Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'originr', 'parallelsugar'
Specified C++11: please drop specification unless essential
‘:::’ call which should be ‘::’: ‘DBItest:::get_default_context’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ‘:::’ call: ‘DBItest:::connect’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  gutsRedIT.c:34:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedIT.c:58:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:36:3: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  gutsRedSD.c:64:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:5:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  odeGUTS_init.c:6:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/odeGUTS.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ogrdbstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_genotype_file
> ### Title: Write the genotype file required by OGRDB
> ### Aliases: write_genotype_file
> 
> ### ** Examples
> 
> genotype_file = tempfile("ogrdb_genotype")
> write_genotype_file(genotype_file, 'V', 'H', example_rep$genotype)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: write_genotype_file ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘OkNNE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OKNNE
> ### Title: Optimal k-Nearest Neighbours Ensemble
> ### Aliases: OKNNE
> ### Keywords: OkNNE Optimal k-NN Bootstraping Regression
> 
> ### ** Examples
> 
>  data(SMSA)
> 
>  anyNA(SMSA)
[1] FALSE
>  #[1] FALSE
> 
>  dim(SMSA)
[1] 59 15
>  #[1] 59 15
> 
>  n=nrow(SMSA)
> 
>  X <- SMSA[names(SMSA)!="NOx"]
>  Y <- SMSA[names(SMSA)=="NOx"]
> 
>  set.seed(25)
>  train.obs <- sample(1:n, 0.7*n, replace = FALSE)
>  test.obs <- (1:n)[-train.obs]
>  xtrain <- X[train.obs,]; ytrain <- Y[train.obs,];
>  xtest <- X[test.obs,]; ytest <- Y[test.obs,]
> 
>  OkNNE.MODEL = OKNNE(xtrain = xtrain, ytrain = ytrain, xtest = xtest, ytest
+  = ytest, k = 10, B = 5, q = trunc(sqrt(ncol(xtrain))), direction = "both",
+  algorithm=c("kd_tree", "cover_tree", "CR", "brute"))
Error in get.knnx(x.train, x.test, k = k, algorithm = algorithm) : 
  DLL requires the use of native symbols
Calls: OKNNE -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Running examples in ‘OncoBayes2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bind_rows_0
> ### Title: Bind rows of multiple data frames with zero fill
> ### Aliases: bind_rows_0
> 
> ### ** Examples
> 
> ## Setting up dummy sampling for fast execution of example
> ## Please use 4 chains and 100x more warmup & iter in practice
> .user_mc_options <- options(OncoBayes2.MC.warmup=10, OncoBayes2.MC.iter=20, OncoBayes2.MC.chains=1,
+                             OncoBayes2.MC.save_warmup=FALSE)
> 
> library(tibble)
> 
> dose_info_A <- tibble(
+    group_id = "hist_A",
+    drug_A = 1
+  )
> 
>  dose_info_B <- tibble(
+    group_id = "hist_B",
+    drug_B = 100 * (1:2)
+  )
> 
> bind_rows_0(dose_info_A, dose_info_B)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: bind_rows_0 ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘ontologics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: new_mapping
> ### Title: Add a new mapping to an ontology
> ### Aliases: new_mapping
> 
> ### ** Examples
> 
> ontoDir <- system.file("extdata", "crops.rds", package = "ontologics")
> onto <- load_ontology(path = ontoDir)
> 
> mapping <- data.frame(old = c("BIOENERGY CROPS", "Bioenergy woody",
+                               "Other bioenergy crops"),
+                       new = c("bioenergy plants", "Wood plantation for fuel",
+                               "Algae for bioenergy"),
+                       type = c("close", "broader", "broader"))
> 
> onto <- new_source(name = "externalDataset",
+                    version = "0.0.1",
+                    description = "a vocabulary",
+                    homepage = "https://www.something.net",
+                    license = "CC-BY-0",
+                    ontology = onto)
> 
> onto <- get_concept(table = data.frame(label = mapping$old), ontology = onto) %>%
+   new_mapping(new = mapping$new,
+               target = .,
+               match = mapping$type,
+               source = "externalDataset",
+               certainty = 3,
+               ontology = onto)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘conversion_to_rdf.Rmd’ using rmarkdown
Quitting from lines 30-34 (conversion_to_rdf.Rmd) 
Error: processing vignette ‘conversion_to_rdf.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘conversion_to_rdf.Rmd’

--- re-building ‘create_an_ontology.Rmd’ using rmarkdown
--- finished re-building ‘create_an_ontology.Rmd’

--- re-building ‘map_new_concepts.Rmd’ using rmarkdown
Quitting from lines 69-78 (map_new_concepts.Rmd) 
Error: processing vignette ‘map_new_concepts.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘map_new_concepts.Rmd’

--- re-building ‘ontology_database_description.Rmd’ using rmarkdown
--- finished re-building ‘ontology_database_description.Rmd’

SUMMARY: processing the following files failed:
  ‘conversion_to_rdf.Rmd’ ‘map_new_concepts.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘openair-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aqStats
> ### Title: Calculate summary statistics for air pollution data by year
> ### Aliases: aqStats
> 
> ### ** Examples
> 
> 
> ## Statistics for 2004. NOTE! these data are in ppb/ppm so the
> ## example is for illustrative purposes only
> aqStats(selectByDate(mydata, year = 2004), pollutant = "no2")
Warning: There was 1 warning in `mutate()`.
ℹ In argument: `date = ymd_hms(date)`.
Caused by warning:
!  366 failed to parse.
Warning: Missing dates detected, removing 366 lines
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: aqStats ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Brief_Introduction_to_openalexR.Rmd’ using rmarkdown
Quitting from lines 276-284 (A_Brief_Introduction_to_openalexR.Rmd) 
Error: processing vignette ‘A_Brief_Introduction_to_openalexR.Rmd’ failed with diagnostics:
Column 3 must be named.
Use `.name_repair` to specify repair.
Caused by error in `repaired_names()`:
! Names can't be empty.
✖ Empty name found at location 3.
--- failed re-building ‘A_Brief_Introduction_to_openalexR.Rmd’

SUMMARY: processing the following file failed:
  ‘A_Brief_Introduction_to_openalexR.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object ‘unary_ops’:
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [37s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 108 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_generalfunctions.R:55:3'): Behavior of summary_map ─────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(summary_map(demo_raster[[1]])) at test_generalfunctions.R:55:2
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. └─OpenLand::summary_map(demo_raster[[1]])
   10.   ├─base::`[<-`(`*tmp*`, i, c(1:2), value = `<list>`)
   11.   └─tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = `<list>`)
   12.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   14.         ├─base::withCallingHandlers(...)
   15.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 108 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(openmeteo)
  > 
  > test_check("openmeteo")
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 36 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-utils.R:10:5'): API queries correctly ──────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─openmeteo::weather_history(...) at test-utils.R:10:4
    2.   └─openmeteo:::.query_openmeteo(...)
    3.     ├─dplyr::mutate(...)
    4.     ├─tidyr::separate(...)
    5.     ├─dplyr::full_join(d, h, by = "date")
    6.     └─dplyr:::full_join.data.frame(d, h, by = "date")
    7.       └─dplyr:::join_mutate(...)
    8.         ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    9.         └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   10.           └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   11.             └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   12.               ├─base::withCallingHandlers(...)
   13.               └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 36 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:33: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ forming offset [176, 183] is out of the bounds [0, 176] of object ‘b’ with type ‘arma::vec’ {aka ‘arma::Col<double>’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ordinalClust.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Running examples in ‘ordinalpattern-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: patternchange
> ### Title: Changepoint Detection Using Ordinal Patterns
> ### Aliases: patternchange plot.change
> 
> ### ** Examples
> 
> set.seed(1066)
> a1 <- cbind(rnorm(100),rnorm(100))
> a2 <- rmvnorm(100,sigma=matrix(c(1,0.8,0.8,1),ncol=2))
> A <- rbind(a1,a2)
> testresult <- patternchange(A[,1],A[,2])
Error in patternseq(tsx, h = h - 1, block = FALSE) : 
  DLL requires the use of native symbols
Calls: patternchange -> patternseq
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘outForest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Data
> ### Title: Extracts Data
> ### Aliases: Data Data.default Data.outForest
> 
> ### ** Examples
> 
> x <- outForest(iris)

Outlier identification by random forests

  Variables to check:		Sepal.Length, Sepal.Width, Petal.Length, Petal.Width
  Variables used to check:	Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, Species

  Checking: Sepal.Length  Sepal.Width  Petal.Length  Petal.Width  Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: outForest -> process_scores -> knnx.index -> get.knnx
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘outForest.Rmd’ using rmarkdown
Quitting from lines 71-92 (outForest.Rmd) 
Error: processing vignette ‘outForest.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘outForest.Rmd’

SUMMARY: processing the following file failed:
  ‘outForest.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘OutliersO3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: O3plotColours
> ### Title: Set colours for O3 plots
> ### Aliases: O3plotColours
> 
> ### ** Examples
> 
> c1 <- O3prep(stackloss, k1=2, method=c("HDo", "BAC"), tolHDo=0.025, tolBAC=0.01)
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: O3prep ... <Anonymous> -> getHDoutliers -> knn.dist -> get.knn
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingO3plots.Rmd’ using rmarkdown
Quitting from lines 25-32 (DrawingO3plots.Rmd) 
Error: processing vignette ‘DrawingO3plots.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘DrawingO3plots.Rmd’

--- re-building ‘MultTolLevels.Rmd’ using rmarkdown
Quitting from lines 24-35 (MultTolLevels.Rmd) 
Error: processing vignette ‘MultTolLevels.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘MultTolLevels.Rmd’

--- re-building ‘PCPsO3.Rmd’ using rmarkdown
Quitting from lines 30-53 (PCPsO3.Rmd) 
Error: processing vignette ‘PCPsO3.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PCPsO3.Rmd’

--- re-building ‘xtraO3methods.Rmd’ using rmarkdown
--- finished re-building ‘xtraO3methods.Rmd’

SUMMARY: processing the following files failed:
  ‘DrawingO3plots.Rmd’ ‘MultTolLevels.Rmd’ ‘PCPsO3.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘result.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Running examples in ‘padr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fill_by_value
> ### Title: Fill missing values by a single value
> ### Aliases: fill_by_value
> 
> ### ** Examples
> 
> library(dplyr) # for the pipe operator

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> x <- seq(as.Date('2016-01-01'), by = 'day', length.out = 366)
> x <- x[sample(1:366, 200)] %>% sort
> x_df <- data_frame(x  = x,
+                    y1 = runif(200, 10, 20) %>% round,
+                    y2 = runif(200, 1, 50) %>% round,
+                    y3 = runif(200, 20, 40) %>% round,
+                    y4 = sample(letters[1:5], 200, replace = TRUE))
> x_padded <- x_df %>% pad
pad applied on the interval: day
> x_padded %>% fill_by_value(y1)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘padr.Rmd’ using rmarkdown
Quitting from lines 27-36 (padr.Rmd) 
Error: processing vignette ‘padr.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘padr.Rmd’

--- re-building ‘padr_custom.Rmd’ using rmarkdown
Quitting from lines 19-41 (padr_custom.Rmd) 
Error: processing vignette ‘padr_custom.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘padr_custom.Rmd’

--- re-building ‘padr_implementation.Rmd’ using rmarkdown
--- finished re-building ‘padr_implementation.Rmd’

SUMMARY: processing the following files failed:
  ‘padr.Rmd’ ‘padr_custom.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘biscale.Rmd’ using rmarkdown
--- finished re-building ‘biscale.Rmd’

--- re-building ‘compatibility.Rmd’ using rmarkdown
--- finished re-building ‘compatibility.Rmd’

--- re-building ‘creating-packages.Rmd’ using rmarkdown
--- finished re-building ‘creating-packages.Rmd’

--- re-building ‘ggplot2.Rmd’ using rmarkdown
--- finished re-building ‘ggplot2.Rmd’

--- re-building ‘gt.Rmd’ using rmarkdown
Quitting from lines 39-69 (gt.Rmd) 
Error: processing vignette ‘gt.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘gt.Rmd’

--- re-building ‘palettes.Rmd’ using rmarkdown
--- finished re-building ‘palettes.Rmd’

SUMMARY: processing the following file failed:
  ‘gt.Rmd’

Error: Vignette re-building failed.
Execution halted
predictSurvProb:
  function(object, newdata, times, ...)
predictSurvProb.pamm:
  function(object, newdata, times)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
rd_info:
  function(obj, ...)
rd_info.ParamSet:
  function(ps, descriptions, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt_impl.h:125:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_impl.h:825:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode.c:58:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/arkode/arkode_adapt.c:42:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/paropt.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-partition.Rmd’ using rmarkdown
Quitting from lines 193-201 (extending-partition.Rmd) 
Error: processing vignette ‘extending-partition.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘extending-partition.Rmd’

--- re-building ‘introduction-to-partition.Rmd’ using rmarkdown
--- finished re-building ‘introduction-to-partition.Rmd’

SUMMARY: processing the following file failed:
  ‘extending-partition.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Running examples in ‘partR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mergeR2
> ### Title: Merge partR2 objects to combine R2s for main effects and
> ###   interactions
> ### Aliases: mergeR2
> 
> ### ** Examples
> 
> 
> data(biomass)
> library(lme4)
Loading required package: Matrix
> 
> # scale data
> biomass[] <- lapply(biomass, function(x) if (is.double(x)) scale(x) else x)
> 
> # Full model
> mod_full <- lmer(Biomass ~  Year + Temperature * Precipitation + SpeciesDiversity + (1|Population),
+             data = biomass)
> # Semi-partial R2 for interaction and all other predictors of interest
> (R2_full <- partR2(mod_full, partvars = c("Temperature:Precipitation", "SpeciesDiversity", "Year"),
+ data = biomass))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: partR2 ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_partR2.Rmd’ using rmarkdown
Quitting from lines 76-78 (Using_partR2.Rmd) 
Error: processing vignette ‘Using_partR2.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Using_partR2.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_partR2.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘PCMBase.Rmd’ using rmarkdown
Quitting from lines 268-302 (PCMBase.Rmd) 
Error: processing vignette ‘PCMBase.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PCMBase.Rmd’

--- re-building ‘PCMCreateModel.Rmd’ using rmarkdown
Quitting from lines 352-386 (PCMCreateModel.Rmd) 
Error: processing vignette ‘PCMCreateModel.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PCMCreateModel.Rmd’

--- re-building ‘PCMParam.Rmd’ using rmarkdown
--- finished re-building ‘PCMParam.Rmd’

--- re-building ‘PCMTracePruning.Rmd’ using rmarkdown
--- finished re-building ‘PCMTracePruning.Rmd’

SUMMARY: processing the following files failed:
  ‘PCMBase.Rmd’ ‘PCMCreateModel.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PythonInR’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  PeakSegJoint_interface.c:113:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PeakSegJoint.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘crrstep’
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘georob’
GNU make is a SystemRequirements.
Running examples in ‘pems.utils-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: 4.1.merge.data.pems
> ### Title: Merging data and pems objects
> ### Aliases: 4.1.merge.data.pems merge.pems align cAlign tAlign
> ###   findLinearOffset stackPEMS C_ylagxCOR
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> ###########
> ##example 1 
> ###########
> 
> ##data vector alignment
> 
> #make two offset ranges
> temp <- rnorm(500)
> x <- temp[25:300]
> y <- temp[10:200]
> 
> #plot pre-alignment data
> plot(x, type="l"); lines(y, col="blue", lty=2)
> 
> #estimated offset
> findLinearOffset(x,y)
[1] -15
> #[1] -15
> 
> #applying linear offset
> ans <- align(x, y, findLinearOffset(x,y))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: align ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) simulate.data.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) simulate.data.Rd:28: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Peptides.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘petrinetR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_PN
> ### Title: Create Petri Net
> ### Aliases: create_PN
> 
> ### ** Examples
> 
> 
> create_PN("place_1",
+ 			"transition_1",
+ 			data.frame(from = "place_1",to = "transition_1"),
+ 			marking = "place_1")
Marking:  place_1 
Enabled transition
            id enabled
1 transition_1    TRUE
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Running examples in ‘phangorn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_ci
> ### Title: Draw Confidences Intervals on Phylogenies
> ### Aliases: add_ci add_boxplot
> ### Keywords: aplot
> 
> ### ** Examples
> 
> data("Laurasiatherian")
> dm <- dist.hamming(Laurasiatherian)
> tree <- upgma(dm)
> set.seed(123)
> trees <- bootstrap.phyDat(Laurasiatherian,
+                           FUN=function(x)upgma(dist.hamming(x)), bs=100)
>                           tree <- plotBS(tree, trees, "phylogram")
> tree <- plotBS(tree, trees, "phylogram")
Error in tabulate(phy$edge[, 1]) : 'bin' must be numeric or a factor
Calls: plotBS ... sapply -> lapply -> FUN -> .is.rooted_ape -> tabulate
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AdvancedFeatures.Rmd’ using rmarkdown
--- finished re-building ‘AdvancedFeatures.Rmd’

--- re-building ‘Ancestral.Rmd’ using rmarkdown
--- finished re-building ‘Ancestral.Rmd’

--- re-building ‘IntertwiningTreesAndNetworks.Rmd’ using rmarkdown
--- finished re-building ‘IntertwiningTreesAndNetworks.Rmd’

--- re-building ‘MLbyHand.Rmd’ using rmarkdown
Quitting from lines 105-107 (MLbyHand.Rmd) 
Error: processing vignette ‘MLbyHand.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘MLbyHand.Rmd’

--- re-building ‘Morphological.Rmd’ using rmarkdown
--- finished re-building ‘Morphological.Rmd’

--- re-building ‘Networx.Rmd’ using rmarkdown
Quitting from lines 30-38 (Networx.Rmd) 
Error: processing vignette ‘Networx.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘Networx.Rmd’

--- re-building ‘Trees.Rmd’ using rmarkdown
--- finished re-building ‘Trees.Rmd’

SUMMARY: processing the following files failed:
  ‘MLbyHand.Rmd’ ‘Networx.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.pdf’
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [13s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PheVis)
  > 
  > test_check("PheVis")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 2 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-traintest_phevis.R:24:9'): test all pipeline is working ────────
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─PheVis::train_phevis(...) at test-traintest_phevis.R:24:8
    2. │ └─PheVis:::fct_surrogate_quanti(...)
    3. │   └─PheVis:::rolling_var(...)
    4. │     └─... %>% arrange(.data$id, .data$start_date)
    5. ├─dplyr::arrange(., .data$id, .data$start_date)
    6. └─base::replace(., is.na(.), 0)
    7.   ├─base::`[<-`(`*tmp*`, list, value = `<dbl>`)
    8.   ├─dplyr:::`[<-.grouped_df`(`*tmp*`, list, value = `<dbl>`)
    9.   ├─base::NextMethod()
   10.   └─tibble:::`[<-.tbl_df`(`*tmp*`, list, value = `<dbl>`)
   11.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   12.       ├─base::withCallingHandlers(...)
   13.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TutoPheVis.Rmd’ using rmarkdown
Quitting from lines 73-81 (TutoPheVis.Rmd) 
Error: processing vignette ‘TutoPheVis.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘TutoPheVis.Rmd’

SUMMARY: processing the following file failed:
  ‘TutoPheVis.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
S3 methods shown with full name in documentation object ‘log’:
  ‘log2.generic_spct’ ‘log10.generic_spct’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
vec_math:
  function(.fn, .x, ...)
vec_math.pillar_num:
  function(op, x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘PKNCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: exclude_nca
> ### Title: Exclude NCA parameters based on examining the parameter set.
> ### Aliases: exclude_nca exclude_nca_span.ratio exclude_nca_max.aucinf.pext
> ###   exclude_nca_min.hl.r.squared
> 
> ### ** Examples
> 
> my_conc <- PKNCAconc(data.frame(conc=1.1^(3:0),
+                                 time=0:3,
+                                 subject=1),
+                      conc~time|subject)
> my_data <- PKNCAdata(my_conc,
+                      intervals=data.frame(start=0, end=Inf,
+                                           aucinf.obs=TRUE,
+                                           aucpext.obs=TRUE))
> my_result <- pk.nca(my_data)
No dose information provided, calculations requiring dose will return NA.
Error in `purrr::pmap()`:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! Please report a bug.
: Error with interval start=0, end=Inf: DLL requires the use of native symbols
Backtrace:
     ▆
  1. ├─PKNCA::pk.nca(my_data)
  2. │ └─purrr::pmap(...)
  3. │   └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
  4. │     ├─purrr:::with_indexed_errors(...)
  5. │     │ └─base::withCallingHandlers(...)
  6. │     ├─purrr:::call_with_cleanup(...)
  7. │     └─PKNCA (local) .f(...)
  8. │       └─base::tryCatch(...)
  9. │         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10. │           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11. │             └─value[[3L]](cond)
 12. │               └─base::stop(e)
 13. └─purrr (local) `<fn>`(`<smplErrr>`)
 14.   └─cli::cli_abort(...)
 15.     └─rlang::abort(...)
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘plsRcox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.autoplsRcox
> ### Title: Cross-validating an autoplsRcox-Model
> ### Aliases: cv.autoplsRcox
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> data(micro.censure)
> data(Xmicro.censure_compl_imp)
> set.seed(123456)
> X_train_micro <- apply((as.matrix(Xmicro.censure_compl_imp)),FUN="as.numeric",MARGIN=2)[1:80,]
> X_train_micro_df <- data.frame(X_train_micro)
> Y_train_micro <- micro.censure$survyear[1:80]
> C_train_micro <- micro.censure$DC[1:80]
> 
> #Should be run with a higher value of nt (at least 10)
> (cv.autoplsRcox.res=cv.autoplsRcox(list(x=X_train_micro,time=Y_train_micro,
+ status=C_train_micro),nt=3,verbose=FALSE))
Error in AUC.sh(object$Surv.rsp, object$Surv.rsp.new, object$lp, object$lpnew,  : 
  DLL requires the use of native symbols
Calls: cv.autoplsRcox -> getIndicCViAUCSH -> AUC.sh
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘pmetar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: metar_decode
> ### Title: Decode METAR report.
> ### Aliases: metar_decode
> 
> ### ** Examples
> 
> metar_decode("EPWA 281830Z 18009KT 140V200 9999 SCT037 03/M01 Q1008 NOSIG")
Getting airport informaiton from the file downloaded from
https://ourairports.com/data/
created by David Megginson
Error: pmetar package error: Incorrect METAR weather report found and cannot be 
           decoded!
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pmetar.Rmd’ using rmarkdown
Quitting from lines 285-286 (pmetar.Rmd) 
Error: processing vignette ‘pmetar.Rmd’ failed with diagnostics:
pmetar package error: Incorrect METAR weather report found and cannot be 
           decoded!

--- failed re-building ‘pmetar.Rmd’

SUMMARY: processing the following file failed:
  ‘pmetar.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘pmlbr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nearest_datasets
> ### Title: ------------------- Select nearest datasets given input 'x'.
> ### Aliases: nearest_datasets nearest_datasets.default
> ###   nearest_datasets.character nearest_datasets.data.frame
> 
> ### ** Examples
> 
> nearest_datasets('penguins')
Error in FNN::get.knnx(summary_i, dataset_stats, k = n_neighbors) : 
  DLL requires the use of native symbols
Calls: nearest_datasets -> nearest_datasets.character -> <Anonymous>
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘pointblank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: activate_steps
> ### Title: Activate one or more of an _agent_'s validation steps
> ### Aliases: activate_steps
> 
> ### ** Examples
> 
> # Create an agent that has the
> # `small_table` object as the
> # target table, add a few inactive
> # validation steps, and then use
> # `interrogate()`
> agent_1 <- 
+   create_agent(
+     tbl = small_table,
+     tbl_name = "small_table",
+     label = "An example."
+   ) %>%
+   col_exists(
+     columns = vars(date),
+     active = FALSE
+   ) %>%
+   col_vals_regex(
+     columns = vars(b),
+     regex = "[0-9]-[a-z]{3}-[0-9]{3}",
+     active = FALSE
+   ) %>%
+   interrogate()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Packages suggested but not available for checking: 'USAboundaries', 'INLA'
Package unavailable to check Rd xrefs: ‘INLA’
'LazyData' is specified without a 'data' directory
Running examples in ‘poio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fix_metadata
> ### Title: Fix metadata in a PO object
> ### Aliases: fix_metadata fix_metadata.po fix_metadata.data.frame
> 
> ### ** Examples
> 
> pot_file <- system.file("extdata/R-summerof69.pot", package = "poio")
> pot <- read_po(pot_file)
> pot_fixed <- fix_metadata(pot, system.file(package = "poio"))
Updating the Project-Id-Version to ‘poio 0.0-4’.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: fix_metadata ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
Running ‘testthat.R’ [20s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PopED)
  > 
  > test_check("PopED")
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 186 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  • Parallel calculations skipped (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_evaluate_design.R:227:3'): Shrinkage evaluation works ──────────
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─PopED::shrinkage(poped.db) at test_evaluate_design.R:227:2
   2.   ├─base::`[<-`(`*tmp*`, data_tmp == 1, value = `<lgl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, data_tmp == 1, value = `<lgl>`)
   4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 1 | WARN 0 | SKIP 2 | PASS 186 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
using C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
using C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
using C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Quitting from lines 911-921 (examples.Rmd) 
Error: processing vignette ‘examples.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘examples.Rmd’

--- re-building ‘intro-poped.Rmd’ using rmarkdown
--- finished re-building ‘intro-poped.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RClone’
Found the following significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  omp_test.c:7:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/poppr.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
Running examples in ‘popstudy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: El_Badry
> ### Title: El-Badry method
> ### Aliases: El_Badry
> 
> ### ** Examples
> 
> 
> CEB_data <- tidyr::gather(CEB, ages, childs, -Children_Ever_Born)
> results <- Moultrie(CEB_data, ages, childs, Children_Ever_Born)
Joining with `by = join_by(age)`
Warning: There was 1 warning in `mutate()`.
ℹ In argument: `Max = ifelse(...)`.
Caused by warning in `ifelse()`:
! NAs introduced by coercion
Joining with `by = join_by(age)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: Moultrie ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [24s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(posterior)
  This is posterior version 1.4.1
  
  Attaching package: 'posterior'
  
  The following objects are masked from 'package:stats':
  
      mad, sd, var
  
  The following objects are masked from 'package:base':
  
      %in%, match
  
  > 
  > test_check("posterior")
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1498 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-summarise_draws.R:18:3'): summarise_draws works correctly ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, 1, value = `<lgl>`) at test-summarise_draws.R:18:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<lgl>`) at test-summarise_draws.R:18:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 1498 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Unknown package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ppmf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agg
> ### Title: Aggregate PPMF Data
> ### Aliases: agg
> 
> ### ** Examples
> 
> data(ppmf_ex)
> ppmf_ex <- ppmf_ex %>% add_geoid()
> blocks <- agg(ppmf_ex)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: agg ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘ppseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_decision_rules
> ### Title: Calculate a decision rule table for interim monitoring of a
> ###   pre-specified design
> ### Aliases: calc_decision_rules
> 
> ### ** Examples
> 
> set.seed(123)
> 
> # One-sample case
> calc_decision_rules(
+   n = seq(5, 25, 5), 
+   N = 25, 
+   theta = 0.86, 
+   ppp = 0.2, 
+   p0 = 0.1, 
+   S = 50
+   )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: calc_decision_rules ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘one_sample_expansion.Rmd’ using rmarkdown
Quitting from lines 113-117 (one_sample_expansion.Rmd) 
Error: processing vignette ‘one_sample_expansion.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘one_sample_expansion.Rmd’

--- re-building ‘two_sample_randomized.Rmd’ using rmarkdown
Quitting from lines 111-115 (two_sample_randomized.Rmd) 
Error: processing vignette ‘two_sample_randomized.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘two_sample_randomized.Rmd’

SUMMARY: processing the following files failed:
  ‘one_sample_expansion.Rmd’ ‘two_sample_randomized.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  prod.c:27:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PreciseSums.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘preregr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: source
> ### Title: Programmatically constructing justifier elements
> ### Aliases: source dcsn jstf asrt srce decide decision assert justify
> 
> ### ** Examples
> 
> ### Programmatically create a partial justification object
> exampleAssertion <-
+   preregr::assert(
+     "This is an assertion",
+     source = c(
+       preregr::source('This is a first source'),
+       preregr::source('This is a second source')));
> 
> ### Programmatically create a justification with two assertions
> ### but without sources
> exampleJustification <-
+   preregr::justify(
+     "Icecream will make me feel less fit",
+     assertion = c(
+       preregr::assert('Icecream is rich in energy'),
+       preregr::assert('Consuming high-energy foods makes me feel less fit')
+     ),
+     weight = -.5
+   );
> 
> ### Show it
> exampleJustification;
Justifier element of type 'justifierJustification' and with id 'ujvn_J7n9twmmk'.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Error(s) in re-building vignettes:
  ...
--- re-building ‘presize.Rmd’ using rmarkdown
Quitting from lines 149-185 (presize.Rmd) 
Error: processing vignette ‘presize.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘presize.Rmd’

SUMMARY: processing the following file failed:
  ‘presize.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd) 
Error: processing vignette ‘getting_started_with_prewas.Rmd’ failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building ‘getting_started_with_prewas.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_prewas.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:22:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:232:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
show:
  function(object)
show.Data:
  function(x, ...)

show:
  function(object)
show.OptimizationProblem:
  function(x, ...)

show:
  function(object)
show.Portfolio:
  function(x, ...)

show:
  function(object)
show.Solution:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘probout-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allProb
> ### Title: Outlier probabilities for all observations
> ### Aliases: allProb
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
>  set.seed(0)
> 
>  lead <- leader(faithful)
Error in get.knnx(data = data[LIST[[r]]$leaders, , drop = F], query = data[i,  : 
  DLL requires the use of native symbols
Calls: leader -> get.knnx
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘probout.Rmd’ using rmarkdown
Quitting from lines 71-72 (probout.Rmd) 
Error: processing vignette ‘probout.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘probout.Rmd’

SUMMARY: processing the following file failed:
  ‘probout.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘processanimateR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: animate_process
> ### Title: Animate cases on a process map
> ### Aliases: animate_process
> 
> ### ** Examples
> 
> data(example_log)
> 
> # Animate the process with default options (absolute time and 60s duration)
> animate_process(example_log)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: animate_process ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘use-external-data-to-change-tokens.Rmd’ using rmarkdown
Quitting from lines 23-49 (use-external-data-to-change-tokens.Rmd) 
Error: processing vignette ‘use-external-data-to-change-tokens.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘use-external-data-to-change-tokens.Rmd’

--- re-building ‘use-shiny-selections.Rmd’ using rmarkdown
--- finished re-building ‘use-shiny-selections.Rmd’

--- re-building ‘use-timestamp-change-token-aes.Rmd’ using rmarkdown
Quitting from lines 59-72 (use-timestamp-change-token-aes.Rmd) 
Error: processing vignette ‘use-timestamp-change-token-aes.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘use-timestamp-change-token-aes.Rmd’

--- re-building ‘use-token_scales.Rmd’ using rmarkdown
Quitting from lines 23-31 (use-token_scales.Rmd) 
Error: processing vignette ‘use-token_scales.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘use-token_scales.Rmd’

--- re-building ‘use-with-shiny.Rmd’ using rmarkdown
--- finished re-building ‘use-with-shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘use-external-data-to-change-tokens.Rmd’
  ‘use-timestamp-change-token-aes.Rmd’ ‘use-token_scales.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘processcheckR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contains_between
> ### Title: Contains Between
> ### Aliases: contains_between
> 
> ### ** Examples
> 
> library(bupaR)

Attaching package: ‘bupaR’

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:utils’:

    timestamp

> library(eventdataR)
> 
> # A patients should have between 0 and 4 blood tests (including 0 and 4).
> patients %>%
+  check_rule(contains_between("Blood test", min = 0, max = 4))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  pause.c:10:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/profvis.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
Quitting from lines 51-52 (quick_start.Rmd) 
Error: processing vignette ‘quick_start.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘quick_start.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_start.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Running examples in ‘prototest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prototest-package
> ### Title: Inference on Prototypes from Clusters of Features
> ### Aliases: prototest-package prototest
> 
> ### ** Examples
> 
> require (prototest)
> 
> ### generate data
> set.seed (12345)
> n = 100
> p = 80
> 
> X = matrix (rnorm(n*p, 0, 1), ncol=p)
> 
> 
> beta = rep(0, p)
> beta[1:3] = 0.1 # three signal variables: number 1, 2, 3
> signal = apply(X, 1, function(col){sum(beta*col)})
> intercept = 3
> 
> y = intercept + signal + rnorm (n, 0, 1)
> 
> ### treat all columns as if in same group and test for signal
> 
> # non-selective ELR test with nuisance intercept
> elr = prototest.univariate (X, y, "ELR", selected.col=1:5)
> # selective F test with nuisance intercept; non-sampling
> f.test = prototest.univariate (X, y, "F", lambda=0.01, hr.iter=0) 
Error in .local(x, ...) : DLL requires the use of native symbols
Calls: prototest.univariate ... FUN -> .local -> reduce -> reduce -> .local -> .Call
Execution halted
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  util.c:6:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pscl.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Pool_Model_Performance.Rmd’ using rmarkdown
--- finished re-building ‘Pool_Model_Performance.Rmd’

--- re-building ‘Pooling_AUC_values.Rmd’ using rmarkdown
--- finished re-building ‘Pooling_AUC_values.Rmd’

--- re-building ‘boot_MI.Rmd’ using rmarkdown
--- finished re-building ‘boot_MI.Rmd’

--- re-building ‘psfmi_CoxModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_CoxModels.Rmd’

--- re-building ‘psfmi_LinearModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_LinearModels.Rmd’

--- re-building ‘psfmi_LogisticModels.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_LogisticModels.Rmd’

--- re-building ‘psfmi_StabilityAnalysis.Rmd’ using rmarkdown
Quitting from lines 60-78 (psfmi_StabilityAnalysis.Rmd) 
Error: processing vignette ‘psfmi_StabilityAnalysis.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘psfmi_StabilityAnalysis.Rmd’

--- re-building ‘psfmi_mice.Rmd’ using rmarkdown
--- finished re-building ‘psfmi_mice.Rmd’

SUMMARY: processing the following file failed:
  ‘psfmi_StabilityAnalysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:120: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Running examples in ‘psycModel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cfa_summary
> ### Title: Confirmatory Factor Analysis
> ### Aliases: cfa_summary
> 
> ### ** Examples
> 
> # REMEMBER, YOU MUST NAMED ALL ARGUMENT EXCEPT THE CFA ITEMS ARGUMENT
> # Fitting a multilevel single factor CFA model
> fit <- cfa_summary(
+   data = lavaan::HolzingerSwineford1939,
+   x1:x3,
+   x4:x6,
+   x7:x9,
+   group = "sex",
+   model_variance = FALSE, # do not print the model_variance
+   model_covariance = FALSE # do not print the model_covariance
+ )

 
[4mModel Summary[24m
[mModel Type = Confirmatory Factor Analysis[m
[mGroup = sex[m
[mModel Formula = 
. DV1 =~ x1 + x2 + x3
  DV2 =~ x4 + x5 + x6
  DV3 =~ x7 + x8 + x9
 [m
[4mFit Measure[24m
──────────────────────────────────────────────────────────────────────────────────────
       Χ²      DF          P    CFI  RMSEA   SRMR    TLI       AIC       BIC      BIC2
──────────────────────────────────────────────────────────────────────────────────────Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: cfa_summary ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘brief-introduction-to-select-syntax.Rmd’ using rmarkdown
--- finished re-building ‘brief-introduction-to-select-syntax.Rmd’

--- re-building ‘quick-introduction.Rmd’ using rmarkdown
Quitting from lines 50-61 (quick-introduction.Rmd) 
Error: processing vignette ‘quick-introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘quick-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘quick-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘psyverse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleSpec <-
+   system.file("inst",
+               "extdata",
+               "example_dct_spec_1.dct",
+               package="psyverse");
> parsedSpecs <- load_dct_specs(exampleSpec);
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: load_dct_specs ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pTITAN2.Rmd’ using rmarkdown
Quitting from lines 566-603 (pTITAN2.Rmd) 
Error: processing vignette ‘pTITAN2.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘pTITAN2.Rmd’

SUMMARY: processing the following file failed:
  ‘pTITAN2.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘pubh-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cosm_reg
> ### Title: Cosmetics for tables of regression coefficients. Converts tables
> ###   generated by 'tbl_regression' to 'huxtable' and adds some cosmetics.
> ### Aliases: cosm_reg
> 
> ### ** Examples
> 
> require(sjlabelled, quietly = TRUE)

Attaching package: ‘sjlabelled’

The following object is masked from ‘package:huxtable’:

    set_label

The following object is masked from ‘package:ggplot2’:

    as_label

> 
> data(diet, package = "Epi")
> diet <- diet %>%
+   var_labels(
+     chd = "Coronary Heart Disease",
+     fibre = "Fibre intake (g/day)"
+   )
> 
> model_binom <- glm(chd ~ fibre, data = diet, family = binomial)
> 
> model_binom %>%
+   tbl_regression(exponentiate = TRUE) %>%
+   cosm_reg(bold = TRUE) %>%
+   theme_pubh(1) %>%
+   add_footnote(get_r2(model_binom), font_size = 9)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 349-353 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction.Rmd’

--- re-building ‘regression.Rmd’ using rmarkdown
Quitting from lines 118-122 (regression.Rmd) 
Error: processing vignette ‘regression.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘regression.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction.Rmd’ ‘regression.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘puls.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'pulssplitv'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Quitting from lines 58-69 (puls.Rmd) 
Error: processing vignette ‘puls.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘puls.Rmd’

SUMMARY: processing the following file failed:
  ‘puls.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘PupilPre-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clean_artifact
> ### Title: Automatically clean artifacts.
> ### Aliases: clean_artifact
> 
> ### ** Examples
> 
> # Load example data
> data("Pupilex4")
> 
> # Writing log file to temporary folder for the example
> dat <- clean_artifact(Pupilex4, MADWindow = 100, MADConstant = 2,
+                       MADPadding = c(200, 200), MahaConstant = 2,
+                       Method = "Robust", XandY = TRUE, Second = TRUE,
+                       MaxValueRun = 5, NAsAroundRun = c(2,2),
+                       LogFile = paste0(tempdir(),"/ArtifactCleanupLog.rds"))

Running cleanup based on MAD (median absolute deviation) and robust Mahalanobis distance.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: clean_artifact ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PupilPre_Basic_Preprocessing.Rmd’ using rmarkdown
Quitting from lines 320-325 (PupilPre_Basic_Preprocessing.Rmd) 
Error: processing vignette ‘PupilPre_Basic_Preprocessing.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PupilPre_Basic_Preprocessing.Rmd’

--- re-building ‘PupilPre_Cleanup.Rmd’ using rmarkdown
Quitting from lines 176-181 (PupilPre_Cleanup.Rmd) 
Error: processing vignette ‘PupilPre_Cleanup.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PupilPre_Cleanup.Rmd’

--- re-building ‘PupilPre_Interpolation_and_Filtering.Rmd’ using rmarkdown
Quitting from lines 18-34 (PupilPre_Interpolation_and_Filtering.Rmd) 
Error: processing vignette ‘PupilPre_Interpolation_and_Filtering.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PupilPre_Interpolation_and_Filtering.Rmd’

--- re-building ‘PupilPre_Message_Alignment.Rmd’ using rmarkdown
--- finished re-building ‘PupilPre_Message_Alignment.Rmd’

--- re-building ‘PupilPre_Plotting.Rmd’ using rmarkdown
--- finished re-building ‘PupilPre_Plotting.Rmd’

SUMMARY: processing the following files failed:
  ‘PupilPre_Basic_Preprocessing.Rmd’ ‘PupilPre_Cleanup.Rmd’
  ‘PupilPre_Interpolation_and_Filtering.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
as.igraph:
  function(x, ...)
as.igraph.qgraph:
  function(object, attributes)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘Parameter_Guidelines.rmd’ using rmarkdown
--- finished re-building ‘Parameter_Guidelines.rmd’

--- re-building ‘User_Guide.rmd’ using rmarkdown
--- finished re-building ‘User_Guide.rmd’

--- re-building ‘Example-full-nca-analysis.rmd’ using knitr
Quitting from lines 47-76 (Example-full-nca-analysis.rmd) 
Error: processing vignette ‘Example-full-nca-analysis.rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Example-full-nca-analysis.rmd’

--- re-building ‘Example-stepwise-nca-analysis.rmd’ using knitr
Quitting from lines 47-76 (Example-stepwise-nca-analysis.rmd) 
Error: processing vignette ‘Example-stepwise-nca-analysis.rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Example-stepwise-nca-analysis.rmd’

SUMMARY: processing the following files failed:
  ‘Example-full-nca-analysis.rmd’ ‘Example-stepwise-nca-analysis.rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 481-486 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
object ‘data_corpus_irishbudget2010’ not found
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Running examples in ‘quanteda.textplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textplot_scale1d
> ### Title: Plot a fitted scaling model
> ### Aliases: textplot_scale1d
> ### Keywords: textplot
> 
> ### ** Examples
> 
> library("quanteda")
Package version: 3.2.4
Unicode version: 15.0
ICU version: 72.1
Parallel computing: 4 of 32 threads used.
See https://quanteda.io for tutorials and examples.
> data(data_corpus_irishbudget2010, package = "quanteda.textmodels")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘quanteda.textmodels’
Calls: data -> find.package
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > library("testthat")
  > library("quanteda")
  Package version: 3.2.4
  Unicode version: 15.0
  ICU version: 72.1
  Parallel computing: 4 of 32 threads used.
  See https://quanteda.io for tutorials and examples.
  > library("quanteda.textmodels")
  Error in library("quanteda.textmodels") : 
    there is no package called 'quanteda.textmodels'
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glmBias.c:84:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/QuasiSeq.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(questionr)
  
  Attaching package: 'questionr'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("questionr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_tables.R:97:3'): prop, cprop and lprop tabyl versions are correct ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% ... at test_tables.R:97:2
    2. ├─tidyr::pivot_longer(., -`qualif/sexe`, names_to = "Var2", values_to = "Freq")
    3. ├─base::as.data.frame(.)
    4. ├─questionr::lprop(.)
    5. └─questionr:::rprop.tabyl(.)
    6.   └─janitor::adorn_totals(tab, c("row", "col"))
    7.     ├─base::`[<-`(`*tmp*`, 1, 1, value = `<chr>`)
    8.     └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 1, value = `<chr>`)
    9.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   10.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   11.           ├─base::withCallingHandlers(...)
   12.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 64 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/r2sundials.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
as.tags:
  function(x, ...)
as.tags.data3js:
  function(x, standalone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘RaceID-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compMean
> ### Title: Function for computing local gene expression averages
> ### Aliases: compMean
> 
> ### ** Examples
> 
> res <- pruneKnn(intestinalDataSmall,knn=10,alpha=1,no_cores=1,FSelect=FALSE)
Warning in irlba(A = t(z), nv = pcaComp, tol = tol) :
  You're computing too large a percentage of total singular values, use a standard svd instead.
Error in get.knn(dimRed, k = knn, algorithm = algorithm) : 
  DLL requires the use of native symbols
Calls: pruneKnn -> get.knn
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RaceID.Rmd’ using rmarkdown
Quitting from lines 591-593 (RaceID.Rmd) 
Error: processing vignette ‘RaceID.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘RaceID.Rmd’

SUMMARY: processing the following file failed:
  ‘RaceID.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in ‘radiant.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.pivotr
> ### Title: Summary method for pivotr
> ### Aliases: summary.pivotr
> 
> ### ** Examples
> 
> pivotr(diamonds, cvars = "cut") %>% summary(chi2 = TRUE)
Pivot table
Data        : diamonds 
Categorical : cut 

       cut n_obs
      Fair   101
      Good   275
 Very Good   677
   Premium   771
     Ideal 1,176
     Total 3,000

Chi-squared: 1202.62 df(4), p.value < .001
0.0% of cells have expected values below 5
> pivotr(diamonds, cvars = "cut", tabsort = "desc(n_obs)") %>% summary()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘algorithmes.Rmd’ using rmarkdown
--- finished re-building ‘algorithmes.Rmd’

--- re-building ‘algorithms_en.Rmd’ using rmarkdown
--- finished re-building ‘algorithms_en.Rmd’

--- re-building ‘introduction_en.Rmd’ using rmarkdown
Quitting from lines 193-195 (introduction_en.Rmd) 
Error: processing vignette ‘introduction_en.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction_en.Rmd’

--- re-building ‘introduction_usage.Rmd’ using rmarkdown
Quitting from lines 205-207 (introduction_usage.Rmd) 
Error: processing vignette ‘introduction_usage.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction_usage.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction_en.Rmd’ ‘introduction_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘blcs.dot’ ‘ex1.dot’ ‘ex1bridge1.dot’ ‘ex1bridge2.dot’
  ‘ex1bridge3.dot’ ‘ex1effect1.dot’ ‘ex1effect2.dot’ ‘gcmlinear.dot’
  ‘latent.dot’ ‘lcs.dot’ ‘mimic.dot’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘googlesheets’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:38:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:172:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sketch.c:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RaProR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  bedrock_leveldb.h:74:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:100:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:102:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.h:103:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:545:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:785:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:797:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  bedrock_leveldb.c:802:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:39:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:136:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:138:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  nbt.c:35:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:44:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:56:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  random.c:90:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  subchunk.c:9:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  support.c:205:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbedrock.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘Building_Benvos.Rmd’ using rmarkdown
--- finished re-building ‘Building_Benvos.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 78-79 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) mn4joint1condi.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) objets.Rd:66: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘rcanvec.cache’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  nonred.c:99:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcdd.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
Found the following significant warnings:
  RClickhouse_init.c:23:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RClickhouse.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
sql_translate_env:
  function(con)
sql_translate_env.ClickhouseConnection:
  function(x)

db_desc:
  function(x)
db_desc.ClickhouseConnection:
  function(con)

db_analyze:
  function(con, table, ...)
db_analyze.ClickhouseConnection:
  function(con, sql, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outcmaesdisp.dat’
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘RcmdrPlugin.RiskDemo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: drawIncidenceFin
> ### Title: Plotting incidence curves of an epidemic with Finnish data
> ### Aliases: drawIncidenceFin
> 
> ### ** Examples
> 
> data(dataCovidFin)
> data(popRegionsFin)
> drawIncidenceFin(data = dataCovidFin, pop = popRegionsFin, 
+     regions = popRegionsFin$Alue[1:5], start = "2020-06-01", end="last", weeks=2, 
+     includeAllRegions = TRUE)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: drawIncidenceFin ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
as_tibble:
  function(x, ..., .rows, .name_repair, rownames)
as_tibble.CompadreDB:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘conics’
Error(s) in re-building vignettes:
  ...
--- re-building ‘climate.Rmd’ using rmarkdown
--- finished re-building ‘climate.Rmd’

--- re-building ‘lidar.Rmd’ using rmarkdown
starting worker pid=1039005 on localhost:11637 at 01:21:15.859
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
starting worker pid=1065317 on localhost:11637 at 01:21:58.697
starting worker pid=1065319 on localhost:11637 at 01:21:58.928
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
--- finished re-building ‘lidar.Rmd’

--- re-building ‘troll.Rmd’ using rmarkdown
--- finished re-building ‘troll.Rmd’

--- re-building ‘workflow.Rmd’ using rmarkdown
Quitting from lines 47-58 (workflow.Rmd) 
Error: processing vignette ‘workflow.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
as.quadratic_constraint:
  function(x, ...)
as.quadratic_constraint.list:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘rredis’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsTMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgeMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.matrix:
  function(x, check.sym)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsCMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.ddiMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsyMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dpoMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgTMatrix:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘PercentCodes’
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘practical_rcurvep.Rmd’ using rmarkdown
Quitting from lines 63-67 (practical_rcurvep.Rmd) 
Error: processing vignette ‘practical_rcurvep.Rmd’ failed with diagnostics:
ℹ In argument: `rcurvep_obj = purrr::pmap(...)`.
Caused by error in `purrr::pmap()`:
ℹ In index: 1.
Caused by error in `dplyr::mutate()`:
ℹ In argument: `fingerprint = purrr::map(.data$output,
  extract_curvep_fingerprint, config = config)`.
Caused by error in `purrr::map()`:
ℹ In index: 2.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘practical_rcurvep.Rmd’

SUMMARY: processing the following file failed:
  ‘practical_rcurvep.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  rDEA_init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rDEA.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
as.integer64:
  function(x, ...)
as.integer64.SNOMEDconcept:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpcops.c:20:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  dsdpsetoptions.c:280:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sdpalloc.c:4:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Dummies.Rmd’ using rmarkdown
--- finished re-building ‘Dummies.Rmd’

--- re-building ‘Ordering.Rmd’ using rmarkdown
--- finished re-building ‘Ordering.Rmd’

--- re-building ‘Roles.Rmd’ using rmarkdown
--- finished re-building ‘Roles.Rmd’

--- re-building ‘Selecting_Variables.Rmd’ using rmarkdown
--- finished re-building ‘Selecting_Variables.Rmd’

--- re-building ‘Skipping.Rmd’ using rmarkdown
--- finished re-building ‘Skipping.Rmd’

--- re-building ‘recipes.Rmd’ using rmarkdown
Quitting from lines 134-136 (recipes.Rmd) 
Error: processing vignette ‘recipes.Rmd’ failed with diagnostics:
Error in `step_impute_knn()`:
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘recipes.Rmd’

SUMMARY: processing the following file failed:
  ‘recipes.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘deduplication.Rmd’ using rmarkdown
--- finished re-building ‘deduplication.Rmd’

--- re-building ‘introduction_to_reclin.Rmd’ using rmarkdown
Quitting from lines 218-220 (introduction_to_reclin.Rmd) 
Error: processing vignette ‘introduction_to_reclin.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction_to_reclin.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction_to_reclin.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘ReDaMoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: confront_data
> ### Title: Confront a RelDataModel to actual data
> ### Aliases: confront_data
> 
> ### ** Examples
> 
> ## Read the model ----
> hpo_model <- read_json_data_model(
+    system.file("examples/HPO-model.json", package="ReDaMoR")
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: read_json_data_model ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Quitting from lines 159-163 (ReDaMoR.Rmd) 
Error: processing vignette ‘ReDaMoR.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘ReDaMoR.Rmd’

SUMMARY: processing the following file failed:
  ‘ReDaMoR.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘cur_plans’
rowwise:
  function(data, ...)
rowwise.redist_map:
  function(x, ...)

rowwise:
  function(data, ...)
rowwise.redist_plans:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  redland.c:771:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:817:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  redland.c:1846:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/redland.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
roclet_process:
  function(x, blocks, env, base_path)
roclet_process.roclet_mergeNamespace:
  function(x, blocks, env, base_path, global_options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
qq:
  function(x, data, ...)
qq.pffr:
  function(object, rep, level, s.rep, type, pch, rl.col, rep.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘regfilter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.rfdata
> ### Title: Print function for class rfdata
> ### Aliases: print.rfdata
> 
> ### ** Examples
> 
> # load the dataset
> data(rock)
> 
> # apply the regression noise filter
> set.seed(9)
> output <- regAENN(x = rock[,-ncol(rock)], y = rock[,ncol(rock)])
Error in get.knn(data = dataset[, -output], k = j, algorithm = "brute") : 
  DLL requires the use of native symbols
Calls: regAENN -> regAENN.default -> get.knn
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Regional_stats.Rmd’ using rmarkdown
Quitting from lines 159-163 (Regional_stats.Rmd) 
Error: processing vignette ‘Regional_stats.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Regional_stats.Rmd’

--- re-building ‘mapping.Rmd’ using rmarkdown
Quitting from lines 234-247 (mapping.Rmd) 
Error: processing vignette ‘mapping.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mapping.Rmd’

--- re-building ‘recode.Rmd’ using rmarkdown
--- finished re-building ‘recode.Rmd’

--- re-building ‘validation.Rmd’ using rmarkdown
--- finished re-building ‘validation.Rmd’

SUMMARY: processing the following files failed:
  ‘Regional_stats.Rmd’ ‘mapping.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:9:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/reglogit.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) pima.Rd:24: Escaped LaTeX specials: \^
checkRd: (-1) reglogit.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:136: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘regtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fineTuning,knnFineTune
> ### Title: Grid Search Plus More
> ### Aliases: fineTuning knnFineTune fineTuningPar plot.tuner
> 
> ### ** Examples
> 
> 
> # mlb data set, predict weight using k-NN, try various values of k
> 
> tc <- function(dtrn,dtst,cmbi,...)
+ {
+    knnout <- kNN(dtrn[,-3],dtrn[,3],dtst[,-3],as.integer(cmbi[1]))
+    preds <- knnout$regests
+    mean(abs(preds - dtst[,3]))
+ }
> 
> data(mlb)
> mlb <- mlb[,3:6]
> mlb.d <- factorsToDummies(mlb)
> fineTuning(mlb.d,list(k=c(5,25)),tc,nTst=100,nXval=2)
Error in FNN::get.knnx(data = x, query = newx, k = kmax1) : 
  DLL requires the use of native symbols
error in comb 5 
Error in fineTuning(mlb.d, list(k = c(5, 25)), tc, nTst = 100, nXval = 2) : 
  
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
render:
  function(x)
render.pdf_image_stream:
  function(x, view)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Anova:
  function(mod, ...)
Anova.resi:
  function(object, alpha, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Running examples in ‘RevGadgets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dropTip
> ### Title: dropTip
> ### Aliases: dropTip
> 
> ### ** Examples
> 
> 
> file <- system.file("extdata",
+                     "sub_models/primates_cytb_GTR_MAP.tre",
+                     package="RevGadgets")
> tree <- readTrees(paths = file)

  |                                              
  |                                        |   0%
  |                                              
  |========================================| 100%
> tree_dropped <- dropTip(tree, "Otolemur_crassicaudatus")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: dropTip ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘customize_support_new_data_model.Rmd’ using rmarkdown
--- finished re-building ‘customize_support_new_data_model.Rmd’

--- re-building ‘customize_support_new_rdbms.Rmd’ using rmarkdown
--- finished re-building ‘customize_support_new_rdbms.Rmd’

--- re-building ‘deploy_bigquery.Rmd’ using rmarkdown
--- finished re-building ‘deploy_bigquery.Rmd’

--- re-building ‘deploy_docker.Rmd’ using rmarkdown
--- finished re-building ‘deploy_docker.Rmd’

--- re-building ‘deploy_local.Rmd’ using rmarkdown
--- finished re-building ‘deploy_local.Rmd’

--- re-building ‘deploy_server.Rmd’ using rmarkdown
--- finished re-building ‘deploy_server.Rmd’

--- re-building ‘usage_connect_to_record_database.Rmd’ using rmarkdown
--- finished re-building ‘usage_connect_to_record_database.Rmd’

--- re-building ‘usage_connect_to_redcap.Rmd’ using rmarkdown
Quitting from lines 55-81 (usage_connect_to_redcap.Rmd) 
Error: processing vignette ‘usage_connect_to_redcap.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘usage_connect_to_redcap.Rmd’

--- re-building ‘usage_perform_chart_review.Rmd’ using rmarkdown
--- finished re-building ‘usage_perform_chart_review.Rmd’

SUMMARY: processing the following file failed:
  ‘usage_connect_to_redcap.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Crash_Sequences.Rmd’ using rmarkdown
trying URL ‘https://static.nhtsa.gov/nhtsa/downloads/FARS/2020/National/FARS2020NationalCSV.zip’
Content type 'application/x-zip-compressed' length 31674692 bytes (30.2 MB)
==================================================
downloaded 30.2 MB

--- finished re-building ‘Crash_Sequences.Rmd’

--- re-building ‘Rural_roads.Rmd’ using rmarkdown
trying URL ‘https://static.nhtsa.gov/nhtsa/downloads/FARS/2018/National/FARS2018NationalCSV.zip’
Content type 'application/x-zip-compressed' length 26874597 bytes (25.6 MB)
==================================================
downloaded 25.6 MB

trying URL ‘https://static.nhtsa.gov/nhtsa/downloads/FARS/2019/National/FARS2019NationalCSV.zip’
Content type 'application/x-zip-compressed' length 26974033 bytes (25.7 MB)
==================================================
downloaded 25.7 MB

trying URL ‘https://static.nhtsa.gov/nhtsa/downloads/FARS/2020/National/FARS2020NationalCSV.zip’
Content type 'application/x-zip-compressed' length 31674692 bytes (30.2 MB)
==================================================
downloaded 30.2 MB

Quitting from lines 81-88 (Rural_roads.Rmd) 
Error: processing vignette ‘Rural_roads.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Rural_roads.Rmd’

SUMMARY: processing the following file failed:
  ‘Rural_roads.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Rglpk_read_file.c:17:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:42:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.persistence_diagram:
  function(x, dimension, alpha, max_intervals, legend, greyblock, n,
           type, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Read 1 item
Quitting from lines 106-110 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  convert.h:12:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  convert.c:79:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ring.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘calculate_d.Rmd’ using rmarkdown
--- finished re-building ‘calculate_d.Rmd’

--- re-building ‘contribute.Rmd’ using rmarkdown
--- finished re-building ‘contribute.Rmd’

--- re-building ‘eh_test.Rmd’ using rmarkdown
--- finished re-building ‘eh_test.Rmd’

--- re-building ‘factor_pvalue.Rmd’ using rmarkdown
--- finished re-building ‘factor_pvalue.Rmd’

--- re-building ‘optimal_d.Rmd’ using rmarkdown
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette ‘optimal_d.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘optimal_d.Rmd’

SUMMARY: processing the following file failed:
  ‘optimal_d.Rmd’

Error: Vignette re-building failed.
Execution halted
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.ate:
  function(x, estimator, type, keep.rownames, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.h:19:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:26:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:30:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rjags.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/stdio2.h:54:35: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’ specified bound 4096 exceeds destination size 512 [-Wstringop-overflow=]
  ./LASlib/lasdefinitions.hpp:673:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 16 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlas.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++14: please drop specification unless essential
Found the following significant warnings:
  RngWrap.c:12:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:23:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  RngWrap.c:304:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  zzz.c:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘USAboundaries’
Specified C++11: please drop specification unless essential
Running examples in ‘RmarineHeatWaves-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detect heatwaves and cold-spells.
> ### Aliases: detect
> 
> ### ** Examples
> 
> ts_dat <- make_whole(sst_WA)
> res <- detect(ts_dat, climatology_start = "1983-01-01",
+               climatology_end = "2012-12-31")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: detect ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘RmdConcord-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: processConcordance
> ### Title: Get the concordance from the "datapos" values and record it in a
> ###   file.
> ### Aliases: processConcordance
> 
> ### ** Examples
> 
> # This example works on the file inst/sample/Sample.Rmd,
> # which should be a copy of the vignette Sample.Rmd.  This
> # is convenient because RStudio doesn't install vignettes by default.
> 
> # First, see the results without concordances:
> 
> library(RmdConcord)
> dir <- tempdir()
> infile <- system.file("sample/Sample.Rmd", package = "RmdConcord")
> outfile1 <- file.path(dir, "html_vignette.html")
> rmarkdown::render(infile,
+                   output_file = outfile1,
+                   quiet = TRUE)
Warning in file(con, "w") :
  cannot open file 'Sample.knit.md': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: <Anonymous> -> <Anonymous> -> write_utf8 -> writeLines -> file
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.meteo_coverage:
  function(mateo_coverage, old_style)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Unknown package ‘StatDA’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘robomit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: o_beta_boot
> ### Title: Bootstrapped beta*s
> ### Aliases: o_beta_boot
> 
> ### ** Examples
> 
> # load data, e.g. the in-build mtcars dataset
> data("mtcars")
> data_oster <- mtcars
> 
> # preview of data
> head(data_oster)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> 
> # load robomit
> require(robomit)
> 
> # estimate bootstrapped beta*s
> o_beta_boot(y = "mpg",            # dependent variable
+             x = "wt",             # independent treatment variable
+             con = "hp + qsec",    # related control variables
+             delta = 1,            # delta
+             R2max = 0.9,          # maximum R-square
+             sim = 100,            # number of simulations
+             obs = 30,             # draws per simulation
+             rep = FALSE,          # bootstrapping with or without replacement
+             type = "lm",          # model type
+             useed = 123,          # seed
+             data = data_oster)    # dataset
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: o_beta_boot ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  monitor.c:15:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robustbase.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  /usr/lib/gcc/x86_64-linux-gnu/12/include/emmintrin.h:131:24: warning: array subscript ‘__m128d_u[0]’ is partly outside array bounds of ‘Eigen::internal::plain_matrix_type<Eigen::Product<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false>, Eigen::Transpose<Eigen::Block<Eigen::Matrix<double, -1, -1>, 1, -1, false> >, 0>, Eigen::Dense>::type [1]’ {aka ‘Eigen::Matrix<double, 1, 1, 0, 1, 1> [1]’} [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RobustGaSP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Running examples in ‘RobustIV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SearchingSampling
> ### Title: Searching-Sampling
> ### Aliases: SearchingSampling
> 
> ### ** Examples
> 
> 
> data("lineardata")
> Y <- lineardata[,"Y"]
> D <- lineardata[,"D"]
> Z <- as.matrix(lineardata[,c("Z.1","Z.2","Z.3","Z.4","Z.5","Z.6","Z.7","Z.8")])
> X <- as.matrix(lineardata[,c("age","sex")])
> Searching.model <- SearchingSampling(Y,D,Z,X, Sampling = FALSE)
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': DLL requires the use of native symbols
Calls: SearchingSampling ... reduce -> .local -> .Call -> .handleSimpleError -> h
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in ‘rock-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_graph_theme
> ### Title: Apply multiple DiagrammeR global graph attributes
> ### Aliases: apply_graph_theme
> 
> ### ** Examples
> 
> exampleSource <- '
+ ---
+ codes:
+   -
+     id: parentCode
+     label: Parent code
+     children:
+       -
+         id: childCode1
+       -
+         id: childCode2
+   -
+     id: childCode3
+     label: Child Code
+     parentId: parentCode
+     children: [grandChild1, grandChild2]
+ ---
+ ';
> parsedSource <-
+   parse_source(text=exampleSource);
> miniGraph <-
+   apply_graph_theme(data.tree::ToDiagrammeRGraph(parsedSource$deductiveCodeTrees),
+                     c("color", "#0000AA", "node"),
+                     c("shape", "triangle", "node"),
+                     c("fontcolor", "#FF0000", "node"));
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: apply_graph_theme ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘Rogue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GraphGeodesic
> ### Title: Graph Geodesic between leaves of unweighted tree
> ### Aliases: GraphGeodesic Cophenetic
> ### Keywords: internal
> 
> ### ** Examples
> 
> GraphGeodesic(TreeTools::BalancedTree(5))
Error in GraphGeodesic(TreeTools::BalancedTree(5)) : 
  DLL requires the use of native symbols
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bayesian.Rmd’ using rmarkdown
Quitting from lines 119-125 (Bayesian.Rmd) 
Error: processing vignette ‘Bayesian.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Bayesian.Rmd’

SUMMARY: processing the following file failed:
  ‘Bayesian.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vendor/boost/intrusive/detail/slist_node.hpp:56:16: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
  vendor/boost/intrusive/detail/hook_traits.hpp:77:10: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RPostgres.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
File ‘RQuantLib/libs/RQuantLib.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘utils.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdalUtils’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Stopwatch.h:13:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Stopwatch.c:4:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rscimark.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abalone
> ### Title: SODAS XML data file.
> ### Aliases: abalone
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(abalone)
> res <- sym.pca(abalone, 'centers')
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: sym.pca ... %in% -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 60-64 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
object ‘tbl_subset_col’ not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Running examples in ‘rshift-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Lanzante
> ### Title: Lanzante L-test
> ### Aliases: Lanzante
> 
> ### ** Examples
> 
> Lanzante(lake_data, "DCA1", "Age")
Warning: `as.tibble()` was deprecated in tibble 2.0.0.
ℹ Please use `as_tibble()` instead.
ℹ The signature and semantics have changed, see `?as_tibble`.
ℹ The deprecated feature was likely used in the rshift package.
  Please report the issue to the authors.
# A tibble: 6 × 2
    Age  p_vals
  <dbl>   <dbl>
1  7520 0.00130
2  7768 0.00250
3  8011 0.00489
4  8254 0.00968
5  8555 0.0193 
6  8855 0.0386 
> Lanzante(lake_data, "DCA1", "Age", p=0.10, merge=TRUE)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: Lanzante ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  vendor/boost/intrusive/detail/slist_node.hpp:56:16: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
  vendor/boost/intrusive/detail/hook_traits.hpp:77:10: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSQLite.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Running examples in ‘rSRD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHeatmapSRD
> ### Title: plotHeatmapSRD
> ### Aliases: plotHeatmapSRD
> 
> ### ** Examples
> 
> srdInput <- data.frame(
+ A=c(32, 52, 44, 44, 47),
+ B=c(73, 75, 65, 76, 70),
+ C=c(60, 59, 57, 55, 60),
+ D=c(35, 24, 44, 83, 47),
+ E=c(41, 52, 46, 50, 65))
> 
> plotHeatmapSRD(srdInput)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plotHeatmapSRD ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  rsyslog.h:15:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rsyslog.c:50:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsyslog.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced_usage.Rmd’ using rmarkdown
--- finished re-building ‘advanced_usage.Rmd’

--- re-building ‘baseline.Rmd’ using rmarkdown
--- finished re-building ‘baseline.Rmd’

--- re-building ‘clinical_trials.Rmd’ using rmarkdown
Quitting from lines 913-923 (clinical_trials.Rmd) 
Error: processing vignette ‘clinical_trials.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘clinical_trials.Rmd’

--- re-building ‘custom_appearance.Rmd’ using rmarkdown
--- finished re-building ‘custom_appearance.Rmd’

--- re-building ‘format_precedence.Rmd’ using rmarkdown
--- finished re-building ‘format_precedence.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘manual_table_construction.Rmd’ using rmarkdown
--- finished re-building ‘manual_table_construction.Rmd’

--- re-building ‘sorting_pruning.Rmd’ using rmarkdown
--- finished re-building ‘sorting_pruning.Rmd’

--- re-building ‘split_functions.Rmd’ using rmarkdown
--- finished re-building ‘split_functions.Rmd’

--- re-building ‘subsetting_tables.Rmd’ using rmarkdown
--- finished re-building ‘subsetting_tables.Rmd’

--- re-building ‘tabulation_concepts.Rmd’ using rmarkdown
--- finished re-building ‘tabulation_concepts.Rmd’

--- re-building ‘tabulation_dplyr.Rmd’ using rmarkdown
--- finished re-building ‘tabulation_dplyr.Rmd’

--- re-building ‘title_footer.Rmd’ using rmarkdown
--- finished re-building ‘title_footer.Rmd’

SUMMARY: processing the following file failed:
  ‘clinical_trials.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘RTL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: efficientFrontier
> ### Title: Markowitz Efficient Frontier
> ### Aliases: efficientFrontier
> 
> ### ** Examples
> 
> x =  RTL::fizdiffs %>% dplyr::select(date, dplyr::contains("WCS"))
> efficientFrontier(nsims = 10, x = x, expectedReturns = NULL)
$data
# A tibble: 13 × 5
     Return  Risk SharpeRatio data             desc                             
      <dbl> <dbl>       <dbl> <list>           <chr>                            
 1 -0.00514 0.632    -0.00813 <tibble [1 × 3]> WCS.CUS = 1, WCS.HOU = 0, WCS.HD…
 2 -0.00510 0.631    -0.00808 <tibble [1 × 3]> WCS.CUS = 0, WCS.HOU = 1, WCS.HD…
 3 -0.00795 1.07     -0.00741 <tibble [1 × 3]> WCS.CUS = 0, WCS.HOU = 0, WCS.HD…
 4 -0.00639 0.642    -0.00997 <tibble [1 × 3]> WCS.CUS = 0.452, WCS.HOU = 0.1, …
 5 -0.00592 0.566    -0.0105  <tibble [1 × 3]> WCS.CUS = 0.423, WCS.HOU = 0.296…
 6 -0.00624 0.613    -0.0102  <tibble [1 × 3]> WCS.CUS = 0.139, WCS.HOU = 0.464…
 7 -0.00631 0.620    -0.0102  <tibble [1 × 3]> WCS.CUS = 0.373, WCS.HOU = 0.209…
 8 -0.00639 0.635    -0.0101  <tibble [1 × 3]> WCS.CUS = 0.225, WCS.HOU = 0.325…
 9 -0.00638 0.634    -0.0101  <tibble [1 × 3]> WCS.CUS = 0.182, WCS.HOU = 0.372…
10 -0.00547 0.561    -0.00975 <tibble [1 × 3]> WCS.CUS = 0.214, WCS.HOU = 0.659…
11 -0.00517 0.571    -0.00906 <tibble [1 × 3]> WCS.CUS = 0.401, WCS.HOU = 0.579…
12 -0.00572 0.557    -0.0103  <tibble [1 × 3]> WCS.CUS = 0.24, WCS.HOU = 0.546,…
13 -0.00601 0.574    -0.0105  <tibble [1 × 3]> WCS.CUS = 0.306, WCS.HOU = 0.381…

$plot

> efficientFrontier(nsims = 10, x = x, expectedReturns = c(0.5,0.8,0.9))
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: efficientFrontier ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
Specified C++14: please drop specification unless essential
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘rubias-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_gsi_sim_mixture
> ### Title: Write a mixture data frame to gsi_sim format baseline and
> ###   repunits file
> ### Aliases: write_gsi_sim_mixture
> 
> ### ** Examples
> 
> # this writes to file prefix "mixfile" in a temporary directory
> dd <- tempdir()
> prefix <- file.path(dd, "mixfile")
> 
> # print that
> prefix
[1] "/home/hornik/tmp/scratch/RtmpC5TNf1/mixfile"
> 
> # note that in practice you will probably want to specify
> # your own directory...
> 
> # run the function
> write_gsi_sim_mixture(chinook_mix, 5, prefix)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: write_gsi_sim_mixture ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [19s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rules)
  Loading required package: parsnip
  > 
  > test_check("rules")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  [ FAIL 1 | WARN 0 | SKIP 34 | PASS 25 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (34)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-c5.R:332:3'): tunable ──────────────────────────────────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─... %>% tunable() at test-c5.R:332:2
    2. ├─generics::tunable(.)
    3. ├─rules:::tunable.C5_rules(.)
    4. ├─base::NextMethod()
    5. ├─parsnip:::tunable.model_spec(.)
    6. │ └─... %>% ...
    7. ├─dplyr::mutate(...)
    8. ├─dplyr::full_join(...)
    9. └─dplyr:::full_join.data.frame(...)
   10.   └─dplyr:::join_mutate(...)
   11.     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   12.     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
   13.       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   14.         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   15.           ├─base::withCallingHandlers(...)
   16.           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 34 | PASS 25 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘results’
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘RVowpalWabbit/libs/RVowpalWabbit.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘parse_args.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘rwicc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit_midpoint_model
> ### Title: Fit model using midpoint imputation
> ### Aliases: fit_midpoint_model
> 
> ### ** Examples
> 
> sim_data = simulate_interval_censoring(
+   "theta" = c(0.986, -3.88),
+   "study_cohort_size" = 4500,
+   "preconversion_interval_length" = 365,
+   "hazard_alpha" = 1,
+   "hazard_beta" = 0.5)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: simulate_interval_censoring ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how-to-use-rwicc.Rmd’ using rmarkdown
Quitting from lines 28-47 (how-to-use-rwicc.Rmd) 
Error: processing vignette ‘how-to-use-rwicc.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘how-to-use-rwicc.Rmd’

SUMMARY: processing the following file failed:
  ‘how-to-use-rwicc.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.qqnorm.spss:
  function(x, plottype, line, l.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [15s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(safetyGraphics)
  > 
  > # Combining testthat and shinytest as described here https://www.r-bloggers.com/unit-testing-shiny-apps-using-testthat/
  > 
  > test_check("safetyGraphics")
  [ FAIL 1 | WARN 4 | SKIP 5 | PASS 90 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (5)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_makeMapping.R:24:1'): (code run outside of `test_that()`) ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─safetyGraphics::makeMapping(testData, meta, TRUE, NULL) at test_makeMapping.R:24:0
    2. │ ├─... %>% select(-.data$current.x, -.data$current.y)
    3. │ ├─dplyr::full_join(...)
    4. │ └─dplyr:::full_join.data.frame(...)
    5. │   └─dplyr:::join_mutate(...)
    6. │     ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    7. │     └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,2]>`)
    8. │       └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. │         └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10. │           ├─base::withCallingHandlers(...)
   11. │           └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
   12. ├─dplyr::select(., -.data$current.x, -.data$current.y)
   13. └─dplyr::mutate(...)
  
  [ FAIL 1 | WARN 4 | SKIP 5 | PASS 90 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Gen_fun.h:17:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  Gen_fun.c:121:8: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  IFscratch.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  load_IFscratch.c:64:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/samon.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Found the following significant warnings:
  init.h:28:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.h:29:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SamplerCompare.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘networkTomography’
Running examples in ‘sandwichr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot
> ### Title: Plot interpolation results
> ### Aliases: autoplot autoplot.sandwich.model
> 
> ### ** Examples
> 
> library(ggplot2)
> data(sim.data)
> sim.sw <- sandwich.model(object=sim.data, sampling.attr="Value", type="shp")
Warning: attribute variables are assumed to be spatially constant throughout all geometries
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: sandwich.model ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sandwichr.R.tutorial.Rmd’ using rmarkdown
Quitting from lines 126-130 (sandwichr.R.tutorial.Rmd) 
Error: processing vignette ‘sandwichr.R.tutorial.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘sandwichr.R.tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘sandwichr.R.tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘sansa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sansa
> ### Title: Title
> ### Aliases: sansa
> 
> ### ** Examples
> 
> 
> library(sansa)
> library(ggplot2)
> minority = data.frame(x1 = rnorm(10, 10, 3),
+                       x2 = rnorm(10, 25, 10),
+                       target = "true")
> majority = data.frame(x1 = rnorm(100, 4, 2),
+                       x2 = rnorm(100, 30, 10),
+                       target = "false")
> 
> dataset = rbind(minority, majority)
> 
> ggplot(dataset) + geom_point(aes(x1, x2, color = target))
> sansaobject = sansa(x = dataset[,1:2], y = dataset$target, lambda = 1, ksel = 3)
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: sansa -> rowSums -> is.data.frame -> <Anonymous> -> get.knn
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘sapfluxnetr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sfn_replacement_methods
> ### Title: sfn_data replacement methods
> ### Aliases: sfn_replacement_methods get_sapf_data<-,sfn_data-method
> ###   get_env_data<-,sfn_data-method get_sapf_flags<-,sfn_data-method
> ###   get_env_flags<-,sfn_data-method get_timestamp<-,sfn_data-method
> ###   get_solar_timestamp<-,sfn_data-method get_si_code<-,sfn_data-method
> ###   get_site_md<-,sfn_data-method get_stand_md<-,sfn_data-method
> ###   get_species_md<-,sfn_data-method get_plant_md<-,sfn_data-method
> ###   get_env_md<-,sfn_data-method
> 
> ### ** Examples
> 
> # preparation
> data('ARG_TRE', package = 'sapfluxnetr')
> sapf_data <- get_sapf_data(ARG_TRE, solar = TRUE)
> 
> # modifying the slot data
> sapf_data[1:10, 2] <- NA
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
‘library’ or ‘require’ call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘scanstatistics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: score_locations
> ### Title: Score each location over zones and duration.
> ### Aliases: score_locations
> 
> ### ** Examples
> 
> # Simple example
> set.seed(1)
> table <- data.frame(zone = 1:5, duration = 1, score = 5:1)
> zones <- list(1:2, 1:3, 2:5, 4:5, c(1, 5))
> x <- list(observed = table, n_locations = 5, max_duration = 1, n_zones = 5)
> score_locations(x, zones)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: score_locations ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 268-295 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  error.h:33:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scclust.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Running examples in ‘scgwr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict0
> ### Title: Spatial prediction using the scalable GWR model
> ### Aliases: predict0
> 
> ### ** Examples
> 
> require(spData)
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
> data(boston)
> 
> id_obs  <-sample(dim(boston.c)[1],400)
> 
> ######################### data at observed sites
> y       <- log(boston.c[id_obs,"MEDV"])
> x       <- boston.c[id_obs, c("CRIM", "INDUS","ZN","NOX","AGE")]
> coords  <- boston.c[id_obs , c("LON", "LAT") ]
> 
> ######################### data at predicted sites
> x0      <- boston.c[-id_obs, c("CRIM", "INDUS","ZN","NOX", "AGE")]
> coords0 <- boston.c[-id_obs , c("LON", "LAT") ]
> 
> mod     <- scgwr( coords = coords, y = y, x = x )
Error in get.knnx(coords, coords_samp, knn - 1) : 
  DLL requires the use of native symbols
Calls: scgwr -> proc -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘scipub_vignette.Rmd’ using rmarkdown
Quitting from lines 172-173 (scipub_vignette.Rmd) 
Error: processing vignette ‘scipub_vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘scipub_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘scipub_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘scistreer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_phylo_heatmap
> ### Title: Plot phylogeny and mutation heatmap
> ### Aliases: plot_phylo_heatmap
> 
> ### ** Examples
> 
> p = plot_phylo_heatmap(tree_small, P_small)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot_phylo_heatmap ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Package suggested but not available for checking: ‘ssvd’
Unexported object imported by a ‘:::’ call: ‘simplifyEnrichment:::is_GO_id’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [22s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sclr)
  > 
  > test_check("sclr")
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 83 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sclr_ideal_data.R:7:3'): ideal data is simulated ───────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─sclr::sclr_ideal_data(...) at test-sclr_ideal_data.R:7:2
   2.   ├─base::`[<-`(...)
   3.   └─tibble:::`[<-.tbl_df`(...)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 83 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘scrutiny-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: duplicate_count_colpair
> ### Title: Count duplicate values by column
> ### Aliases: duplicate_count_colpair
> 
> ### ** Examples
> 
> # Basic usage:
> mtcars %>%
+   duplicate_count_colpair()
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [113s/189s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > 
  > library(testthat)
  > library(scrutiny)
  > 
  > test_check("scrutiny")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 491 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-duplicate-count-colpair.R:2:1'): (code run outside of `test_that()`) ──
  Error in `vectbl_assign(x[[j]], cells[[j]], value)`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─mtcars %>% duplicate_count_colpair() at test-duplicate-count-colpair.R:2:0
    2. ├─scrutiny::duplicate_count_colpair(.)
    3. │ └─... %>% dplyr::rename(count = "r")
    4. ├─dplyr::rename(., count = "r")
    5. ├─dplyr::arrange(., dplyr::desc(.data$r))
    6. ├─corrr::stretch(., na.rm = TRUE, remove.dups = FALSE)
    7. ├─corrr::shave(.)
    8. └─corrr:::shave.cor_df(.)
    9.   ├─base::`[<-`(`*tmp*`, upper.tri(x), value = `<lgl>`)
   10.   └─tibble:::`[<-.tbl_df`(`*tmp*`, upper.tri(x), value = `<lgl>`)
   11.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
   12.       ├─base::withCallingHandlers(...)
   13.       └─tibble:::vectbl_assign(x[[j]], cells[[j]], value)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 491 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘scutr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SCUT
> ### Title: SMOTE and cluster-based undersampling technique.
> ### Aliases: SCUT SCUT_parallel
> 
> ### ** Examples
> 
> ret <- SCUT(iris, "Species", undersample = undersample_hclust,
+             usamp_opts = list(dist_calc="manhattan"))
> ret2 <- SCUT(chickwts, "feed", undersample = undersample_kmeans)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: SCUT ... <Anonymous> -> SMOTE -> knearest -> <Anonymous> -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘sdcSpatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mask_grid
> ### Title: Mask coordinates using a grid
> ### Aliases: mask_grid
> 
> ### ** Examples
> 
> x <- cbind(
+   x = c(2.5, 3.5, 7.2, 1.5),
+   y = c(6.2, 3.8, 4.4, 2.1)
+ )
> 
> # plotting is only useful from small datasets!
> 
> # grid masking
> x_g <- mask_grid(x, r=1, plot=TRUE)
> 
> # random pertubation
> set.seed(3)
> x_r <- mask_random(x, r=1, plot=TRUE)
> 
> if (requireNamespace("FNN", quietly = TRUE)){
+   # weighted random pertubation
+   x_wr <- mask_weighted_random(x, k = 2, r = 4, plot=TRUE)
+ }
Error in FNN::get.knn(x, k = k) : DLL requires the use of native symbols
Calls: mask_weighted_random -> <Anonymous>
Execution halted
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spgrass6’
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in ‘selectiveInference-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: groupfs
> ### Title: Select a model with forward stepwise.
> ### Aliases: groupfs
> 
> ### ** Examples
> 
> x = matrix(rnorm(20*40), nrow=20)
> index = sort(rep(1:20, 2))
> y = rnorm(20) + 2 * x[,1] - x[,4]
> fit = groupfs(x, y, index, maxsteps = 5)
> out = groupfsInf(fit)
Step 1/5: computing P-value for group 1 
Error in .local(x, ...) : DLL requires the use of native symbols
Calls: groupfsInf ... <Anonymous> -> .local -> reduce -> reduce -> .local -> .Call
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:28: Escaped LaTeX specials: \^
checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sequoia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcBYprobs
> ### Title: Birth year probabilities
> ### Aliases: CalcBYprobs
> 
> ### ** Examples
> 
> BYprobs <- CalcBYprobs(Pedigree = SeqOUT_griffin$Pedigree,
+                        LifeHistData = SeqOUT_griffin$LifeHist)
Error in GetRelA(Ped.R, patmat = TRUE, GenBack = 1, List = TRUE) : 
  DLL requires the use of native symbols
Calls: CalcBYprobs -> MakeAgePrior -> GetRelA
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PedComp.Rmd’ using rmarkdown
--- finished re-building ‘PedComp.Rmd’

--- re-building ‘quick_start_example1.rmd’ using rmarkdown
Quitting from lines 80-83 (quick_start_example1.rmd) 
Error: processing vignette ‘quick_start_example1.rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘quick_start_example1.rmd’

--- re-building ‘vignette-age.Rmd’ using rmarkdown
Quitting from lines 183-184 (vignette-age.Rmd) 
Error: processing vignette ‘vignette-age.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘vignette-age.Rmd’

--- re-building ‘vignette-main.Rmd’ using rmarkdown
Quitting from lines 650-652 (vignette-main.Rmd) 
Error: processing vignette ‘vignette-main.Rmd’ failed with diagnostics:
argument is of length zero
--- failed re-building ‘vignette-main.Rmd’

--- re-building ‘flowchart.pdf.asis’ using asis
--- finished re-building ‘flowchart.pdf.asis’

SUMMARY: processing the following files failed:
  ‘quick_start_example1.rmd’ ‘vignette-age.Rmd’ ‘vignette-main.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘sfc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sfc
> ### Title: Substance Flow Computation
> ### Aliases: sfc
> 
> ### ** Examples
> 
> library(sfc)
> 
> ## model as txt
> data <- system.file("extdata", "data_utf8.csv", package = "sfc")
> model <- system.file("extdata", "model_utf8.txt", package = "sfc")
> sfc(data, model, sample.size = 100, fileEncoding = "UTF-8")
Read 12 items
Warning: `funs()` was deprecated in dplyr 0.8.0.
ℹ Please use a list of either functions or lambdas:

# Simple named list: list(mean = mean, median = median)

# Auto named with `tibble::lst()`: tibble::lst(mean, median)

# Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
ℹ The deprecated feature was likely used in the sfc package.
  Please report the issue at <https://github.com/ctfysh/sfc/issues>.
Warning: `mutate_each_()` was deprecated in dplyr 0.7.0.
ℹ Please use `across()` instead.
ℹ The deprecated feature was likely used in the dplyr package.
  Please report the issue at <https://github.com/tidyverse/dplyr/issues>.
Warning: `arrange_()` was deprecated in dplyr 0.7.0.
ℹ Please use `arrange()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the sfc package.
  Please report the issue at <https://github.com/ctfysh/sfc/issues>.
Warning: `group_by_()` was deprecated in dplyr 0.7.0.
ℹ Please use `group_by()` instead.
ℹ See vignette('programming') for more help
ℹ The deprecated feature was likely used in the sfc package.
  Please report the issue at <https://github.com/ctfysh/sfc/issues>.
Joining with `by = join_by(NAME, TIME)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: sfc ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
st_precision:
  function(x)
st_precision.sfnetwork:
  function(x, active, ...)

st_z_range:
  function(obj, ...)
st_z_range.sfnetwork:
  function(x, active, ...)

st_geometry:
  function(obj, ...)
st_geometry.sfnetwork:
  function(x, active, ...)

st_bbox:
  function(obj, ...)
st_bbox.sfnetwork:
  function(x, active, ...)

st_set_precision:
  function(x, precision)
st_set_precision.sfnetwork:
  function(x, value)

st_m_range:
  function(obj, ...)
st_m_range.sfnetwork:
  function(x, active, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘sfnetworks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: st_network_join
> ### Title: Join two spatial networks based on equality of node geometries
> ### Aliases: st_network_join
> 
> ### ** Examples
> 
> library(sf, quietly = TRUE)
Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
> 
> node1 = st_point(c(0, 0))
> node2 = st_point(c(1, 0))
> node3 = st_point(c(1,1))
> node4 = st_point(c(0,1))
> edge1 = st_sfc(st_linestring(c(node1, node2)))
> edge2 = st_sfc(st_linestring(c(node2, node3)))
> edge3 = st_sfc(st_linestring(c(node3, node4)))
> 
> net1 = as_sfnetwork(c(edge1, edge2))
> net2 = as_sfnetwork(c(edge2, edge3))
> 
> joined = st_network_join(net1, net2)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: st_network_join ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sfn01_structure.Rmd’ using rmarkdown
--- finished re-building ‘sfn01_structure.Rmd’

--- re-building ‘sfn02_preprocess_clean.Rmd’ using rmarkdown
--- finished re-building ‘sfn02_preprocess_clean.Rmd’

--- re-building ‘sfn03_join_filter.Rmd’ using rmarkdown
Quitting from lines 289-302 (sfn03_join_filter.Rmd) 
Error: processing vignette ‘sfn03_join_filter.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘sfn03_join_filter.Rmd’

--- re-building ‘sfn04_routing.Rmd’ using rmarkdown
--- finished re-building ‘sfn04_routing.Rmd’

--- re-building ‘sfn05_morphers.Rmd’ using rmarkdown
--- finished re-building ‘sfn05_morphers.Rmd’

SUMMARY: processing the following file failed:
  ‘sfn03_join_filter.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Quitting from lines 86-91 (sf4.Rmd) 
Error: processing vignette ‘sf4.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
--- finished re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
--- finished re-building ‘sf6.Rmd’

--- re-building ‘sf7.Rmd’ using rmarkdown
--- finished re-building ‘sf7.Rmd’

SUMMARY: processing the following file failed:
  ‘sf4.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘sftime.Rmd’ using rmarkdown
Quitting from lines 142-147 (sftime.Rmd) 
Error: processing vignette ‘sftime.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘sftime.Rmd’

SUMMARY: processing the following file failed:
  ‘sftime.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
Running examples in ‘shattering-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_number_hyperplanes
> ### Title: Function to estimate the number of hyperplanes required to
> ###   classify such a data sample.
> ### Aliases: estimate_number_hyperplanes
> ### Keywords: estimate hyperplanes number
> 
> ### ** Examples
> 
> 
> # Generating some random dataset with 2 classes:
> # 50 examples in class 1 and 50 in class 2 (last column)
> data = cbind(rnorm(mean=1, sd=1, n=50), rnorm(mean=1, sd=1, n=50), rep(1, 50))
> data = rbind(data, cbind(rnorm(mean=-1, sd=1, n=50), rnorm(mean=-1, sd=1, n=50), rep(2, 50)))
> 
> # Building up the input and output sets
> X = data[,1:2]
> Y = data[,3]
> 
> # Plotting our dataset using classes as colors
> plot(X, col=Y, main="Original dataset", xlab="Attribute 1", ylab="Attribute 2")
> 
> # Here we estimate the number of hyperplanes required to shatter (divide) the given sample
> # in all possible ways according to the organization of points in the input space
> Hyperplanes = estimate_number_hyperplanes(X, Y, length=10, quantile.percentage=0.1, epsilon=1e-7)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: estimate_number_hyperplanes -> equivalence_relation -> <Anonymous> -> get.knnx
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shattering)
  > 
  > test_check("shattering")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test01.r:4:1'): (code run outside of `test_that()`) ─────────────────
  Error in `get.knnx(data, query, k, algorithm)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─shattering::estimate_number_hyperplanes(...) at test01.r:4:0
   2.   └─shattering::equivalence_relation(...)
   3.     └─FNN::knnx.dist(...)
   4.       └─FNN::get.knnx(data, query, k, algorithm)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
shinytest requires PhantomJS to record and run tests.
• To install it, run shinytest::installDependencies()
• If it is installed, please check it is available on the PATH

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  cairodev.h:86:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  cairodev.c:11:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.h:64:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.h:47:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  outline.c:169:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  register_routines.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  showtext.c:111:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:43:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  util.c:53:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/showtext.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sift)
  > 
  > test_check("sift")
  Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
    DLL requires the use of native symbols
  Calls: test_check ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
  Execution halted
Package suggested but not available for checking: ‘copynumber’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) chol_s2Dp.Rd:147: Escaped LaTeX specials: \&
checkRd: (-1) chol_s2Dp.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) precision_builder.Rd:87: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_RandSet_HPPP.Rd:93: Escaped LaTeX specials: \&
checkRd: (-1) sim2D_binarymap.Rd:157: Escaped LaTeX specials: \&
checkRd: (-1) sim_MVN_X.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_Binary_X.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) sim_Y_MVN_X.Rd:213: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘simaerep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check_df_visit
> ### Title: Integrity check for df_visit.
> ### Aliases: check_df_visit
> 
> ### ** Examples
> 
> 
> df_visit <- sim_test_data_study(
+   n_pat = 100,
+   n_sites = 5,
+   frac_site_with_ur = 0.4,
+   ur_rate = 0.6
+ )
> 
> df_visit$study_id <- "A"
> 
> df_visit_filt <- df_visit %>%
+   dplyr::filter(visit != 3)
> 
> df_visit_corr <- check_df_visit(df_visit_filt)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: check_df_visit ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘simcausal_vignette.Rnw’ using knitr
Quitting from lines 1665-1674 (simcausal_vignette.Rnw) 
Error: processing vignette ‘simcausal_vignette.Rnw’ failed with diagnostics:
setActions(): some intervention node(s) do not exist in the original DAG: A1_0
--- failed re-building ‘simcausal_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘simcausal_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
Specified C++11: please drop specification unless essential
Running examples in ‘simIReff-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: effCont_norm
> ### Title: Continuous Effectiveness as Truncated Normal Distribution.
> ### Aliases: effCont_norm
> 
> ### ** Examples
> 
> e <- effCont_norm(web2010ap[,1])
Error in truncnorm::etruncnorm(a = 0, b = 1, mean = mu, sd = sigma) : 
  DLL requires the use of native symbols
Calls: effCont_norm -> <Anonymous>
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Found the following files/directories:
  ‘simu.pheno’ ‘usedpars.txt’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [24s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simpr)
  
  Attaching package: 'simpr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("simpr")
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_calc_tidy.R:86:3'): Errors show up in tidied output. ─────────
  buggy_fit$.fit_error not equal to c(...).
  2/4 mismatches
  x[1]: "Error in eval(substitute(expr), data, enclos = parent.frame()): object 'y
  x[1]: ' not found\n"
  y[1]: "Error in t.test(y): object 'y' not found\n"
  
  x[2]: "Error in eval(substitute(expr), data, enclos = parent.frame()): object 'y
  x[2]: ' not found\n"
  y[2]: "Error in is.data.frame(x): object 'y' not found\n"
  
  [ FAIL 1 | WARN 9 | SKIP 0 | PASS 50 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘SimRAD-exampleRefSeq-Fasta.fa’ ‘SimRAD-exampleRefSeq.fa’
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘fg_step_tab_pp’
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustered.Rmd’ using rmarkdown
--- finished re-building ‘clustered.Rmd’

--- re-building ‘corelationmat.Rmd’ using rmarkdown
--- finished re-building ‘corelationmat.Rmd’

--- re-building ‘correlated.Rmd’ using rmarkdown
--- finished re-building ‘correlated.Rmd’

--- re-building ‘double_dot_extension.Rmd’ using rmarkdown
--- finished re-building ‘double_dot_extension.Rmd’

--- re-building ‘longitudinal.Rmd’ using rmarkdown
--- finished re-building ‘longitudinal.Rmd’

--- re-building ‘missing.Rmd’ using rmarkdown
--- finished re-building ‘missing.Rmd’

--- re-building ‘ordinal.Rmd’ using rmarkdown
--- finished re-building ‘ordinal.Rmd’

--- re-building ‘simstudy.Rmd’ using rmarkdown
--- finished re-building ‘simstudy.Rmd’

--- re-building ‘spline.Rmd’ using rmarkdown
--- finished re-building ‘spline.Rmd’

--- re-building ‘survival.Rmd’ using rmarkdown
Quitting from lines 161-162 (survival.Rmd) 
Error: processing vignette ‘survival.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘survival.Rmd’

--- re-building ‘treat_and_exposure.Rmd’ using rmarkdown
--- finished re-building ‘treat_and_exposure.Rmd’

SUMMARY: processing the following file failed:
  ‘survival.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘SIPmg-vignette.Rmd’ using rmarkdown
Quitting from lines 247-255 (SIPmg-vignette.Rmd) 
Error: processing vignette ‘SIPmg-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘SIPmg-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘SIPmg-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in ‘sjlabelled-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_factor
> ### Title: Convert variable into factor and keep value labels
> ### Aliases: as_factor to_factor as_factor.data.frame
> 
> ### ** Examples
> 
> if (require("sjmisc") && require("magrittr")) {
+   data(efc)
+   # normal factor conversion, loses value attributes
+   x <- as.factor(efc$e42dep)
+   frq(x)
+ 
+   # factor conversion, which keeps value attributes
+   x <- as_factor(efc$e42dep)
+   frq(x)
+ 
+   # create partially labelled vector
+   x <- set_labels(
+     efc$e42dep,
+     labels = c(
+       `1` = "independent",
+       `4` = "severe dependency",
+       `9` = "missing value"
+    ))
+ 
+   # only copy existing value labels
+   as_factor(x) %>% head()
+   get_labels(as_factor(x), values = "p")
+ 
+   # also add labels to non-labelled values
+   as_factor(x, add.non.labelled = TRUE) %>% head()
+   get_labels(as_factor(x, add.non.labelled = TRUE), values = "p")
+ 
+ 
+   # easily coerce specific variables in a data frame to factor
+   # and keep other variables, with their class preserved
+   as_factor(efc, e42dep, e16sex, c172code) %>% head()
+ 
+   # use select-helpers from dplyr-package
+   if (require("dplyr")) {
+     as_factor(efc, contains("cop"), c161sex:c175empl) %>% head()
+   }
+ }
Loading required package: sjmisc
Loading required package: magrittr
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: frq ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sjlabelled.Rmd’ using rmarkdown
Quitting from lines 217-225 (intro_sjlabelled.Rmd) 
Error: processing vignette ‘intro_sjlabelled.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘intro_sjlabelled.Rmd’

--- re-building ‘labelleddata.Rmd’ using rmarkdown
--- finished re-building ‘labelleddata.Rmd’

--- re-building ‘quasiquotation.Rmd’ using rmarkdown
Quitting from lines 32-57 (quasiquotation.Rmd) 
Error: processing vignette ‘quasiquotation.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘quasiquotation.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_sjlabelled.Rmd’ ‘quasiquotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘design_philosophy.Rmd’ using rmarkdown
--- finished re-building ‘design_philosophy.Rmd’

--- re-building ‘exploringdatasets.Rmd’ using rmarkdown
Quitting from lines 38-39 (exploringdatasets.Rmd) 
Error: processing vignette ‘exploringdatasets.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘exploringdatasets.Rmd’

--- re-building ‘recodingvariables.Rmd’ using rmarkdown
Quitting from lines 43-53 (recodingvariables.Rmd) 
Error: processing vignette ‘recodingvariables.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘recodingvariables.Rmd’

SUMMARY: processing the following files failed:
  ‘exploringdatasets.Rmd’ ‘recodingvariables.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sjPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_frq
> ### Title: Plot frequencies of variables
> ### Aliases: plot_frq
> 
> ### ** Examples
> 
> library(sjlabelled)
> data(efc)
> data(iris)
> 
> # simple plots, two different notations
> plot_frq(iris, Species)
> plot_frq(efc$tot_sc_e)
> 
> # boxplot
> plot_frq(efc$e17age, type = "box")
Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
ℹ Please use the `fun` argument instead.
ℹ The deprecated feature was likely used in the sjPlot package.
  Please report the issue at <https://github.com/strengejacke/sjPlot/issues>.
> 
> if (require("dplyr")) {
+   # histogram, pipe-workflow
+   efc %>%
+     dplyr::select(e17age, c160age) %>%
+     plot_frq(type = "hist", show.mean = TRUE)
+ 
+   # bar plot(s)
+   plot_frq(efc, e42dep, c172code)
+ }
Loading required package: dplyr

Attaching package: ‘dplyr’

The following object is masked from ‘package:sjlabelled’:

    as_label

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot_frq ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown
Quitting from lines 141-145 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following file failed:
  ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Quitting from lines 83-84 (basic_usage.Rmd) 
Error: processing vignette ‘basic_usage.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘basic_usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ‘:::’ call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ex0723.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ex0915.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) ex1515.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Unknown package ‘InformationValue’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Specified C++11: please drop specification unless essential
Running examples in ‘smotefamily-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ANS
> ### Title: Adaptive Neighbor Synthetic Majority Oversampling TEchnique
> ### Aliases: ANS
> ### Keywords: manip methods
> 
> ### ** Examples
> 
> 	data_example = sample_generator(5000,ratio = 0.80)
> 	genData = ANS(data_example[,-3],data_example[,3])
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: ANS -> <Anonymous> -> get.knnx
Execution halted
Running examples in ‘SMOTEWB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SMOTE
> ### Title: Synthetic Minority Oversampling Technique (SMOTE)
> ### Aliases: SMOTE
> 
> ### ** Examples
> 
> 
> set.seed(1)
> x <- rbind(matrix(rnorm(2000, 3, 1), ncol = 2, nrow = 1000),
+            matrix(rnorm(100, 5, 1), ncol = 2, nrow = 50))
> y <- as.factor(c(rep("negative", 1000), rep("positive", 50)))
> 
> plot(x, col = y)
> 
> # resampling
> m <- SMOTE(x = x, y = y, k = 7)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: SMOTE -> <Anonymous> -> get.knnx
Execution halted
Found the following files/directories:
  ‘my_new_social_media_plot.png’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  SnowballC_init.c:7:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  stem.c:59:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SnowballC.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.solveEnv’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.som.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) som.Rd:128: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘r2cytoscape’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘spatial_multivariate.Rmd’ using rmarkdown
Quitting from lines 91-104 (spatial_multivariate.Rmd) 
Error: processing vignette ‘spatial_multivariate.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘spatial_multivariate.Rmd’

SUMMARY: processing the following file failed:
  ‘spatial_multivariate.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.tbl_spark:
  function(tbl, size, replace, weight, .env)

slice_:
  function(.data, ..., .dots)
slice_.tbl_spark:
  function(x, ...)

op_vars:
  function(op)
op_vars.tbl_spark:
  function(x)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.tbl_spark:
  function(tbl, size, replace, weight, .env)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Unknown package ‘sparsebn’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘sparseR.Rmd’ using rmarkdown
Quitting from lines 325-330 (sparseR.Rmd) 
Error: processing vignette ‘sparseR.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘sparseR.Rmd’

SUMMARY: processing the following file failed:
  ‘sparseR.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘RStoolbox’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
checkRd: (-1) sarorderedprobit.Rd:84: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Running examples in ‘spatialTIME-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: subset_mif
> ### Title: Subset mif object on cellular level
> ### Aliases: subset_mif
> 
> ### ** Examples
> 
> #' #Create mif object
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> x <- create_mif(clinical_data = example_clinical %>% 
+ mutate(deidentified_id = as.character(deidentified_id)),
+ sample_data = example_summary %>% 
+ mutate(deidentified_id = as.character(deidentified_id)),
+ spatial_list = example_spatial,
+ patient_id = "deidentified_id", 
+ sample_id = "deidentified_sample")
> 
> markers = c("CD3..Opal.570..Positive","CD8..Opal.520..Positive",
+ "FOXP3..Opal.620..Positive","PDL1..Opal.540..Positive",
+ "PD1..Opal.650..Positive","CD3..CD8.","CD3..FOXP3.")
> 
> mif_tumor = subset_mif(mif = x, classifier = 'Classifier.Label', 
+ level = 'Tumor', markers = markers)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: subset_mif ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 315-319 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat.data', 'spatstat',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'

Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package unavailable to check Rd xrefs: ‘RandomFields’
Packages suggested but not available for checking:
  'RandomFields', 'RandomFieldsUtils'
Package unavailable to check Rd xrefs: ‘RandomFields’
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.geom', 'spatstat.random',
  'spatstat.explore', 'spatstat.model', 'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spDataLarge’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BWR
> ### Title: BW ratio calculation
> ### Aliases: BWR
> 
> ### ** Examples
> 
> res=makeSimulatedData();
> X=res$data;
> groupLabel=res$label;
> peakList <- detectSpecPeaks(X,
+                             nDivRange = c(128),
+                             scales = seq(1, 16, 2),
+                             baselineThresh = 50000,
+                             SNR.Th = -1,
+                             verbose=FALSE
+ );
> resFindRef<- findRef(peakList);
> refInd <- resFindRef$refInd;
> maxShift = 50;
> Y <- dohCluster(X,
+                 peakList = peakList,
+                 refInd = refInd,
+                 maxShift  = maxShift,
+                 acceptLostPeak = TRUE, verbose=FALSE);
Warning in min(peakList) :
  no non-missing arguments to min; returning Inf
Warning in max(peakList) :
  no non-missing arguments to max; returning -Inf
Error in startP:(minpeakList - 1) : result would be too long a vector
Calls: dohCluster -> .withMaxShift -> hClustAlign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'Unaligned_spectral_plots'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'Peak_detection'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'Reference_finding'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'Spectral_alignment'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Quitting from lines 111-120 (classic_speaq_vignette.Rmd) 
Error: processing vignette ‘classic_speaq_vignette.Rmd’ failed with diagnostics:
result would be too long a vector
--- failed re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 71-83 (speaq2_illustrations.Rmd) 
Error: processing vignette ‘speaq2_illustrations.Rmd’ failed with diagnostics:
invalid ‘times’ argument
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following files failed:
  ‘classic_speaq_vignette.Rmd’ ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
spFSR:
  function(x, ...)
spFSR.default:
  function(task, wrapper, scoring, perturb.amount, gain.min, gain.max,
           change.min, change.max, bb.bottom.threshold, mon.gain.A,
           mon.gain.a, mon.gain.alpha, hot.start.num.ft.factor,
           hot.start.max.auto.num.ft, use.hot.start, hot.start.range,
           rf.n.estimators, gain.type, num.features.selected,
           iters.max, stall.limit, n.samples.max, ft.weighting,
           encoding.type, is.debug, stall.tolerance, random.state,
           rounding, run.parallel, n.jobs, show.info, print.freq,
           num.cv.folds, num.cv.reps.eval, num.cv.reps.grad,
           num.grad.avg, perf.eval.method)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
Specified C++11: please drop specification unless essential
checkRd: (-1) PimaIndiansDiabetes_long.Rd:14: Escaped LaTeX specials: \^
checkRd: (-1) PimaIndiansDiabetes_wide.Rd:16: Escaped LaTeX specials: \^
Running examples in ‘spinifex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basis_guided
> ### Title: Solve for the last basis of a guided tour.
> ### Aliases: basis_guided
> 
> ### ** Examples
> 
> dat <- scale_sd(wine[, 2:6])
> basis_guided(data = dat, index_f = tourr::holes())
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: basis_guided ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_spinifex.Rmd’ using rmarkdown
Quitting from lines 224-230 (getting_started_with_spinifex.Rmd) 
Error: processing vignette ‘getting_started_with_spinifex.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘getting_started_with_spinifex.Rmd’

--- re-building ‘ggproto_api.Rmd’ using rmarkdown
--- finished re-building ‘ggproto_api.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_spinifex.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  spMC.h:44:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  spMC.c:303:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spMC.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Parallel computation will not perform. CPU cores in use: 1.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘spqdep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.test
> ### Title: A function to compute Q test for spatial qualitative data
> ### Aliases: Q.test
> 
> ### ** Examples
> 
> 
> # Case 1: With coordinates
> N <- 200
> cx <- runif(N)
> cy <- runif(N)
> coor <- cbind(cx,cy)
> p <- c(1/6,3/6,2/6)
> rho = 0.3
> listw <- spdep::nb2listw(spdep::knn2nb(spdep::knearneigh(cbind(cx,cy), k = 4)))
> fx <- dgp.spq(list = listw, p = p, rho = rho)
> q.test <- Q.test(fx = fx, coor = coor, m = 3, r = 1)
> summary(q.test)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: summary ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spq_userguide.Rmd’ using rmarkdown
Quitting from lines 172-174 (spq_userguide.Rmd) 
Error: processing vignette ‘spq_userguide.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘spq_userguide.Rmd’

SUMMARY: processing the following file failed:
  ‘spq_userguide.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
autoplot:
  function(object, ...)
autoplot.qts_sample:
  function(x, memberships, highlighted, with_animation, ...)

autoplot:
  function(object, ...)
autoplot.qts:
  function(x, highlighted_points, ...)

autoplot:
  function(object, ...)
autoplot.prcomp_qts:
  function(x, what, ...)

autoplot:
  function(object, ...)
autoplot.kma_qts:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ssdtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ssd_hc_bcanz
> ### Title: BCANZ Hazard Concentrations
> ### Aliases: ssd_hc_bcanz
> 
> ### ** Examples
> 
> fits <- ssd_fit_bcanz(ssddata::ccme_boron)
> ssd_hc_bcanz(fits, nboot = 100)
Error in (function (.x, .f, ..., .progress = FALSE)  : ℹ In index: 1.
ℹ With name: gamma.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
Calls: ssd_hc_bcanz ... resolve.list -> signalConditionsASAP -> signalConditions
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘distributions.Rmd’ using rmarkdown
--- finished re-building ‘distributions.Rmd’

--- re-building ‘exposure-plots.Rmd’ using rmarkdown
--- finished re-building ‘exposure-plots.Rmd’

--- re-building ‘faqs.Rmd’ using rmarkdown
--- finished re-building ‘faqs.Rmd’

--- re-building ‘small-sample-bias-ref.Rmd’ using rmarkdown
--- finished re-building ‘small-sample-bias-ref.Rmd’

--- re-building ‘ssdtools.Rmd’ using rmarkdown
Quitting from lines 190-193 (ssdtools.Rmd) 
Error: processing vignette ‘ssdtools.Rmd’ failed with diagnostics:
ℹ In index: 1.
ℹ With name: llogis.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘ssdtools.Rmd’

--- re-building ‘small-sample-bias.pdf.asis’ using asis
--- finished re-building ‘small-sample-bias.pdf.asis’

SUMMARY: processing the following file failed:
  ‘ssdtools.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in ‘ssrn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_passenger_matrix
> ### Title: Convert passenger and station data to origin-destination matrix
> ### Aliases: make_passenger_matrix
> 
> ### ** Examples
> 
> jreast_jt_od %>%
+   make_passenger_matrix(jreast_jt,
+                         departure_st_code,
+                         arrive_st_code,
+                         st_code,
+                         volume)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
estfun:
  function(x, ...)
estfun.ssym:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) Snacks.Rd:6: Escaped LaTeX specials: \~
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Bug fixes
Error(s) in re-building vignettes:
  ...
--- re-building ‘stabiliser.Rmd’ using knitr
Quitting from lines 63-64 (stabiliser.Rmd) 
Error: processing vignette ‘stabiliser.Rmd’ failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘stabiliser.Rmd’

SUMMARY: processing the following file failed:
  ‘stabiliser.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Quitting from lines 195-223 (basics.Rmd) 
Error: processing vignette ‘basics.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘basics.Rmd’

--- re-building ‘classification.Rmd’ using rmarkdown
Quitting from lines 142-162 (classification.Rmd) 
Error: processing vignette ‘classification.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘classification.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘classification.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 302-324 (stacomir.Rmd) 
Error: processing vignette ‘stacomir.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) katrina.Rd:36: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘staRdom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eem_metatemplate
> ### Title: Create table that contains sample names and locations of files.
> ### Aliases: eem_metatemplate
> 
> ### ** Examples
> 
> folder <- system.file("extdata/EEMs", package = "staRdom") # load example data
> eem_list <- eem_read(folder, recursive = TRUE, import_function = eem_csv)
> data(absorbance)
> 
> eem_metatemplate(eem_list,absorbance)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: eem_metatemplate ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Package suggested but not available for checking: ‘starsdata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘stars1.Rmd’ using rmarkdown
Quitting from lines 182-184 (stars1.Rmd) 
Error: processing vignette ‘stars1.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
--- finished re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
--- finished re-building ‘stars5.Rmd’

--- re-building ‘stars6.Rmd’ using rmarkdown
--- finished re-building ‘stars6.Rmd’

--- re-building ‘stars7.Rmd’ using rmarkdown
--- finished re-building ‘stars7.Rmd’

--- re-building ‘stars8.Rmd’ using rmarkdown
Quitting from lines 26-29 (stars8.Rmd) 
Error: processing vignette ‘stars8.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘stars8.Rmd’

SUMMARY: processing the following files failed:
  ‘stars1.Rmd’ ‘stars8.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: join
> ### Title: Join two data frames together
> ### Aliases: join
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> x <- data.frame(a = rep(1:2, each = 3), b=1:6)
> y <- data.frame(a = 0:1, bb = 10:11)
> join(x, y, kind = "full")
Joining with `by = join_by(a)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: join ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘skip-download.R’ [0s/1s]
  Running ‘testthat.R’ [5s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stats19)
  Data provided under OGL v3.0. Cite the source and link to:
  www.nationalarchives.gov.uk/doc/open-government-licence/version/3/
  > 
  > test_check("stats19")
  trying URL 'https://data.dft.gov.uk/road-accidents-safety-data/dft-road-casualty-statistics-accident-2017.csv'
  Content type 'application/vnd.ms-excel' length 21356274 bytes (20.4 MB)
  ==================================================
  downloaded 20.4 MB
  
  [ FAIL 1 | WARN 1 | SKIP 10 | PASS 24 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (10)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-format.R:84:3'): format_ppp exclude events with missing coordinates ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, "location_easting_osgr", value = `<lgl>`) at test-format.R:84:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, "location_easting_osgr", value = `<lgl>`) at test-format.R:84:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 1 | SKIP 10 | PASS 24 ]
  Error: Test failures
  Execution halted
Running examples in ‘statsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot_bandit_posterior ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘INLA’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
rowwise:
  function(data, ...)
rowwise.sticky_rowwise_df:
  function(.data, ..., .add)

rowwise:
  function(data, ...)
rowwise.sticky_grouped_df:
  function(.data, ..., .add)

rowwise:
  function(data, ...)
rowwise.sticky_tbl_df:
  function(.data, ..., .add)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [38s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(strand)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("strand")
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 67 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_Simulation.R:125:1'): (code run outside of `test_that()`) ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, simple_pricing_data$id %in% "101", , value = `<dbl>`) at test_Simulation.R:125:0
   2. └─tibble:::`[<-.tbl_df`(...) at test_Simulation.R:125:0
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xo, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 67 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘strand.Rmd’ using rmarkdown
Quitting from lines 471-472 (strand.Rmd) 
Error: processing vignette ‘strand.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘strand.Rmd’

SUMMARY: processing the following file failed:
  ‘strand.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘StratifiedRF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: varimp_stratified_rf
> ### Title: Heuristic on variable importance
> ### Aliases: varimp_stratified_rf
> 
> ### ** Examples
> 
> data(iris)
> groups <- list(c("Sepal.Length","Sepal.Width"),c("Petal.Length","Petal.Width"))
> mtry <- c(1,1)
> m <- stratified_rf(iris,"Species",groups,mtry,ntrees=2,multicore=FALSE)
> varimp_stratified_rf(m)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: varimp_stratified_rf ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘STraTUS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build.edgelist
> ### Title: For a sample, produce the transmission tree as a 'igraph' object
> ### Aliases: build.edgelist
> 
> ### ** Examples
> 
> generator <- tt.generator(stratus.example.tree)
> samples <- sample.tt(generator, 1)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: sample.tt ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘stray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: display_HDoutliers
> ### Title: Display outliers with a scatterplot
> ### Aliases: display_HDoutliers
> 
> ### ** Examples
> 
> data <- c(rnorm(100), 7, 7.5, rnorm(100, 20), 45)
> output <- find_HDoutliers(data, knnsearchtype = "kd_tree")
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: find_HDoutliers -> use_KNN -> <Anonymous> -> get.knn
Execution halted
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Running examples in ‘stRoke-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generic_stroke
> ### Title: Generic stroke study outcome
> ### Aliases: generic_stroke
> 
> ### ** Examples
> 
> generic_stroke(df = stRoke::talos, group = "rtreat", score = "mrs_6", 
+ variables = c("hypertension","diabetes","civil"))
Waiting for profiling to be done...
$`Table 1`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘toolbox.Rmd’ using rmarkdown
Quitting from lines 113-117 (toolbox.Rmd) 
Error: processing vignette ‘toolbox.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘toolbox.Rmd’

SUMMARY: processing the following file failed:
  ‘toolbox.Rmd’

Error: Vignette re-building failed.
Execution halted
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘stxplore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hovmoller
> ### Title: Computes the data structure for the Hovmoller plots
> ### Aliases: hovmoller hovmoller.data.frame hovmoller.stars
> ###   autoplot.hovmoller
> 
> ### ** Examples
> 
> # dataframe examples
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data(NOAA_df_1990)
> Tmax <- filter(NOAA_df_1990,
+   proc == "Tmax" &
+   month %in% 5:9 &
+   year == 1993 &
+   id < 4000)
> Tmax$t <- Tmax$julian - min(Tmax$julian) + 1
> hov <- hovmoller(lat_or_lon = "lat",
+           x = Tmax,
+           lat_or_lon_col = 'lat',
+           t_col = 't',
+           z_col = 'z')
Consider reducing xlen to eliminate empty patches.
> autoplot(hov)
> 
> # stars examples
> library(stars)
Loading required package: abind
Loading required package: sf
Linking to GEOS 3.11.1, GDAL 3.6.2, PROJ 9.1.1; sf_use_s2() is TRUE
> prec_file = system.file("nc/test_stageiv_xyt.nc", package = "stars")
> prec <- read_ncdf(prec_file)
no 'var' specified, using Total_precipitation_surface_1_Hour_Accumulation
other available variables:
 lat, lon, time
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: read_ncdf ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘subrank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: corc
> ### Title: Function to estimate copula using ranks and sub-sampling
> ### Aliases: corc
> 
> ### ** Examples
> 
> lon <- 30
> a <- 2
> x <- rnorm(lon)
> y = a*x^2+rnorm(lon)
> datatable = as.data.frame(cbind(x,y))
> c=corc(datatable,c("x","y"),8)
Error in corc0(obs, nnm, dimension, subsampsize, nboot, u, mixties, nthreads = nthreads) : 
  DLL requires the use of native symbols
Calls: corc -> corc0
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘suddengains-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_byperson
> ### Title: Create a data set with one gain per person
> ### Aliases: create_byperson
> 
> ### ** Examples
> 
> # Create byperson data set, selecting the largest gain in case of muliple gains
> create_byperson(data = sgdata,
+                 sg_crit1_cutoff = 7,
+                 id_var_name = "id",
+                 tx_start_var_name = "bdi_s1",
+                 tx_end_var_name = "bdi_s12",
+                 sg_var_list = c("bdi_s1", "bdi_s2", "bdi_s3",
+                                 "bdi_s4", "bdi_s5", "bdi_s6",
+                                 "bdi_s7", "bdi_s8", "bdi_s9",
+                                 "bdi_s10", "bdi_s11", "bdi_s12"),
+                 sg_measure_name = "bdi",
+                 multiple_sg_select = "largest")
First, second, and third sudden gains criteria were applied.
The critical value for the third criterion was adjusted for missingness.
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: create_byperson ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shinygains.Rmd’ using rmarkdown
--- finished re-building ‘shinygains.Rmd’

--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Quitting from lines 402-412 (suddengains-tutorial.Rmd) 
Error: processing vignette ‘suddengains-tutorial.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sugarbag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allocate
> ### Title: Allocate polygon centroids to hexagons in a grid
> ### Aliases: allocate
> 
> ### ** Examples
> 
> # Create centroids set
> centroids <- create_centroids(tas_lga, sf_id = "lga_code_2016")
> # Smaller set for faster example
> centroids <- centroids[1:10,] 
> # Create hexagon location grid
> data(capital_cities)
> grid <- create_grid(centroids = centroids, hex_size = 0.2, buffer_dist = 1.2)
> # Allocate polygon centroids to hexagon grid points
> hex_allocated <- allocate(
+   centroids = centroids,
+   hex_grid = grid,
+   hex_size = 0.2, # same size used in create_grid
+   hex_filter = 3,
+   focal_points = capital_cities,
+   width = 30, 
+   verbose = TRUE
+ )
Finding closest point in focal_points data set.
Allocating centroids, in order of distance to closest focal point.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: allocate ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tasmania.Rmd’ using rmarkdown
Quitting from lines 77-87 (Tasmania.Rmd) 
Error: processing vignette ‘Tasmania.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Tasmania.Rmd’

SUMMARY: processing the following file failed:
  ‘Tasmania.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘frame-calendar.Rmd’ using rmarkdown
Quitting from lines 146-161 (frame-calendar.Rmd) 
Error: processing vignette ‘frame-calendar.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘frame-calendar.Rmd’

SUMMARY: processing the following file failed:
  ‘frame-calendar.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:106:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_linearsolver.c:28:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_matrix.c:29:11: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nonlinearsolver.c:26:20: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  sundials/sundials/sundials_nvector.c:28:10: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sundialr.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘supercompress-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: supercompress
> ### Title: Supervised Data Compression via Clustering.
> ### Aliases: supercompress
> 
> ### ** Examples
> 
> #########################################################################
> # One dimensional example
> #########################################################################
> # generate big data
> set.seed(1)
> N <- 3000
> x <- seq(0,1,length=N)
> f <- function(x) dnorm(x, mean = 0.4, sd = 0.01)
> y <- f(x) + 0.1 * rnorm(N)
> x <- matrix(x, ncol=1)
> # visualize big data
> plot(x,y,cex=.5,main="Big Data",cex.main=3,xlab="x",ylab="y",cex.lab=2, cex.axis=2)
> # big data reduction via supercompress
> n <- 30
> sc <- supercompress(n,x,y,lam=0)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: supercompress -> knnx.index -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Unknown package ‘extraTrees’ in Rd xrefs
Package suggested but not available for checking: ‘extraTrees’
Specified C++11: please drop specification unless essential
Running examples in ‘superml-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KNNTrainer
> ### Title: K Nearest Neighbours Trainer
> ### Aliases: KNNTrainer
> 
> ### ** Examples
> 
> data("iris")
> 
> iris$Species <- as.integer(as.factor(iris$Species))
> 
> xtrain <- iris[1:100,]
> xtest <- iris[101:150,]
> 
> bst <- KNNTrainer$new(k=3, prob=TRUE, type="class")
> bst$fit(xtrain, xtest, 'Species')
Error in get.knnx(data = train, query = test, k = k, algorithm) : 
  DLL requires the use of native symbols
Calls: <Anonymous> -> <Anonymous> -> get.knnx
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Guide-to-CountVectorizer.Rmd’ using rmarkdown
--- finished re-building ‘Guide-to-CountVectorizer.Rmd’

--- re-building ‘Guide-to-TfidfVectorizer.Rmd’ using rmarkdown
--- finished re-building ‘Guide-to-TfidfVectorizer.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 111-116 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
autoplot:
  function(object, ...)
autoplot.pairwise:
  function(x, ...)

tbl_sum:
  function(x)
tbl_sum.pairwise_tbl:
  function(x, setup, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘survAUC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AUC.cd
> ### Title: AUC estimator proposed by Chambless and Diao
> ### Aliases: AUC.cd
> ### Keywords: classif
> 
> ### ** Examples
> 
> data(cancer,package="survival")
> TR <- ovarian[1:16,]
> TE <- ovarian[17:26,]
> train.fit  <- survival::coxph(survival::Surv(futime, fustat) ~ age,
+                     x=TRUE, y=TRUE, method="breslow", data=TR)
> 
> lp <- predict(train.fit)
> lpnew <- predict(train.fit, newdata=TE)
> Surv.rsp <- survival::Surv(TR$futime, TR$fustat)
> Surv.rsp.new <- survival::Surv(TE$futime, TE$fustat)
> times <- seq(10, 1000, 10)                  
> 
> AUC_CD <- AUC.cd(Surv.rsp, Surv.rsp.new, lp, lpnew, times)
Error in AUC.cd(Surv.rsp, Surv.rsp.new, lp, lpnew, times) : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Running examples in ‘surveillance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: epidataCS_aggregate
> ### Title: Conversion (aggregation) of '"epidataCS"' to '"epidata"' or
> ###   '"sts"'
> ### Aliases: epidataCS2sts as.epidata.epidataCS
> ### Keywords: spatial manip methods
> 
> ### ** Examples
> 
> data("imdepi")
> load(system.file("shapes", "districtsD.RData", package="surveillance"))
> 
> ## convert imdepi point pattern into multivariate time series
> imdsts <- epidataCS2sts(imdepi, freq = 12, start = c(2002, 1),
+                         neighbourhood = NULL, # not needed here
+                         tiles = districtsD)
> 
> ## check the overall number of events by district
> stopifnot(all.equal(colSums(observed(imdsts)),
+                     c(table(imdepi$events$tile))))
> 
> ## compare plots of monthly number of cases
> opar <- par(mfrow = c(2, 1))
> plot(imdepi, "time")
> plot(imdsts, type = observed ~ time)
> par(opar)
> 
> ## Don't show: 
> if (surveillance.options("allExamples"))
+ ## End(Don't show)
+ ## plot number of cases by district
+ plot(imdsts, type = observed ~ unit)
> 
> ## also test conversion to an SIS event history ("epidata") of the "tiles"
> if (requireNamespace("intervals")) {
+     imdepi_short <- subset(imdepi, time < 50)  # to reduce the runtime
+     imdepi_short$stgrid <- subset(imdepi_short$stgrid, start < 50)
+     imdepidata <- as.epidata(imdepi_short,
+                              tileCentroids = coordinates(districtsD))
+     summary(imdepidata)
+ }
Loading required namespace: intervals
Error in .local(x, ...) : DLL requires the use of native symbols
Calls: as.epidata ... as.matrix -> <Anonymous> -> <Anonymous> -> .local -> .Call
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) estweights.Rd:42: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘INLA’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘distr6’
Unknown package ‘distr6’ in Rd xrefs
Specified C++11: please drop specification unless essential
Unknown package ‘survJamda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [104s/163s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(survParamSim)
  > 
  > # options(lifecycle_verbosity = "error")
  > test_check("survParamSim")
  [ FAIL 1 | WARN 4 | SKIP 4 | PASS 51 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  • Too heavy to run routinely (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-calc_hr_pi.R:45:3'): error if you have NA in treatment ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, "trt", value = `<lgl>`) at test-calc_hr_pi.R:45:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, "trt", value = `<lgl>`) at test-calc_hr_pi.R:45:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 4 | SKIP 4 | PASS 51 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) diabetes.Rd:18: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Unknown package ‘robets’ in Rd xrefs
Running examples in ‘sweep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidiers_robets
> ### Title: Tidying methods for robets (Robust Error, Trend, Seasonal)
> ###   exponential smoothing modeling of time series
> ### Aliases: tidiers_robets sw_tidy.robets sw_glance.robets
> ###   sw_augment.robets sw_tidy_decomp.robets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(robets)
Error in library(robets) : there is no package called ‘robets’
Execution halted
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sweep)
  > library(timetk)
  > library(forecast)
  > library(tidyverse)
  ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
  ✔ dplyr     1.1.0     ✔ readr     2.1.4
  ✔ forcats   1.0.0     ✔ stringr   1.5.0
  ✔ ggplot2   3.4.1     ✔ tibble    3.2.0
  ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
  ✔ purrr     1.0.1     
  ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
  ✖ readr::edition_get()   masks testthat::edition_get()
  ✖ dplyr::filter()        masks stats::filter()
  ✖ purrr::is_null()       masks testthat::is_null()
  ✖ dplyr::lag()           masks stats::lag()
  ✖ readr::local_edition() masks testthat::local_edition()
  ✖ dplyr::matches()       masks tidyr::matches(), testthat::matches()
  ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
  > library(robets)
  Error in library(robets) : there is no package called 'robets'
  Execution halted
Package suggested but not available for checking: ‘swephRdata’
Found the following significant warnings:
  libswe/swephlib.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.h:130:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.h:120:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swepcalc.c:373:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/sweph.c:7099:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  libswe/swephlib.c:3033:7: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/swephR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Running examples in ‘SWMPr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_quants
> ### Title: Create a plot of data for a single year overlaid on historical
> ###   data.
> ### Aliases: plot_quants plot_quants.swmpr
> 
> ### ** Examples
> 
> # qaqc
> dat <- qaqc(apacpwq)
> 
> # generate a plot of salinity for 2013 overlaid on 2012-2013 data
> plot_quants(dat, 'sal', yr = 2013, yrstart = 2012, yrend = 2013)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: plot_quants ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
bread:
  function(x, ...)
bread.systemfit:
  function(obj, ...)

estfun:
  function(x, ...)
estfun.systemfit:
  function(obj, residFit, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.xls’ ‘attenu.xls’ ‘chick1.xls’ ‘chick2.xls’ ‘generic1.xls’
  ‘hands.xls’ ‘table1.xls’
Error(s) in re-building vignettes:
  ...
--- re-building ‘default_rounder.Rmd’ using rmarkdown
--- finished re-building ‘default_rounder.Rmd’

--- re-building ‘table_guide.Rmd’ using rmarkdown
Quitting from lines 89-108 (table_guide.Rmd) 
Error: processing vignette ‘table_guide.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘table_guide.Rmd’

SUMMARY: processing the following file failed:
  ‘table_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘tame-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: employ
> ### Title: Employ a Clustering to New Data
> ### Aliases: employ
> 
> ### ** Examples
> 
> part1 <- complications[1:100,]
> part2 <- complications[101:149,]
> 
> clust <- medic(part1, id = id, atc = atc, k = 3)
> 
> # Nearest cluster matching
> employ(clust, part2)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: employ ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
'LazyData' is specified without a 'data' directory
is_valid:
  function(x, ...)
is_valid.Stacked_table:
  function(x)

is_valid:
  function(x, ...)
is_valid.Mashed_table:
  function(x)

is_valid:
  function(x, ...)
is_valid.TT_meta:
  function(dat)

is_valid:
  function(x, ...)
is_valid.Tatoo_report:
  function(x)

as.data.table:
  function(x, keep.rownames, ...)
as.data.table.Composite_table:
  function(x, multinames, sep, ...)

as.data.table:
  function(x, keep.rownames, ...)
as.data.table.Mashed_table:
  function(x, mash_method, insert_blank_row, id_vars, suffixes)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘taxonbridge-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate
> ### Title: Annotate a custom taxonomy
> ### Aliases: annotate
> 
> ### ** Examples
> 
> sample <- load_sample()

#####  ##   #    #   ###   #    #  ####   ####   #####  ####    #####  #####
  #   #  #   #  #   #   #  ##   #  #   #  #   #    #    #   #   #      #    
  #   ####    #     #   #  # #  #  #####  #####    #    #    #  #  ##  #####
  #   #  #   #  #   #   #  #  # #  #   #  #  #     #    #   #   #   #  #    
  #   #  #  #    #   ###   #    #  ####   #   #  #####  ####    #####  #####

A sample containing 2000 rows by 29 columns has been loaded.
Visit the following links to learn more about Taxonbridge:
https://github.com/MoultDB/taxonbridge#available-methods-and-how-to-use-them
https://github.com/MoultDB/taxonbridge/blob/master/taxonbridge_workflow.pdf
https://rdocumentation.org/packages/taxonbridge/
https://CRAN.R-project.org/package=taxonbridge
> lineages <- get_lineages(sample)
> kingdom <- get_validity(lineages, rank = "kingdom", valid = FALSE)
Term conversion carried out on kingdom taxonomic rank
> family <- get_validity(lineages, rank = "family", valid = FALSE)
> candidates <- list(kingdom, family)
> binomials <- get_inconsistencies(candidates, uninomials = FALSE, set = "intersect")
> x <- annotate(sample, binomials, new_column = "inconsistencies", "Accepted but ambigious")
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: annotate ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown
Quitting from lines 100-102 (Examples.Rmd) 
Error: processing vignette ‘Examples.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Examples.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘TDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterTree
> ### Title: Density clustering: the cluster tree
> ### Aliases: clusterTree print.clusterTree
> ### Keywords: nonparametric
> 
> ### ** Examples
> 
> ## Generate data: 3 clusters
> n <- 1200    #sample size
> Neach <- floor(n / 4) 
> X1 <- cbind(rnorm(Neach, 1, .8), rnorm(Neach, 5, 0.8))
> X2 <- cbind(rnorm(Neach, 3.5, .8), rnorm(Neach, 5, 0.8))
> X3 <- cbind(rnorm(Neach, 6, 1), rnorm(Neach, 1, 1))
> X <- rbind(X1, X2, X3)
> 
> k <- 100     #parameter of knn
> 
> ## Density clustering using knn and kde
> Tree <- clusterTree(X, k, density = "knn")
Error in FNN::get.knn(X, k = k, algorithm = "kd_tree") : 
  DLL requires the use of native symbols
Calls: clusterTree -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rnw’ using Sweave

Error: processing vignette ‘article.Rnw’ failed with diagnostics:
 chunk 3 (label = eq2) 
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols

--- failed re-building ‘article.Rnw’

SUMMARY: processing the following file failed:
  ‘article.Rnw’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘R2wd’
checkRd: (-1) R2txt.Rd:164: Escaped LaTeX specials: \#
checkRd: (-1) bct.Rd:18: Escaped LaTeX specials: \^
checkRd: (-1) bct.Rd:19: Escaped LaTeX specials: \^
checkRd: (-1) ineq.Rd:10: Escaped LaTeX specials: \&
checkRd: (-1) put.points.demo.Rd:39: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:10: Escaped LaTeX specials: \^
checkRd: (-1) run.cor.examp.Rd:31: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘packages_introduction.Rmd’ using rmarkdown
Quitting from lines 43-65 (packages_introduction.Rmd) 
Error: processing vignette ‘packages_introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘packages_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘packages_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages which this enhances but not available for checking:
  'mnlogit', 'Zelig'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘textreuse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lsh_compare
> ### Title: Compare candidates identified by LSH
> ### Aliases: lsh_compare
> 
> ### ** Examples
> 
> dir <- system.file("extdata/legal", package = "textreuse")
> minhash <- minhash_generator(200, seed = 234)
> corpus <- TextReuseCorpus(dir = dir,
+                           tokenizer = tokenize_ngrams, n = 5,
+                           minhash_func = minhash)
> buckets <- lsh(corpus, bands = 50)
> candidates <- lsh_candidates(buckets)
> lsh_compare(candidates, corpus, jaccard_similarity)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: lsh_compare ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(textreuse)
  > 
  > test_check("textreuse")
  [ FAIL 1 | WARN 3 | SKIP 2 | PASS 129 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lsh.R:11:1'): (code run outside of `test_that()`) ──────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─textreuse::lsh_compare(candidates, corpus, jaccard_similarity) at test-lsh.R:11:0
   2.   ├─base::`[<-`(`*tmp*`, i, "score", value = `<dbl>`)
   3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, i, "score", value = `<dbl>`)
   4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   5.       └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   6.         ├─base::withCallingHandlers(...)
   7.         └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 3 | SKIP 2 | PASS 129 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘textreuse-alignment.Rmd’ using rmarkdown
--- finished re-building ‘textreuse-alignment.Rmd’

--- re-building ‘textreuse-introduction.Rmd’ using rmarkdown
--- finished re-building ‘textreuse-introduction.Rmd’

--- re-building ‘textreuse-minhash.Rmd’ using rmarkdown
Quitting from lines 86-87 (textreuse-minhash.Rmd) 
Error: processing vignette ‘textreuse-minhash.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘textreuse-minhash.Rmd’

--- re-building ‘textreuse-pairwise.Rmd’ using rmarkdown
--- finished re-building ‘textreuse-pairwise.Rmd’

SUMMARY: processing the following file failed:
  ‘textreuse-minhash.Rmd’

Error: Vignette re-building failed.
Execution halted
Unknown package ‘textreadr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘thurstonianIRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit_TIRT_lavaan
> ### Title: Fit Thurstonian IRT models in lavaan
> ### Aliases: fit_TIRT_lavaan
> 
> ### ** Examples
> 
> # load the data
> data("triplets")
> 
> # define the blocks of items
> blocks <-
+   set_block(c("i1", "i2", "i3"), traits = c("t1", "t2", "t3"),
+           signs = c(1, 1, 1)) +
+   set_block(c("i4", "i5", "i6"), traits = c("t1", "t2", "t3"),
+             signs = c(-1, 1, 1)) +
+   set_block(c("i7", "i8", "i9"), traits = c("t1", "t2", "t3"),
+             signs = c(1, 1, -1)) +
+   set_block(c("i10", "i11", "i12"), traits = c("t1", "t2", "t3"),
+             signs = c(1, -1, 1))
> 
> # generate the data to be understood by 'thurstonianIRT'
> triplets_long <- make_TIRT_data(
+   data = triplets, blocks = blocks, direction = "larger",
+   format = "pairwise", family = "bernoulli", range = c(0, 1)
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: make_TIRT_data ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [5s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidycharts)
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Loading required package: knitr
  > 
  > test_check("tidycharts")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-column_chart_functions.R:69:3'): Stacked column charts are generating ──
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 1, 2:4, value = `<df[,3]>`) at test-column_chart_functions.R:69:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 1, 2:4, value = `<df[,3]>`) at test-column_chart_functions.R:69:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 75 ]
  Error: Test failures
  Execution halted
Running examples in ‘tidycmprsk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_cuminc
> ### Title: Additional Functions for 'tbl_cuminc()'
> ### Aliases: add_cuminc add_p.tbl_cuminc add_n.tbl_cuminc
> ###   add_nevent.tbl_cuminc inline_text.tbl_cuminc
> 
> ### ** Examples
> 
> # Example 1 ----------------------------------
> add_cuminc_ex1 <-
+   cuminc(Surv(ttdeath, death_cr) ~ 1, trial) %>%
+   tbl_cuminc(times = c(12, 24), label_header = "**Month {time}**") %>%
+   add_nevent() %>%
+   add_n()
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [19s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidycomm)
  
  Attaching package: 'tidycomm'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("tidycomm")
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 153 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-icr.R:49:3'): test_icr produces warning with missing data ──────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 4, 4, value = `<lgl>`) at test-icr.R:49:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 4, 4, value = `<lgl>`) at test-icr.R:49:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  ── Error ('test-icr.R:58:3'): test_icr removes missing data if specified ───────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 4, 4, value = `<lgl>`) at test-icr.R:58:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 4, 4, value = `<lgl>`) at test-icr.R:58:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 2 | WARN 14 | SKIP 0 | PASS 153 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘tidygate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gate
> ### Title: DEPRECATED - use gate_chr, gate_int instead inside a
> ###   dplyr::mutate() statement
> ### Aliases: gate gate.spec_tbl_df gate.tbl_df
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> 
> library(magrittr)
> 
> tidygate::tidygate_data  %>%
+  gate(
+    .element = c(`ct 1`, `ct 2`),
+    Dim1, Dim2,
+    gate_list = tidygate::gate_list
+  )
Warning: `gate()` was deprecated in tidygate 0.3.0.
ℹ Please use `gate_chr()` instead.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introdution.Rmd’ using knitr
Quitting from lines 90-98 (introdution.Rmd) 
Error: processing vignette ‘introdution.Rmd’ failed with diagnostics:
ℹ In argument: `gate = gate_chr(Dim1, Dim2, gate_list = my_gates)`.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘introdution.Rmd’

SUMMARY: processing the following file failed:
  ‘introdution.Rmd’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Running examples in ‘tidygraph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_join
> ### Title: Join graphs on common nodes
> ### Aliases: graph_join
> 
> ### ** Examples
> 
> gr1 <- create_notable('bull') %>%
+   activate(nodes) %>%
+   mutate(name = letters[1:5])
> gr2 <- create_ring(10) %>%
+   activate(nodes) %>%
+   mutate(name = letters[4:13])
> 
> gr1 %>% graph_join(gr2)
Joining with `by = join_by(name)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [12s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidylda)
  tidylda is under active development. The API and behavior may change.
  > 
  > test_check("tidylda")
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 186 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tidy-methods.R:200:3'): augment.tidylda behaves nicely ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. ├─generics::augment(...) at test-tidy-methods.R:200:2
    2. └─tidylda:::augment.tidylda(...)
    3.   ├─dplyr::right_join(tidy_lambda, data, by = c(token = term_col))
    4.   └─dplyr:::right_join.data.frame(tidy_lambda, data, by = c(token = term_col))
    5.     └─dplyr:::join_mutate(...)
    6.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    8.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   10.             ├─base::withCallingHandlers(...)
   11.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 5 | SKIP 0 | PASS 186 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Running examples in ‘tidync-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hyper_filter
> ### Title: Subset NetCDF variable by expression
> ### Aliases: hyper_filter hyper_filter.tidync
> 
> ### ** Examples
> 
> f <- "S20080012008031.L3m_MO_CHL_chlor_a_9km.nc"
> l3file <- system.file("extdata/oceandata", f, package= "tidync")
> ## filter by value
> tidync(l3file) %>% hyper_filter(lon = lon < 100)

Data Source (1): S20080012008031.L3m_MO_CHL_chlor_a_9km.nc ...

Grids (4) <dimension family> : <associated variables> 

[1]   D1,D0 : chlor_a    **ACTIVE GRID** ( 9331200  values per variable)
[2]   D3,D2 : palette
[3]   D0    : lat
[4]   D1    : lon
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘netcdf-with-tidync.Rmd’ using rmarkdown
Quitting from lines 100-102 (netcdf-with-tidync.Rmd) 
Error: processing vignette ‘netcdf-with-tidync.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘netcdf-with-tidync.Rmd’

SUMMARY: processing the following file failed:
  ‘netcdf-with-tidync.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown
--- finished re-building ‘cubist.Rmd’

--- re-building ‘glm.Rmd’ using rmarkdown
--- finished re-building ‘glm.Rmd’

--- re-building ‘lm.Rmd’ using rmarkdown
--- finished re-building ‘lm.Rmd’

--- re-building ‘mars.Rmd’ using rmarkdown
Quitting from lines 40-41 (mars.Rmd) 
Error: processing vignette ‘mars.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mars.Rmd’

--- re-building ‘non-r.Rmd’ using rmarkdown
--- finished re-building ‘non-r.Rmd’

--- re-building ‘ranger.Rmd’ using rmarkdown
--- finished re-building ‘ranger.Rmd’

--- re-building ‘regression.Rmd’ using rmarkdown
--- finished re-building ‘regression.Rmd’

--- re-building ‘rf.Rmd’ using rmarkdown
--- finished re-building ‘rf.Rmd’

--- re-building ‘save.Rmd’ using rmarkdown
--- finished re-building ‘save.Rmd’

--- re-building ‘sql.Rmd’ using rmarkdown
--- finished re-building ‘sql.Rmd’

--- re-building ‘tree.Rmd’ using rmarkdown
--- finished re-building ‘tree.Rmd’

--- re-building ‘xgboost.Rmd’ using rmarkdown
--- finished re-building ‘xgboost.Rmd’

SUMMARY: processing the following file failed:
  ‘mars.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘tidyterra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as_tibble.Spat
> ### Title: Coerce a Spat* object to data frames
> ### Aliases: as_tibble.Spat as_tibble.SpatRaster as_tibble.SpatVector
> 
> ### ** Examples
> 
> 
> library(terra)
terra 1.7.18
> # SpatRaster
> f <- system.file("extdata/cyl_temp.tif", package = "tidyterra")
> r <- rast(f)
> 
> as_tibble(r, na.rm = TRUE)
# A tibble: 6,522 × 3
   tavg_04 tavg_05 tavg_06
     <dbl>   <dbl>   <dbl>
 1    3.18    6.79    11.1
 2    5.30    8.73    12.7
 3    4.59    8.05    12.1
 4    6.38    9.72    13.6
 5    4.05    7.58    11.8
 6    2.90    6.54    10.9
 7    5.05    8.49    12.5
 8    2.58    6.17    10.5
 9    9.30   12.5     15.4
10    9.84   13.0     15.9
# … with 6,512 more rows
> 
> as_tibble(r, xy = TRUE)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: as_tibble ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Running examples in ‘tidytransit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: set_dates_services
> ### Title: Returns all possible date/service_id combinations as a data
> ###   frame
> ### Aliases: set_dates_services
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> local_gtfs_path <- system.file("extdata", "google_transit_nyc_subway.zip", package = "tidytransit")
> nyc <- read_gtfs(local_gtfs_path)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: read_gtfs ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘frequency.Rmd’ using rmarkdown
Quitting from lines 53-55 (frequency.Rmd) 
Error: processing vignette ‘frequency.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘frequency.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 73-79 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘introduction.Rmd’

--- re-building ‘servicepatterns.Rmd’ using rmarkdown
Quitting from lines 40-43 (servicepatterns.Rmd) 
Error: processing vignette ‘servicepatterns.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘servicepatterns.Rmd’

--- re-building ‘timetable.Rmd’ using rmarkdown
Quitting from lines 28-31 (timetable.Rmd) 
Error: processing vignette ‘timetable.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘timetable.Rmd’

SUMMARY: processing the following files failed:
  ‘frequency.Rmd’ ‘introduction.Rmd’ ‘servicepatterns.Rmd’
  ‘timetable.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tidytree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ancestor
> ### Title: ancestor
> ### Aliases: ancestor ancestor.tbl_tree
> 
> ### ** Examples
> 
> library(ape)
> tree <- rtree(4)
> x <- as_tibble(tree)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: as_tibble ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘data-validation-rules.Rmd’ using rmarkdown
--- finished re-building ‘data-validation-rules.Rmd’

--- re-building ‘smells.Rmd’ using rmarkdown
Quitting from lines 141-157 (smells.Rmd) 
Error: processing vignette ‘smells.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘smells.Rmd’

--- re-building ‘tidyxl.Rmd’ using rmarkdown
--- finished re-building ‘tidyxl.Rmd’

SUMMARY: processing the following file failed:
  ‘smells.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  common.c:36:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tiff.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
Running examples in ‘timbeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi_logs
> ### Title: Simulate log extraction using a Bi (2000) variable-form taper
> ###   equation that describes the taper of the tree.
> ### Aliases: bi_logs
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(minpack.lm)
> library(timbeR)
> 
> tree_scaling <- tree_scaling %>%
+ mutate(did = di/dbh,
+        hih = hi/h)
> 
> bi <-  nlsLM(di ~ taper_bi(dbh, h, hih, b0, b1, b2, b3, b4, b5, b6),
+ data=tree_scaling,
+ start=list(b0=1.8,b1=-0.2,b2=-0.04,b3=-0.9,b4=-0.0006,b5=0.07,b6=-.14))
> 
> coef_bi <- coef(bi)
> 
> dbh <- 25
> h <- 20
> 
> assortments <- data.frame(
+   NAME = c('15-25','4-15'),
+   SED = c(15,4),
+   MINLENGTH = c(2.65,2),
+   MAXLENGTH = c(2.65,4.2),
+   LOSS = c(5,5)
+ )
> 
> bi_logs(dbh, h, coef_bi, assortments)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: bi_logs ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_timbeR.Rmd’ using rmarkdown
Quitting from lines 270-273 (Intro_to_timbeR.Rmd) 
Error: processing vignette ‘Intro_to_timbeR.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Intro_to_timbeR.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_timbeR.Rmd’

Error: Vignette re-building failed.
Execution halted
rowwise:
  function(data, ...)
rowwise.forest:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘robets’
Running examples in ‘Tinflex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Tinflex-package
> ### Title: Tinflex - Universal non-uniform random number generator
> ### Aliases: Tinflex-package Tinflex
> ### Keywords: package distribution datagen
> 
> ### ** Examples
> 
> ## Bimodal density
> ##   f(x) = exp( -|x|^alpha + s*|x|^beta + eps*|x|^2 )
> ##   with alpha > beta >= 2 and s, eps > 0
> 
> alpha <- 4.2
> beta <- 2.1
> s <- 1
> eps <- 0.1
> 
> ## Log-density and its derivatives.
> lpdf   <- function(x) { -abs(x)^alpha + s*abs(x)^beta + eps*abs(x)^2 }
> dlpdf  <- function(x) { (sign(x) * (-alpha*abs(x)^(alpha-1)
+                            + s*beta*abs(x)^(beta-1) + 2*eps*abs(x))) }
> d2lpdf <- function(x) { (-alpha*(alpha-1)*abs(x)^(alpha-2)
+                           + s*beta*(beta-1)*abs(x)^(beta-2) + 2*eps) }
> 
> ## Parameter cT=0 (default):
> ##   There are two inflection points on either side of 0.
> ib <- c(-Inf, 0, Inf)
> 
> ## Create generator object.
> gen <- Tinflex.setup.C(lpdf, dlpdf, d2lpdf, ib=c(-Inf,0,Inf), rho=1.1)
> 
> ## Print data about generator object.
> print(gen)
Object of class 'TinflexC':

       log-density(x) = {-abs(x)^alpha+s*abs(x)^beta+eps*abs(x)^2}
       used 2nd derivative: TRUE

       area below hat = 2.993174 
   area below squeeze = 2.770046 
    ratio hat/squeeze = 1.08055    [= upper bound for rejection constant ]
          # intervals = 16 

    initial intervals = -Inf | 0 | Inf 
                   cT = 0 
                  rho = 1.1 
 
> 
> ## Draw a random sample
> Tinflex.sample(gen, n=10)
Error in Tinflex.sample(gen, n = 10) : 
  DLL requires the use of native symbols
Execution halted
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘tinyscholar.Rmd’ using rmarkdown
Quitting from lines 78-81 (tinyscholar.Rmd) 
Error: processing vignette ‘tinyscholar.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tinyscholar.Rmd’

SUMMARY: processing the following file failed:
  ‘tinyscholar.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TKCat.Rcheck/00install.out’ for details.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘polling_districts.Rmd’ using rmarkdown
Quitting from lines 86-103 (polling_districts.Rmd) 
Error: processing vignette ‘polling_districts.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘polling_districts.Rmd’

--- re-building ‘tongfen-ca-estimate.Rmd’ using rmarkdown
--- finished re-building ‘tongfen-ca-estimate.Rmd’

--- re-building ‘tongfen.Rmd’ using rmarkdown
--- finished re-building ‘tongfen.Rmd’

--- re-building ‘tongfen_ca.Rmd’ using rmarkdown
--- finished re-building ‘tongfen_ca.Rmd’

--- re-building ‘tongfen_us.Rmd’ using rmarkdown
--- finished re-building ‘tongfen_us.Rmd’

SUMMARY: processing the following file failed:
  ‘polling_districts.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘corpus.JSS.papers’
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘topicmodels.Rnw’ using Sweave
Warning: unable to access index for repository https://datacube.wu.ac.at/src/contrib:
  cannot open URL ‘https://datacube.wu.ac.at/src/contrib/PACKAGES’
Warning: package 'corpus.JSS.papers' is not available for this version of R

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages

Error: processing vignette ‘topicmodels.Rnw’ failed with diagnostics:
 chunk 6 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.JSS.papers'

--- failed re-building 'topicmodels.Rnw'

SUMMARY: processing the following file failed:
  'topicmodels.Rnw'

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘toscaData’
qnormal:
  function(object, ...)
qnormal.toureg:
  function(object, nsim, level, envelope)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘tourr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: display_andrews
> ### Title: Andrews' curves tour path animation.
> ### Aliases: display_andrews animate_andrews
> ### Keywords: hplot
> 
> ### ** Examples
> 
> animate_andrews(flea[, 1:6])
Converting input data to the required matrix format.
> animate_andrews(flea[, 1:6], grand_tour(d = 3))
Converting input data to the required matrix format.
> animate_andrews(flea[, 1:6], grand_tour(d = 6))
Converting input data to the required matrix format.
> 
> # It's easy to experiment with different tour paths:
> animate_andrews(flea[, 1:6], guided_tour(cmass()))
Converting input data to the required matrix format.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: animate_andrews ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edges.Rmd’ using rmarkdown
--- finished re-building ‘edges.Rmd’

--- re-building ‘tourr.Rmd’ using rmarkdown
Quitting from lines 65-68 (tourr.Rmd) 
Error: processing vignette ‘tourr.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tourr.Rmd’

SUMMARY: processing the following file failed:
  ‘tourr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘toweranNA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeTower
> ### Title: Nonimputational method for dealing with NA values in prediction
> ###   application
> ### Aliases: makeTower predict.tower
> 
> ### ** Examples
> 
> towerOut <- makeTower(mtcars,'mpg','lm')
> 
> newx <- mtcars[-c(1:10),-1]
> for(i in 1:10)
+   newx[i, i] <- NA
> 
> head(newx)
                    cyl  disp  hp drat    wt  qsec vs am gear carb
Merc 280C            NA 167.6 123 3.92 3.440 18.90  1  0    4    4
Merc 450SE            8    NA 180 3.07 4.070 17.40  0  0    3    3
Merc 450SL            8 275.8  NA 3.07 3.730 17.60  0  0    3    3
Merc 450SLC           8 275.8 180   NA 3.780 18.00  0  0    3    3
Cadillac Fleetwood    8 472.0 205 2.93    NA 17.98  0  0    3    4
Lincoln Continental   8 460.0 215 3.00 5.424    NA  0  0    3    4
> #                     cyl  disp  hp drat    wt  qsec vs am gear carb
> # Merc 280C            NA 167.6 123 3.92 3.440 18.90  1  0    4    4
> # Merc 450SE            8    NA 180 3.07 4.070 17.40  0  0    3    3
> # Merc 450SL            8 275.8  NA 3.07 3.730 17.60  0  0    3    3
> # Merc 450SLC           8 275.8 180   NA 3.780 18.00  0  0    3    3
> # Cadillac Fleetwood    8 472.0 205 2.93    NA 17.98  0  0    3    4
> # Lincoln Continental   8 460.0 215 3.00 5.424    NA  0  0    3    4
>  
> predict(towerOut,newx,k=3)
Error in get.knnx(data = xic, query = rwm, k = kThisTime) : 
  DLL requires the use of native symbols
Calls: predict -> predict.tower -> nearNeighborIndices -> get.knnx
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in ‘toxEval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_chemical_summary
> ### Title: Compute EAR values
> ### Aliases: get_chemical_summary
> 
> ### ** Examples
> 
> path_to_tox <-  system.file("extdata", package="toxEval")
> file_name <- "OWC_data_fromSup.xlsx"
> full_path <- file.path(path_to_tox, file_name)
> 
> tox_list <- create_toxEval(full_path)
> 
> ACC <- get_ACC(tox_list$chem_info$CAS)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: get_ACC ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(toxEval)
  USGS Research Package:
  https://owi.usgs.gov/R/packages.html#research
  ToxCast database: version 3.2
  > test_check("toxEval")
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 0 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests_summary.R:12:1'): (code run outside of `test_that()`) ─────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─toxEval::get_ACC(chem_info$CAS) at tests_summary.R:12:0
    2.   ├─dplyr::right_join(ACC, chem_list, by = c(CAS = "casrn"))
    3.   └─dplyr:::right_join.data.frame(ACC, chem_list, by = c(CAS = "casrn"))
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 6 | PASS 0 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘PrepareData.Rmd’ using rmarkdown
--- finished re-building ‘PrepareData.Rmd’

--- re-building ‘basicWorkflow.Rmd’ using rmarkdown
Quitting from lines 55-62 (basicWorkflow.Rmd) 
Error: processing vignette ‘basicWorkflow.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘basicWorkflow.Rmd’

--- re-building ‘shinyApp.Rmd’ using rmarkdown
--- finished re-building ‘shinyApp.Rmd’

SUMMARY: processing the following file failed:
  ‘basicWorkflow.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tplyr.Rmd’ using rmarkdown
Quitting from lines 317-324 (Tplyr.Rmd) 
Error: processing vignette ‘Tplyr.Rmd’ failed with diagnostics:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘Tplyr.Rmd’

--- re-building ‘count.Rmd’ using rmarkdown
Quitting from lines 99-106 (count.Rmd) 
Error: processing vignette ‘count.Rmd’ failed with diagnostics:
ℹ In index: 1.
Caused by error in `vectbl_assign()`:
! DLL requires the use of native symbols
--- failed re-building ‘count.Rmd’

--- re-building ‘custom-metadata.Rmd’ using rmarkdown
--- finished re-building ‘custom-metadata.Rmd’

--- re-building ‘denom.Rmd’ using rmarkdown
Quitting from lines 221-235 (denom.Rmd) 
Error: processing vignette ‘denom.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘denom.Rmd’

--- re-building ‘desc.Rmd’ using rmarkdown
--- finished re-building ‘desc.Rmd’

--- re-building ‘desc_layer_formatting.Rmd’ using rmarkdown
--- finished re-building ‘desc_layer_formatting.Rmd’

--- re-building ‘general_string_formatting.Rmd’ using rmarkdown
--- finished re-building ‘general_string_formatting.Rmd’

--- re-building ‘layer_templates.Rmd’ using rmarkdown
--- finished re-building ‘layer_templates.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown
--- finished re-building ‘metadata.Rmd’

--- re-building ‘options.Rmd’ using rmarkdown
--- finished re-building ‘options.Rmd’

--- re-building ‘post_processing.Rmd’ using rmarkdown
--- finished re-building ‘post_processing.Rmd’

--- re-building ‘shift.Rmd’ using rmarkdown
--- finished re-building ‘shift.Rmd’

--- re-building ‘table.Rmd’ using rmarkdown
--- finished re-building ‘table.Rmd’

SUMMARY: processing the following files failed:
  ‘Tplyr.Rmd’ ‘count.Rmd’ ‘denom.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
anti_join:
  function(x, y, by, copy, ...)
anti_join.track:
  function(.data, ...)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.track:
  function(.data, ...)

ungroup:
  function(x, ...)
ungroup.track:
  function(.data, ...)

semi_join:
  function(x, y, by, copy, ...)
semi_join.track:
  function(.data, ...)

nest_join:
  function(x, y, by, copy, keep, name, ...)
nest_join.track:
  function(.data, ...)

rowwise:
  function(data, ...)
rowwise.track:
  function(.data, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.track:
  function(.data, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.track:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.track:
  function(.data, ...)

full_join:
  function(x, y, by, copy, suffix, ..., keep)
full_join.track:
  function(.data, ...)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.track:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Enhancements
    Other changes
'LazyData' is specified without a 'data' directory
Running examples in ‘trafo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gpower
> ### Title: Gpower transformation for linear models
> ### Aliases: gpower
> 
> ### ** Examples
> 
> # Load data
> data("cars", package = "datasets")
> 
> # Fit linear model
> lm_cars <- lm(dist ~ speed, data = cars)
> 
> # Transform dependent variable using divergence minimization following 
> # Kullback-Leibler
> gpower(object = lm_cars, method = "div.kl", plotit = FALSE)
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: gpower -> oneparam -> oneparam.lm -> est_lm
Execution halted
Package suggested but not available for checking: ‘taxidata’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dcc.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) seascorr.Rd:128: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘TreeDistData’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [17s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat", warn.conflicts = FALSE)
  > library("TreeDist")
  > 
  > test_check("TreeDist")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1280 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-lap.R:291:3'): Avoid infinite loop in LAP ──────────────────────
  Error in `NeworderPhylo(nTip, edge[, 1], edge[, 2], nEdge, 1)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─testthat::expect_lt(...) at test-lap.R:291:2
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─TreeDist::ClusteringInfoDistance(...)
   5. │ └─TreeDist::MutualClusteringInfo(...)
   6. │   └─TreeDist::CalculateTreeDistance(...)
   7. ├─TreeTools::Cladewise(...)
   8. └─TreeTools:::Cladewise.phylo(...)
   9.   └─TreeTools::NeworderPhylo(nTip, edge[, 1], edge[, 2], nEdge, 1)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 1280 ]
  Deleting unused snapshots:
  • Plot3/plotting-order.svg
  • plot/jrf-vm-matchzeros-false.svg
  • plot/rf-collapse-a-node.svg
  • plot/rf-collapse-and-change.svg
  • plot/rf-vm-single-splits-plainedges.svg
  • plot/test-lc-letters.svg
  • plot/test-uc-letters.svg
  • plot/test-vmr.svg
  • plot/test-without-space.svg
  • plot/visualize-mci-matching.svg
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Generalized-RF.Rmd’ using rmarkdown
--- finished re-building ‘Generalized-RF.Rmd’

--- re-building ‘Robinson-Foulds.Rmd’ using rmarkdown
--- finished re-building ‘Robinson-Foulds.Rmd’

--- re-building ‘Using-TreeDist.Rmd’ using rmarkdown
--- finished re-building ‘Using-TreeDist.Rmd’

--- re-building ‘compare-treesets.Rmd’ using rmarkdown
Quitting from lines 143-171 (compare-treesets.Rmd) 
Error: processing vignette ‘compare-treesets.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘compare-treesets.Rmd’

--- re-building ‘different-leaves.Rmd’ using rmarkdown
--- finished re-building ‘different-leaves.Rmd’

--- re-building ‘information.Rmd’ using rmarkdown
--- finished re-building ‘information.Rmd’

--- re-building ‘landscapes.Rmd’ using rmarkdown
--- finished re-building ‘landscapes.Rmd’

--- re-building ‘treespace.Rmd’ using rmarkdown
--- finished re-building ‘treespace.Rmd’

--- re-building ‘using-distances.Rmd’ using rmarkdown
--- finished re-building ‘using-distances.Rmd’

SUMMARY: processing the following file failed:
  ‘compare-treesets.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘TreeSearch-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AdditionTree
> ### Title: Addition tree
> ### Aliases: AdditionTree
> 
> ### ** Examples
> 
> data("Lobo", package = "TreeTools")
> AdditionTree(Lobo.phy, concavity = 10)
Error in mpl_new_Morphy() : DLL requires the use of native symbols
Calls: AdditionTree ... TreeLength -> TreeLength.list -> lapply -> FUN -> mpl_new_Morphy
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom.Rmd’ using rmarkdown
Quitting from lines 163-175 (custom.Rmd) 
Error: processing vignette ‘custom.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘custom.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘profile-scores.Rmd’ using rmarkdown
--- finished re-building ‘profile-scores.Rmd’

--- re-building ‘profile.Rmd’ using rmarkdown
Quitting from lines 67-71 (profile.Rmd) 
Error: processing vignette ‘profile.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘profile.Rmd’

--- re-building ‘tree-search.Rmd’ using rmarkdown
Quitting from lines 84-85 (tree-search.Rmd) 
Error: processing vignette ‘tree-search.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tree-search.Rmd’

--- re-building ‘tree-space.Rmd’ using rmarkdown
Quitting from lines 94-141 (tree-space.Rmd) 
Error: processing vignette ‘tree-space.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘tree-space.Rmd’

SUMMARY: processing the following files failed:
  ‘custom.Rmd’ ‘profile.Rmd’ ‘tree-search.Rmd’ ‘tree-space.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++14: please drop specification unless essential
Running examples in ‘TreeTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EnforceOutgroup
> ### Title: Generate a tree with a specified outgroup
> ### Aliases: EnforceOutgroup EnforceOutgroup.phylo
> ###   EnforceOutgroup.character
> 
> ### ** Examples
> 
> tree <- EnforceOutgroup(letters[1:9], letters[1:3])
Error in NeworderPhylo(nTip, edge[, 1], edge[, 2], nEdge, 2L) : 
  DLL requires the use of native symbols
Calls: EnforceOutgroup ... ApePostorder -> ApePostorder.phylo -> NeworderPhylo
Execution halted
'LazyData' is specified without a 'data' directory
Running examples in ‘trend-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: br.test
> ### Title: Buishand Range Test for Change-Point Detection
> ### Aliases: br.test
> ### Keywords: htest ts univar
> 
> ### ** Examples
> 
> data(Nile)
> (out <- br.test(Nile))
Error in br.test(Nile) : DLL requires the use of native symbols
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘trend.Rnw’ using Sweave
Loading required package: trend

Error: processing vignette ‘trend.Rnw’ failed with diagnostics:
 chunk 13 
Error in br.test(Nile) : DLL requires the use of native symbols

--- failed re-building ‘trend.Rnw’

SUMMARY: processing the following file failed:
  ‘trend.Rnw’

Error: Vignette re-building failed.
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
GNU make is a SystemRequirements.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (require("testthat"))
  +   test_check("truncnorm")
  Loading required package: testthat
  Loading required package: truncnorm
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-sanity_checks.R:22:1'): (code run outside of `test_that()`) ────
  Error in `etruncnorm(a, b, mean, sd)`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. └─truncnorm (local) check_dev(-3, Inf, 0, 1) at test-sanity_checks.R:22:0
   2.   └─truncnorm::etruncnorm(a, b, mean, sd) at test-sanity_checks.R:7:2
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 13 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [92s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tsbox)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("tsbox")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 622 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (17)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-error_handling.R:55:3'): errors work as expected ───────────────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
      ▆
   1. ├─base::`[<-`(`*tmp*`, 2, 1, value = `<lgl>`) at test-error_handling.R:55:2
   2. └─tibble:::`[<-.tbl_df`(`*tmp*`, 2, 1, value = `<lgl>`) at test-error_handling.R:55:2
   3.   └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   4.     └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
   5.       ├─base::withCallingHandlers(...)
   6.       └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 17 | PASS 622 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.grnnForecast:
  function(forecast, highlight)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updates for the development version (0.1.0.9000) on Github
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Running examples in ‘TT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: treetable
> ### Title: Display tree structured data using 'datatable' widget
> ### Aliases: treetable
> 
> ### ** Examples
> 
> data("org")
> data("col_order")
> colnames <- factor(c("org",org$attributesAll),
+                    levels =  col_order)
> treetable(org, color="#FFFFFF", colnames=colnames)
Warning: Automatic coercion from double to character was deprecated in purrr 1.0.0.
ℹ Please use an explicit call to `as.character()` within `map_chr()` instead.
ℹ The deprecated feature was likely used in the TT package.
  Please report the issue to the authors.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: treetable ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Running examples in ‘tune-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conf_mat_resampled
> ### Title: Compute average confusion matrix across resamples
> ### Aliases: conf_mat_resampled
> 
> ### ** Examples
> 
> library(parsnip)
> library(rsample)
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> data(two_class_dat, package = "modeldata")
> 
> set.seed(2393)
> res <-
+   logistic_reg() %>%
+   set_engine("glm") %>%
+   fit_resamples(
+     Class ~ .,
+     resamples = vfold_cv(two_class_dat, v = 3),
+     control = control_resamples(save_pred = TRUE)
+   )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) lindner.Rd:44: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘sl3’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Found the following significant warnings:
  interface.c:114:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ucminf.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MortalityLaws’
Unknown package ‘MortalityLaws’ in Rd xrefs
Running examples in ‘unheadr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: unbreak_vals
> ### Title: Unbreak values using regex to match the lagging half of the
> ###   broken value
> ### Aliases: unbreak_vals
> 
> ### ** Examples
> 
> data(primates2017_broken)
> # regex matches strings starting in lowercase (broken species epithets)
> unbreak_vals(primates2017_broken, "^[a-z]", scientific_name, sciname_new)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: unbreak_vals ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘unheadr-vignette.Rmd’ using rmarkdown
Quitting from lines 74-77 (unheadr-vignette.Rmd) 
Error: processing vignette ‘unheadr-vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘unheadr-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘unheadr-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ursa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: band_group
> ### Title: Extract certain statistics of each band.
> ### Aliases: band_mean band_sd band_sum band_min band_max band_n band_nNA
> ###   band_quantile
> ### Keywords: spatial
> 
> ### ** Examples
> 
> session_grid(NULL)
> a <- ursa_dummy()
Error in .Cursa("resampl4", x = x$value, nodata = as.numeric(nodata),  : 
  DLL requires the use of native symbols
Calls: ursa_dummy -> regrid -> .Cursa -> .C
Execution halted
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘ushr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summarize_model
> ### Title: Summarize model output
> ### Aliases: summarize_model
> 
> ### ** Examples
> 
> 
> set.seed(1234567)
> 
> simulated_data <- simulate_data(nsubjects = 20)
Joining with `by = join_by(id)`
> 
> model_output <- ushr(data = simulated_data)
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
Warning in sqrt(diag(fisher_info)) : NaNs produced
> 
> summarize_model(model_output, data = simulated_data)
Joining with `by = join_by(id, Model)`
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: summarize_model ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Quitting from lines 151-158 (Vignette.Rmd) 
Error: processing vignette ‘Vignette.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  rand.c:90:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:92:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:103:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  rand.c:138:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/uuid.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Running examples in ‘uwot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lvish
> ### Title: Dimensionality Reduction with a LargeVis-like method
> ### Aliases: lvish
> 
> ### ** Examples
> 
> # Default number of epochs is much larger than for UMAP, assumes random
> # initialization. Use perplexity rather than n_neighbors to control the size
> # of the local neighborhood 20 epochs may be too small for a random
> # initialization
> iris_lvish <- lvish(iris,
+   perplexity = 50, learning_rate = 0.5,
+   init = "random", n_epochs = 20
+ )
Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
Calls: lvish ... data2set -> x2set -> x2nn -> find_nn -> FNN_nn -> <Anonymous>
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(uwot)
  Loading required package: Matrix
  > 
  > test_check("uwot")
  Error in FNN::get.knn(X, k) : DLL requires the use of native symbols
  Calls: test_check ... eval -> create_data -> find_nn -> FNN_nn -> <Anonymous>
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Running examples in ‘validata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: confirm_overlap
> ### Title: Confirm Overlap
> ### Aliases: confirm_overlap co_find_only_in_1 co_find_only_in_2
> ###   co_find_in_both
> 
> ### ** Examples
> 
> 
> confirm_overlap(iris$Sepal.Width, iris$Sepal.Length) -> iris_overlap
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: confirm_overlap ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PackageIntroduction.Rmd’ using rmarkdown
Quitting from lines 101-104 (PackageIntroduction.Rmd) 
Error: processing vignette ‘PackageIntroduction.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘PackageIntroduction.Rmd’

SUMMARY: processing the following file failed:
  ‘PackageIntroduction.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [36s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(vdiffr)
  > library(valr)
  > 
  > test_check("valr")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 435 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (2)
  • run db tests manually. (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_projection.r:20:1'): (code run outside of `test_that()`) ───────
  Error in `vectbl_assign(x[[j]], i, recycled_value[[j]])`: DLL requires the use of native symbols
  Backtrace:
       ▆
    1. └─valr::bed_projection(x, y, genome) at test_projection.r:20:0
    2.   ├─dplyr::full_join(y, genome, by = "chrom")
    3.   └─dplyr:::full_join.data.frame(y, genome, by = "chrom")
    4.     └─dplyr:::join_mutate(...)
    5.       ├─base::`[<-`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    6.       └─tibble:::`[<-.tbl_df`(`*tmp*`, new_rows, merge, value = `<tibble[,1]>`)
    7.         └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    8.           └─tibble:::tbl_subassign_row(xj, i, value, i_arg, value_arg, call)
    9.             ├─base::withCallingHandlers(...)
   10.             └─tibble:::vectbl_assign(x[[j]], i, recycled_value[[j]])
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 435 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
toMlm:
  function(x, ...)
toMlm.varest:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) irf.Rd:111: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Running examples in ‘VBLPCM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VBLPCM-package
> ### Title: VBLPCM: Variational Bayes for the Latent Position Cluster Model
> ###   for networks
> ### Aliases: VBLPCM-package VBLPCM
> ### Keywords: graphs networks variational package models latentnet
> 
> ### ** Examples
> 
> ### Sampson's monks with sender random effects ###
> data(sampson,package="VBLPCM")
> v.start<-vblpcmstart(samplike,G=3,model="rreceiver",LSTEPS=1e3)
Error in Y_to_E(N, NE, g.network$gal$directed, Y) : 
  DLL requires the use of native symbols
Calls: vblpcmstart -> Y_to_E
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  computeCox.c:15:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vdra.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) checkTS.VGAMextra.Rd:176: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
sql_translation:
  function(con)
sql_translation.wfsConnection:
  function(conn)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW FEATURES
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘visR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate_cuminc
> ### Title: Competing Events Cumulative Incidence
> ### Aliases: estimate_cuminc
> 
> ### ** Examples
> 
> cuminc <-
+   visR::estimate_cuminc(
+     data = tidycmprsk::trial,
+     strata = "trt",
+     CNSR = "death_cr",
+     AVAL = "ttdeath"
+   )
> cuminc

── cuminc() ────────────────────────────────────────────────────────────────────
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CDISC_ADaM.Rmd’ using rmarkdown
Quitting from lines 60-63 (CDISC_ADaM.Rmd) 
Error: processing vignette ‘CDISC_ADaM.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘CDISC_ADaM.Rmd’

--- re-building ‘Consort_flow_diagram.Rmd’ using rmarkdown
--- finished re-building ‘Consort_flow_diagram.Rmd’

--- re-building ‘Styling_KM_plots.Rmd’ using rmarkdown
--- finished re-building ‘Styling_KM_plots.Rmd’

--- re-building ‘Time_to_event_analysis.Rmd’ using rmarkdown
Quitting from lines 69-78 (Time_to_event_analysis.Rmd) 
Error: processing vignette ‘Time_to_event_analysis.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘Time_to_event_analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘CDISC_ADaM.Rmd’ ‘Time_to_event_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.csl_dates:
  function(x)

vec_proxy_order:
  function(x, ...)
vec_proxy_order.list_of_csl_names:
  function(x)

vec_proxy_order:
  function(x, ...)
vec_proxy_order.csl_dates:
  function(x)

knit_print:
  function(x, ...)
knit_print.vitae_brief:
  function(x, options)

knit_print:
  function(x, ...)
knit_print.vitae_detailed:
  function(x, options)

knit_print:
  function(x, ...)
knit_print.vitae_bibliography:
  function(x, options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Running examples in ‘voice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conv_df
> ### Title: Convolute data frames using multicore.
> ### Aliases: conv_df
> 
> ### ** Examples
> 
> library(voice)
> 
> # get path to audio file
> path2wav <- list.files(system.file('extdata', package = 'wrassp'),
+ pattern <- glob2rx('*.wav'), full.names = TRUE)
> 
> # getting Media data frame
> M <- extract_features(dirname(path2wav), features = c('f0','formants'),
+ mc.cores = 1, verbose = FALSE)
Error in vectbl_assign(x[[j]], cells[[j]], value) : 
  DLL requires the use of native symbols
Calls: extract_features ... tbl_subassign_matrix -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘VoxR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_noise
> ### Title: Statistical filtering of a point cloud.
> ### Aliases: filter_noise
> 
> ### ** Examples
> 
> #- import tls data
> tls=data.table::fread(system.file("extdata", "Tree_t0.asc", package="VoxR"))
> 
> #- run noise filter
> clean=VoxR::filter_noise(tls,store_noise = TRUE)
Error in get.knn(data, k, algorithm) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... eval -> rowSums -> is.data.frame -> <Anonymous> -> get.knn
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/vprr.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘WASP.Rmd’ using rmarkdown
Quitting from lines 472-582 (WASP.Rmd) 
Error: processing vignette ‘WASP.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘WASP.Rmd’

SUMMARY: processing the following file failed:
  ‘WASP.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Running examples in ‘Wats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: polar_periodic
> ### Title: Polar Plot with Periodic Elements
> ### Aliases: polar_periodic
> ### Keywords: polar
> 
> ### ** Examples
> 
> requireNamespace("grid")
> library(Wats)
> ds_linear <-
+   Wats::county_month_birth_rate_2005_version |>
+   dplyr::filter(county_name == "oklahoma") |>
+   augment_year_data_with_month_resolution(date_name = "date")
> 
> h_spread <- function(scores) { quantile(x = scores, probs = c(.25, .75)) }
> portfolio <- annotate_data(
+   ds_linear       = ds_linear,
+   dv_name         = "birth_rate",
+   center_function = median,
+   spread_function = h_spread
+ )
> rm(ds_linear)
> 
> polarized <- polarize_cartesian(
+   portfolio$ds_linear,
+   portfolio$ds_stage_cycle,
+   y_name        = "birth_rate",
+   stage_id_name = "stage_id"
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: polarize_cartesian ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mbr-figures.Rmd’ using rmarkdown
Quitting from lines 255-279 (mbr-figures.Rmd) 
Error: processing vignette ‘mbr-figures.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘mbr-figures.Rmd’

SUMMARY: processing the following file failed:
  ‘mbr-figures.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running examples in ‘waywiser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.ww_area_of_applicability
> ### Title: Predict from a 'ww_area_of_applicability'
> ### Aliases: predict.ww_area_of_applicability
> 
> ### ** Examples
> 
> ## Don't show: 
> if (rlang::is_installed("vip")) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ library(vip)
+ train <- gen_friedman(1000, seed = 101)  # ?vip::gen_friedman
+ test <- train[701:1000, ]
+ train <- train[1:700, ]
+ pp <- stats::ppr(y ~ ., data = train, nterms = 11)
+ importance <- vi_permute(
+   pp,
+   target = "y",
+   metric = "rsquared",
+   pred_wrapper = predict
+ )
+ 
+ aoa <- ww_area_of_applicability(y ~ ., train, test, importance = importance)
+ predict(aoa, test)
+ ## Don't show: 
+ }) # examplesIf
> library(vip)

Attaching package: ‘vip’

The following object is masked from ‘package:utils’:

    vi

> train <- gen_friedman(1000, seed = 101)
> test <- train[701:1000, ]
> train <- train[1:700, ]
> pp <- stats::ppr(y ~ ., data = train, nterms = 11)
> importance <- vi_permute(pp, target = "y", metric = "rsquared", pred_wrapper = predict)
> aoa <- ww_area_of_applicability(y ~ ., train, test, importance = importance)
> predict(aoa, test)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: <Anonymous> ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘prepr’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
plot_pop_vis:
  function(p_obj, ...)
plot_pop_vis.plotly:
  function(p_obj, tbl_pop, title_trace)

plot_pop_vis:
  function(p_obj, ...)
plot_pop_vis.ggplot:
  function(p_obj, tbl_pop, title_trace)

plot_prob_vis:
  function(p_obj, ...)
plot_prob_vis.plotly:
  function(p_obj, tbl_prob, distribution, title_main, title_x, title_y,
           title_trace)

plot_prob_vis:
  function(p_obj, ...)
plot_prob_vis.ggplot:
  function(p_obj, tbl_prob, distribution, title_main, title_x, title_y,
           title_trace)

plot_layout_vis:
  function(p_obj, ...)
plot_layout_vis.ggplot:
  function(p_obj, x, distribution, title_main, title_x, title_y)

plot_layout_vis:
  function(p_obj, ...)
plot_layout_vis.plotly:
  function(p_obj, x, distribution, title_main, title_x, title_y)

plot_conf_vis:
  function(p_obj, ...)
plot_conf_vis.ggplot:
  function(p_obj, tbl_p, title_trace)

plot_conf_vis:
  function(p_obj, ...)
plot_conf_vis.plotly:
  function(p_obj, tbl_p, title_trace)

plot_mod_vis:
  function(p_obj, ...)
plot_mod_vis.plotly:
  function(p_obj, tbl_pred, title_trace)

plot_mod_vis:
  function(p_obj, ...)
plot_mod_vis.ggplot:
  function(p_obj, tbl_pred, title_trace)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  init.c:11:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WeightedCluster.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ATE’
Missing or unexported object: ‘MNP::predict.mnp’
Unknown package ‘ATE’ in Rd xrefs
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown
Quitting from lines 77-97 (united_nations.Rmd) 
Error: processing vignette ‘united_nations.Rmd’ failed with diagnostics:
DLL requires the use of native symbols
--- failed re-building ‘united_nations.Rmd’

SUMMARY: processing the following file failed:
  ‘united_nations.Rmd’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘WinRatio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: winratio
> ### Title: Win Ratio for Prioritized Outcomes and 95% Confidence Interval
> ### Aliases: winratio
> 
> ### ** Examples
> 
> # Load survival package to use the dataset 'bladder1'
> library(survival)
> 
> # Creation of dataset 'df' with 3 outcomes:
> #   Outcome 1: death (survival event)
> #   Outcome 2: cancer recurrence (repeated survival event)
> #   Outcome 3: size of largest initial tumour (continuous event) 
> data1 <- bladder1  %>%  
+   mutate(trt = if_else(treatment == "placebo", "Placebo", "Treatment")) %>%
+   group_by(id) %>% 
+   mutate(death = if_else(max(status) %in% c(2, 3), 1, 0),
+          t2death = max(stop)) %>% 
+   ungroup() %>%
+   select(id, trt, death, t2death, number, size) %>% 
+  unique()
> 
> data2 <- bladder1 %>% 
+   filter(status == 1) %>% 
+   select(id, t2recurr = stop) %>%
+   mutate(recurr = 1) %>% 
+   arrange(id, t2recurr) %>% 
+   group_by(id) %>% 
+   mutate(nrecurr = row_number()) %>% 
+   ungroup() %>% 
+   full_join((data1 %>% select(id)), by = "id") %>% 
+   complete(id, nrecurr) %>%
+   filter(!is.na(nrecurr)) %>% 
+   full_join((data1 %>% select(id, t2death)), by = "id") %>% 
+   mutate(
+     recurr = replace(recurr, is.na(recurr), 0),
+     t2recurr = if_else(is.na(t2recurr), t2death, t2recurr)
+   ) %>% 
+   select(id, nrecurr, recurr, t2recurr)
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: %>% ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following significant warnings:
  make-collection-filter.c:228:79: warning: pointer ‘collection_filter’ used after ‘free’ [-Wuse-after-free]
  make-linestring-filter.c:215:79: warning: pointer ‘linestring_filter’ used after ‘free’ [-Wuse-after-free]
  make-polygon-filter.c:285:76: warning: pointer ‘polygon_filter’ used after ‘free’ [-Wuse-after-free]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  random_wrap.c:9:15: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/wnominate.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used Fortran compiler: ‘GNU Fortran (Debian 12.2.0-14) 12.2.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
  ...
--- re-building ‘evaluating-different-predictor-sets.Rmd’ using rmarkdown
Quitting from lines 89-127 (evaluating-different-predictor-sets.Rmd) 
Error: processing vignette ‘evaluating-different-predictor-sets.Rmd’ failed with diagnostics:
There were 20 workflows that had no results.
--- failed re-building ‘evaluating-different-predictor-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘evaluating-different-predictor-sets.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘aphiainfo.csv’ ‘tax.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Running examples in ‘wrappedtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_n_qualvars
> ### Title: Comparison for columns of factors for more than 2 groups with
> ###   post-hoc
> ### Aliases: compare_n_qualvars
> 
> ### ** Examples
> 
> # Separate lines for each factor level:
> compare_n_qualvars(
+   data = mtcars, dep_vars = c("am", "cyl", "carb"), indep_var = "gear",
+   spacer = " "
+ )
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: compare_n_qualvars ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RP2_data_1.txt’ ‘RP2_data_4.txt’ ‘RP2_qtl_1.txt’ ‘RP2_qtl_4.txt’
  ‘hp1_effect_qtl.txt’ ‘hp1_freq_mrk.txt’ ‘hp1_freq_qtl.txt’
  ‘hp1_genome.txt’ ‘hp1_last_hp_data.txt’ ‘hp1_lm_mrk.txt’
  ‘hp1_lm_qtl.txt’ ‘hp1_lm_qtl_mrk.txt’ ‘hp1_mrk.txt’ ‘hp1_qtl.txt’
  ‘hp2_effect_qtl.txt’ ‘hp2_freq_mrk.txt’ ‘hp2_freq_qtl.txt’
  ‘hp2_genome.txt’ ‘hp2_last_hp_data.txt’ ‘hp2_lm_mrk.txt’
  ‘hp2_lm_qtl.txt’ ‘hp2_lm_qtl_mrk.txt’ ‘hp2_mrk.txt’ ‘hp2_qtl.txt’
  ‘my_RP_data_1.txt’ ‘my_RP_data_4.txt’ ‘my_RP_mrk_1.txt’
  ‘my_RP_mrk_4.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xgb.plot.multi.trees
> ### Title: Project all trees on one tree and plot it
> ### Aliases: xgb.plot.multi.trees
> 
> ### ** Examples
> 
> 
> data(agaricus.train, package='xgboost')
> 
> bst <- xgboost(data = agaricus.train$data, label = agaricus.train$label, max_depth = 15,
+                eta = 1, nthread = 2, nrounds = 30, objective = "binary:logistic",
+                min_child_weight = 50, verbose = 0)
> 
> p <- xgb.plot.multi.trees(model = bst, features_keep = 3)
Column 2 ['No'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for  backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: xgb.plot.multi.trees ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
predictdf:
  function(model, xseq, se, level)
predictdf.polr:
  function(model, xseq, se, level, data, method, formula, method.args,
           weight, n_boot)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Running examples in ‘xkcdcolors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nearest_named
> ### Title: Find nearest named color to a specified color.
> ### Aliases: nearest_named
> ### Keywords: graphics
> 
> ### ** Examples
> 
> nearest_named("#8f7303")
Error in get.knnx(data, query, k, algorithm) : 
  DLL requires the use of native symbols
Calls: nearest_named -> knnx.index -> get.knnx
Execution halted
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:24:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:25:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:71:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
  init.c:72:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/xml2.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-12 (Debian 12.2.0-14) 12.2.0’
* used C++ compiler: ‘g++-12 (Debian 12.2.0-14) 12.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xopen)
  > 
  > if (ps::ps_is_supported()) {
  +   reporter <- ps::CleanupReporter(testthat::SummaryReporter)$new()
  + } else {
  +   ## ps does not support this platform
  +   reporter <- "progress"
  + }
  > 
  > test_check("xopen", reporter = reporter)
  test: 
  xopen: 1
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error ('test.R:4:1'): (code run outside of `test_that()`) ────────────────
  Error in `not_null(.Call("psll_connections", p))`: DLL requires the use of native symbols
  Backtrace:
    1. testthat::test_that(...)
         at test.R:4:0
    2. testthat:::test_code(desc, code, env = parent.frame(), reporter = reporter)
    3. reporter$start_test(context = reporter$.context, test = test)
    4. testthat:::o_apply(self$reporters, "start_test", context, test)
    5. base::lapply(objects, f)
    6. testthat (local) FUN(X[[i]], ...)
    7. x$start_test(...)
    8. ps::ps_connections(ps_handle())
    9. ps:::psl_connections(p)
   10. ps:::not_null(.Call("psll_connections", p))
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Don't worry, you'll get it.
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) read.npc.vpc.results.Rd:16: Escaped LaTeX specials: \_
checkRd: (-1) read.npc.vpc.results.Rd:19: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) read.npc.vpc.results.Rd:22: Escaped LaTeX specials: \_
Running examples in ‘xrf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef.xrf
> ### Title: Produce rules & coefficients for the RuleFit model
> ### Aliases: coef.xrf
> 
> ### ** Examples
> 
> m <- xrf(Petal.Length ~ ., iris,
+          xgb_control = list(nrounds = 2, max_depth = 2),
+          family = 'gaussian')
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: xrf ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
Found the following files/directories:
  ‘OPT.csv’ ‘testTecan_defaultLiquid.csv’ ‘testTecan_setLiquid.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RNRCS', 'metScanR'
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in ‘zmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: zingle
> ### Title: Return the single (unique) value found in a vector
> ### Aliases: zingle
> 
> ### ** Examples
> 
> # If all elements are identical, all is good.
> # The value of the element is returned.
> zingle(c("Alpha", "Alpha", "Alpha"))
[1] "Alpha"
> 
> # If any elements differ, an error is thrown
> tryCatch(zingle(c("Alpha", "Beta", "Alpha")), error=wrap_error)
#E> all(x[1] == x) is not TRUE
> 
> if (require("dplyr", quietly=TRUE, warn.conflicts=FALSE)) {
+   d <- tibble::tribble(
+     ~id, ~name, ~fouls,
+     1, "James", 3,
+     2, "Jack",  2,
+     1, "James", 4
+   )
+ 
+   # If the data is of the correct format, all is good
+   d %>%
+     dplyr::group_by(id) %>%
+     dplyr::summarise(name=zingle(name), total_fouls=sum(fouls))
+  }
# A tibble: 2 × 3
     id name  total_fouls
  <dbl> <chr>       <dbl>
1     1 James           7
2     2 Jack            2
> 
> if (require("dplyr", quietly=TRUE, warn.conflicts=FALSE)) {
+   # If a name does not match its ID, we should get an error
+   d[1,"name"] <- "Jammes"
+   tryCatch({
+     d %>%
+       dplyr::group_by(id) %>%
+       dplyr::summarise(name=zingle(name), total_fouls=sum(fouls))
+   }, error=wrap_error)
+ }
Error in vectbl_assign(x[[j]], i, recycled_value[[j]]) : 
  DLL requires the use of native symbols
Calls: [<- ... tbl_subassign_row -> withCallingHandlers -> vectbl_assign
Execution halted
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘zdat’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    NEW DEPENDENCIES
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘SDMTools’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 134469 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Undeclared package ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘acceldata2.RData’
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hunspell’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
‘configure’: /bin/bash is not portable
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  13.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppProgress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 305 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.1Mb
    help   1.4Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Example.jpeg’
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(adace)
  > 
  > test_check("adace")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-adace_func.R:98:3'): adace main function ─────────────────────
  message1$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  ── Failure ('test-adace_func.R:101:3'): adace main function ────────────────────
  message2$message (`actual`) not equal to "prediction from a rank-deficient fit may be misleading" (`expected`).
  
  actual vs expected
  - "prediction from rank-deficient fit; attr(*, \"non-estim\") has doubtful cases"
  + "prediction from a rank-deficient fit may be misleading"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘HI’, ‘MHadaptive’ in Rd xrefs
Unknown packages ‘HI’, ‘MHadaptive’ in Rd xrefs
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.0Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared packages ‘timereg’, ‘rms’, ‘ranger’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
  ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
  ‘sandwich’ ‘sjstats’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘table_AeRobiology’
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(africamonitor)
  africamonitor 0.2.3, see help(africamonitor)
  > 
  > test_check("africamonitor")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-accessdb.R:6:3'): reshaping works ──────────────────────────────
  Error in `alc(qDT_raw(X, row.names.col, keep.attr, if (length(class) || 
      keep.attr) class else c("data.table", "data.frame"), if (is.atomic(X) && 
      !is.matrix(X)) l1orlst(as.character(substitute(X))) else NULL))`: cannot take a writable DATAPTR of an ALTLIST [class: wrap_list, pkg: base]
  Backtrace:
       ▆
    1. ├─testthat::expect_equal(data, am_pivot_wider(am_pivot_longer(data))) at test-accessdb.R:6:2
    2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─africamonitor::am_pivot_wider(am_pivot_longer(data))
    5. │ └─collapse::ftransformv(data, names_from, qF, sort = FALSE)
    6. └─africamonitor::am_pivot_longer(data)
    7.   ├─data.table::melt(...)
    8.   │ └─data.table::is.data.table(data)
    9.   └─collapse::qDT(data)
   10.     └─collapse:::alc(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘mFilter’ ‘regclass’ ‘writexl’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Undeclared packages ‘epiR’, ‘cccrm’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
S3 methods shown with full name in documentation object 'intervals.freq':
  ‘intervals.freq’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
checkRd: (-1) BerryMielke.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) BlairLacy.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) Kvalseth.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) consensus.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) dsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) l.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) lsquared.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) var.variance.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) adapt.Rd:41: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘multcomp’, ‘gmodels’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
  ‘utils’
  All declared Imports should be used.
Note: found 53 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       2.0Mb
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
'LazyData' is specified without a 'data' directory
Undeclared package ‘SnowballC’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘hyperSpec’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 114 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 171 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘metaboliteIDmapping’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'library' or 'require' call to ‘network’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘dplyr’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
as.url:
  function(x, ...)
as.url.domain:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) deshrink.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) deshrink.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) plot.mat.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) plot.wa.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) predict.prcurve.Rd:5: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
Note: found 231 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
Namespaces in Imports field not imported from:
  ‘cli’ ‘crayon’ ‘rstudioapi’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    test_v8    2.2Mb
    testdata   2.1Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mcclust’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘geepack’, ‘dispmod’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘AER’ ‘ChainLadder’ ‘ISLR’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘APIS/libs/APIS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
checkRd: (-1) AQuadtree-package.Rd:11: Escaped LaTeX specials: \$
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Undeclared package ‘RCurl’ in Rd xrefs
Note: found 76 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘bannerCommenter’ ‘config’ ‘feather’ ‘here’ ‘knitr’ ‘log4r’ ‘ps’
  ‘rmarkdown’ ‘skimr’ ‘snakecase’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘rmarkdown’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Undeclared packages ‘survey’, ‘Matching’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs  39.0Mb
Undeclared package ‘readr’ in Rd xrefs
Note: found 1409 marked UTF-8 strings
Package which this enhances but not available for checking: ‘ARTP’
Found the following significant warnings:
  ARTP2_init.c:17:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ARTP2.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘assertive.properties’, ‘assertive.types’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘rstudioapi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘sets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pryr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘asteRiskData’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
ihasNext:
  function(obj, ...)
ihasNext.default:
  function(obj)

ihasNext:
  function(obj, ...)
ihasNext.ihasNextOr:
  function(x)

ihasNext:
  function(obj, ...)
ihasNext.iteror:
  function(iter, ...)

compile:
  function(x, level, ...)
compile.coroutine:
  function(x, level)

as.promise:
  function(x)
as.promise.channel:
  function(ch, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
add_name_to_statistics:
  function(x, name)
add_name_to_statistics.data.frame:
  function(x, name, colname_for_variable)

add_name_to_tests:
  function(x, name)
add_name_to_tests.data.frame:
  function(x, name, colname_for_variable)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Error(s) in re-building vignettes:
--- re-building ‘PeakSegDisk.Rmd’ using knitr
--- finished re-building ‘PeakSegDisk.Rmd’

--- re-building ‘binseg.Rmd’ using knitr
--- finished re-building ‘binseg.Rmd’

--- re-building ‘cum_median.Rmd’ using knitr
--- finished re-building ‘cum_median.Rmd’

--- re-building ‘data.table.Rmd’ using knitr
--- finished re-building ‘data.table.Rmd’

--- re-building ‘git.Rmd’ using knitr
Quitting from lines 92-100 (git.Rmd) 
Error: processing vignette 'git.Rmd' failed with diagnostics:
! in callr subprocess.
Caused by error: 
! there is no package called ‘binsegRcpp.dcd0808f52b0b9858352106cc7852e36d7f5b15d’
--- failed re-building ‘git.Rmd’

--- re-building ‘optseg.Rmd’ using knitr
--- finished re-building ‘optseg.Rmd’

--- re-building ‘regex.Rmd’ using knitr
--- finished re-building ‘regex.Rmd’

SUMMARY: processing the following file failed:
  ‘git.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘lubridate’ ‘openair’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘snpar’ in Rd xrefs
Unknown package ‘snpar’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dlnm’ ‘ggplot2’ ‘mvmeta’ ‘pbs’ ‘tsModel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  driver.c:114:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:161:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  driver.c:199:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/audio.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Undeclared package ‘gtable’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 54582 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 552 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tensorflow’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.rsp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘readxl’ ‘reshape2’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bslib’ ‘rclipboard’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MixAll’ ‘dplyr’ ‘lqmm’ ‘matrixcalc’ ‘rmutil’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Undeclared package ‘AzureAuth’ in Rd xrefs
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘lixoftConnectors’
Specified C++14: please drop specification unless essential
Note: found 64209 marked UTF-8 strings
Note: found 133353 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ in Rd xrefs
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
posterior_predict:
  function(object, ...)
posterior_predict.baggr:
  function(object, draws, newdata, transform, summary, message,
           interval)

pp_check:
  function(object, ...)
pp_check.baggr:
  function(x, type, nsamples)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 260 marked UTF-8 strings
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘fs’ ‘testthat’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.3Mb
    doc    1.8Mb
Undeclared package ‘akima’ in Rd xrefs
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fdpbandsdata’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 148 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
Undeclared package ‘YaleToolkit’ in Rd xrefs
Note: found 13825 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 73-75 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.4Mb
Specified C++11: please drop specification unless essential
Undeclared package ‘Rraven’ in Rd xrefs
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘jsonlite’, ‘arrow’ in Rd xrefs
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Earlier versions
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘circlize’ ‘hexbin’ ‘scales’ ‘sna’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘rPython’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rmpi’ in Rd xrefs
Namespace in Imports field not imported from: ‘vtable’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
Found the following significant warnings:
  bayesDccGarch.c:48:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:110:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  bayesDccGarch.c:172:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/bayesDccGarch.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   6.4Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘StanHeaders’ ‘astsa’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RcppParallel’ ‘mlbench’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘fGarch’ in Rd xrefs
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
rhat:
  function(x, ...)
rhat.bayesmanecfit:
  function(object, rhat_cutoff, ...)

rhat:
  function(x, ...)
rhat.bayesnecfit:
  function(object, rhat_cutoff, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)

plot:
  function(x)
plot.posterior:
  function(x, add_prior, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘MCMCpack’ ‘R2WinBUGS’ ‘R2jags’ ‘carData’ ‘rjags’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
Note: found 1924 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘matrixcalc’ ‘stats’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bart.Rd:271: Escaped LaTeX specials: \_
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 385 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) create_ThetaMatrix.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) create_ThetaMatrix.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Undeclared package ‘formula.tools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘betareg’ in Rd xrefs
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   3.3Mb
sql_translation:
  function(con)
sql_translation.wfsConnection:
  function(conn)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following files/directories:
  ‘fabiabreast.txt’
checkRd: (-1) tlsce.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:55: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) tlsce.Rd:93: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'kBET', 'lisi', 'dlfUtils'
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘splatter’
  All declared Imports should be used.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2666 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.plm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.gplm:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.tournament:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.gplm0:
  function(x, type, param, transformed, ...)

autoplot:
  function(object, ...)
autoplot.plm0:
  function(x, type, param, transformed, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘dump.txt’
Package suggested but not available for checking: ‘flowCore’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘beast_plot_toy.pdf’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  load.c:11:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./nanotime.h:7:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:75:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:118:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  mark.c:119:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:61:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotime.c:71:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  process_memory.c:79:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/bench.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘zoo’ in Rd xrefs
Namespace in Imports field not imported from: ‘BiDAG’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘SoDA’
Specified C++11: please drop specification unless essential
Note: found 10089 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 582 marked UTF-8 strings
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Undeclared package ‘conf.design’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is 155.7Mb
  sub-directories of 1Mb or more:
    include  155.6Mb
Specified C++11: please drop specification unless essential
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 99 marked UTF-8 strings
Note: found 1904 marked UTF-8 strings
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DAAG’ ‘datasets’ ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Found the following significant warnings:
  rbimax.c:326:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/biclust.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespace in Imports field not imported from: ‘RBGL’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ffbase’
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 940 marked Latin-1 strings
Found the following significant warnings:
  ./lib.h:6:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib.c:3:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigGP.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Specified C++11: please drop specification unless essential
Undeclared package ‘bigrquery’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘outputs’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmio’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Binarize.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Undeclared package ‘BoolNet’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BinaryEPPM.Rd:159: Escaped LaTeX specials: \&
Undeclared packages ‘CountsEPPM’, ‘betareg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tint’, ‘pinp’, ‘linl’ in Rd xrefs
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘genalg’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘msa’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared packages ‘rgeos’, ‘pvclust’ in Rd xrefs
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
Undeclared package ‘seqinr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘desc’ ‘lme4’ ‘mitml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 46 marked UTF-8 strings
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘magrittr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  ./binarizeBASCA.h:37:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC.c:258:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  TASC_min.c:256:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  binarizeBASCA.c:358:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/BiTrinA.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Undeclared package ‘BoolNet’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RColorBrewer’ in Rd xrefs
Package suggested but not available for checking: ‘RQuantLib’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘digest’ ‘ergm’ ‘foreign’ ‘gWidgets2’ ‘gWidgets2tcltk’ ‘haven’
  ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       4.6Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.9Mb
Undeclared packages ‘biomod2’, ‘gstat’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘np’ in Rd xrefs
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
GNU make is a SystemRequirements.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   5.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  ./include/register.h:46:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:75:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:76:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./include/register.h:82:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:15:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  globals.c:33:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:26:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  test.counter.c:35:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
as.mcmc:
  function(x, ...)
as.mcmc.multNRMI:
  function(fitlist, thinning_to, ncores)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Package suggested but not available for checking: ‘sangerseqR’
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 47.7Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      36.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘HSAUR3’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    modules 0.x
Undeclared packages ‘data.table’, ‘readxl’, ‘openxlsx’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) bpca.Rd:85: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Note: found 2487 marked UTF-8 strings
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) R2txtJG.Rd:90: Escaped LaTeX specials: \#
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘generics’ in Rd xrefs
GNU make is a SystemRequirements.
Undeclared package ‘brglm’ in Rd xrefs
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘cmdstanr’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   3.6Mb
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) brr-package.Rd:33: Escaped LaTeX specials: \&
Found the following significant warnings:
  BugsHelper.c:76:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:87:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  BugsHelper.c:88:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/BRugs.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   1.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Undeclared package ‘data.table’ in Rd xrefs
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    fonts   3.0Mb
    lib     5.3Mb
Undeclared package ‘plotly’ in Rd xrefs
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘grDevices’ ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   2.7Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘mitools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘magrittr’ ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Undeclared packages ‘Hmisc’, ‘gtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.performance:
  function(x, type, format, keep.rownames, ...)

iid:
  function(x, ...)
iid.BuyseTTEM:
  function(x, treatment, strata, cause)

iid:
  function(x, ...)
iid.BuyseTestAuc:
  function(object, ...)

iid:
  function(x, ...)
iid.prodlim:
  function(object, add0, ...)

iid:
  function(x, ...)
iid.BuyseTestBrier:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Undeclared packages ‘quadprog’, ‘nnls’ in Rd xrefs
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 179 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following significant warnings:
  cairobem.c:50:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:9:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./Rapi.h:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:661:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1552:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cairotalk.c:1588:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  xlib-backend.c:156:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Cairo.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Note: found 58 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RxODE’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tesseract’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.2Mb
Undeclared package ‘plotrix’ in Rd xrefs
Note: found 287 marked UTF-8 strings
Note: found 512 marked UTF-8 strings
Note: found 23 marked UTF-8 strings
Found the following files/directories:
  ‘tmp.txt’
Undeclared packages ‘yacca’, ‘CCA’ in Rd xrefs
Found the following files/directories:
  ‘MDA231_tree.pdf’
checkRd: (-1) caic-class.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) caic-class.Rd:15: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘methods’ ‘readr’ ‘recipes’ ‘sf’ ‘stringr’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
oob_pred:
  function(x, ...)
oob_pred.rfe:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.train:
  function(x, best, average)

oob_pred:
  function(x, ...)
oob_pred.sbf:
  function(x, average)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Undeclared package ‘limma’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘plotrix’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GAMBoost’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    doc  37.7Mb
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Undeclared packages ‘pixmap’, ‘XML’, ‘exactRankTests’, ‘coin’, ‘ROCR’, ‘Epi’, ‘verification’, ‘Hmisc’, ‘gtools’, ‘magic’, ‘zoo’ in Rd xrefs
checkRd: (-1) belt.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) bipf.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) crime.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) da.cat.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) dabipf.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) ecm.cat.Rd:77: Escaped LaTeX specials: \&
checkRd: (-1) em.cat.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) ipf.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) logpost.cat.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) mda.cat.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) mi.inference.Rd:140: Escaped LaTeX specials: \&
checkRd: (-1) older.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) prelim.cat.Rd:67: Escaped LaTeX specials: \&
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘forcats’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CBPS’ ‘spelling’
  All declared Imports should be used.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Undeclared package ‘graph’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 1 marked UTF-8 string
Undeclared package ‘sitmo’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘GeneNet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hotcold.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘CirceR’
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
Specified C++11: please drop specification unless essential
Note: found 907 marked UTF-8 strings
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.2Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Running examples in ‘CensSpatial-Ex.R’ failed
The error most likely occurred in:

> ### Name: algnaive12
> ### Title: Naive 1 and Naive 2 method for spatial prediction.
> ### Aliases: algnaive12
> ### Keywords: Spatial Censored SAEM
> 
> ### ** Examples
> 
> ###simulated coordinates
> n<-200 ### sample size for estimation.
> n1=100 ### number of observation used in the prediction.
> 
> ###simulated coordinates
> r1=sample(seq(1,30,length=400),n+n1)
> r2=sample(seq(1,30,length=400),n+n1)
> coords=cbind(r1,r2)### total coordinates (used in estimation and prediction).
> 
> coords1=coords[1:n,]####coordinates used for estimation.
> 
> type="matern"### covariance structure.
> 
> xtot<-cbind(1,runif((n+n1)),runif((n+n1),2,3))## X matrix for estimation and prediction.
> xobs=xtot[1:n,]## X matrix for estimation.
> 
> ###simulated data
> obj=rspacens(cov.pars=c(3,.3,0),beta=c(5,3,1),x=xtot,coords=coords,kappa=1.2,
+ cens=0.25,n=(n+n1),n1=n1,cov.model=type,cens.type="left")
> 
> data2=obj$datare
> data2[,4:5]=xobs[,-1]
> 
> cc=obj$cc
> y=obj$datare[,3]
> cutoff=rep(obj$cutoff,length(y[cc==1]))
> 
> 
> aux2=algnaive12(data=data2,cc=obj$cc,covar=TRUE,covar.col=4:5,
+ copred=obj$coords1,thetaini=c(.1,.2),y.col=3,coords.col=1:2,
+ fix.nugget=TRUE,nugget=0,kappa=1.2,cutoff=cutoff,trend=~V4+V5,
+ cov.model=type)
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 104 marked UTF-8 strings
Undeclared package ‘vegan’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘alr3’
Namespaces in Imports field not imported from:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘batchtools’ ‘data.table’ ‘dplyr’ ‘ggplot2’ ‘htmltools’
  ‘jsonlite’ ‘magrittr’ ‘methods’ ‘plotly’ ‘reshape’ ‘rlang’ ‘shiny’
  ‘shinyWidgets’ ‘shinyjqui’ ‘shinyjs’ ‘shinymaterial’ ‘sortable’ ‘ssh’
  ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major refactoring of the code
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.5Mb
  sub-directories of 1Mb or more:
    include  38.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Malformed Title field: should not end in a period.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared packages ‘dplyr’, ‘matrixStats’, ‘filesstrings’, ‘pracma’, ‘sf’, ‘rgeos’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bench’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘AER’ ‘graphics’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘darts’
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hyptis.Rd:31: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘stepres00.txt’
Package suggested but not available for checking: ‘clusterCrit’
Unknown package ‘clusterCrit’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘countreg’
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 32 marked UTF-8 strings
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Note: found 8119 marked UTF-8 strings
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘cmdstanr’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘entab’
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
  All declared Imports should be used.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 28982 marked UTF-8 strings
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Package suggested but not available for checking: ‘userfriendlyscience’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘networkD3’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
resolved:
  function(x, ...)
resolved.CivisFuture:
  function(future, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    help   1.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘reshape’ in Rd xrefs
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘bslib’, ‘shiny’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 27934 marked UTF-8 strings
Note: found 10332 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 8737 marked UTF-8 strings
checkRd: (-1) diagwl.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) diagwl.Rd:5: Escaped LaTeX specials: \&
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Undeclared package ‘s2dv’ in Rd xrefs
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mlbench’, ‘fpc’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
checkRd: (-1) genRandomClust.Rd:228: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:259: Escaped LaTeX specials: \_
checkRd: (-1) genRandomClust.Rd:327: Escaped LaTeX specials: \_
checkRd: (-1) plot1DProjection.Rd:95: Escaped LaTeX specials: \_ \_
checkRd: (-1) plot2DProjection.Rd:117: Escaped LaTeX specials: \_ \_
checkRd: (-1) simClustDesign.Rd:235: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:268: Escaped LaTeX specials: \_
checkRd: (-1) simClustDesign.Rd:331: Escaped LaTeX specials: \_
Found the following files/directories:
  ‘clusterhap_reports’
Specified C++11: please drop specification unless essential
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘mvoutlier’, ‘fpc’, ‘ellipse’, ‘sfsmisc’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) HINoV.Mod.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) HINoV.Symbolic.rd:3: Escaped LaTeX specials: \&
checkRd: (-1) cluster.Gen.rd:14: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:18: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:29: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) cluster.Gen.rd:33: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:34: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:38: Escaped LaTeX specials: \_ \_
checkRd: (-1) cluster.Gen.rd:51: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:52: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:54: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:55: Escaped LaTeX specials: \_
checkRd: (-1) cluster.Gen.rd:62: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) comparing.Partitions.rd:12: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.BC.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.GDM.rd:33: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) dist.SM.rd:10: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.C.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G2.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.G3.rd:11: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.H.rd:16: Escaped LaTeX specials: \$ \_ \_
checkRd: (-1) index.S.rd:12: Escaped LaTeX specials: \$ \_ \_
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘sp’ ‘spdep’
  All declared Imports should be used.
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  optimal_assignment.c:47:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/clv.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 4622 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crr.Rd:22: Escaped LaTeX specials: \#
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘R.utils’ ‘SearchTrees’ ‘colorspace’ ‘colourpicker’
  ‘data.table’ ‘fields’ ‘mapproj’ ‘maps’ ‘maptools’ ‘ncdf4’ ‘raster’
  ‘rworldxtra’ ‘shinyFiles’ ‘shinyWidgets’ ‘shinyjs’ ‘shinythemes’ ‘sp’
  ‘tcltk’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tobit1’
'LazyData' is specified without a 'data' directory
Undeclared package ‘wavethresh’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Package suggested but not available for checking: ‘PopGenome’
autoplot:
  function(object, ...)
autoplot.bal.tab:
  function(x, stats, abs, agg.fun, var.order, drop.missing,
           drop.distance, thresholds, line, stars, grid, limits,
           colors, shapes, alpha, size, wrap, var.names, title,
           sample.names, labels, position, themes, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) drqssbc.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) qbsks.Rd:81: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘nnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 14729 marked UTF-8 strings
Package which this enhances but not available for checking: ‘rkward’
Undeclared package ‘pls’ in Rd xrefs
Package which this enhances but not available for checking: ‘rkward’
Note: found 27 marked UTF-8 strings
Package suggested but not available for checking: ‘userfriendlyscience’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
Note: found 30244 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4186 marked UTF-8 strings
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 742 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.1Mb
Note: found 2 marked UTF-8 strings
Unexported object imported by a ':::' call: ‘crayon:::mypaste’
  See the note in ?`:::` about the use of this operator.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘chi’ ‘dplyr’ ‘spatstat.utils’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘GGally’ ‘RColorBrewer’ ‘abind’ ‘diagram’ ‘ggplot2’ ‘grid’ ‘gtable’
  ‘igraph’ ‘magrittr’ ‘plyr’ ‘purrr’ ‘reshape2’ ‘scales’ ‘useful’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘CAM’
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 92 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kernlab’ ‘purrr’ ‘survminer’ ‘tidyverse’
  All declared Imports should be used.
File ‘condmixt/libs/condmixt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘mvtnorm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘base’ ‘lwgeom’ ‘s2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘dplyr’ ‘foreign’ ‘lavaan’ ‘openxlsx’ ‘purrr’ ‘semTools’
  ‘shinyWidgets’ ‘stringr’ ‘summarytools’ ‘waiter’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘scales’ ‘sna’
  All declared Imports should be used.
Note: found 244 marked UTF-8 strings
Undeclared package ‘ggplot2’ in Rd xrefs
File ‘ConsReg/libs/ConsReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  brentmin.c:237:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ContaminatedMixt.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     2.2Mb
    doc   3.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘re2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
checkRd: (-1) BrownBigrams.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownLOBPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownPassives.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BrownStats.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) KrennPPV.Rd:74: Escaped LaTeX specials: \&
Note: found 1187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 578 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) sgt.Rd:16: Escaped LaTeX specials: \&
Note: found 438 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) egde.Rd:26: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
ggplot:
  function(data, mapping, ..., environment)
ggplot.cosinor.lm:
  function(object, x_str)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘xaringan’, ‘beepr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 139613 marked UTF-8 strings
Undeclared package ‘betareg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘colourpicker’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘covfefe_inauguration.txt’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.7Mb
Note: found 1934235 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapview’ ‘plotly’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
merge_coverage:
  function(x)
merge_coverage.list:
  function(coverage_objs)

merge_coverage:
  function(x)
merge_coverage.character:
  function(files)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘gsl’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘multicolor’
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘GENESIS’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  bcplm.c:84:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/cplm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Non-visible changes:
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
crps:
  function(y, ...)
crps.crch:
  function(object, newdata, average, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conos', 'pagoda2'
‘cleanup’: /bin/bash is not portable
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.NumericVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.DatetimeVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalArrayVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CategoricalVariable:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.CrunchCubeCalculation:
  function(x, plot_type, ...)

autoplot:
  function(object, ...)
autoplot.tbl_crunch_cube:
  function(x, plot_type, measure)

autoplot:
  function(object, ...)
autoplot.CrunchCube:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.MultipleResponseVariable:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major features
    Minor features
checkRd: (-1) handmovement.Rd:9: Escaped LaTeX specials: \_ \_
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 500 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘geosphere’ ‘mapdata’ ‘maps’ ‘marmap’ ‘shinydashboard’
  ‘shinyjs’ ‘stringr’ ‘swfscDAS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘copula’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Note: found 282 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Note: found 3031 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:11:47: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctmcd.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 1350 marked UTF-8 strings
Specified C++14: please drop specification unless essential
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.6Mb
    doc    1.2Mb
    libs   9.7Mb
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘par-7269706c6579’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Hello.csv’
slice_head:
  function(.data, ..., n, prop, by)
slice_head.cubble_df:
  function(data, ...)

slice_tail:
  function(.data, ..., n, prop, by)
slice_tail.cubble_df:
  function(data, ...)

summarise:
  function(.data, ..., .by, .groups)
summarise.cubble_df:
  function(data, ...)

ungroup:
  function(x, ...)
ungroup.cubble_df:
  function(data, ...)

slice_max:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_max.cubble_df:
  function(data, ...)

group_by:
  function(.data, ..., .add, .drop)
group_by.cubble_df:
  function(data, ...)

slice_min:
  function(.data, order_by, ..., n, prop, by, with_ties, na_rm)
slice_min.cubble_df:
  function(data, ...)

vec_cast.data.frame:
  function(x, to, ...)
vec_cast.data.frame.cubble_df:
  function(x, y, ...)

tbl_sum:
  function(x)
tbl_sum.cubble_df:
  function(data)

slice_sample:
  function(.data, ..., n, prop, by, weight_by, replace)
slice_sample.cubble_df:
  function(data, ...)

vec_cast:
  function(x, to, ..., x_arg, to_arg, call)
vec_cast.cubble_df.data.frame:
  function(x, y, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 459 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    doc    1.2Mb
    help   1.0Mb
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
survfit:
  function(formula, ...)
survfit.cyclopsFit:
  function(cyclopsFit, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    demos         4.4Mb
    extdata       1.4Mb
    htmlwidgets   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    img   4.4Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘plyr’ ‘simpleboot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 109157 marked UTF-8 strings
checkRd: (-1) dspg.Rd:29: Escaped LaTeX specials: \^ \^
checkRd: (-1) dspgd2015.Rd:31: Escaped LaTeX specials: \^ \^
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Note: found 2020 marked UTF-8 strings
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 212 marked Latin-1 strings
  Note: found 12719 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pca3d’
Package suggested but not available for checking: ‘dash’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    deps  10.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dash’
Package suggested but not available for checking: ‘dash’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Undeclared package ‘gdata’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘my new data set.rds’
Note: found 36560 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Package suggested but not available for checking: ‘stubthat’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Datastream DWE - now decommissioned by Refinitiv
    CRAN
Note: found 8 marked Latin-1 strings
Found the following significant warnings:
  init.c:29:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:30:45: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:31:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:33:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:34:52: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:36:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:37:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/datastructures.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
‘cleanup’: ‘env bash’ is not portable as bash need not be installed
Namespaces in Imports field not imported from:
  ‘R6’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("dataverse")
  > 
  > if (!requireNamespace("yaml", quietly = TRUE)) {
  +   warning("The 'yaml' package must be present to test the dataverse package.")
  + } else if (!requireNamespace("checkmate", quietly = TRUE)) {
  +   warning("The 'checkmate' package must be present to test the dataverse package.")
  + } else {
  +   server  <- Sys.getenv("DATAVERSE_SERVER")
  +   key     <- Sys.getenv("DATAVERSE_KEY")
  + 
  +   if (server == "" | key == "") {
  +     config  <- yaml::read_yaml(system.file("constants.yml", package = "dataverse"))
  +     # config  <- yaml::read_yaml("inst/constants.yml")
  + 
  +     Sys.setenv("DATAVERSE_SERVER" = config$server)
  +     Sys.setenv("DATAVERSE_KEY"    = config$api_token)
  + 
  +     # To better identify the source of problems, check if the token is expired.
  +     #   This check *should* be unnecessary on CRAN, since not CRAN tests should
  +     #   try to access any server.
  +     if (Sys.getenv("NOT_CRAN") %in% c("", "true")) {
  +       if (as.Date(config$api_token_expiration) < Sys.Date()) {
  +         stop(
  +           "The API token expired on `",
  +           config$api_token_expiration,
  +           "`, so the tests would probably fail.  ",
  +           "Please regenerate a new token and update `inst/constants.yml`"
  +         )
  +       }
  +     }
  +     rm(config)
  +   }
  +   rm(server, key)
  + 
  +   message("Using Dataverse server `", Sys.getenv("DATAVERSE_SERVER"), "`.")
  + 
  +   test_check("dataverse")
  + }
  Error: The API token expired on `2023-03-10`, so the tests would probably fail.  Please regenerate a new token and update `inst/constants.yml`
  Execution halted
Specified C++11: please drop specification unless essential
Undeclared package ‘FCPS’ in Rd xrefs
Package suggested but not available for checking: ‘SASxport’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 54315 marked UTF-8 strings
Note: found 1 marked Latin-1 string
  Note: found 360 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tidyverse’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘withr’ in Rd xrefs
Undeclared package ‘duckdb’ in Rd xrefs
Package suggested but not available for checking: ‘dblog’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PqConnection:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.PostgreSQL:
  function(con, df, types, lvl)

sql_values_subquery:
  function(con, df, types, lvl, ...)
sql_values_subquery.Microsoft SQL Server:
  function(con, df, types, lvl)

db_write_table:
  function(con, table, types, values, temporary, ...)
db_write_table.PostgreSQLConnection:
  function(con, table, types, values, temporary, overwrite, ....)

sql_select:
  function(con, select, from, where, group_by, having, order_by, limit,
           distinct, ...)
sql_select.DBIConnection:
  function(con, select, from, where, group_by, having, window,
           order_by, limit, distinct, ..., subquery)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘html5’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘lubridate’ ‘tseries’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘bslib’ ‘knitr’ ‘matrixStats’ ‘rmarkdown’ ‘shinythemes’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Undeclared package ‘fda.usc’ in Rd xrefs
Found the following significant warnings:
  ./difeq.h:65:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  difeq.c:123:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./dopri.h:208:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dopri.c:245:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/dde.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘qpdf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘future’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Note: found 1 marked Latin-1 string
  Note: found 46826 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘e1071’, ‘nloptr’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘shinyBS’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes from previous package DecompHoriuchi
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘smd_table.docx’
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
ggplot:
  function(data, mapping, ..., environment)
ggplot.ggdend:
  function(data, segments, labels, nodes, horiz, theme, offset_labels,
           na.rm, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘DEoptim’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   2.1Mb
Package suggested but not available for checking: ‘Rdonlp2’
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘Rdonlp2’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./deque.h:73:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  constructor.c:43:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  deque.c:31:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dequer_native.c:9:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/dequer.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.ddplot:
  function(data, axis.location, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.timeseries:
  function(data, edges, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.histogram:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.barplot:
  function(data, spine, ...)

ggplot:
  function(data, mapping, ..., environment)
ggplot.parcoords:
  function(data, absoluteX, absoluteY, edges, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) geom_axis.Rd:10: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Undeclared package ‘FactoMineR’ in Rd xrefs
Note: found 5764 marked UTF-8 strings
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.N’ ‘.Nmiss’ ‘.Q1’ ‘.Q3’ ‘.factorN’ ‘.factorNmiss’ ‘.factorQ1’
  ‘.factorQ3’ ‘.factormax’ ‘.factormean’ ‘.factormedian’ ‘.factormin’
  ‘.factorsd’ ‘.max’ ‘.mean’ ‘.median’ ‘.min’ ‘.sd’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.5Mb
Undeclared packages ‘ineq’, ‘randtests’, ‘Hmisc’, ‘plotrix’, ‘caret’, ‘pcaPP’, ‘polycor’, ‘lmtest’, ‘car’, ‘gmp’, ‘vcdExtra’, ‘chron’, ‘coin’, ‘caTools’, ‘forecast’, ‘sfsmisc’, ‘vcd’, ‘areaplot’, ‘corrgram’, ‘UsingR’, ‘memisc’, ‘gtools’, ‘BSDA’, ‘prettyR’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Note: found 47 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  void_dev.c:103:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:182:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  void_dev.c:197:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/devoid.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘plyr’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) phihat.Rd:34: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # install.packages("testthat")
  > library(testthat)
  > # install.packages("forecast")
  > # library(forecast)
  > # install.packages("stats")
  > # library(stats)
  > # install.packages("future.apply")
  > # library(future.apply)
  > library(dhReg)
  Loading required package: forecast
  Loading required package: future.apply
  Loading required package: future
  > Data1 <- runif(runif(200,100,1000)) #To generate random number for example
  > Data_ts <- ts(Data1)
  > 
  > test_that("summary of Dynamic harmonic regression model", {
  +   M <- dhr(Data=Data_ts,XREG=NULL,Range=list(1:2,1),Frequency=c(24,168),Criteria="aicc")
  + })
  ── Error (???): summary of Dynamic harmonic regression model ───────────────────
  <defunctError/error/condition>
  Error: Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
  Backtrace:
   1. dhReg::dhr(...)
   2. future::plan(future::multiprocess)
   3. future (local) plan_set(newStack, skip = .skip, cleanup = .cleanup, init = .init)
   4. future (local) warn_about_multiprocess(newStack)
   5. future (local) warn_about_deprecated(stack, strategy = "multiprocess", fmtstr = sprintf("Strategy '%%s' is %%s in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'."))
   6. base (local) dfcn(msg = msg, package = .packageName)
  
  Error in reporter$stop_if_needed() : Test failed
  Calls: test_that -> <Anonymous>
  Execution halted
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Note: found 8014 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘purrr’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)

colnames:
  function(x, do.NULL, prefix)
colnames.MultivariateAnalysis:
  function(x)

rownames:
  function(x, do.NULL, prefix)
rownames.MultivariateAnalysis:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘CVST’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘gamlss’, ‘flexsurv’ in Rd xrefs
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
checkRd: (-1) sammy.Rd:51: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘discreteMTP’
Unknown package ‘discreteMTP’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
Undeclared package ‘Hmisc’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘diversitree’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Undeclared package ‘robustbase’ in Rd xrefs
log_quantile:
  function(x, q, ...)
log_quantile.dist_na:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.distribution:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_lognormal:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_default:
  function(x, p, ...)

log_quantile:
  function(x, q, ...)
log_quantile.dist_normal:
  function(x, p, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘RobAStBase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘RobAStBase’ in Rd xrefs
Undeclared package ‘distrTEst’ in Rd xrefs
Undeclared package ‘distr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘truncnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggmulti’ ‘loon’ ‘loon.data’ ‘loon.ggplot’ ‘loon.shiny’ ‘loon.tourr’
  ‘stats’ ‘zenplots’
  All declared Imports should be used.
Found the following significant warnings:
  ./rfftw.h:34:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rfftw.c:149:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  util.c:231:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:10:33: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./zzz.h:44:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/diversitree.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘clang version 16.0.0’
Package suggested but not available for checking: ‘BOLTSSIRR’
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plotly’ ‘pryr’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
checkRd: (-1) dlsem.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:20: Escaped LaTeX specials: \&
checkRd: (-1) unirootTest.Rd:26: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Note: found 9796 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
checkRd: (-1) block.catlg.Rd:61: Escaped LaTeX specials: \^ \^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘uuid’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    data      2.0Mb
    extdata   2.3Mb
Undeclared package ‘molaR’ in Rd xrefs
Note: found 100 marked UTF-8 strings
Found the following significant warnings:
  alive.c:200:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  alive.c:277:7: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/doRedis.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New features
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘DT’ ‘DoseFinding’ ‘Rsolnp’ ‘ggplot2’ ‘kableExtra’ ‘knitr’
  ‘latticeExtra’ ‘purrr’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘stringr’ ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘OpenMPController’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Note: found 2 marked UTF-8 strings
Undeclared package ‘broomExtra’ in Rd xrefs
Unknown package ‘broomExtra’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Running ‘testthat.R’ [4m/21m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  [ FAIL 2 | WARN 270 | SKIP 305 | PASS 2764 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (305)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-filter.R:301:3'): hybrid function row_number does not trigger warning in filter (#3750) ──
  `out` is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-join-by.R:236:3'): nicely catches missing arguments when wrapped ──
  `fn(a)` did not throw the expected error.
  
  [ FAIL 2 | WARN 270 | SKIP 305 | PASS 2764 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘ggplot2’ ‘nloptr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Undeclared package ‘RcppEigen’ in Rd xrefs
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘sitmo’ in Rd xrefs
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
Undeclared package ‘SimMultiCorrData’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    tutorials   5.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 8 marked UTF-8 strings
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘data.table’ in Rd xrefs
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘EvalEst’ in Rd xrefs
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 149 marked UTF-8 strings
Note: found 4891 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘dsBaseClient’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘dstat’, ‘sensitivity2x2xk’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 1 marked Latin-1 string
'LazyData' is specified without a 'data' directory
Note: found 281 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
dt_has_computation:
  function(x)
dt_has_computation.dtplyr_step:
  function(x, needs_copy)

count:
  function(x, ..., wt, sort, name)
count.dtplyr_step:
  function(.data, ..., wt, sort, name)

pull:
  function(.data, var, name, ...)
pull.dtplyr_step:
  function(.data, var, name)

show_query:
  function(x, ...)
show_query.dtplyr_step:
  function(x)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.dtplyr_step:
  function(tbl, size, replace, weight)

sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.dtplyr_step:
  function(tbl, size, replace, weight)

group_modify:
  function(.data, .f, ..., .keep)
group_modify.dtplyr_step:
  function(.tbl, .f, ..., keep)

add_count:
  function(x, ..., wt, sort, name, .drop)
add_count.dtplyr_step:
  function(.data, ..., wt, sort, name)

tally:
  function(x, wt, sort, name)
tally.dtplyr_step:
  function(.data, wt, sort, name)

ungroup:
  function(x, ...)
ungroup.dtplyr_step:
  function(.data, ...)

group_map:
  function(.data, .f, ..., .keep)
group_map.dtplyr_step:
  function(.tbl, .f, ..., keep)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘vctrs’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.1Mb
File ‘dualtrees/libs/dualtrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  35.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2854 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘GenEst’ ‘expint’ ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘quadprog’ in Rd xrefs
Undeclared package ‘stringdist’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   2.2Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    data   7.0Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘NatureSounds’ ‘av’ ‘magrittr’ ‘stats’
  All declared Imports should be used.
Undeclared package ‘warbleR’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lle’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Found the following significant warnings:
  arms.c:105:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:902:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/dynsurv.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Note: found 9 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘leaps’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    20181118
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.estimate:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    breaking changes
    major changes
    minor changes
    Internal
Namespace in Imports field not imported from: ‘qcr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’ ‘urca’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following significant warnings:
  include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos_bb/ecos_bb_preproc.c:298:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ecos/include/ecos_bb.h:161:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ECOSolveR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
GNU make is a SystemRequirements.
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Undeclared package ‘installr’ in Rd xrefs
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
Note: found 22 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.edbl_unit:
  function(x)

tbl_sum:
  function(x)
tbl_sum.edbl_table:
  function(.data)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.edbl_unit:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘tibble’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘ndl’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘T2EQ’ in Rd xrefs
glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)

glm:
  function(formula, family, data, weights, subset, na.action, start,
           etastart, mustart, offset, control, model, method, x, y,
           singular.ok, contrasts, ...)
glm.sdf:
  function(formula, family, data, weightVar, relevels, varMethod,
           jrrIMax, omittedLevels, defaultConditions, recode,
           returnNumberOfPSU, returnVarEstInputs)

lm:
  function(formula, data, subset, weights, na.action, method, model, x,
           y, qr, singular.ok, contrasts, offset, ...)
lm.sdf:
  function(formula, data, weightVar, relevels, varMethod, jrrIMax,
           omittedLevels, defaultConditions, recode,
           returnVarEstInputs, returnNumberOfPSU,
           standardizeWithSamplingVar, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘PCovR’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘carData’ in Rd xrefs
Undeclared packages ‘carData’, ‘faraway’ in Rd xrefs
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/eflm.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Note: found 24 marked UTF-8 strings
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
Specified C++14: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
Note: found 7 marked UTF-8 strings
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./eicm.h:70:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/eicm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘eRm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘EloRating’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
File ‘elsa/libs/elsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘textrecipes’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 155 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘mvtnorm’ in Rd xrefs
Note: found 50 marked Latin-1 strings
Found the following significant warnings:
  emd-rubner.c:143:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:153:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  emd-rubner.c:640:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/emdist.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘osmar’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./utilities.h:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  utilities.c:14:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/emoa.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 16919 marked UTF-8 strings
Undeclared packages ‘Kendall’, ‘geoR’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 23639 marked Latin-1 strings
Namespace in Imports field not imported from: ‘BBmisc’
  All declared Imports should be used.
Math2:
  function(x, digits)
Math2.trackdata:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘DECIPHER’ ‘ggplot2’ ‘reshape2’ ‘usethis’
  All declared Imports should be used.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RStoolbox’
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.4Mb
checkRd: (-1) calibrate.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) cdfCompareCensored.Rd:299: Escaped LaTeX specials: \&
checkRd: (-1) detectionLimitCalibrate.Rd:149: Escaped LaTeX specials: \&
checkRd: (-1) ecdfPlotCensored.Rd:169: Escaped LaTeX specials: \&
checkRd: (-1) egammaAltCensored.Rd:344: Escaped LaTeX specials: \&
checkRd: (-1) egammaCensored.Rd:340: Escaped LaTeX specials: \&
checkRd: (-1) elnormAltCensored.Rd:694: Escaped LaTeX specials: \&
checkRd: (-1) elnormCensored.Rd:270: Escaped LaTeX specials: \&
checkRd: (-1) enormCensored.Rd:852: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:343: Escaped LaTeX specials: \&
checkRd: (-1) enparCensored.Rd:358: Escaped LaTeX specials: \&
checkRd: (-1) epoisCensored.Rd:354: Escaped LaTeX specials: \&
checkRd: (-1) ppointsCensored.Rd:406: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) predIntGammaSimultaneous.Rd:171: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:136: Escaped LaTeX specials: \&
checkRd: (-1) predIntLnormSimultaneous.Rd:137: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:204: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneous.Rd:205: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) predIntNormSimultaneousK.Rd:278: Escaped LaTeX specials: \&
checkRd: (-1) qqPlotCensored.Rd:261: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTest.Rd:276: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:324: Escaped LaTeX specials: \&
checkRd: (-1) twoSampleLinearRankTestCensored.Rd:331: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Net1-fromR.inp’
Namespaces in Imports field not imported from:
  ‘RSpectra’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
  Note: found 1508 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
as.igraph:
  function(x, ...)
as.igraph.epicontacts:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tinytest’
  All declared Imports should be used.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Package suggested but not available for checking: ‘epidict’
Specified C++11: please drop specification unless essential
AaJ:
  function(Lx, ...)
AaJ.Lexis:
  function(Lx, formula, timeScale)

addCov:
  function(Lx, ...)
addCov.Lexis:
  function(Lx, clin, timescale, exnam, tfc)

addDrug:
  function(Lx, ...)
addDrug.Lexis:
  function(Lx, pdat, amt, dpt, apt, method, maxt, grace, tnam, prefix,
           sepfix, verbose)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘taskscheduleR’

Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘knitr’ ‘plyr’ ‘rgdal’ ‘tidyverse’ ‘tokenizers’ ‘xml2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 15 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘OpenMx’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘methods’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Undeclared package ‘margins’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   1.8Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc  13.1Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘metafor’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘EMMAgeo’ ‘limSolve’ ‘shinyFiles’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Note: found 1054 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘curl’ ‘scales’ ‘stringr’ ‘tidyquant’
  All declared Imports should be used.
Undeclared package ‘R6’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
Undeclared packages ‘ks’, ‘evd’, ‘ismev’, ‘mixtools’, ‘evir’, ‘smoothtail’ in Rd xrefs
Found the following significant warnings:
  Warning: replacing previous import ‘geiger::rescale’ by ‘phytools::rescale’ when loading ‘evobiR’
See ‘/data/gannet/ripley/R/packages/tests-clang/evobiR.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘sample .nwk’
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘exact2x2’ in Rd xrefs
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘ExactData’
checkRd: (-1) exams2sakai.Rd:152: Escaped LaTeX specials: \&
Undeclared package ‘tth’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 342 marked UTF-8 strings
Undeclared package ‘iptools’ in Rd xrefs
Unknown package ‘iptools’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
Undeclared packages ‘tseriesChaos’, ‘rSFA’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cec2013’
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
Undeclared package ‘quantreg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc      3.5Mb
    images   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Note: found 1 marked UTF-8 string
Error(s) in re-building vignettes:
--- re-building ‘expp.Rmd’ using rmarkdown
Loading required package: expp
This is expp 1.2.5 For a tutorial type vignette("expp")

Attaching package: 'expp'

The following object is masked from 'package:base':

    as.data.frame

Quitting from lines 103-105 (expp.Rmd) 
Error: processing vignette 'expp.Rmd' failed with diagnostics:
unable to find an inherited method for function 'as.data.frame' for signature '"list"'
--- failed re-building ‘expp.Rmd’

SUMMARY: processing the following file failed:
  ‘expp.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) outlierPlot.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) outlierPlot.Rd:32: Escaped LaTeX specials: \$
File ‘extremis/libs/extremis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘exuberdata’
autoplot_radf_distr:
  function(x, ...)
autoplot_radf_distr.sb_distr:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
tidy:
  function(x, ...)
tidy.VAR:
  function(x)

tidy:
  function(x, ...)
tidy.AR:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘lmtest’ in Rd xrefs
ungroup:
  function(x, ...)
ungroup.fbl_ts:
  function(.data, ...)

ungroup:
  function(x, ...)
ungroup.grouped_fbl:
  function(.data, ...)

fortify:
  function(model, data, ...)
fortify.fbl_ts:
  function(object, level)

key_data:
  function(.data)
key_data.mdl_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘future’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘hier.part’
Undeclared package ‘SciViews’ in Rd xrefs
Unknown package ‘hier.part’ in Rd xrefs
Note: found 5 marked Latin-1 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
autoplot:
  function(object, ...)
autoplot.fairadapt:
  function(x, when, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘data.table’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  chli.c:5:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/fame.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

See section ‘Good practice’ in '?.onAttach'.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.0Mb
    help   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 179 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘RWeka’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1430 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./lu.h:44:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lu.c:828:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/fastclime.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘default5.eps’
Specified C++11: please drop specification unless essential
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘clusterCrit’
Error(s) in re-building vignettes:
--- re-building ‘fasthplus.Rmd’ using rmarkdown
Quitting from lines 298-300 (fasthplus.Rmd) 
Error: processing vignette 'fasthplus.Rmd' failed with diagnostics:
there is no package called 'clusterCrit'
--- failed re-building ‘fasthplus.Rmd’

SUMMARY: processing the following file failed:
  ‘fasthplus.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘coxKM’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ICSNP’, ‘ICS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) FastPCS-package.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) FastPCS.Rd:104: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) Scent.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) Traffic.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) Lemons.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) Lemons.Rd:5: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘NNLM’
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘collapse’ ‘data.table’ ‘kit’ ‘magrittr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rsolnp’ ‘assertthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.9Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.Rprofile’
Specified C++11: please drop specification unless essential
Unexported objects imported by ':::' calls:
  ‘fdapace:::GCVLwls1D1’ ‘fdapace:::GetSmoothedMeanCurve’
  ‘fdapace:::HandleNumericsAndNAN’ ‘fdapace:::interp2lin’
  See the note in ?`:::` about the use of this operator.
Note: found 75 marked UTF-8 strings
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘FastGP’ ‘MASS’ ‘fdapace’
  All declared Imports should be used.
Note: found 76 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘vert.txt’
vec_arith:
  function(op, x, y, ...)
vec_arith.cf_lag:
  function(op, x, y)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘treesAll.txt’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) noRegMin.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) regMin.Rd:24: Escaped LaTeX specials: \#
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘panelView’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    New Stuff
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 43825 marked UTF-8 strings
Note: found 134 marked UTF-8 strings
checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./f2c.h:185:49: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:186:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:187:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:188:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:189:38: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:190:35: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:191:42: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:192:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:193:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:194:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./f2c.h:195:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/FGSG.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    extdata   2.8Mb
Undeclared packages ‘MLEcens’, ‘Icens’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘MicrobeDS’
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R         4.3Mb
    doc       1.9Mb
    extdata   2.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rclipboard’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘FinePop’ in Rd xrefs
Package suggested but not available for checking: ‘diveRsity’
Unknown package ‘diveRsity’ in Rd xrefs
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 7 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Undeclared package ‘conicfit’ in Rd xrefs
Undeclared package ‘ks’ in Rd xrefs
checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
Undeclared package ‘extraDistr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fivethirtyeightdata’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
Note: found 584 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) fk_regression.Rd:32: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
levelplot:
  function(x, data, ...)
levelplot.JPtest:
  function(JPobj, what, rotate, plot, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 82 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cclust.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) randIndex.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) vacmot.Rd:28: Escaped LaTeX specials: \&
Undeclared package ‘mixture’ in Rd xrefs
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘FPCEnv’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/sugar/functions/sapply.h:36:26: warning: 'result_of<double (*(double))(double)>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/flexsurv.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Note: found 710 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc   9.0Mb
Undeclared package ‘flip’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Undeclared package ‘Kendall’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Undeclared package ‘HMR’ in Rd xrefs
Found the following files/directories:
  ‘flux.CH4.txt’
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) pseudoOptim.Rd:27: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘XICOR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 446 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 234 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ForecastCombinations’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘Rcpp’ ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Previous versions (not tagged nor released)
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.6Mb
Note: found 31 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘LaplacesDemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RandomFields’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
checkRd: (-1) CatalogueAccessors.Rd:249: Escaped LaTeX specials: \^ \^
checkRd: (-1) FrF2.Rd:574: Escaped LaTeX specials: \^
checkRd: (-1) FrF2.Rd:629: Escaped LaTeX specials: \^ \^
checkRd: (-1) IAPlot.Rd:87: Escaped LaTeX specials: \$
checkRd: (-1) block.Rd:121: Escaped LaTeX specials: \^
checkRd: (-1) block.Rd:150: Escaped LaTeX specials: \^ \^
checkRd: (-1) blockpick.Rd:114: Escaped LaTeX specials: \^ \^
Note: found 50 marked UTF-8 strings
Package suggested but not available for checking: ‘dggrids’
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.8Mb
    libs   1.5Mb
Undeclared packages ‘frm’, ‘frmpd’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
Undeclared packages ‘frm’, ‘frmhet’ in Rd xrefs
Unknown package ‘frm’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘chillR’ in Rd xrefs
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Found the following significant warnings:
  init.c:20:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/FSelectorRcpp.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Warning in formals(fun) : argument is not a function
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 39 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean.fts.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) median.fts.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) plot.fm.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) residuals.fm.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) sd.fts.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) var.fts.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) Spec_compare_localize_freq.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 120 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
semi_join:
  function(x, y, by, copy, ...)
semi_join.tbl_funnel:
  function(.data, ...)

anti_join:
  function(x, y, by, copy, ...)
anti_join.tbl_funnel:
  function(.data, ...)

inner_join:
  function(x, y, by, copy, suffix, ..., keep)
inner_join.tbl_funnel:
  function(.data, ...)

left_join:
  function(x, y, by, copy, suffix, ..., keep)
left_join.tbl_funnel:
  function(.data, ...)

right_join:
  function(x, y, by, copy, suffix, ..., keep)
right_join.tbl_funnel:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘completeTrial_byArm_eventPriorRateC3=0.001_eventPriorRateT1=0_eventPriorRateT2=0_eventPriorWt=0.5.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.2.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.4.RData’
  ‘completeTrial_byArm_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03_eventPriorWt=0.6.RData’
  ‘completeTrial_pooled_eventPriorRate=0.001_eventPriorWt=0.5.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.2.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.4.RData’
  ‘completeTrial_pooled_eventPriorRate=0.06_eventPriorWt=0.6.RData’
  ‘rcdf_byArm_arm=T1_eventPriorRateC3=0.06_eventPriorRateT1=0.03_eventPriorRateT2=0.03.pdf’
  ‘rcdf_pooled_eventPriorRate=0.06.pdf’
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘cffdrs’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Undeclared package ‘mfdb’ in Rd xrefs
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gargle’ ‘getProxy’ ‘rappsflyer’ ‘rfacebookstat’ ‘rgoogleads’
  ‘rmytarget’ ‘rvkstat’ ‘ryandexdirect’ ‘rym’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  gamlr.c:87:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/gamlr.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LGAclaims.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) LGAclaims.Rd:36: Escaped LaTeX specials: \_
Undeclared package ‘gamlss’ in Rd xrefs
Undeclared packages ‘gamlss.dist’, ‘gamlss.add’ in Rd xrefs
Undeclared package ‘hyperSpec’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GSE.Test.Main.Rd:23: Escaped LaTeX specials: \_
Note: found 2 marked UTF-8 strings
checkRd: (-1) meyer.Rd:11: Escaped LaTeX specials: \&
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Specified C++14: please drop specification unless essential
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc  44.3Mb
':::' call which should be '::': ‘graphics:::grid’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      1.9Mb
Undeclared package ‘RcppEigen’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘fortunes’, ‘rmsfact’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘checkdata.csv’ ‘gbmforest.sas’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fitgbd.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) fitgld.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) gb.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) gbd.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) gld.Rd:36: Escaped LaTeX specials: \&
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Note: found 103 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘gcmr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    libs     3.4Mb
Undeclared package ‘reshape’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’
  All declared Imports should be used.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
checkRd: (-1) plot_summary.Rd:14: Escaped LaTeX specials: \_
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘poibin’ in Rd xrefs
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘genderdata’
Undeclared package ‘mmap’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘R.utils’ ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
Undeclared package ‘RColorBrewer’ in Rd xrefs
Package suggested but not available for checking: ‘rrvgo’
Malformed Description field: should contain one or more complete sentences.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘GGEBiplots’ ‘calibrate’ ‘graphics’ ‘matrixStats’ ‘prettydoc’
  ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘bootstrap’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘GenSA/libs/GenSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  arms.c:99:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  arms.c:900:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/genscore.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 144 marked UTF-8 strings
Note: found 58 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   3.0Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Note: found 80 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘RiemBase’ in Rd xrefs
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 646 marked UTF-8 strings
Note: found 76726 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    R         9.6Mb
    extdata   2.6Mb
    help      2.4Mb
Undeclared package ‘ggmap’ in Rd xrefs
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘nloptr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘loo’ in Rd xrefs
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
Note: found 64 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘GWmodel’ ‘beepr’ ‘cartography’ ‘dplyr’ ‘raster’ ‘readxl’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinyjs’ ‘sp’
  ‘spdep’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
checkRd: (-1) getopt.Rd:60: Escaped LaTeX specials: \#
Package suggested but not available for checking: ‘argon2’
checkRd: (-1) gexp.Rd:123: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘RGtk2’
checkRd: (-1) estGF.Rd:106: Escaped LaTeX specials: \&
checkRd: (-1) estGF.Rd:107: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘googlesheets4’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘glue’, ‘magrittr’ in Rd xrefs
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       5.2Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘gge’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 2356 marked UTF-8 strings
Running examples in ‘ggESDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cardiological
> ### Title: Cardiological data example
> ### Aliases: Cardiological
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cardiological)
> ggInterval_index(Cardiological, aes(x = Syst))
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: ggInterval_index ... as.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ggESDA.Rmd’ using rmarkdown
Quitting from lines 47-57 (ggESDA.Rmd) 
Error: processing vignette 'ggESDA.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘ggESDA.Rmd’

SUMMARY: processing the following file failed:
  ‘ggESDA.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘utils’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘ggExtra/R/ggMarginalGadget.R’:
  assign(plotname, eval(parse(text = origPlot)), envir = .GlobalEnv)
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘interp’, ‘quantreg’ in Rd xrefs
grid.draw:
  function(x, recording)
grid.draw.ggmultiplot:
  function(plot)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
Undeclared package ‘rlang’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:37: Escaped LaTeX specials: \&
':::' call which should be '::': ‘scales:::censor’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘productplots:::bound’
  See the note in ?`:::` about the use of this operator.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggsci’ ‘memes’ ‘universalmotif’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Undeclared package ‘dwlm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘scales’, ‘labeling’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggOceanMapsData’
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggdensity’ in Rd xrefs
sample_frac:
  function(tbl, size, replace, weight, .env, ...)
sample_frac.periodic_df:
  function(tbl, size, replace, weight, .env)

fortify:
  function(model, data, ...)
fortify.periodic_df:
  function(data, ...)

sample_n:
  function(tbl, size, replace, weight, .env, ...)
sample_n.periodic_df:
  function(tbl, size, replace, weight, .env)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   1.9Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
makeContext:
  function(x)
makeContext.dotstackGrob:
  function(x, recording)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘interp’, ‘akima’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    History
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'nlmixr', 'lixoftConnectors'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.3Mb
    testdata   4.8Mb
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Note: found 6242 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * Changes all data options to .data to decrease possibility of column naming overlap
Undeclared package ‘RColorBrewer’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Undeclared packages ‘chemometrics’, ‘rlang’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 138 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Win CRAN check results - R Windows
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
Note: found 203 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘refund’ ‘stats’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   2.5Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘Runuran’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Undeclared packages ‘ineq’, ‘IC2’ in Rd xrefs
Unknown package ‘IC2’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1178 marked UTF-8 strings
Note: found 866 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MCMCpack’ ‘ggplot2’ ‘moments’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlr3proba’
'LazyData' is specified without a 'data' directory
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.5Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ordinal’
  All declared Imports should be used.
checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
checkRd: (-1) glmc.Rd:241: Escaped LaTeX specials: \&
checkRd: (-1) glmc.control.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) glmc.control.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
VarCorr:
  function(x, sigma, ...)
VarCorr.lmertree:
  function(object, ...)

VarCorr:
  function(x, sigma, ...)
VarCorr.glmertree:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘GMMBoost’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs            6.2Mb
    test_data       2.2Mb
    vignette_data   1.1Mb
isLMM:
  function(x, ...)
isLMM.glmmTMB:
  function(object)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) coef.glmulti.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) consensus.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) getfit.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti-class.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) glmulti.Rd:99: Escaped LaTeX specials: \&
checkRd: (-1) summary.glmulti.Rd:72: Escaped LaTeX specials: \&
Malformed Description field: should contain one or more complete sentences.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rnaturalearthdata’
  All declared Imports should be used.
Note: found 1191 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 2629 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Undeclared package ‘glmmLasso’ in Rd xrefs
Undeclared package ‘sandwich’ in Rd xrefs
Undeclared package ‘rms’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) replace_in_file.Rd:40: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘repeated’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) barleyHeights.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) barleyHeights.Rd:22: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Undeclared package ‘gdata’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘goftest’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 1352 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:16: Escaped LaTeX specials: \& \&
checkRd: (-1) BVDWSTOXX.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
Undeclared package ‘fBasics’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Undeclared packages ‘rcmdcheck’, ‘covr’, ‘devtools’, ‘pkgdown’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.drive_id:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
sfNEmpty:
  function(sf)
sfNEmpty.sfc:
  function(sfc)

sfGeometryType:
  function(sf)
sfGeometryType.sfc:
  function(sfc)

sfEpsg:
  function(sf)
sfEpsg.sfc:
  function(sfc)

sfPrecision:
  function(sf)
sfPrecision.sfc:
  function(sfc)

sfProj:
  function(sf)
sfProj.sfc:
  function(sfc)

sfDimension:
  function(sf)
sfDimension.sfc:
  function(sfc)

sfGeometryAttributes:
  function(sf)
sfGeometryAttributes.sfc:
  function(sfc)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Unexported objects imported by ':::' calls:
  ‘gargle:::secret_can_decrypt’ ‘gargle:::secret_read’
  See the note in ?`:::` about the use of this operator.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.sheets_id:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘jsonlite’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’
  All declared Imports should be used.
.access_result:
  function(res, accessor)
.access_result.character:
  function(js, accessor)

.access_result:
  function(res, accessor)
.access_result.list:
  function(lst, accessor)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R   6.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Package suggested but not available for checking: ‘gvcm.cat’
Specified C++11: please drop specification unless essential
Unknown package ‘gvcm.cat’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) barplot2.Rd:219: Escaped LaTeX specials: \_
checkRd: (-1) colorpanel.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) qqnorm.aov.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) venn.Rd:59: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gratia’ in Rd xrefs
Package suggested but not available for checking: ‘quanteda.textmodels’
Note: found 5030 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘PairedData’ ‘RColorBrewer’ ‘agricolae’ ‘corrplot’ ‘desplot’
  ‘dplyr’ ‘ggplot2’ ‘ggpubr’ ‘gridGraphics’ ‘gtools’ ‘kableExtra’
  ‘knitr’ ‘magrittr’ ‘pastecs’ ‘reshape2’ ‘rmarkdown’ ‘shinyWidgets’
  ‘summarytools’
  All declared Imports should be used.
checkRd: (-1) corrApp.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) crdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) descApp.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) layoutApp.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) rbdApp.Rd:46: Escaped LaTeX specials: \&
checkRd: (-1) ttApp.Rd:43: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘glasso’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) mlGraphicalVAR.Rd:79: Escaped LaTeX specials: \~
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cubature’ ‘magicaxis’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
Found the following significant warnings:
  Offset.c:3:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:12:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:5:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_diagnose.c:18:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/grattan.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/sugar/functions/sapply.h:36:26: warning: 'result_of<int (*(SEXPREC *))(SEXPREC *)>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/gRbase.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Found the following significant warnings:
  init.c:11:46: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/gRc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Note: found 989 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
pot:
  function(obj, ...)
pot.BlockGraph:
  function(newg, newd, ...)

h_edges:
  function(obj, ...)
h_edges.RootDepSet:
  function(obj, g)

createObj:
  function(obj, ...)
createObj.HRMBG:
  function(obj, data)

resetParams:
  function(obj, ...)
resetParams.MLE1params:
  function(obj, cnames)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ungroup:
  function(x, ...)
ungroup.igrouped_df:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared packages ‘repeated’, ‘gnlm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Found the following files/directories:
  ‘p1_20up-vs-p2_25up_in_str1.txt’ ‘p1_20up-vs-p2_25up_in_str2.txt’
  ‘p2_25up-vs-p1_20up_in_str1.txt’ ‘p2_25up-vs-p1_20up_in_str2.txt’
  ‘s0_20up.txt’ ‘s0_30up.txt’ ‘s0_f2up.txt’ ‘strs.vec_01mx.txt’
  ‘strs.vec_02mx.txt’ ‘strs.vec_03mx.txt’ ‘strs.vec_04mx.txt’
  ‘strs.vec_05mx.txt’ ‘strs.vec_06mx.txt’ ‘strs.vec_30up.txt’
  ‘strs.vec_50up.txt’ ‘strs.vec_f2up.txt’ ‘uni_p1_20up-p2_25up.txt’
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘FMD mag discontinuities_disc.png’ ‘FMD mag
  discontinuities_disc1.res’ ‘FMD mag discontinuities_disc2.res’
  ‘IDYLLWILD_bvmed.png’ ‘IDYLLWILD_fig.png’ ‘Schuster's
  diagram_schu.png’ ‘hour.res’
Undeclared package ‘nflfastR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) gsym.point.Rd:143: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 116 marked UTF-8 strings
Note: found 269 marked UTF-8 strings
Note: found 42384 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘RRprof.out’
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
Undeclared package ‘permute’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Note: found 18981 marked UTF-8 strings
checkRd: (-1) GUTS-package.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:201: Escaped LaTeX specials: \&
checkRd: (-1) GUTS.Rd:209: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
checkRd: (-1) luzdat.Rd:21: Escaped LaTeX specials: \~
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘testdata1.txt’ ‘testdata2.txt’ ‘testdata3.txt’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 182.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    java  179.7Mb
Running ‘testthat.R’ [12s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(h3jsr)
  > 
  > test_check("h3jsr")
  Reading layer `nc' from data source 
    `/data/gannet/ripley/R/test-clang/sf/shape/nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  Geometry type: MULTIPOLYGON
  Dimension:     XY
  Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  Geodetic CRS:  NAD27
  free(): double free detected in tcache 2
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    HaDeX   4.1Mb
    doc     4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.ga.breed’ ‘.ga.fitness’ ‘.ga.init’ ‘.ga.mutate’ ‘.ga.step’
  ‘.ga.weight’
Specified C++11: please drop specification unless essential
Undeclared package ‘mnis’ in Rd xrefs
Note: found 8248 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hash-accessors.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) hash-class.Rd:45: Escaped LaTeX specials: \$
checkRd: (-1) hash-package.Rd:39: Escaped LaTeX specials: \#
Undeclared package ‘dplyr’ in Rd xrefs
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.7Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) prm09.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) prm09.Rd:26: Escaped LaTeX specials: \&
Note: found 3 marked UTF-8 strings
Note: found 104392 marked UTF-8 strings
checkRd: (-1) schools.Rd:18: Escaped LaTeX specials: \&
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘questionr’ ‘rprojroot’ ‘tidyverse’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Namespaces in Imports field not imported from:
  ‘TidyDensity’ ‘healthyR’ ‘healthyR.ai’ ‘healthyR.data’ ‘healthyR.ts’
  ‘tidyAML’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Specified C++11: please drop specification unless essential
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
expand_state:
  function(x, ...)
expand_state.uneval_init:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_state_list:
  function(x, state_name, cycles)

expand_state:
  function(x, ...)
expand_state.uneval_matrix:
  function(x, state_pos, state_name, cycles, n)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘Sleuth2’, ‘rrcov’, ‘carData’, ‘archdata’, ‘qqtest’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘synbreed’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) erode.hexbin.Rd:43: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ohio.Rd:104: Escaped LaTeX specials: \&
checkRd: (-1) ohio.Rd:105: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘lme4’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Undeclared packages ‘sp’, ‘rgeos’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
':::' call which should be '::': ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RiskPortfolios’
  All declared Imports should be used.
Note: found 11 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) Snow.Rd:118: Escaped LaTeX specials: \&
checkRd: (-1) Snow.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) Yeast.Rd:56: Escaped LaTeX specials: \&
Undeclared packages ‘Guerry’, ‘alr4’, ‘agridat’, ‘coin’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘trackr’
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘HadoopStreaming’
Note: found 9638 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
pp_check:
  function(object, ...)
pp_check.hmcdm:
  function(object, plotfun, type)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) disc42.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) discrimination.Rd:31: Escaped LaTeX specials: \&
Undeclared package ‘genalg’ in Rd xrefs
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.hms:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.hms:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmmADMB’
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
Undeclared packages ‘nlreg’, ‘cond’, ‘marg’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ROI.plugin.mosek’
'LazyData' is specified without a 'data' directory
Undeclared package ‘rgl’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 124 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'RGtk2', 'cairoDevice'
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘quantreg’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.5Mb
checkRd: (-1) attributes_speclib.Rd:73: Escaped LaTeX specials: \$
checkRd: (-1) get_reflectance.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./useful.h:6:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/hSDM.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Running ‘test-all.R’ [15s/39s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(htmltools)
  > 
  > test_check("htmltools")
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Chinese locale not available (2)
  • On CRAN (3)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tags.r:29:3'): Hanging commas don't break things ─────────────
  `as.character(div("one", , ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 2 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div("one", , )), "is empty") at test-tags.r:29:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div("one", , )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  ── Failure ('test-tags.r:31:3'): Hanging commas don't break things ─────────────
  `as.character(div(, "one", ))` threw an error with unexpected message.
  Expected match: "is empty"
  Actual message: "Argument 1 can't be empty."
  Backtrace:
      ▆
   1. ├─testthat::expect_error(as.character(div(, "one", )), "is empty") at test-tags.r:31:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. ├─htmltools::div(, "one", )
   7. │ └─rlang::dots_list(...)
   8. └─rlang::abort(message = message)
  
  [ FAIL 2 | WARN 0 | SKIP 5 | PASS 2049 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    2.1Mb
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Undeclared package ‘sp’ in Rd xrefs
checkRd: (-1) Trancura9414001.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) Trancura9414001.Rd:28: Escaped LaTeX specials: \_
checkRd: (-1) hydroPSO.Rd:390: Escaped LaTeX specials: \&
checkRd: (-1) hydroPSO.Rd:408: Escaped LaTeX specials: \&
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘rgdal’ in Rd xrefs
checkRd: (-1) SandP500.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:7: Escaped LaTeX specials: \&
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    exdata   6.1Mb
Package suggested but not available for checking: ‘flowCore’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) palettes.Rd:25: Escaped LaTeX specials: \#
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 38558 marked UTF-8 strings
Note: found 1058038 marked UTF-8 strings
Package suggested but not available for checking: ‘switchr’
autoplot:
  function(object, ...)
autoplot.grid_search:
  function(x, type, ...)

autoplot:
  function(object, ...)
autoplot.stability_analysis:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.roc_curve:
  function(x, ...)

autoplot:
  function(object, ...)
autoplot.similarity_comparison:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘AIC.txt’ ‘AICc.txt’ ‘IAS.pdf’ ‘IAS2.pdf’ ‘IAS3.pdf’
  ‘P.microlepis-AIC.txt’ ‘P.microlepis-AICc.txt’ ‘P.microlepis-IAS.pdf’
  ‘P.microlepis-IAS2.pdf’ ‘P.microlepis-IAS3.pdf’
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Note: found 359 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘SparkR’
Specified C++11: please drop specification unless essential
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 356712 marked UTF-8 strings
Package suggested but not available for checking: ‘icd’
Note: found 55 marked UTF-8 strings
Undeclared package ‘tibble’ in Rd xrefs
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘digest’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 10 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pulmonary.Rd:13: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘mlogit’, ‘logitr’ in Rd xrefs
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared packages ‘sfsmisc’, ‘RColorBrewer’, ‘hexbin’ in Rd xrefs
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 40 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Running ‘testthat.R’ [30m/39m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # NOTE: This will not test an uninstalled package.
  > library(testthat)
  > test_check('ifaTools')
  Loading required package: ifaTools
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: reshape2
  Loading required package: rpf
  Loading required package: parallel
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  Welcome to ifaTools!
   Use itemModelExplorer() to explore item models.
   Use modelBuilder() to build an IFA model.
Package suggested but not available for checking: ‘IFCdata’
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.4Mb
    libs   3.3Mb
Malformed Description field: should contain one or more complete sentences.
knit_print:
  function(x, ...)
knit_print.Iheatmap:
  function(x, options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.5Mb
Undeclared packages ‘bmp’, ‘jpeg’, ‘png’, ‘tiff’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘tesseract’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.1Mb
    include   3.0Mb
    libs      3.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘accdata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pscl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Undeclared package ‘minfi’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 151 marked UTF-8 strings
Namespace in Imports field not imported from: ‘optimr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Found the following significant warnings:
  keyplayer-utils.c:24:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/influenceR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘c.txt’ ‘rho.txt’ ‘sta.txt’ ‘topo.txt’
'LazyData' is specified without a 'data' directory
Undeclared package ‘R.methodsS3’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    INSPECTumours (development version)
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘splines2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Error_Estimation_Response_1.tiff’ ‘Error_Estimation_Response_2.tiff’
  ‘Error_Estimation_Response_3.tiff’
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘methods’ ‘mlbench’ ‘parallel’ ‘utils’
  All declared Imports should be used.
Undeclared packages ‘quantreg’, ‘effects’, ‘Hmisc’, ‘rockchalk’, ‘pequod’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘colorspace’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
# NOTE - CRAN check detected: limiting maximum number of cores [2/24]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Intervals-class.Rd:109: Escaped LaTeX specials: \_
checkRd: (-1) Intervals-class.Rd:110: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:68: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:76: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:77: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:79: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:81: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:89: Escaped LaTeX specials: \_
checkRd: (-1) Intervals_virtual-class.Rd:90: Escaped LaTeX specials: \_
checkRd: (-1) sgd.Rd:12: Escaped LaTeX specials: \_
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
Undeclared package ‘DT’ in Rd xrefs
Specified C++11: please drop specification unless essential
Running ‘testthat.R’ [35m/44m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(intkrige)
  Loading required package: sp
  Loading required package: gstat
  Loading required package: raster
  > 
  > test_check("intkrige")
  OMP: Warning #96: Cannot form a team with 12 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 12106 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘nlstools’, ‘lme4’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fdrtool’ ‘nimble’
  All declared Imports should be used.
Package suggested but not available for checking: ‘surveyspec’
Specified C++11: please drop specification unless essential
Note: found 102 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘gmodels’ ‘lmtest’ ‘testthat’ ‘tidyverse’ ‘zoo’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘Rpadrino’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) constrained.Rd:49: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) bp.coeff.raw.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp.coeff.raw.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) fleiss.kappa.raw.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) landis.koch.bf.Rd:17: Escaped LaTeX specials: \&
checkRd: (-1) ir_to_transmittance.Rd:49: Escaped LaTeX specials: \&
Undeclared package ‘irr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
checkRd: (-1) pine.Rd:20: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Note: found 104 marked UTF-8 strings
Undeclared packages ‘IsingFit’, ‘IsingSampler’ in Rd xrefs
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  trace_islasso.c:39:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/islasso.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘Unicode’ in Rd xrefs
Note: found 7528 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Undeclared package ‘multtest’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘curl’ ‘modules’
  All declared Imports should be used.
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS1.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_deriv_loglikelihood.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) ISOpureS2.model_optimize.kappa.kappa_loglikelihood.Rd:11: Escaped LaTeX specials: \$
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   3.7Mb
GNU make is a SystemRequirements.
Undeclared package ‘surveillance’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Note: found 87 marked UTF-8 strings
Specified C++14: please drop specification unless essential
Note: found 1 marked UTF-8 string
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
Found the following files/directories:
  ‘RMTplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘AER’ in Rd xrefs
Package suggested but not available for checking: ‘gurobi’
Note: found 58 marked UTF-8 strings
Package suggested but not available for checking: ‘locClass’
checkRd: (-1) ivmodel.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) ivmodelFormula.Rd:79: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Note: found 2261 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_1km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.mesh_100m:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Note: found 461377 marked UTF-8 strings
Note: found 1984 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘grid’ ‘mcmcplots’ ‘tidyverse’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘JavaGD/libs/JavaGD.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘jGDtalk.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘knitr’ ‘markdown’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 85 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    i18n   4.0Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘dplyr’ ‘emmeans’ ‘ggrepel’ ‘ggridges’ ‘lavaan’
  ‘multcomp’ ‘mvnormtest’ ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘remMap’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘boot’ ‘fds’ ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_250m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_10km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_80km:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_100m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_500m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_125m:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.grid_1km:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Note: found 925830 marked UTF-8 strings
Note: found 176 marked UTF-8 strings
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.json2:
  function(x)

vec_ptype_full:
  function(x, ...)
vec_ptype_full.json2:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    examples      2.9Mb
    htmlwidgets   1.1Mb
    www           2.7Mb
Note: found 17 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release juicr (2017 - 2021)
Specified C++14: please drop specification unless essential
Undeclared package ‘ggplot2’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Superpower’ ‘pwr’ ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘song.wav’ ‘song4karaoke.wav’
Namespace in Imports field not imported from: ‘gifski’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
r_to_py:
  function(x, convert)
r_to_py.keras_layer_wrapper:
  function(fn, convert)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘keras’
  All declared Imports should be used.
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘splines’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘fitdistrplus’ ‘plotly’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘rkward’
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘kml3d’ in Rd xrefs
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Killed after ’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘VARSEDIG’
Undeclared packages ‘usdm’, ‘car’, ‘IDPmisc’, ‘psych’, ‘REdaS’, ‘candisc’ in Rd xrefs
Unknown package ‘VARSEDIG’ in Rd xrefs
Note: found 9 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'koRpus.lang.de', 'koRpus.lang.es', 'koRpus.lang.fr',
  'koRpus.lang.it', 'koRpus.lang.nl', 'koRpus.lang.pt',
  'koRpus.lang.ru'

Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘KSEA Bar Plot.tiff’ ‘KSEA Kinase Scores.csv’
  ‘KSEA.Merged.Heatmap.png’ ‘Kinase-Substrate Links.csv’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
checkRd: (-1) alphaOnly.Rd:25: Escaped LaTeX specials: \^
checkRd: (-1) alphaOnly.Rd:26: Escaped LaTeX specials: \$
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
checkRd: (-1) natlongsurv.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
calibrate:
  function(dsvord, ...)
calibrate.dsvord:
  function(dsvord, site, dims, family, gamma, keep.models)

varplot:
  function(pca, ...)
varplot.pca:
  function(x, dim)

loadings:
  function(pca, ...)
loadings.pca:
  function(x, dim, digits, cutoff)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘fso’ in Rd xrefs
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘carData’, ‘factoextra’, ‘labstatR’ in Rd xrefs
Found the following files/directories:
  ‘MYSLID.csv’ ‘tabelle.csv’
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
Undeclared package ‘spdep’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Undeclared package ‘plyr’ in Rd xrefs
Undeclared package ‘gsl’ in Rd xrefs
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) LaplaceApproximation.Rd:485: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) LossMatrix.Rd:117: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:19:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/largeList.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘example.llo’
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘glmnet’ in Rd xrefs
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘ergm.userterms’
checkRd: (-1) simulate.ergmm.Rd:35: Escaped LaTeX specials: \$
checkRd: (-1) simulate.ergmm.Rd:36: Escaped LaTeX specials: \$
Unknown package ‘ergm.userterms’ in Rd xrefs
GNU make is a SystemRequirements.
Found the following significant warnings:
  init.c:12:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:18:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:24:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:27:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:51:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/later.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'akmedoids', 'clusterCrit'
Unknown packages ‘clusterCrit’, ‘akmedoids’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Undeclared package ‘ggplot2’ in Rd xrefs
checkRd: (-1) LKrig.MLE.Rd:114: Escaped LaTeX specials: \$ \$
checkRd: (-1) LKrig.MLE.Rd:115: Escaped LaTeX specials: \$
Undeclared package ‘zoo’ in Rd xrefs
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tseries’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) goodnessfit.Rd:105: Escaped LaTeX specials: \&
checkRd: (-1) lba.Rd:252: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) pregnancy.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    lcars.0.3.1
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘gridExtra’ in Rd xrefs
Found the following files/directories:
  ‘temp.float.csv’ ‘temp.result.athena.csv’
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  lcopula-init.c:15:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/lcopula.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘chinese.misc’ ‘dplyr’ ‘factoextra’ ‘glasso’
  ‘highcharter’ ‘htmlwidgets’ ‘ldatuning’ ‘qgraph’ ‘quanteda’ ‘rvest’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinybusy’ ‘shinycssloaders’
  ‘shinydashboard’ ‘shinyjs’ ‘stringr’ ‘textmineR’ ‘textplot’ ‘tidyr’
  ‘topicmodels’
  All declared Imports should be used.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘tm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RcppProgress’ ‘rgen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Note: found 1096 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    light.interception.voxels() - This function create the Fraction absorbed incident light
    light.interception.raster() - Create a raster of Fraction absorbed incident light
    light.incident.voxels() - This function create the Fraction incident light
    light.incident.raster() - Create a raster of the Fraction incident light
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) leaps.Rd:38: Escaped LaTeX specials: \&
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘pracma’ in Rd xrefs
Note: found 78 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Found the following significant warnings:
  lemna.c:98:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:109:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:120:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:129:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lemna.c:138:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/lemna.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Undeclared packages ‘purrr’, ‘dplyr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.5Mb
Undeclared package ‘MESS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 22 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘libstableR/libs/libstableR.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘stable_integration.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gWidgets', 'gWidgetsRGtk2', 'RGtk2'
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Undeclared package ‘future’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:6:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/liGP.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
Undeclared package ‘tidyselect’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) LIMEcoli.Rd:125: Escaped LaTeX specials: \_
checkRd: (-1) Read.Rd:88: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:92: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:98: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:104: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:105: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:106: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:107: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:108: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:109: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:110: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:111: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:112: Escaped LaTeX specials: \# \#
checkRd: (-1) Read.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) Read.Rd:114: Escaped LaTeX specials: \# \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘magrittr’ in Rd xrefs
Note: found 60640 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 32 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared package ‘keras’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 435 marked UTF-8 strings
checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Note: found 266 marked UTF-8 strings
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        1.6Mb
    testdata   1.3Mb
Undeclared packages ‘sfsmisc’, ‘mnormt’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘agridat’ ‘ggplot2’ ‘maps’ ‘sp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) cauchypoly.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) normpoly.Rd:38: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) normpoly.Rd:39: Escaped LaTeX specials: \_
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘tTestTable.rda’
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘base’ ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SPSloess.Rd:71: Escaped LaTeX specials: \^ \^
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) ACS.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) EmployedACS.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSale.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCA.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleCanton.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) HomesForSaleNY.Rd:11: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) MustangPrice.Rd:24: Escaped LaTeX specials: \$
checkRd: (-1) SalaryGender.Rd:9: Escaped LaTeX specials: \$
checkRd: (-1) SandP500.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:24: Escaped LaTeX specials: \&
checkRd: (-1) SandP500.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) SandwichAnts2.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:11: Escaped LaTeX specials: \&
checkRd: (-1) StockChanges.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) TrafficFlow.Rd:18: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘lestat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘colorspace’ in Rd xrefs
Running examples in ‘LogConcDEAD-Ex.R’ failed
The error most likely occurred in:

> ### Name: EMmixlcd
> ### Title: Estimate the mixture proportions and component densities using
> ###   EM algorithm
> ### Aliases: EMmixlcd
> ### Keywords: nonparametric multivariate EM classification
> 
> ### ** Examples
> 
> ##Simple bivariate normal data
>   set.seed( 1 )
>   n = 15
>   d = 2
>   props=c( 0.6, 0.4 )
>   shift=2
>   x <- matrix( rnorm( n*d ), ncol = d )
>   shiftvec <- ifelse( runif( n ) > props[ 1 ], 0, shift )
>   x[,1] <- x[,1] + shiftvec
>   EMmixlcd( x, k = 2, max.iter = 2)
*** buffer overflow detected ***: terminated
Error(s) in re-building vignettes:
--- re-building ‘LogConcDEAD.Rnw’ using Sweave
Loading required package: LogConcDEAD
Loading required package: mvtnorm
*** buffer overflow detected ***: terminated
Note: found 12 marked UTF-8 strings
Found the following significant warnings:
  ./veclib.h:316:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/logistf.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.nri.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) maxauc.s.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) nri.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) roc.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) roc.s.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) sensspec.s.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 994 marked Latin-1 strings
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   1.6Mb
    tcl   1.3Mb
Found the following files/directories:
  ‘Model_1.cm’ ‘dambacher.dot’ ‘levins.dot’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  LowRankQP.c:278:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  LowRankQP_init.c:29:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/LowRankQP.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) lpepa.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:51: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) lpepa.Rd:90: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:61: Escaped LaTeX specials: \&
checkRd: (-1) lpridge.Rd:65: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kerdiest’
Note: found 55 marked UTF-8 strings
checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
Note: found 2096 marked UTF-8 strings
Undeclared package ‘MCMCglmm’ in Rd xrefs
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
Undeclared package ‘zoo’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as_string:
  function(x, ...)
as_string.character:
  function(x, sep, conj)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘orthogene’
Namespace in Imports field not imported from: ‘fmsb’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘orthogene’
Undeclared package ‘rnaturalearth’ in Rd xrefs
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Note: found 134 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘maptools’ ‘sp’
  All declared Imports should be used.
checkRd: (-1) read.magpie.Rd:20: Escaped LaTeX specials: \_ \_
checkRd: (-1) read.magpie.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:35: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:36: Escaped LaTeX specials: \_
checkRd: (-1) read.magpie.Rd:65: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:24: Escaped LaTeX specials: \_ \_
checkRd: (-1) write.magpie.Rd:27: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:42: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:43: Escaped LaTeX specials: \_
checkRd: (-1) write.magpie.Rd:70: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘tesseract’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import ‘golem::pkg_version’ by ‘pkgload::pkg_version’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_name’ by ‘pkgload::pkg_name’ when loading ‘MainExistingDatasets’
  Warning: replacing previous import ‘golem::pkg_path’ by ‘pkgload::pkg_path’ when loading ‘MainExistingDatasets’
See ‘/data/gannet/ripley/R/packages/tests-clang/MainExistingDatasets.Rcheck/00install.out’ for details.
Note: found 41 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘nomnoml’
  All declared Imports should be used.
Package suggested but not available for checking: ‘testthat’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
Note: found 17524 marked UTF-8 strings
File ‘MAMS/libs/MAMS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘testthat’
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
Note: found 328 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 55 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.5Mb
Package suggested but not available for checking: ‘RGtk2’
Undeclared package ‘nparLD’ in Rd xrefs
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.3Mb
    libs          2.6Mb
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 29618 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    data   2.4Mb
Namespace in Imports field not imported from: ‘pbmcapply’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    To do
Note: found 55 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 996 marked UTF-8 strings
Note: found 13138 marked UTF-8 strings
Note: found 1763 marked UTF-8 strings
Undeclared package ‘rgdal’ in Rd xrefs
Note: found 1 marked UTF-8 string
checkRd: (-1) sw_sfac.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) Interpolation-class.Rd:41: Escaped LaTeX specials: \#
checkRd: (-1) MareyMap-class.Rd:85: Escaped LaTeX specials: \_
checkRd: (-1) MareyMap-methods.Rd:11: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) MareyMap-methods.Rd:12: Escaped LaTeX specials: \_
checkRd: (-1) SpeciesMaps-methods.Rd:11: Escaped LaTeX specials: \_
checkRd: (-1) interpolation-methods.Rd:13: Escaped LaTeX specials: \_
Note: found 5210 marked UTF-8 strings
Undeclared package ‘car’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
autoplot:
  function(object, ...)
autoplot.bathy:
  function(x, geom, mapping, coast, ...)

fortify:
  function(model, data, ...)
fortify.bathy:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘flashier’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
checkRd: (-1) size_t-class.Rd:6: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
File ‘Matrix/libs/Matrix.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
    Object: ‘validity.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘utilities.R’
Undeclared package ‘tracerer’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) maxControl.Rd:83: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
Note: found 54 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘map_5.png’ ‘maze_5.html’
Note: found 66 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Undeclared packages ‘logistf’, ‘brglm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 6 marked Latin-1 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cplexAPI’
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
checkRd: (-1) mc.lnOR.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) MCtest.Rd:39: Escaped LaTeX specials: \#
checkRd: (-1) MCtest.Rd:40: Escaped LaTeX specials: \#
Note: found 46 marked UTF-8 strings
Undeclared package ‘NLP’ in Rd xrefs
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘coda’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) eigp.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) imcdiag.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) mc.plot.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) mctest.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:39: Escaped LaTeX specials: \&
checkRd: (-1) omcdiag.Rd:41: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial version.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) glass.Rd:23: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) glass.Rd:25: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) glass.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./threat-safe-random.h:58:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./threat-safe-random.h:70:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/mdgc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) mriTest.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) riTest.Rd:9: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2866 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MethylCapSig’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mebootSpear.Rd:88: Escaped LaTeX specials: \_
checkRd: (-1) ullwan.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ullwan.Rd:8: Escaped LaTeX specials: \& \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
residualPlots:
  function(model, ...)
residualPlots.expData:
  function(object, ...)

residualPlots:
  function(model, ...)
residualPlots.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.neModel:
  function(object, ...)

residualPlot:
  function(model, ...)
residualPlot.expData:
  function(object, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Data_Correlation.txt’ ‘correlation_FDR_table.txt’
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) Soybean.Rd:15: Escaped LaTeX specials: \#
checkRd: (-1) Soybean.Rd:33: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
VarCorr:
  function(x, sigma, ...)
VarCorr.merModList:
  function(x, sigma, rdig)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Package suggested but not available for checking: ‘ropls’
Package suggested but not available for checking: ‘genuMet’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘cycHumanBloodData.csv’ ‘cycHumanBloodDesign.csv’
  ‘cycMouseLiverProtein.txt’ ‘cycMouseLiverRNA.csv’ ‘cycSimu4h2d.csv’
  ‘cycYeastCycle.csv’ ‘example’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Suggests orphaned package: ‘udunits2’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘netmeta’, ‘metasens’, ‘robumeta’ in Rd xrefs
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metadat’
  All declared Imports should be used.
Note: found 1496 marked UTF-8 strings
Note: found 3302 marked UTF-8 strings
checkRd: (-1) dslp.Rd:11: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) cardiac.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) plvol.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) sbp.Rd:16: Escaped LaTeX specials: \&
Undeclared package ‘R2WinBUGS’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘MetProc_output.pdf’ ‘sample_removed.csv’ ‘sample_retained.csv’
Note: found 1 marked UTF-8 string
guide_train:
  function(guide, scale, aesthetic)
guide_train.vector:
  function(guide, scale, output)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘rlang’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.6Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    mev v.1.9x
    mev v.1.8x
Undeclared packages ‘hoa’, ‘evir’ in Rd xrefs
Note: found 7 marked Latin-1 strings
  Note: found 14 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘knitr’ ‘qlcMatrix’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘structSSI’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ProteoMM’
Undeclared package ‘DAPAR’ in Rd xrefs
Package unavailable to check Rd xrefs: ‘DAPAR’
S3 methods shown with full name in documentation object 'complete.miceadds':
  ‘complete.mids.nmi’ ‘complete.mids.1chain’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘micEconAids’, ‘micEconSNQP’ in Rd xrefs
Specified C++11: please drop specification unless essential
checkRd: (-1) IPDNa.Rd:42: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Note: found 9345 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./do_nothing.h:4:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  do_nothing.c:11:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:7:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nanotimer.c:88:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/microbenchmark.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Undeclared package ‘tibble’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
    lib   1.6Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘curl’ ‘jsonlite’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Undeclared package ‘scatterplot3d’ in Rd xrefs
Undeclared packages ‘pspline’, ‘lme4’ in Rd xrefs
Undeclared package ‘maxLik’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘list’ in Rd xrefs
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘l1_similarity’
checkRd: (-1) AKMCS.Rd:215: Escaped LaTeX specials: \&
checkRd: (-1) BMP.Rd:164: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) IRW.Rd:151: Escaped LaTeX specials: \&
checkRd: (-1) MP.Rd:142: Escaped LaTeX specials: \&
checkRd: (-1) MetropolisHastings.Rd:58: Escaped LaTeX specials: \&
checkRd: (-1) SubsetSimulation.Rd:152: Escaped LaTeX specials: \&
checkRd: (-1) oscillator_d6.Rd:14: Escaped LaTeX specials: \&
Packages suggested but not available for checking:
  'karyoploteR', 'regioneR'
Found the following files/directories:
  ‘par-7269706c6579’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘AnalyzeFMRI’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
    Update Old .R files
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) mixmeta-package.Rd:115: Escaped LaTeX specials: \&
checkRd: (-1) mixmeta.ml.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ml.igls.Rd:62: Escaped LaTeX specials: \&
Undeclared package ‘mvmeta’ in Rd xrefs
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘rms’ in Rd xrefs
Undeclared packages ‘rms’, ‘Hmisc’, ‘genefilter’ in Rd xrefs
checkRd: (-1) ssize.propCI.Rd:38: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Found the following significant warnings:
  waveform.c:31:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  waveform.c:44:16: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/mlbench.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
checkRd: (-1) BreastCancer.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) Ionosphere.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) PimaIndiansDiabetes.Rd:19: Escaped LaTeX specials: \^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ConfusionTableR’ ‘OddsPlotty’ ‘caret’ ‘dplyr’ ‘ggplot2’ ‘parsnip’
  ‘ranger’ ‘recipes’ ‘rsample’ ‘varhandle’ ‘workflows’
  All declared Imports should be used.
checkRd: (-1) AutumnLab.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) gp.list.Rd:16: Escaped LaTeX specials: \#
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'

Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘ClusterR’ ‘MASS’ ‘Rdpack’ ‘multiwave’ ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Found the following significant warnings:
  ./mlpack/core/data/save_impl.hpp:107:30: warning: 'quiet_save' is deprecated [-Wdeprecated-declarations]
  ./mlpack/core/data/save_impl.hpp:128:33: warning: 'quiet_save' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/mlpack.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 16.0.0’
Specified C++14: please drop specification unless essential
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bit64’
  All declared Imports should be used.
as_learner:
  function(x, ...)
as_learner.PipeOp:
  function(x, clone)

as_learner:
  function(x, ...)
as_learner.Graph:
  function(x, clone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘htmlwidgets’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘MM2S_Predictions_Heatmap.pdf’ ‘MM2S_Predictions_StackedBarplot.pdf’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.6Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘geeM’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘magrittr’ ‘reticulate’ ‘tensorflow’ ‘usethis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Flury’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘energy’ in Rd xrefs
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘geomorph’ in Rd xrefs
Package suggested but not available for checking: ‘alstructure’

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'

Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: 'ensembldb'
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘caret’ in Rd xrefs
Note: found 313 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
train:
  function(x, ...)
train.model_grid:
  function(mg, train_all, resample_seed)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 18 marked Latin-1 strings
predictor_vars:
  function(model)
predictor_vars.default:
  function(model, data)

response_var:
  function(model)
response_var.default:
  function(model, data)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared packages ‘lme4’, ‘rstanarm’, ‘dplyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
Could not detect any Conda Python Environments with `reticulate::conda_list()`. Conda is required for 'modeltime.gluonts'. Try using `reticulate::install_miniconda()`.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5238 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 20578 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    * efourier with default norm=TRUE now messages about how wrong it may be
Note: found 16 marked UTF-8 strings
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘seewave’ in Rd xrefs
Found the following significant warnings:
  ordsampler.c:59:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:113:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:124:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:386:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:544:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:560:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:710:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ordsampler.c:1102:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:52:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:149:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:158:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sampler.c:729:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/monoreg.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Note: found 13 marked UTF-8 strings
File ‘morse/libs/morse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘MortalityLaws’
'LazyData' is specified without a 'data' directory
Note: found 56 marked UTF-8 strings
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Undeclared package ‘cubature’ in Rd xrefs
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘graphlayouts’ in Rd xrefs
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Specified C++11: please drop specification unless essential
checkRd: (-1) Context.Rd:27: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:48: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) psyfun.boot.Rd:28: Escaped LaTeX specials: \&
Undeclared package ‘lme4’ in Rd xrefs
checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
checkRd: (-1) genotype_data.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) phenotype_data.Rd:15: Escaped LaTeX specials: \_
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Undeclared package ‘proxy’ in Rd xrefs
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) F.huggins.estim.Rd:199: Escaped LaTeX specials: \$ \$
checkRd: (-1) F.huggins.estim.Rd:205: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:206: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:207: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:208: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:209: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:210: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:212: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:213: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:214: Escaped LaTeX specials: \$
checkRd: (-1) F.huggins.estim.Rd:215: Escaped LaTeX specials: \$
checkRd: (-1) lines.cjs.Rd:15: Escaped LaTeX specials: \$
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘processx’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared package ‘speedglm’ in Rd xrefs
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 75 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   4.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test.txt’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R   5.9Mb
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Acceleration.pdf’ ‘File1.pdf’ ‘Forecast.pdf’ ‘Series.pdf’
  ‘Velocity.pdf’
checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_sev.Rd:31: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘markdown’ ‘methods’ ‘vctrs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Missing or unexported object: ‘rqPen::rq.lasso.fit’
MTElasso: no visible global function definition for ‘rq.lasso.fit’
Undefined global functions or variables:
  rq.lasso.fit
Running examples in ‘MTE-Ex.R’ failed
The error most likely occurred in:

> ### Name: MTElasso
> ### Title: MTE-Lasso estimator
> ### Aliases: MTElasso
> 
> ### ** Examples
> 
> set.seed(2017)
> n=200; d=500
> X=matrix(rnorm(n*d), nrow=n, ncol=d)
> beta=c(rep(2,6), rep(0, d-6))
> y=X%*%beta+c(rnorm(150), rnorm(30,10,10), rnorm(20,0,100))
> output.MTELasso=MTElasso(X, y, p=2, t=0.05, method="MTE")
Error in rq.lasso.fit(x = X, y = as.vector(y), lambda = 0.1, intercept = intercept) : 
  could not find function "rq.lasso.fit"
Calls: MTElasso
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mkjnw.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) mkjnw.Rd:6: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
checkRd: (-1) MultBiplotR-package.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) MultBiplotR-package.Rd:52: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Undeclared package ‘slam’ in Rd xrefs
checkRd: (-1) print.multcompLetters.Rd:20: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
pull:
  function(.data, var, name, ...)
pull.multidplyr_party_df:
  function(.data, var)

ungroup:
  function(x, ...)
ungroup.multidplyr_party_df:
  function(.data, ...)

collect:
  function(x, ...)
collect.multidplyr_party_df:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plsgenomics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 15 marked UTF-8 strings
Specified C++14: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   9.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘fields’ ‘optmatch’ ‘rcbalance’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 6 marked UTF-8 strings
Specified C++14: please drop specification unless essential
Undeclared package ‘lfe’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared packages ‘AICcmodavg’, ‘bbmle’, ‘glmulti’, ‘arm’, ‘performance’, ‘wgeesel’, ‘ape’, ‘bestglm’, ‘leaps’, ‘glmmTMB’, ‘brglm’, ‘quantreg’, ‘maxlike’, ‘RMark’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Undeclared package ‘dosresmeta’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
Undeclared package ‘VGAM’ in Rd xrefs
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
Undeclared package ‘mev’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘sampleSelection’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) mvr.Rd:113: Escaped LaTeX specials: \#
checkRd: (-1) mvr.Rd:115: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'BioNet', 'DLBCL'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 50 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’ ‘rpart’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘asreml’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
Found the following significant warnings:
  namespace.c:4:11: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/namespace.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Malformed Description field: should contain one or more complete sentences.
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.0Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Package suggested but not available for checking: ‘gurobi’
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_menu:
  function(x)

vec_ptype_abbr:
  function(x, ..., prefix_named, suffix_shape)
vec_ptype_abbr.navigatr_nav_input:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘CBPS’ in Rd xrefs
Note: found 140 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘sSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Namespace in Imports field not imported from: ‘magick’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘reader’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘re2r’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Undeclared package ‘DescTools’ in Rd xrefs
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) netCoin-package.Rd:38: Escaped LaTeX specials: \&
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
':::' call which should be '::': ‘lhs:::maximinLHS’
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) exportToTSPlibFormat.Rd:32: Escaped LaTeX specials: \_ \_
checkRd: (-1) makeNetwork.Rd:31: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Undeclared package ‘mediation’ in Rd xrefs
Undeclared package ‘crossnma’ in Rd xrefs
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 2 marked Latin-1 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 4894 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Undeclared package ‘yaml’ in Rd xrefs
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.3Mb
    classic-bugs   1.6Mb
    include        5.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       4.0Mb
    extdata   1.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Undeclared packages ‘cshapes’, ‘mapdata’ in Rd xrefs
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘knitr’ ‘nlraa’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘vpc’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Undeclared package ‘tm’ in Rd xrefs
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) nltm.control.Rd:29: Escaped LaTeX specials: \$
Package suggested but not available for checking: ‘DAISIE’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
# NOTE - CRAN check detected: limiting maximum number of cores [2/24]

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./veclib.h:302:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/nncc.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Found the following significant warnings:
  geodesic.c:57:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/nngeo.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
Undeclared package ‘sfheaders’ in Rd xrefs
Undeclared packages ‘quadprog’, ‘bvls’ in Rd xrefs
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘copula’ in Rd xrefs
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  init.c:16:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/norm.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) prepareplot.Rd:64: Escaped LaTeX specials: \#
checkRd: (-1) prepareplot.Rd:68: Escaped LaTeX specials: \#
Undeclared package ‘tidyselect’ in Rd xrefs
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
checkRd: (-1) Ardechedata.Rd:18: Escaped LaTeX specials: \_
checkRd: (-1) nsRFA-package.Rd:231: Escaped LaTeX specials: \&
Note: found 1 marked UTF-8 string
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘optparse’ ‘vcfR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘ensurer’, ‘validate’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Packages suggested but not available for checking:
  'originr', 'parallelsugar'

Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘rnaturalearthdata’ ‘spocc’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1242 marked UTF-8 strings
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    doc       5.7Mb
    extdata   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.0Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
':::' call which should be '::': ‘DBItest:::get_default_context’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘DBItest:::connect’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Undeclared package ‘gam’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Found the following significant warnings:
  gutsRedIT.c:34:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedIT.c:58:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:36:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  gutsRedSD.c:64:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:5:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  odeGUTS_init.c:6:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/odeGUTS.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘sp’ in Rd xrefs
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘lubridate’ in Rd xrefs
Specified C++11: please drop specification unless essential
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 32 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘quanteda.textmodels’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘worldmet’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'unary_ops':
  ‘log10.ProcessNode’ ‘log10.ProcessGraphParameter’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
Note: found 2524 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R        2.6Mb
    data     1.5Mb
    libs     6.4Mb
    models   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Package suggested but not available for checking: ‘openNLPmodels.en’
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Note: found 167 marked UTF-8 strings
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   1.4Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘alabama’, ‘cccp’, ‘nloptr’ in Rd xrefs
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
Package suggested but not available for checking: ‘rrelaxiv’
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Undeclared package ‘vegan’ in Rd xrefs
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Undeclared package ‘pillar’ in Rd xrefs
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘microplot’ in Rd xrefs
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Undeclared package ‘orloca.es’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘knitr’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Note: found 263 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘survey’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘astsa’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘result.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘h-block-crossvalidation.Rmd’ using rmarkdown
# A tibble: 1 × 1
   RMSE
  <dbl>
1  1.28
Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) :
  longer object length is not a multiple of shorter object length
# A tibble: 1 × 1
      h
  <dbl>
1   900
Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) :
  longer object length is not a multiple of shorter object length
# A tibble: 1 × 1
      h
  <dbl>
1   900
--- finished re-building ‘h-block-crossvalidation.Rmd’

--- re-building ‘randomTF-spatial.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
SUMMARY: processing the following file failed:
  ‘randomTF-spatial.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 314 marked UTF-8 strings
Package which this enhances but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘bison_example.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 16 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Namespaces in Imports field not imported from:
  ‘DT’ ‘dbplyr’ ‘downloadthis’ ‘ggExtra’ ‘htmlwidgets’ ‘methods’
  ‘rmarkdown’ ‘scales’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
predictSurvProb:
  function(object, newdata, times, ...)
predictSurvProb.pamm:
  function(object, newdata, times)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Undeclared package ‘AER’ in Rd xrefs
Undeclared packages ‘parameters’, ‘performance’, ‘gt’ in Rd xrefs
'LazyData' is specified without a 'data' directory
checkRd: (-1) pan.bd.Rd:65: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Undeclared packages ‘partykit’, ‘Cubist’, ‘rules’, ‘h2o’, ‘agua’, ‘baguette’, ‘ipred’, ‘dbarts’, ‘lightgbm’, ‘bonsai’, ‘mboost’, ‘mda’, ‘sda’, ‘sparsediscrim’, ‘klaR’, ‘workflows’, ‘brulee’, ‘glmnet’, ‘rstan’, ‘rstanarm’, ‘naivebayes’, ‘plsmod’, ‘pscl’, ‘aorsf’, ‘randomForest’, ‘xrf’, ‘flexsurv’, ‘broom’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
S3 methods shown with full name in documentation object 'prune.modelparty':
  ‘prune.modelparty’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \# \# \#
checkRd: (-1) regul.Rd:52: Escaped LaTeX specials: \#
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    data   1.5Mb
Undeclared package ‘pathfindR’ in Rd xrefs
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Undeclared package ‘future’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   2.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   2.7Mb
---- unloading
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Note: information on .o files is not available
'LazyData' is specified without a 'data' directory
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Undeclared packages ‘tibble’, ‘data.table’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
Undeclared packages ‘combinat’, ‘unifDAG’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  10.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 11 marked UTF-8 strings
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘sm’, ‘spdep’ in Rd xrefs
Package suggested but not available for checking: ‘PythonInR’
Package suggested but not available for checking: ‘tesseract’
'LazyData' is specified without a 'data' directory
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  PeakSegJoint_interface.c:113:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/PeakSegJoint.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘crrstep’
checkRd: (-1) pec.Rd:250: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:251: Escaped LaTeX specials: \&
checkRd: (-1) pec.Rd:256: Escaped LaTeX specials: \&
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.7Mb
Package suggested but not available for checking: ‘georob’
Note: found 7326 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) simulate.data.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) simulate.data.Rd:28: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
Specified C++11: please drop specification unless essential
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Found the following significant warnings:
  init.c:13:51: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peptides.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 4 marked UTF-8 strings
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Undeclared packages ‘timeSeries’, ‘tseries’, ‘car’, ‘gplots’ in Rd xrefs
Package suggested but not available for checking: ‘DMwR’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dendextendRcpp’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘classInt’, ‘maptools’, ‘PMCMR’, ‘agricolae’, ‘rgdal’, ‘plotrix’, ‘AICcmodavg’ in Rd xrefs
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    application   5.0Mb
Namespaces in Imports field not imported from:
  ‘rJava’ ‘shinyWidgets’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘phase1RMD’ in Rd xrefs
Undeclared package ‘aricode’ in Rd xrefs
Found the following files/directories:
  ‘test.pdf’
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘vowels’ in Rd xrefs
Found the following files/directories:
  ‘1khz.wav’ ‘snd.wav’
S3 methods shown with full name in documentation object 'log':
  ‘log2.generic_spct’ ‘log10.generic_spct’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Note: found 13 marked UTF-8 strings
checkRd: (-1) phylo4d-methods.Rd:209: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Undeclared packages ‘future’, ‘geiger’, ‘caper’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Undeclared package ‘picante’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘cowplot’ ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/sugar/functions/sapply.h:36:26: warning: 'result_of<float (*(double))(float)>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/physiology.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Undeclared package ‘BsMD’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
vec_math:
  function(.fn, .x, ...)
vec_math.pillar_num:
  function(op, x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2048 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
Package suggested but not available for checking: ‘ggsubplot’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sanitize_latex.Rd:49: Escaped LaTeX specials: \$
Undeclared package ‘Hmisc’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘usethis’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
Undeclared package ‘htmlwidgets’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: ‘RStoolbox’
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
Packages suggested but not available for checking:
  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    tests   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.0Mb
Undeclared package ‘exams’ in Rd xrefs
Undeclared package ‘scape’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘sm’ in Rd xrefs
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘DiagrammeR’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘USAboundaries’
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘ISOcodes’ in Rd xrefs
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Undeclared package ‘flexmix’ in Rd xrefs
Note: found 21 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 52 marked UTF-8 strings
Undeclared package ‘purrr’ in Rd xrefs
Note: found 805 marked Latin-1 strings
  Note: found 12681 marked UTF-8 strings
Undeclared package ‘modelObj’ in Rd xrefs
Package suggested but not available for checking: ‘pollimetrydata’
Specified C++11: please drop specification unless essential
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘polyfreqs-mcmc.out’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.6Mb
Specified C++11: please drop specification unless essential
Undeclared packages ‘polymapR’, ‘BSgenome’ in Rd xrefs
Undeclared package ‘Rcmdr’ in Rd xrefs
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Kendall.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) countCDFxt.Rd:63: Escaped LaTeX specials: \&
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: ‘RClone’
Found the following significant warnings:
  init.c:24:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  omp_test.c:7:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/poppr.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
checkRd: (-1) genetic_distance.Rd:106: Escaped LaTeX specials: \~
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘psych’ ‘zoo’
  All declared Imports should be used.
File ‘population/libs/population.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) tradelist-class.Rd:91: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Undeclared package ‘bslib’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Undeclared package ‘advclust’ in Rd xrefs
Unknown package ‘advclust’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sum.c:358:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  prod.c:27:32: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:28:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/PreciseSums.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata  11.6Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘ffbase’
Unknown package ‘ffbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 83 marked UTF-8 strings
Note: found 42966 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    shinyApp   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘parsnip’ in Rd xrefs
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 136-141 (getting_started_with_prewas.Rmd) 
Error: processing vignette 'getting_started_with_prewas.Rmd' failed with diagnostics:
Strategy 'multiprocess' is defunct in future (>= 1.32.0) [2023-03-06]. Instead, explicitly specify either 'multisession' (recommended) or 'multicore'.
--- failed re-building ‘getting_started_with_prewas.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_with_prewas.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 165 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  init.c:17:43: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:22:48: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:232:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zhegv.c:3715:13: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/PRIMME.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'gurobi', 'Rcplex'
Specified C++11: please drop specification unless essential
show:
  function(object)
show.Data:
  function(x, ...)

show:
  function(object)
show.OptimizationProblem:
  function(x, ...)

show:
  function(object)
show.Portfolio:
  function(x, ...)

show:
  function(object)
show.Solution:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.6Mb
Undeclared packages ‘ipflasso’, ‘mvtnorm’ in Rd xrefs
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.6Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) prodlim.Rd:119: Escaped LaTeX specials: \&
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ProFit’
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  pause.c:10:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/profvis.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cin’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
Undeclared package ‘RProtoBuf’ in Rd xrefs
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘XML’ in Rd xrefs
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
Specified C++11: please drop specification unless essential
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  util.c:6:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/pscl.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespaces in Imports field not imported from:
  ‘LambertW’ ‘gtools’ ‘mstate’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 26 marked Latin-1 strings
Undeclared package ‘spsur’ in Rd xrefs
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Undeclared package ‘entropy’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) esa.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:9: Escaped LaTeX specials: \&
checkRd: (-1) meta_varcov.Rd:120: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    doc        4.0Mb
    examples   2.5Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘sjPlot’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘lazyeval’ ‘mgcv’
  All declared Imports should be used.
Undeclared package ‘tibble’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch0C-plot.cpd.PwrGSD.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘exampleplot_1_blockdist_1.png’ ‘exampleplot_1_blockdist_2.png’
  ‘exampleplot_1_blockdist_3.png’ ‘exampleplot_1_bootdist.png’
  ‘exampleplot_1_dist.png’ ‘exampleplot_1_histogramtest_EMD.png’
  ‘exampleplot_1_roc_dynamic.png’ ‘exampleplot_1_slidedist_1.png’
  ‘exampleplot_1_slidedist_2.png’ ‘exampleplot_1_slidedist_3.png’
  ‘exampleplot_1_trimmeddist.png’ ‘exampleplot_blockdist_1.png’
  ‘exampleplot_blockdist_2.png’ ‘exampleplot_blockdist_3.png’
  ‘exampleplot_bootdist.png’ ‘exampleplot_dist.png’
  ‘exampleplot_lim_dyn.png’ ‘exampleplot_lim_sig.png’
  ‘exampleplot_lim_sta.png’ ‘exampleplot_noc.png’
  ‘exampleplot_roc_dyn.png’ ‘exampleplot_roc_sta.png’
  ‘exampleplot_slidedist_1.png’ ‘exampleplot_slidedist_2.png’
  ‘exampleplot_slidedist_3.png’ ‘exampleplot_trimmeddist.png’
  ‘myworkflow_result.xml’ ‘test_2_roc_dynamic.png’ ‘test_4_dist.png’
  ‘test_5_blockdist_1.png’ ‘test_5_blockdist_2.png’
  ‘test_5_blockdist_3.png’ ‘test_6_slidedist_1.png’
  ‘test_6_slidedist_2.png’ ‘test_6_slidedist_3.png’
  ‘test_7_trimmeddist.png’ ‘test_8_bootdist.png’ ‘test_emd_1d.png’
  ‘test_emd_2d.png’ ‘test_jsd_1d.png’ ‘test_jsd_2d.png’
  ‘test_kld_1d.png’ ‘test_kld_2d.png’ ‘test_ms_1d.png’ ‘test_ms_2d.png’
  ‘test_rms_1d.png’ ‘test_rms_2d.png’
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    gui          1.7Mb
    staticdocs   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘qdap’ in Rd xrefs
Undeclared package ‘gplots’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
as.igraph:
  function(x, ...)
as.igraph.qgraph:
  function(object, attributes)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++14: please drop specification unless essential
Note: found 76102 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘readxl’ ‘reshape2’ ‘sjmisc’ ‘stringr’ ‘xlsx’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘lambda.pdf’ ‘qqplot.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Undeclared package ‘qrNLMM’ in Rd xrefs
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      1.7Mb
Specified C++11: please drop specification unless essential
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GRI.Rd:3: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’
  All declared Imports should be used.
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Note: found 4 marked UTF-8 strings
Error(s) in re-building vignettes:
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 481-486 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
object 'data_corpus_irishbudget2010' not found
--- failed re-building ‘quickstart.Rmd’

SUMMARY: processing the following file failed:
  ‘quickstart.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quanteda.textmodels’
Specified C++11: please drop specification unless essential
Unknown package ‘quanteda.textmodels’ in Rd xrefs
Running examples in ‘quanteda.textplots-Ex.R’ failed
The error most likely occurred in:

> ### Name: textplot_scale1d
> ### Title: Plot a fitted scaling model
> ### Aliases: textplot_scale1d
> ### Keywords: textplot
> 
> ### ** Examples
> 
> library("quanteda")
Package version: 3.2.4
Unicode version: 13.0
ICU version: 69.1
Parallel computing: 24 of 24 threads used.
See https://quanteda.io for tutorials and examples.
> data(data_corpus_irishbudget2010, package = "quanteda.textmodels")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘quanteda.textmodels’
Calls: data -> find.package
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > library("testthat")
  > library("quanteda")
  Package version: 3.2.4
  Unicode version: 13.0
  ICU version: 69.1
  Parallel computing: 24 of 24 threads used.
  See https://quanteda.io for tutorials and examples.
  > library("quanteda.textmodels")
  Error in library("quanteda.textmodels") : 
    there is no package called 'quanteda.textmodels'
  Execution halted
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  glmBias.c:84:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/QuasiSeq.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Note: found 8504 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘psych’ ‘psychTools’
  All declared Imports should be used.
Undeclared package ‘reshape’ in Rd xrefs
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fastshp', 'visualTest'
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Undeclared package ‘PredictABEL’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 12928 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc         2.9Mb
    shiny_app   1.4Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) qwraps2.Rd:73: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ReGenesees’
Undeclared package ‘gplots’ in Rd xrefs
installed size is  5.0Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘generics’ in Rd xrefs
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ../inst/include/sundials/sundials_nvector.h:163:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_nonlinearsolver.h:131:56: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_matrix.h:105:41: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../inst/include/sundials/sundials_linearsolver.h:137:50: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nonlinearsolver.c:26:40: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_matrix.c:29:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_nvector.c:28:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  lib/sundials/sundials_linearsolver.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/r2sundials.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc           5.3Mb
    htmlwidgets   1.8Mb
as.tags:
  function(x, ...)
as.tags.data3js:
  function(x, standalone)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.6Mb
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Note: found 3 marked UTF-8 strings
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Undeclared packages ‘longitudinal’, ‘gRbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets       10.0Mb
    super-tiny-icons   1.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘googlesheets’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘igraph’ in Rd xrefs
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘reshape’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  sketch.c:33:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:38:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:172:9: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sketch.c:206:6: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/RaProR.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gurobi’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘arm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘exactci’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    etc    1.9Mb
    po     1.2Mb
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Note: found 8 marked UTF-8 strings
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
GNU make is a SystemRequirements.
Undeclared packages ‘MCMCpack’, ‘gtools’ in Rd xrefs
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    blp   7.1Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) mn4joint1condi.Rd:39: Escaped LaTeX specials: \$
checkRd: (-1) mn4joint1condi.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) objets.Rd:66: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 26334 marked UTF-8 strings
Found the following files/directories:
  ‘rcanvec.cache’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
Found the following significant warnings:
  cddmp.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp.c:63:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:24:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  cddmp_f.c:64:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  nonred.c:99:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcdd.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    cont  24.3Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘data.csv’
Found the following significant warnings:
  RClickhouse_init.c:23:54: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:373:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  vendor/clickhouse-cpp/contrib/lz4/lz4.c:1474:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/RClickhouse.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
sql_translate_env:
  function(con)
sql_translate_env.ClickhouseConnection:
  function(x)

db_desc:
  function(x)
db_desc.ClickhouseConnection:
  function(con)

db_analyze:
  function(con, table, ...)
db_analyze.ClickhouseConnection:
  function(con, sql, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Found the following files/directories:
  ‘outcmaesdisp.dat’
Undeclared package ‘car’ in Rd xrefs
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Undeclared packages ‘BsMD’, ‘rsm’, ‘AlgDesign’, ‘lhs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Undeclared packages ‘car’, ‘leaps’, ‘latticeExtra’, ‘rgl’ in Rd xrefs
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Undeclared package ‘randtests’ in Rd xrefs
Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
    po    2.5Mb
as_tibble:
  function(x, ..., .rows, .name_repair, rownames)
as_tibble.CompadreDB:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Note: found 345 marked UTF-8 strings
Undeclared package ‘remotes’ in Rd xrefs
Package suggested but not available for checking: ‘conics’
Note: found 1 marked UTF-8 string
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    include  45.2Mb
Undeclared package ‘RcppExamples’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘configure’: /bin/bash is not portable
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    include    6.4Mb
    tinytest   1.0Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rredis’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include        2.0Mb
    jsonexamples   3.9Mb
    libs           1.7Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsTMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgeMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.matrix:
  function(x, check.sym)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsCMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.ddiMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dsyMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dpoMatrix:
  function(x)

as.simple_triplet_sym_matrix:
  function(x, ...)
as.simple_triplet_sym_matrix.dgTMatrix:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘PercentCodes’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  rDEA_init.c:11:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rDEA.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Undeclared package ‘Rglpk’ in Rd xrefs
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘devAll’
'LazyData' is specified without a 'data' directory
as.integer64:
  function(x, ...)
as.integer64.SNOMEDconcept:
  function(x)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   1.7Mb
Undeclared package ‘Rtsne’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./deps/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_product_op<float> (const float &, const float &)>' is deprecated [-Wdeprecated-declarations]
  ./deps/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_abs_op<float> (const float &)>' is deprecated [-Wdeprecated-declarations]
  ./deps/eigen-3.3.9/Eigen/src/Core/util/Meta.h:320:25: warning: 'result_of<Eigen::internal::scalar_score_coeff_op<float> (const float &)>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/rDppDiversity.Rcheck/00install.out’ for details.
* used C++ compiler: ‘clang version 16.0.0’
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  dsdp/include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ../../include/dsdp5.h:206:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:20:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpcops.c:28:34: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdpsetoptions.c:280:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpalloc.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  sdpexit.c:4:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  dsdperror.c:129:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rdsdp.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   1.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) re2_syntax.Rd:539: Escaped LaTeX specials: \_
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘readMzXmlData’, ‘MALDIquantForeign’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘MALDIquantForeign’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tidyselect’, ‘vctrs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 8 marked UTF-8 strings
Undeclared package ‘rebus.unicode’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared packages ‘fastICA’, ‘dimRed’ in Rd xrefs
Specified C++11: please drop specification unless essential
Undeclared package ‘snow’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 1036 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Undeclared package ‘car’ in Rd xrefs
Package suggested but not available for checking: ‘opencv’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.9Mb
Undeclared package ‘jpeg’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Found the following files/directories:
  ‘Filled.RData’ ‘cleaned.RData’ ‘days’ ‘gridded’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   1.4Mb
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘cur_plans’
rowwise:
  function(data, ...)
rowwise.redist_map:
  function(x, ...)

rowwise:
  function(data, ...)
rowwise.redist_plans:
  function(x, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  redland.c:771:37: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:817:31: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  redland.c:1846:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/redland.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
roclet_process:
  function(x, blocks, env, base_path)
roclet_process.roclet_mergeNamespace:
  function(x, blocks, env, base_path, global_options)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
qq:
  function(x, data, ...)
qq.pffr:
  function(object, rep, level, s.rep, type, pch, rl.col, rep.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  init.c:9:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:13:25: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/reglogit.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
checkRd: (-1) pima.Rd:24: Escaped LaTeX specials: \^
checkRd: (-1) reglogit.Rd:120: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:124: Escaped LaTeX specials: \&
checkRd: (-1) reglogit.Rd:136: Escaped LaTeX specials: \&
Undeclared package ‘monomvn’ in Rd xrefs
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘psych’ in Rd xrefs
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc.relimp.Rd:41: Escaped LaTeX specials: \~
checkRd: (-1) classesmethods.relaimpo.Rd:27: Escaped LaTeX specials: \$
checkRd: (-1) classesmethods.relaimpo.Rd:104: Escaped LaTeX specials: \$
checkRd: (-1) mianalyze.relimp.Rd:69: Escaped LaTeX specials: \~
checkRd: (-1) mianalyze.relimp.Rd:73: Escaped LaTeX specials: \~
checkRd: (-1) relimplm-class.Rd:63: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbootMI-class.Rd:121: Escaped LaTeX specials: \$
checkRd: (-1) relimplmbooteval-class.Rd:146: Escaped LaTeX specials: \$
Package which this enhances but not available for checking: ‘Rcplex’
Undeclared package ‘graph’ in Rd xrefs
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Undeclared package ‘magrittr’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) ena.plot.group.Rd:44: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:46: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.group.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:38: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:40: Escaped LaTeX specials: \$
checkRd: (-1) ena.plot.trajectory.Rd:42: Escaped LaTeX specials: \$
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 6034 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘ggplot2’ in Rd xrefs
Undeclared package ‘wesanderson’ in Rd xrefs
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
Anova:
  function(mod, ...)
Anova.resi:
  function(object, alpha, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
checkRd: (-1) Burns.Rd:28: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 26 marked UTF-8 strings
Undeclared package ‘robustbase’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Undeclared package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
Note: found 514 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rfieldclimate)
  > 
  > test_check("rfieldclimate")
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 3 ]
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • Sys.getenv("FC_PRIVATE_KEY") == "" is TRUE (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-fc_request.R:4:3'): fc_request fails with invalid credentials ──
  `fc_request("GET", "/user", public_key = "invalid", private_key = "invalid")` threw an error with unexpected message.
  Expected match: "fieldclimate API request failed"
  Actual message: "lexical error: invalid char in json text.\n                                       <br /> <b>Fatal error</b>:  Unc\n                     (right here) ------^\n"
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-fc_request.R:4:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─rfieldclimate::fc_request(...)
    7. │ └─... %>% jsonlite::fromJSON(simplifyVector = FALSE)
    8. └─jsonlite::fromJSON(., simplifyVector = FALSE)
    9.   └─jsonlite:::parse_and_simplify(...)
   10.     └─jsonlite:::parseJSON(txt, bigint_as_char)
   11.       └─jsonlite:::parse_string(txt, bigint_as_char)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 3 ]
  Error: Test failures
  Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
checkRd: (-1) CardioRiskFactors.Rd:35: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  pcg_basic.c:69:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/RGBM.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        3.7Mb
    pictures   1.3Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Undeclared package ‘Matching’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Rglpk_read_file.c:17:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  init.c:42:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rglpk.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
checkRd: (-1) Rglpk_read_file.Rd:6: Escaped LaTeX specials: \_
Undeclared packages ‘lpSolve’, ‘ROI’, ‘Rsymphony’ in Rd xrefs
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    fonts   1.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) columbus.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) columbus.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) columbus.Rd:30: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
autoplot:
  function(object, ...)
autoplot.persistence_diagram:
  function(x, dimension, alpha, max_intervals, legend, greyblock, n,
           type, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Note: found 1473 marked UTF-8 strings
Undeclared package ‘DBI’ in Rd xrefs
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.3Mb
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
'LazyData' is specified without a 'data' directory
Undeclared packages ‘tseries’, ‘TSA’ in Rd xrefs
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./convert.h:12:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  convert.c:79:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/ring.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 169 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
    libs     14.4Mb
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
as.data.table:
  function(x, keep.rownames, ...)
as.data.table.ate:
  function(x, estimator, type, keep.rownames, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
Undeclared package ‘utility’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  ./init.h:19:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:26:28: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:30:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rjags.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used C++ compiler: ‘clang version 16.0.0’
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   2.9Mb
    libs      2.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
'LazyData' is specified without a 'data' directory
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Undeclared package ‘rgdal’ in Rd xrefs
Found the following significant warnings:
  RngWrap.c:12:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:23:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:304:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  RngWrap.c:328:24: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:11:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:13:26: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  zzz.c:17:30: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rlecuyer.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    1.9Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    lib       3.5Mb
    libs      1.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘USAboundaries’
Note: found 31 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    minizinc   3.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
Undeclared package ‘coda’ in Rd xrefs
GNU make is a SystemRequirements.
Undeclared package ‘fortunes’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    2.2Mb
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Undeclared package ‘raster’ in Rd xrefs
Note: found 416 marked Latin-1 strings
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Undeclared packages ‘fossil’, ‘raster’ in Rd xrefs
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.2Mb
'LazyData' is specified without a 'data' directory
Undeclared package ‘metafor’ in Rd xrefs
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
autoplot:
  function(object, ...)
autoplot.meteo_coverage:
  function(mateo_coverage, old_style)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘rappdirs’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) addLR.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) addLRinv.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) adtestWrapper.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) arcticLake.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cenLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) cenLRinv.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) expenditures.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) gemas.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) machineOperators.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) plot.imp.Rd:138: Escaped LaTeX specials: \&
checkRd: (-1) robCompositions-package.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) skyeLavas.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) variation.Rd:45: Escaped LaTeX specials: \&
Undeclared package ‘StatDA’ in Rd xrefs
Unknown package ‘StatDA’ in Rd xrefs
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Undeclared package ‘distrEx’ in Rd xrefs
Undeclared package ‘ROptEst’ in Rd xrefs
Undeclared packages ‘bridgesampling’, ‘metafor’, ‘extraDistr’ in Rd xrefs
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘extraDistr’ in Rd xrefs
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘graphics’ ‘methods’ ‘utils’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Undeclared package ‘extraDistr’ in Rd xrefs
GNU make is a SystemRequirements.
Note: found 6 marked UTF-8 strings
Found the following significant warnings:
  monitor.c:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/robustbase.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
checkRd: (-1) aircraft.Rd:8: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘readroper’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘pROC’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    libs   1.1Mb
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Package suggested but not available for checking: ‘RandomFields’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘tree’ in Rd xrefs
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Undeclared package ‘rsoi’ in Rd xrefs
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Undeclared package ‘htmlwidgets’ in Rd xrefs
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘scalreg’ in Rd xrefs
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.bpl’ ‘test.cr’ ‘test.ct’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘evolqg’
Unknown package ‘evolqg’ in Rd xrefs
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gdalUtils’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./Stopwatch.h:13:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Stopwatch.c:4:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rscimark.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared packages ‘keras’, ‘tensorflow’, ‘devtools’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: abalone
> ### Title: SODAS XML data file.
> ### Aliases: abalone
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(abalone)
> res <- sym.pca(abalone, 'centers')
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'tbl_subset_col' not found
Calls: sym.pca ... %in% -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 60-64 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'tbl_subset_col' not found
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  tls.c:29:15: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_InputHandlers’,
    ‘R_Outputfile’, ‘R_TempDir’, ‘R_Visible’, ‘addInputHandler’,
    ‘ptr_R_Busy’, ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’,
    ‘ptr_R_ReadConsole’, ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 467 marked UTF-8 strings
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Vdgraph’
Unknown package ‘Vdgraph’ in Rd xrefs
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    help   1.4Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.8Mb
    libs  15.2Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
Undeclared packages ‘gamm4’, ‘shiny’ in Rd xrefs
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    lib    2.1Mb
    libs   7.4Mb
Undeclared packages ‘coda’, ‘rstanarm’ in Rd xrefs
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘bitops’ ‘httpuv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    swipl  24.2Mb
GNU make is a SystemRequirements.
Undeclared packages ‘lpSolve’, ‘Rglpk’ in Rd xrefs
Found the following significant warnings:
  ./rsyslog.h:15:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  rsyslog.c:50:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/rsyslog.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R           1.3Mb
    bootstrap   1.6Mb
    doc         1.2Mb
    help        2.8Mb
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    rmarkdown   7.3Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 40 marked UTF-8 strings
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      3.4Mb
    extdata   1.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.9Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘lubridate’ ‘rstantools’
  All declared Imports should be used.
Unknown package ‘cmdstanr’ in Rd xrefs
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RQuantLib’
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R   3.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) tracker.Rd:70: Escaped LaTeX specials: \&
checkRd: (-1) tracker.Rd:73: Escaped LaTeX specials: \&
Found the following files/directories:
  ‘results’
checkRd: (-1) run.jags.study.Rd:67: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘glmmADMB’
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘cli’ ‘withr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    include   5.0Mb
    libs      5.0Mb
Undeclared package ‘wdm’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    test   4.5Mb
File ‘RVowpalWabbit/libs/RVowpalWabbit.so’:
  Found ‘sprintf’, possibly from ‘sprintf’ (C)
    Object: ‘parse_args.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rWCVPdata’
Undeclared package ‘scales’ in Rd xrefs
Note: found 16 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mapBubbles.Rd:62: Escaped LaTeX specials: \$
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package required and available but unsuitable version: ‘rxode2parse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rxode2parse.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘rxode2parse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
Undeclared package ‘rym’ in Rd xrefs
'LazyData' is specified without a 'data' directory
ggplot:
  function(data, mapping, ..., environment)
ggplot.qqnorm.spss:
  function(x, plottype, line, l.col, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Undeclared package ‘jsonlite’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Undeclared package ‘sf’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 37 marked Latin-1 strings
  Note: found 172 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Undeclared package ‘magrittr’ in Rd xrefs
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  ./Gen_fun.h:17:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  Gen_fun.c:121:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./IFscratch.h:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_IFscratch.c:64:12: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  load_env.c:162:14: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/samon.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Found the following significant warnings:
  ./init.h:28:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
  ./init.h:29:19: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/SamplerCompare.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-4)’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.5Mb
Specified C++11: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
Package suggested but not available for checking: ‘networkTomography’
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘FitARMA’
Specified C++11: please drop specification unless essential
checkRd: (-1) generef.Rd:29: Escaped LaTeX specials: \&
'library' or 'require' call to ‘progress’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
Undeclared package ‘evd’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Found the following significant warnings:
  ./error.h:33:21: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/scclust.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SingleCellSignalR’
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘DuoClustering2018’
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'ssvd', 'conos', 'pagoda2'
Unexported object imported by a ':::' call: ‘simplifyEnrichment:::is_GO_id’
  See the note in ?`:::` about the use of this operator.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘AUCell’
Undeclared package ‘SeuratObject’ in Rd xrefs
File ‘scquantum/libs/scquantum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  linsys/cpu/direct/private.c:4:36: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]
See ‘/data/gannet/ripley/R/packages/tests-clang/scs.Rcheck/00install.out’ for details.
* used C compiler: ‘clang version 16.0.0’
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmGamPoi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘tibble’ in Rd xrefs
Note: found 1 marked UTF-8 string
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Undeclared package ‘RegSDC’ in Rd xrefs
Found the following files/directories:
  ‘MC p-value.ps’ ‘Output.csv’ ‘Rh.ps’ ‘Th.ps’ ‘dataratio .Rdata’
  ‘featuresRmax.csv’ ‘featuresT.csv’
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
Note: found 5 marked Latin-1 strings
  Note: found 51869 marked UTF-8 strings
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Undeclared package ‘raster’ in Rd xrefs
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking:
  'xbioc', 'MuSiC', 'seAMLessData'
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
Note: found 3 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘rsbml’
Undeclared packages ‘EDNE.EQ’, ‘T2EQ’ in Rd xrefs
'LazyData' is specified without a 'data' directory
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Package suggested but not available for checking: ‘spgrass6’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Undeclared package ‘cate’ in Rd xrefs
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Undeclared packages ‘NetworkToolbox’, ‘SemNetCleaner’ in Rd xrefs
Undeclared package ‘qgraph’ in Rd xrefs
checkRd: (-1) escape.Rd:28: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fahst.rd:39: Escaped LaTeX specials: \^
checkRd: (-1) fahst.rd:36: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:46: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:42: Escaped LaTeX specials: \^
checkRd: (-1) fasnt.rd:43: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:49: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:44: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) fast.Rd:46: Escaped LaTeX specials: \^
checkRd: (-1) hsortplot.rd:24: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:30: Escaped LaTeX specials: \^
checkRd: (-1) nappesortplot.Rd:28: Escaped LaTeX specials: \^
checkRd: (-1) plot.fahst.rd:45: Escaped LaTeX specials: \^
checkRd: (-1) plot.fasnt.Rd:47: Escaped LaTeX specials: \^
checkRd: (-1) plot.fast.Rd:45: Escaped LaTeX specials: \^
checkRd: (-1) print.fahst.rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fasnt.Rd:22: Escaped LaTeX specials: \^
checkRd: (-1) print.fast.Rd:22: Escaped LaTeX specials: \^
Specified C++11: please drop specification unless essential
Note: found 836 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Undeclared package ‘lexicon’ in Rd xrefs
Note: found 3128 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 52 marked UTF-8 strings
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.5Mb
    sequences   1.9Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Package required but not available: ‘copynumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘plotly’ in Rd xrefs
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Specified C++11: please drop specification unless essential
Undeclared package ‘Signac’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
st_precision:
  function(x)
st_precision.sfnetwork:
  function(x, active, ...)

st_z_range:
  function(obj, ...)
st_z_range.sfnetwork:
  function(x, active, ...)

st_geometry:
  function(obj, ...)
st_geometry.sfnetwork:
  function(x, active, ...)

st_bbox:
  function(obj, ...)
st_bbox.sfnetwork:
  function(x, active, ...)

st_set_precision:
  function(x, precision)
st_set_precision.sfnetwork:
  function(x, value)

st_m_range:
  function(obj, ...)
st_m_range.sfnetwork:
  function(x, active, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    libs     1.1Mb
    sqlite   1.5Mb
Specified C++11: please drop specification unless essential
Undeclared package ‘vctrs’ in Rd xrefs
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Undeclared package ‘tripack’ in Rd xrefs
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
checkRd: (-1) gPLS.Rd:72: Escaped LaTeX specials: \^
checkRd: (-1) gPLS.Rd:74: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:67: Escaped LaTeX specials: \^
checkRd: (-1) sPLS.Rd:69: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:75: Escaped LaTeX specials: \^
checkRd: (-1) sgPLS.Rd:77: Escaped LaTeX specials: \^
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.0Mb
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Other ideas
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘huge’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
'LazyData' is specified without a 'data' directory
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Undeclared package ‘finetune’ in Rd xrefs
'LazyData' is specified without a 'data' directory
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    shinyApp  21.4Mb