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installed size is 63.2Mb
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GNU make is a SystemRequirements.
Packages required but not available:
  'minfi', 'IlluminaHumanMethylationEPICanno.ilm10b4.hg19',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
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installed size is 18.0Mb
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Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
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Package suggested but not available for checking: ‘Rmpi’
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Package suggested but not available for checking: ‘epidict’
Packages suggested but not available for checking:
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Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘cmdstanr’
installed size is 140.8Mb
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Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
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Packages unavailable to check Rd xrefs: ‘OpenMx’, ‘semTools’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
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checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘ExactData’
CCRR: no visible global function definition for ‘%||%’
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TetrachoricCorrelationMatrix: no visible global function definition for
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createBinaryFunction : <anonymous>: no visible global function
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stanine: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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Package suggested but not available for checking: ‘INLA’
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checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
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checkRd: (-1) sp500.Rd:5: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘exuberdata’
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    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    minor changes
installed size is  7.7Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Factoshiny.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
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Running examples in ‘familial-Ex.R’ failed
The error most likely occurred in:

> ### Name: center.test
> ### Title: Center test
> ### Aliases: center.test
> 
> ### ** Examples
> 
> set.seed(123)
> 
> test <- center.test(MASS::galaxies, mu = 21000, nboot = 100)
> print(test)
-----------------------------------------------
familial test of centers with huber family
-----------------------------------------------
mu = 21000 
posterior probabilities: 
  H0   H1 
0.59 0.41 
optimal decision: indeterminate 
> plot(test)
Error in validObject(.Object) : 
  invalid class “FncBand” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: plot ... initialize -> initialize -> initMatrix -> validObject
Execution halted
Running ‘testthat.R’ [78s/200s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(familial)
  > 
  > test_check("familial")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-center-test.R:27:3'): plot function returns a plot ─────────────
  Error in `validObject(.Object)`: invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
       ▆
    1. ├─testthat::expect_s3_class(plot(test), "ggplot") at test-center-test.R:27:3
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. ├─base::plot(test)
    5. └─familial:::plot.center.test(test)
    6.   └─base::lapply(band, bands)
    7.     └─familial (local) FUN(X[[i]], ...)
    8.       ├─base::data.frame(...)
    9.       └─DepthProc::fncGetBand(DepthProc::fncDepth(boot.wide), level)
   10.         └─methods::new("FncBand", bands, index = obj@index, level = band)
   11.           ├─methods::initialize(value, ...)
   12.           └─methods::initialize(value, ...)
   13.             └─methods (local) initMatrix(.Object, ...)
   14.               └─methods::validObject(.Object)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 56-57 [unnamed-chunk-3] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
invalid class "FncBand" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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installed size is 11.9Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
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.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
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installed size is 10.2Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘DESeq2’
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installed size is 32.1Mb
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GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fcl.Rcheck/00install.out’ for details.
installed size is 10.9Mb
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Package suggested but not available for checking: ‘fields’
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installed size is 41.0Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is  5.0Mb
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installed size is 12.0Mb
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checkRd: (-1) morse.Rd:40: Escaped LaTeX specials: \#
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checkRd: (-1) fermicatsR.Rd:31: Escaped LaTeX specials: \&
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installed size is  8.5Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Package suggested but not available for checking: ‘gridlayout’
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Packages suggested but not available for checking:
  'benchden', 'reliaR', 'STAR'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘fivethirtyeightdata’
Package unavailable to check Rd xrefs: ‘fivethirtyeightdata’
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    3.6Mb
    libs   5.2Mb
'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  7.8Mb
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    doc    1.9Mb
    help   2.3Mb
    libs   3.2Mb
installed size is  7.5Mb
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'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: \&
Package suggested but not available for checking: ‘ExperimentHub’
Error(s) in re-building vignettes:
--- re-building ‘FLASHMM-vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
* installing *source* package ‘FLASHMM’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FLASHMM)

Quitting from lines 216-242 [Reference dataset] (FLASHMM-vignette.Rmd)
Error: processing vignette 'FLASHMM-vignette.Rmd' failed with diagnostics:
there is no package called 'ExperimentHub'
--- failed re-building ‘FLASHMM-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 315.7Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc   9.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.8Mb
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    libs  33.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
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    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   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘minet’
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  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
'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:
    Previous versions (not tagged nor released)
'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 19.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    help   1.0Mb
    libs  13.8Mb
'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: ‘Mcomp’
Package suggested but not available for checking: ‘RandomFields’
'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 12.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    help   2.6Mb
    libs   6.6Mb
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) MultiAsset.Rd:26: Escaped LaTeX specials: \&
Error(s) in re-building vignettes:
--- re-building ‘lala2015frbs.ltx’ using tex
--- finished re-building ‘lala2015frbs.ltx’

--- re-building ‘lala2015pmml.Rtex’ using Sweave
Warning in mean.default((real.val - res.test)^2) :
  argument is not numeric or logical: returning NA
Error: processing vignette 'lala2015pmml.Rtex' failed with diagnostics:
Running 'texi2dvi' on 'lala2015pmml.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'lala2015pmml.Rtex'

SUMMARY: processing the following file failed:
  ‘lala2015pmml.Rtex’

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MARSS’
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.2Mb
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.6Mb
Package suggested but not available for checking: ‘dggrids’
installed size is 106.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    doc    1.8Mb
    libs  98.1Mb
Running examples in ‘froggeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: quarto_project
> ### Title: Create a Custom 'Quarto' Project
> ### Aliases: quarto_project
> 
> ### ** Examples
> 
> if (quarto::quarto_version() >= "1.4") {
+   # Create a temporary directory for testing
+   tmp_dir <- tempdir()
+ 
+   # Create the Quarto project with custom YAML & associated files
+   quarto_project("frogs", path = tempdir(), custom_yaml = TRUE)
+ 
+   # Confirms files were created (optional, for user confirmation)
+   file.exists(file.path(tmp_dir, "frogs.rproj"))  # Rproj file
+   file.exists(file.path(tmp_dir, "frog.qmd"))     # Quarto doc
+   file.exists(file.path(tmp_dir, "_quarto.yml"))  # project YAML file
+ 
+   # Create a new Quarto project with standard Quarto YAML
+   # quarto_project('frogs_standard', path = tempdir(), custom_yaml = FALSE)
+ 
+   # Clean up: Remove the created temp directory and all files
+   unlink(list.files(tempdir(), full.names = TRUE), recursive = TRUE)
+ }
Error in `find_quarto()`:
! Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
    ▆
 1. └─quarto::quarto_version()
 2.   └─quarto:::find_quarto()
 3.     └─cli::cli_abort(quarto_not_found_msg)
 4.       └─rlang::abort(...)
Execution halted
installed size is 39.4Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'extraTrees', 'foba', 'nodeHarvest', 'obliqueRF', 'relaxo', 'rrlda'
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
Malformed Description field: should contain one or more complete sentences.
'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
Package suggested but not available for checking: ‘WGCNA’
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    help   4.6Mb
installed size is 39.2Mb
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installed size is 26.3Mb
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    doc    2.0Mb
    libs  22.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.0Mb
Error(s) in re-building vignettes:
--- re-building ‘gamboostLSS_Tutorial.Rnw’ using Sweave
Loading required package: R2BayesX
Loading required package: BayesXsrc
Loading required package: colorspace
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-42. For overview type 'help("mgcv-package")'.
Loading required package: gamboostLSS
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs

Attaching package: 'gamboostLSS'

The following object is masked from 'package:stats':

    model.weights

Loading required namespace: BayesX
Error: processing vignette 'gamboostLSS_Tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'gamboostLSS_Tutorial.Rnw'

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

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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Package suggested but not available for checking: ‘caret’
Package which this enhances but not available for checking: ‘doMPI’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    doc   31.8Mb
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  10.0Mb
installed size is 114.3Mb
  sub-directories of 1Mb or more:
    libs  113.8Mb
GNU make is a SystemRequirements.
installed size is 60.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     57.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Specified C++11: please drop specification unless essential
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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: \&
checkRd: (-1) estprops.Rd:40: Escaped LaTeX specials: \&
Package suggested but not available for checking: ‘gputools’
Package suggested but not available for checking: ‘paleofire’
'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 284.6Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    281.1Mb
installed size is 261.8Mb
  sub-directories of 1Mb or more:
    libs  259.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
installed size is  5.3Mb
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    libs   5.0Mb
Package suggested but not available for checking: ‘gdxrrw’
'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.4Mb
    libs      1.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘genderdata’
Package suggested but not available for checking: ‘rrvgo’
Specified C++11: please drop specification unless essential
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xgboost’
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘simplifyEnrichment’
Package suggested but not available for checking: ‘pwalign’
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.0Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘reactome.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
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    extdata   3.0Mb
    libs      4.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
'LazyData' is specified without a 'data' directory
installed size is 105.4Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    libs  104.0Mb
GNU make is a SystemRequirements.
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:
    doc       2.1Mb
    extdata   3.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.6Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.3Mb
Package suggested but not available for checking: ‘geomarocdata’
'LazyData' is specified without a 'data' directory
installed size is 15.7Mb
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    extdata   2.5Mb
    help      3.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/GeoModels.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    libs   5.1Mb
installed size is 113.8Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  111.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘RandomFields’

Package which this enhances but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Specified C++11: please drop specification unless essential
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.7Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    extdata   4.9Mb
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘ggmsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
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    libs      3.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
'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:
    libs   5.1Mb
'LazyData' is specified without a 'data' directory
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
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
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
'LazyData' is specified without a 'data' directory
installed size is 19.7Mb
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    libs  17.8Mb
'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  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   7.3Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'car', 'NetworkToolbox', 'NetworkComparisonTest'
Specified C++11: please drop specification unless essential
checkRd: (-1) boot_eip.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) constrained.Rd:93: Escaped LaTeX specials: \&
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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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  sub-directories of 1Mb or more:
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    doc    2.3Mb
    help   1.2Mb
'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: ‘lixoftConnectors’
installed size is  8.9Mb
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    help       2.4Mb
    testdata   4.8Mb
'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  7.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
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
'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:
    Win CRAN check results - R Windows
installed size is 11.0Mb
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    doc    9.5Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
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installed size is  7.5Mb
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GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'psych', 'psychTools'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   3.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.4Mb
'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:
    libs   6.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'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.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is  7.8Mb
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Specified C++11: please drop specification unless essential
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checkRd: (-1) randPIT.Rd:52: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 209.7Mb
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installed size is 26.0Mb
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checkRd: (-1) glmc.Rd:232: Escaped LaTeX specials: \&
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checkRd: (-1) glmc.summaries.Rd:79: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mlmRev’
installed size is 67.4Mb
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GNU make is a SystemRequirements.
installed size is  8.1Mb
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    libs   7.5Mb
installed size is 67.4Mb
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GNU make is a SystemRequirements.
installed size is 164.5Mb
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    libs  163.2Mb
GNU make is a SystemRequirements.
installed size is 45.9Mb
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    libs  45.7Mb
installed size is 99.5Mb
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    doc             1.3Mb
    libs           93.0Mb
    test_data       2.3Mb
    vignette_data   2.1Mb
installed size is 34.8Mb
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checkRd: (-1) coef.glmulti.Rd:26: Escaped LaTeX specials: \&
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Malformed Description field: should contain one or more complete sentences.
installed size is 11.5Mb
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    libs   9.8Mb
'LazyData' is specified without a 'data' directory
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
Package unavailable to check Rd xrefs: ‘caret’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘SeqVarTools’
installed size is  7.9Mb
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    libs   5.9Mb
installed size is  6.3Mb
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    doc   5.0Mb
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Package unavailable to check Rd xrefs: ‘repeated’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    data   4.2Mb
installed size is  5.5Mb
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    libs   5.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) BVDWSTOXX.Rd:14: Escaped LaTeX specials: \&
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checkRd: (-1) BVDWSTOXX.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:34: Escaped LaTeX specials: \&
checkRd: (-1) BVDWSTOXX.Rd:37: Escaped LaTeX specials: \&
installed size is  7.4Mb
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'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
installed size is 51.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'Overview.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
pandoc: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/governor.Rcheck/vign_test/governor/vignettes/Overview.html: withFile: resource exhausted (No space left on device)
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
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    R   7.0Mb
installed size is 36.8Mb
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    libs  36.3Mb
installed size is 205.1Mb
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    libs  204.2Mb
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Failure ('test_predict.GP.R:64:9'): check predict.GP ─────────────────────
  smse2 >= 0 & smse2 < 30 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── 2. Failure ('test_predict.GP.R:81:9'): check predict.GP ─────────────────────
  sum(gpp2$complete_data[, 5] - ms2 < 1e-05) >= 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted
installed size is  8.0Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘gplm-examples.Rnw’ using Sweave
Loading required package: AER
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: survival
Error: processing vignette 'gplm-examples.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'gplm-examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `wasysym.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.20 \usepackage
                {comment}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘gplm-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘gplm-examples.Rnw’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
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    data   1.4Mb
    doc    3.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 54.4Mb
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    libs  51.9Mb
Error(s) in re-building vignettes:
--- re-building ‘custom_ocl_gpuR.Rnw’ using knitr
Error: processing vignette 'custom_ocl_gpuR.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'custom_ocl_gpuR.tex' failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
! Emergency stop.
<inserted text> 
                $
l.116 custom_
             ocl_gpuR.R\end{kframe}
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘custom_ocl_gpuR.Rnw’

--- re-building ‘gpuR.Rnw’ using knitr
--- finished re-building ‘gpuR.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
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    libs   5.2Mb
'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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   5.2Mb
Package suggested but not available for checking: ‘monocle’
Package unavailable to check Rd xrefs: ‘monocle’
'LazyData' is specified without a 'data' directory
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Specified C++11: please drop specification unless essential
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    help   2.0Mb
    libs   3.4Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  10.0Mb
Specified C++11: please drop specification unless essential
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
GNU make is a SystemRequirements.
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
jagam2greta: no visible global function definition for ‘%||%’
Undefined global functions or variables:
  %||%
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.8Mb
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
GNU make is a SystemRequirements.
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
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs                     5.6Mb
    supplementary_material   3.1Mb
Package required but not available: ‘EnsDb.Hsapiens.v75’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
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Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 14.0Mb
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    libs  13.6Mb
installed size is  6.0Mb
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    extdata   5.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages unavailable to check Rd xrefs: ‘repeated’, ‘gnlm’
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmddisc.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:46: Escaped LaTeX specials: \_
checkRd: (-1) schuster.Rd:54: Escaped LaTeX specials: \&
installed size is 12.5Mb
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installed size is  5.2Mb
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    libs   4.6Mb
'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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   3.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    data   1.1Mb
    help   2.2Mb
'LazyData' is specified without a 'data' directory
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs  68.5Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.5Mb
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    extdata   2.5Mb
    libs      2.4Mb
installed size is  8.3Mb
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    htmlwidgets   8.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 29.5Mb
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    data   1.5Mb
    libs  27.1Mb
'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 275.7Mb
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    R       2.1Mb
    help    1.0Mb
    java  272.1Mb
'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
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    libs    1.5Mb
    shiny   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
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    HaDeX   4.0Mb
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installed size is  5.8Mb
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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’
Package required but not available: ‘handwriterRF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
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    libs   3.0Mb
Package suggested but not available for checking: ‘Rmpi’
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.4Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 173.0Mb
  sub-directories of 1Mb or more:
    libs  171.4Mb
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         3.0Mb
    extdata   1.3Mb
GNU make is a SystemRequirements.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
Specified C++11: please drop specification unless essential
installed size is  8.2Mb
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    libs   5.6Mb
installed size is  7.3Mb
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    libs   6.5Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    libs   5.7Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 11.0Mb
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    data   5.8Mb
    libs   4.9Mb
installed size is  7.6Mb
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    libs   6.9Mb
installed size is 36.7Mb
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    libs  35.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HDXBoxeR.Rmd’ using rmarkdown
Error: processing vignette 'HDXBoxeR.Rmd' failed with diagnostics:
Error writing to connection:  No space left on device
--- failed re-building ‘HDXBoxeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'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:
    libs   6.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.9Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  20.3Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.4Mb
'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: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
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    libs   7.4Mb
'LazyData' is specified without a 'data' directory
installed size is 11.1Mb
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Package suggested but not available for checking: ‘geojsonio’
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
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    data   2.3Mb
    libs   3.9Mb
Specified C++11: please drop specification unless essential
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.6Mb
Package suggested but not available for checking: ‘INLA’
installed size is 55.9Mb
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Package suggested but not available for checking: ‘colorfulVennPlot’
Specified C++11: please drop specification unless essential
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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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.9Mb
installed size is 84.0Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package which this enhances but not available for checking: ‘HadoopStreaming’
installed size is  5.1Mb
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    libs   5.0Mb
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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    data   3.5Mb
    libs   4.0Mb
installed size is 11.5Mb
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html_describe_con: multiple local function definitions for ‘g’ with
  different formal arguments
Specified C++11: please drop specification unless essential
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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: \&
installed size is 60.4Mb
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installed size is  6.2Mb
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    doc    4.0Mb
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Package suggested but not available for checking: ‘glmmADMB’
Package suggested but not available for checking: ‘microViz’
installed size is  5.3Mb
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    doc   3.3Mb
installed size is  9.9Mb
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    libs   9.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
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installed size is 15.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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installed size is  8.3Mb
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installed size is  7.9Mb
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Note: skipping ‘Ch_cluster_analysis.Rnw’ due to unavailable dependencies:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 69.9Mb
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘HTSFilter’
installed size is  6.8Mb
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    doc    2.3Mb
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Specified C++14: please drop specification unless essential
installed size is 10.3Mb
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checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
installed size is  9.1Mb
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GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘data_extraction_naiades.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘data_extraction_naiades.Rmd’

--- re-building ‘example_ecoulement_api.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 101-119 [unnamed-chunk-8] (example_ecoulement_api.Rmd)
Error: processing vignette 'example_ecoulement_api.Rmd' failed with diagnostics:
Chrome debugging port not open after 10 seconds.
--- failed re-building ‘example_ecoulement_api.Rmd’

--- re-building ‘example_niveaux_nappes_api.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 176-183 [unnamed-chunk-13] (example_niveaux_nappes_api.Rmd)
Error: processing vignette 'example_niveaux_nappes_api.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘example_niveaux_nappes_api.Rmd’

SUMMARY: processing the following files failed:
  ‘example_ecoulement_api.Rmd’ ‘example_niveaux_nappes_api.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  9.3Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.8Mb
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installed size is  8.0Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘microViz’
installed size is  8.0Mb
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installed size is  5.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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Package suggested but not available for checking: ‘flowCore’
installed size is 21.6Mb
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Error(s) in re-building vignettes:
--- re-building ‘hypergeometric.Rnw’ using Sweave
Loading required package: hypergeo
Loading required package: elliptic

Attaching package: ‘elliptic’

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

    sd, sigma

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

    is.primitive

Error: processing vignette 'hypergeometric.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'hypergeometric.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘hypergeometric.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
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installed size is  5.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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Specified C++11: please drop specification unless essential
installed size is  7.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SparkR’
installed size is  5.1Mb
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    libs   1.0Mb
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
installed size is  6.4Mb
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'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: ‘LTRCtrees’
Package unavailable to check Rd xrefs: ‘LTRCtrees’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘icd’
installed size is  5.8Mb
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checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: Escaped LaTeX specials: \$
installed size is 15.6Mb
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Package suggested but not available for checking: ‘mixAK’
installed size is  9.1Mb
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    libs   5.5Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 32.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rggobi’
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘IFCdata’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
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    libs   4.6Mb
'LazyData' is specified without a 'data' directory
installed size is 23.6Mb
  sub-directories of 1Mb or more:
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    doc    1.2Mb
    help   2.0Mb
    libs  18.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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 34.7Mb
  sub-directories of 1Mb or more:
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    doc       3.7Mb
    extdata   1.0Mb
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    libs     24.7Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
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    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Specified C++11: please drop specification unless essential
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.1Mb
'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
'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  5.3Mb
  sub-directories of 1Mb or more:
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installed size is 95.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  12.2Mb
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘minfi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘INLA’
installed size is  5.7Mb
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    data   5.3Mb
'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:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  29.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
Specified C++11: please drop specification unless essential
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Specified C++11: please drop specification unless essential
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘surveyspec’
installed size is  5.1Mb
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    libs           1.9Mb
    shiny-server   1.0Mb
Specified C++11: please drop specification unless essential
installed size is  6.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rhdf5’
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'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:
    libs  12.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.2Mb
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Package suggested but not available for checking: ‘Rmpi’
checkRd: (-1) constrained.Rd:49: 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
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: \&
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘xcms’
'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  6.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
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
installed size is 95.2Mb
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GNU make is a SystemRequirements.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
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    libs  16.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘iucnrdata’
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘locClass’
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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
installed size is 19.7Mb
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    libs          17.3Mb
GNU make is a SystemRequirements.
installed size is 31.5Mb
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Packages suggested but not available for checking: 'lfa', 'gcatest'
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
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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’, 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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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installed size is  8.6Mb
  sub-directories of 1Mb or more:
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    extdata   4.0Mb
    help      2.0Mb
installed size is 103.7Mb
  sub-directories of 1Mb or more:
    libs  102.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Specified C++11: please drop specification unless essential
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
'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:
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    libs   5.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
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    i18n   6.7Mb
'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:
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    libs   3.9Mb
Package suggested but not available for checking: ‘remMap’
'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:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 32.8Mb
  sub-directories of 1Mb or more:
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installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
'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
    libs   3.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.7Mb
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    htmlwidgets   1.1Mb
    www           2.7Mb
'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)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kanjistat.data’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.2Mb
  sub-directories of 1Mb or more:
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    help   8.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    help   2.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 11.6Mb
  sub-directories of 1Mb or more:
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'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
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘rkward’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RGeostats’
'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 required but not available: ‘pwalign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seqLogo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘kadmin’
'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  6.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
'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
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installed size is 13.2Mb
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installed size is  8.3Mb
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GNU make is a SystemRequirements.
installed size is  5.3Mb
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installed size is 10.4Mb
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    libs   6.1Mb
'LazyData' is specified without a 'data' directory
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installed size is  5.4Mb
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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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘mixAK’
Package unavailable to check Rd xrefs: ‘mixAK’
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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    doc   6.4Mb
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'xcms', 'MSnbase'
'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
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Package suggested but not available for checking: ‘VariantAnnotation’
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 25.9Mb
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    libs  24.6Mb
'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:
    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
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
installed size is 17.6Mb
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installed size is  5.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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installed size is 11.9Mb
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installed size is 95.4Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) hydro.Rd:17: Escaped LaTeX specials: \&
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checkRd: (-1) predict.lb.Rd:16: Escaped LaTeX specials: \$
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Package suggested but not available for checking: ‘org.Mm.eg.db’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 22-30 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'org.Mm.eg.db'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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Error(s) in re-building vignettes:
--- re-building ‘linevis.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 50-51 [unnamed-chunk-2] (linevis.Rmd)
Error: processing vignette 'linevis.Rmd' failed with diagnostics:
Chrome debugging port not open after 10 seconds.
--- failed re-building ‘linevis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
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checkRd: (-1) solveLP.Rd:119: Escaped LaTeX specials: \&
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checkRd: (-1) lstats.liu.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) MHDI.Rd:23: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘pbkrtest’
Package unavailable to check Rd xrefs: ‘pbkrtest’
installed size is 55.3Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) cauchypoly.Rd:39: Escaped LaTeX specials: \_ \_ \_
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checkRd: (-1) lmSubsets-package.Rd:48: Escaped LaTeX specials: \&
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Package unavailable to check Rd xrefs: ‘car’
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Author
    Maintainer
Specified C++11: please drop specification unless essential
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Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) TrafficFlow.Rd:25: Escaped LaTeX specials: \#
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Package suggested but not available for checking: ‘EnsDb.Hsapiens.v75’
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Specified C++11: please drop specification unless essential
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installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘QSutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) butstrap.Rd:44: Escaped LaTeX specials: \&
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checkRd: (-1) butstrap.s.Rd:44: Escaped LaTeX specials: \&
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Package suggested but not available for checking: ‘scio’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 64.3Mb
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Packages suggested but not available for checking:
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checkRd: (-1) specialchars.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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installed size is 45.9Mb
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    libs  43.7Mb
'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: package or namespace load failed for ‘LSTbook’:
 .onLoad failed in loadNamespace() for 'LSTbook', details:
  call: loadNamespace(name)
  error: there is no package called ‘mosaicData’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
checkRd: (-1) LS.kalman.Rd:65: Escaped LaTeX specials: \&
checkRd: (-1) spectral.density.Rd:55: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
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    data   2.1Mb
    libs   3.7Mb
installed size is  6.2Mb
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    R      2.0Mb
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installed size is  6.0Mb
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    R   5.0Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘depth’
'LazyData' is specified without a 'data' directory
installed size is 26.1Mb
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'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: ‘rnaturalearthhires’
installed size is  7.4Mb
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installed size is 32.8Mb
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    libs  32.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘maestro-1-quick-start.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
--- finished re-building ‘maestro-1-quick-start.Rmd’

--- re-building ‘maestro-5-directed-acyclic-graphs.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 186-191 [unnamed-chunk-9] (maestro-5-directed-acyclic-graphs.Rmd)
Error: processing vignette 'maestro-5-directed-acyclic-graphs.Rmd' failed with diagnostics:
attempt to apply non-function
--- failed re-building ‘maestro-5-directed-acyclic-graphs.Rmd’

--- re-building ‘maestro-2-motivation-concepts.qmd’ using html
Quarto binary is required to build Quarto vignettes but is not available.
ℹ Please make sure it is installed and found by `find_quarto()`.
--- finished re-building ‘maestro-2-motivation-concepts.qmd’

--- re-building ‘maestro-3-use-cases.qmd’ using html
Quarto binary is required to build Quarto vignettes but is not available.
ℹ Please make sure it is installed and found by `find_quarto()`.
--- finished re-building ‘maestro-3-use-cases.qmd’

--- re-building ‘maestro-4-advanced-scheduling.qmd’ using html
Quarto binary is required to build Quarto vignettes but is not available.
ℹ Please make sure it is installed and found by `find_quarto()`.
--- finished re-building ‘maestro-4-advanced-scheduling.qmd’

--- re-building ‘maestro-6-logging.qmd’ using html
Quarto binary is required to build Quarto vignettes but is not available.
ℹ Please make sure it is installed and found by `find_quarto()`.
--- finished re-building ‘maestro-6-logging.qmd’

SUMMARY: processing the following file failed:
  ‘maestro-5-directed-acyclic-graphs.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘quitte’
Package suggested but not available for checking: ‘SeqVarTools’
installed size is  6.9Mb
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installed size is 71.8Mb
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'LazyData' is specified without a 'data' directory
installed size is 25.1Mb
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Package suggested but not available for checking: ‘dittoSeq’
Packages suggested but not available for checking:
  'ssize', 'WGCNA', 'KEGGgraph', 'pdInfoBuilder', 'lumi', 'oligo',
  'affy', 'genefilter', 'beadarray', 'GOstats', 'Category', 'impute'
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BiocCheck’
installed size is 10.4Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
Running ‘testthat.R’ [4s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(makepipe)
  > 
  > test_check("makepipe")
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  i Targets are out of date. Updating...
  
  v Finished updating
  
  i Targets are out of date. Updating...
  
  v Finished updating
  
  v Targets are up to date
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 110 ]
  
  ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
  • On CRAN (4): 'test-Pipeline.R:189:3', 'test-Pipeline.R:282:3',
    'test-make.R:109:3', 'test-make.R:171:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-Pipeline.R:199:3'): pipeline can be saved as html ──────────────
  Error in `pandoc_self_contained_html(file, file)`: Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
  Backtrace:
      ▆
   1. └─makepipe::save_pipeline(temp_html, pipeline = pipe, as = "visnetwork") at test-Pipeline.R:199:3
   2.   └─pipeline$save_visnetwork(file, ...)
   3.     └─visNetwork::visSave(out, file, selfcontained, background)
   4.       └─htmlwidgets::saveWidget(...)
   5.         └─htmlwidgets:::pandoc_self_contained_html(file, file)
  
  [ FAIL 1 | WARN 0 | SKIP 4 | PASS 110 ]
  Deleting unused snapshots:
  • Pipeline/pipeline.png
  Error: Test failures
  Execution halted
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installed size is 10.2Mb
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘DescTools’
installed size is  5.3Mb
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    doc    3.5Mb
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installed size is  6.1Mb
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installed size is 33.5Mb
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installed size is 21.9Mb
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    htmlwidgets   3.5Mb
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Bug Fixes
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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installed size is 12.5Mb
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    R      2.8Mb
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    libs   4.7Mb
GNU make is a SystemRequirements.
installed size is  5.4Mb
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    doc    2.6Mb
    libs   2.0Mb
installed size is  5.8Mb
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GNU make is a SystemRequirements.
installed size is  7.6Mb
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    doc   6.4Mb
checkRd: (-1) mma.Rd:67: Escaped LaTeX specials: \&
Packages suggested but not available for checking: 'csampling', 'nlreg'
checkRd: (-1) residuals.rsm.Rd:74: Escaped LaTeX specials: \&
checkRd: (-1) marima.Rd:223: Escaped LaTeX specials: \&
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installed size is 14.5Mb
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    libs      10.5Mb
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installed size is 10.2Mb
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    libs   8.6Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.6Mb
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Package suggested but not available for checking: ‘marssTMB’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.NCBI.GRCh38', 'org.Mm.eg.db', 'wiggleplotr'
installed size is  8.7Mb
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installed size is  9.0Mb
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installed size is 50.2Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is 13.3Mb
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    java   3.3Mb
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Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘gurobi’
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Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
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installed size is 11.0Mb
  sub-directories of 1Mb or more:
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    libs   8.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBSP’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
qr.X: no visible binding for global variable ‘R’
Undefined global functions or variables:
  R
'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  6.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.3Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
* checking re-building of vignette outputs ...* using check arguments '--no-clean-on-error '
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: \#
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
'LazyData' is specified without a 'data' directory
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  18.7Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'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
checkRd: (-1) pBED.Rd:34: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Package suggested but not available for checking: ‘RGtk2’
'LazyData' is specified without a 'data' directory
'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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Package suggested but not available for checking: ‘cmdstanr’
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    libs  63.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
'LazyData' is specified without a 'data' directory
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
  %dorng%
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 157.0Mb
  sub-directories of 1Mb or more:
    libs  155.5Mb
'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: \#
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'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 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.5Mb
Package suggested but not available for checking: ‘INLA’
'LazyData' is specified without a 'data' directory
installed size is 109.1Mb
  sub-directories of 1Mb or more:
    libs  108.3Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'ropls', 'xcms'
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    help   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data       3.0Mb
    examples  10.3Mb
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
Package suggested but not available for checking: ‘caret’
installed size is  5.2Mb
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    R   4.9Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘InteractiveComplexHeatmap’
installed size is 56.8Mb
  sub-directories of 1Mb or more:
    libs  56.3Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
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    libs  22.2Mb
'LazyData' is specified without a 'data' directory
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.1Mb
    libs   6.8Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
installed size is 19.9Mb
  sub-directories of 1Mb or more:
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    libs  17.3Mb
'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: ‘structSSI’
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'DAPAR', 'ProteoMM'
installed size is  7.4Mb
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    libs   5.8Mb
Specified C++11: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘dada2’
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
Running examples in ‘MicroSEC-Ex.R’ failed
The error most likely occurred in:

> ### Name: fun_load_genome
> ### Title: Genome loading function.
> ### Aliases: fun_load_genome
> 
> ### ** Examples
> 
> fun_load_genome("Human")
Error: Install BSgenome.Hsapiens.UCSC.hg38 package.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 125-195 [analysis] (my-vignette.Rmd)
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg38'
--- failed re-building ‘my-vignette.Rmd’

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

Execution halted
installed size is 20.5Mb
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    libs   4.6Mb
installed size is  5.5Mb
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    doc    1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘midfielddata’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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    libs   6.1Mb
Package suggested but not available for checking: ‘gurobi’
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Package required but not available: ‘InteractiveComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.7Mb
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 44.3Mb
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    libs        1.4Mb
    redengine  42.7Mb
'LazyData' is specified without a 'data' directory
installed size is 112.9Mb
  sub-directories of 1Mb or more:
    libs  112.2Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Packages unavailable to check Rd xrefs: ‘lme4’, ‘mixAK’
Package required but not available: ‘dada2’

Packages suggested but not available for checking: 'ANCOMBC', 'mia'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.2Mb
    libs      1.6Mb
installed size is  6.8Mb
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Package suggested but not available for checking: ‘glmmTMB’
Packages suggested but not available for checking:
  'clustree', 'karyoploteR', 'regioneR'
installed size is 25.2Mb
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    libs  22.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) SLD.Rd:20: Escaped LaTeX specials: \&
Package which this enhances but not available for checking: ‘pbdMPI’
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
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
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: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘mixRasch’
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘genefilter’
installed size is  5.2Mb
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    R      2.8Mb
    help   2.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) Texture.Rd:35: Escaped LaTeX specials: \&
checkRd: (-1) binom.diagnostics.Rd:33: 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
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Packages suggested but not available for checking:
  'ueadata1', 'ueadata2', 'ueadata3', 'ueadata4', 'ueadata5',
  'ueadata6', 'ueadata7', 'ueadata8'
installed size is 244.5Mb
  sub-directories of 1Mb or more:
    include   10.0Mb
    libs     234.0Mb
Package suggested but not available for checking: ‘mlr3proba’
Package suggested but not available for checking: ‘mlr3proba’
Package unavailable to check Rd xrefs: ‘mlr3proba’
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.6Mb
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    data   2.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 141.3Mb
  sub-directories of 1Mb or more:
    doc     1.2Mb
    libs  139.3Mb
GNU make is a SystemRequirements.
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.4Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  14.8Mb
'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 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
'LazyData' is specified without a 'data' directory
installed size is 121.9Mb
  sub-directories of 1Mb or more:
    libs  120.1Mb
'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 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
'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:
    libs  10.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'doMPI', 'alstructure'

Packages which this enhances but not available for checking:
  'miraculix', 'RandomFieldsUtils', 'MoBPSmaps'
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'ArchR', 'motifmatchr', 'TxDb.Hsapiens.UCSC.hg38.refGene',
  'BSgenome.Hsapiens.UCSC.hg19', 'chromVAR'
'LazyData' is specified without a 'data' directory
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
'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: ‘survey’
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    libs   4.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) CHECKSUCCESS.Rd:44: Escaped LaTeX specials: \&
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
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    R      2.0Mb
    doc    1.7Mb
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installed size is  7.3Mb
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installed size is 14.8Mb
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    htmlwidgets  14.7Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fftw', 'RODBC'
Packages unavailable to check Rd xrefs: ‘seewave’, ‘RODBC’
Package suggested but not available for checking: ‘lixoftConnectors’
installed size is  5.9Mb
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    theo   1.1Mb
GNU make is a SystemRequirements.
installed size is 11.0Mb
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    data   2.0Mb
    libs   7.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    raster   2.2Mb
Package suggested but not available for checking: ‘ergm’
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
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    libs   2.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
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Error: there is no package called ‘knitr’
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7: asNamespace(ns)
6: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
5: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPat
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘knitr’
Calls: <Anonymous>
Execution halted
Error: package or namespace load failed for ‘movieROC’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘knitr’
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, cha
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.4Mb
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--- re-building ‘NBLAST-Clustering.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 21:31:32.757 R[43986:2287591920] XType: Using static font registry.

Quitting from lines 57-60 [unnamed-chunk-5] (NBLAST-Clustering.Rmd)
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. See here to learn more https://bookdown.org/yihui/rmarkdown-cookbook/install-pandoc.html
--- failed re-building ‘NBLAST-Clustering.Rmd’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
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GNU make is a SystemRequirements.
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Error(s) in re-building vignettes:
--- re-building ‘partitionspaper.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'partitionspaper.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘partitionspaper.Rnw’

--- re-building ‘scrabble.Rnw’ using Sweave
Error: processing vignette 'scrabble.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'scrabble.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘scrabble.Rnw’

--- re-building ‘setpartitions.Rnw’ using Sweave
Loading required package: partitions
Error: processing vignette 'setpartitions.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'setpartitions.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘setpartitions.Rnw’

SUMMARY: processing the following files failed:
  ‘partitionspaper.Rnw’ ‘scrabble.Rnw’ ‘setpartitions.Rnw’

Error: Vignette re-building failed.
Execution halted
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Package required but not available: ‘ggkegg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘anomalize’
installed size is  5.6Mb
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Running examples in ‘patterncausality-Ex.R’ failed
The error most likely occurred in:

> ### Name: stateSpace
> ### Title: State Space Reconstruction
> ### Aliases: stateSpace
> 
> ### ** Examples
> 
> ts <- c(1:100)
> result <- stateSpace(ts, E = 3, tau = 2)
> plot(result)
tcltk DLL is linked to '/opt/R/x86_64/lib/libtk8.6.dylib'
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
  call: fun(libname, pkgname)
  error: Tcl/Tk libraries are missing: install the Tcl/Tk component from the R installer
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is 11.1Mb
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installed size is  7.6Mb
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/pbdMPI.Rcheck/00install.out’ for details.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘PerformanceAnalytics’
installed size is  6.8Mb
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installed size is  5.4Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  6.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 28.2Mb
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GNU make is a SystemRequirements.
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installed size is 140.0Mb
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GNU make is a SystemRequirements.
installed size is  5.0Mb
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installed size is 33.3Mb
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installed size is 32.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 21.4Mb
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installed size is  7.3Mb
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Packages suggested but not available for checking:
  'car', 'fields', 'georob', 'gstat'
Packages unavailable to check Rd xrefs: ‘fields’, ‘gstat’, ‘car’
installed size is 126.0Mb
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
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GNU make is a SystemRequirements.
installed size is  8.1Mb
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GNU make is a SystemRequirements.
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installed size is 63.8Mb
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Packages suggested but not available for checking: 'INLA', 'DHARMa', 'rr2'
installed size is 12.4Mb
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
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installed size is  7.4Mb
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  'gurobi', 'Rcplex', 'rcbc'
installed size is 10.7Mb
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Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 20.4Mb
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Package suggested but not available for checking: ‘glmSparseNet’
Error(s) in re-building vignettes:
--- re-building ‘priorityelasticnet-vignettes.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.

Quitting from lines 427-450 [unnamed-chunk-23] (priorityelasticnet-vignettes.Rmd)
Error: processing vignette 'priorityelasticnet-vignettes.Rmd' failed with diagnostics:
there is no package called 'glmSparseNet'
--- failed re-building ‘priorityelasticnet-vignettes.Rmd’

SUMMARY: processing the following file failed:
  ‘priorityelasticnet-vignettes.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'cmdstanr', 'iwmm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 235.9Mb
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GNU make is a SystemRequirements.
installed size is 20.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.5Mb
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    htmlwidgets   2.5Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
installed size is 15.3Mb
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'LazyData' is specified without a 'data' directory
installed size is 18.2Mb
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Package suggested but not available for checking: ‘cmdstanr’
installed size is  5.0Mb
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installed size is 18.4Mb
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installed size is 123.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.4Mb
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GNU make is a SystemRequirements.
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Package required but not available: ‘UniProt.ws’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  6.7Mb
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installed size is 40.1Mb
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installed size is 139.0Mb
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GNU make is a SystemRequirements.
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installed size is  5.3Mb
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installed size is  7.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 11.5Mb
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'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 27.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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installed size is 47.6Mb
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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
installed size is 33.2Mb
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'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 ‘PvSTATEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: generate_plate_report
> ### Title: Generate a report for a plate.
> ### Aliases: generate_plate_report
> 
> ### ** Examples
> 
> 
> plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "PvSTATEM")
> # a plate file with reduced number of analytes to speed up the computation
> layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
> note <- "This is a test report.\n**Author**: Jane Doe \n**Tester**: John Doe"
> 
> plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)
> example_dir <- tempdir(check = TRUE) # a temporary directory
> generate_plate_report(plate,
+   output_dir = example_dir,
+   counts_lower_threshold = 40,
+   counts_higher_threshold = 50,
+   additional_notes = note
+ )
Generating report...This will take approximately 30 seconds.
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is 15.5Mb
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checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
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installed size is  5.9Mb
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'LazyData' is specified without a 'data' directory
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installed size is  5.4Mb
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installed size is 114.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
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Package suggested but not available for checking: ‘spDataLarge’
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  7.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
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installed size is 15.7Mb
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Specified C++11: please drop specification unless essential
installed size is  7.9Mb
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Packages suggested but not available for checking: 'glmmTMB', 'DHARMa'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 11.0Mb
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installed size is  9.6Mb
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GNU make is a SystemRequirements.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
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Malformed Description field: should contain one or more complete sentences.
installed size is  9.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is 15.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 44.3Mb
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installed size is  6.5Mb
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installed size is 11.8Mb
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Packages suggested but not available for checking:
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'LazyData' is specified without a 'data' directory
installed size is 16.0Mb
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installed size is  8.0Mb
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installed size is 10.9Mb
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installed size is  9.2Mb
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Package suggested but not available for checking: ‘survey’
Package unavailable to check Rd xrefs: ‘survey’
installed size is  9.6Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is 15.5Mb
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Package suggested but not available for checking: ‘ReGenesees’
Warning: package needs dependence on R (>= 2.10)
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
'library' or 'require' call to ‘RDCOMClient’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  7.9Mb
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'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is 11.5Mb
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installed size is 25.4Mb
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installed size is  5.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is  5.4Mb
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installed size is  5.2Mb
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installed size is 46.0Mb
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installed size is  5.8Mb
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installed size is 35.7Mb
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installed size is 11.9Mb
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installed size is  6.0Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building ‘RankAggreg.Rnw’ using Sweave
Loading required package: cluster
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: ‘kohonen’

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

    map

Error: processing vignette 'RankAggreg.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.28 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘RankAggreg.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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installed size is  6.5Mb
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'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘gurobi’
installed size is 16.5Mb
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    extdata   4.1Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.5Mb
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
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installed size is 68.5Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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installed size is 21.7Mb
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installed size is 10.6Mb
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checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
installed size is 16.2Mb
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Package suggested but not available for checking: ‘raybevel’
installed size is  7.2Mb
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installed size is 13.4Mb
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installed size is  5.4Mb
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GNU make is a SystemRequirements.
installed size is 67.3Mb
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GNU make is a SystemRequirements.
installed size is 60.1Mb
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GNU make is a SystemRequirements.
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rblpapi.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rbm25.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
installed size is 64.3Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
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Package suggested but not available for checking: ‘rqubic’

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: \&
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Package suggested but not available for checking: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
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    po    2.4Mb
Package suggested but not available for checking: ‘conics’
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installed size is  7.6Mb
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Packages suggested but not available for checking:
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rcplex.Rcheck/00install.out’ for details.
installed size is 21.0Mb
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installed size is  6.5Mb
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installed size is  9.6Mb
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Specified C++11: please drop specification unless essential
installed size is  8.6Mb
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    libs   8.4Mb
installed size is 40.3Mb
  sub-directories of 1Mb or more:
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    libs      2.3Mb
Specified C++11: please drop specification unless essential
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 46.6Mb
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    include  46.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
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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
installed size is 34.7Mb
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    libs     24.7Mb
Specified C++11: please drop specification unless essential
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
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  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RcppMeCab.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Specified C++11: please drop specification unless essential
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      5.0Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs          12.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      5.9Mb
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
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
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  16.3Mb
'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  7.2Mb
  sub-directories of 1Mb or more:
    R      4.6Mb
    data   1.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.7Mb
    libs   1.1Mb
'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  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   3.0Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs        1.5Mb
    redengine  29.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘Rmpi’
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs  14.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
'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
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.8Mb
'LazyData' is specified without a 'data' directory
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'cdparcoord', 'partools'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggpubr’
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   5.2Mb
'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
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'PADOG', 'GSVA'
Packages unavailable to check Rd xrefs: ‘GSVA’, ‘PADOG’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.1Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    1.2Mb
    libs  13.7Mb
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: \_ \_
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Package suggested but not available for checking: ‘resourcecodedata’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs      3.4Mb
    swagger   1.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     24.4Mb
    models    1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Package suggested but not available for checking: ‘ccdata’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg38’

See section ‘The DESCRIPTION file’ 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
Unknown package ‘btergm’ in Rd xrefs
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running ‘testthat.R’ [64s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─testthat::expect_error(...) at test-forestry.R:48:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─Rforestry::forestry(x = iris[, -1], y = iris[, 1], seed = seed_i)
    7.   └─base::tryCatch(...)
    8.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
    9.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   10.         └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1422 ]
  Error: Test failures
  Execution halted
'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:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs   25.6Mb
'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 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'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:
  'mimic.demo', 'eicu.demo'
Running examples in ‘ridge-Ex.R’ failed
The error most likely occurred in:

> ### Name: pvals
> ### Title: Compute p-values for ridgeLinear and ridgeLogistic models
> ### Aliases: pvals pvals.ridgeLinear pvals.ridgeLogistic
> ###   plot.pvalsRidgeLinear plot.pvalsRidgeLogistic print.pvalsRidgeLinear
> ###   print.pvalsRidgeLogistic
> 
> ### ** Examples
> 
> data(GenBin)
> mod <- logisticRidge(Phenotypes ~ ., data = as.data.frame(GenBin))

Execution halted
Specified C++11: please drop specification unless essential
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  16.0Mb
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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'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
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
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
'LazyData' is specified without a 'data' directory
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘portfolioBacktest’
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.7Mb
'LazyData' is specified without a 'data' directory
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 ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)

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.

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
'LazyData' is specified without a 'data' directory
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs     51.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  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 28.3Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  23.8Mb
'LazyData' is specified without a 'data' directory
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
installed size is 44.9Mb
  sub-directories of 1Mb or more:
    libs  44.3Mb
'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: \$
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    lemon   2.8Mb
    libs   17.0Mb
'LazyData' is specified without a 'data' directory
installed size is 165.9Mb
  sub-directories of 1Mb or more:
    libs  164.9Mb
GNU make is a SystemRequirements.
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   7.3Mb
    lib      37.8Mb
    libs     26.4Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'EnhancedVolcano', 'RcppPlanc', 'reactome.db'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   6.2Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
'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
Package suggested but not available for checking: ‘rnaturalearthhires’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.0Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RMark.Rcheck/00install.out’ for details.
Warning: Software mark not found in path.
         If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
installed size is 135.1Mb
  sub-directories of 1Mb or more:
    libs  134.7Mb
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/RmecabKo.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   6.0Mb
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  6.9Mb
  sub-directories of 1Mb or more:
    R          1.0Mb
    libs       1.1Mb
    minizinc   3.3Mb
Specified C++11: please drop specification unless essential
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.4Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rmpi.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
installed size is 85.0Mb
  sub-directories of 1Mb or more:
    libs  84.4Mb
Package unavailable to check Rd xrefs: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
GNU make is a SystemRequirements.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.4Mb
Package required but not available: ‘R4RNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package suggested but not available for checking: ‘recount3’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.3Mb
Package suggested but not available for checking: ‘rnaturalearthhires’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
Packages which this enhances but not available for checking:
  'pbdMPI', 'Rmpi'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages unavailable to check Rd xrefs: ‘pbdMPI’, ‘Rmpi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 120.9Mb
  sub-directories of 1Mb or more:
    extdata    2.0Mb
    libs     118.7Mb
'LazyData' is specified without a 'data' directory
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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installed size is 12.2Mb
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installed size is 18.4Mb
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installed size is  8.7Mb
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installed size is 19.9Mb
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Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
installed size is  5.4Mb
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installed size is  7.1Mb
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Error(s) in re-building vignettes:
--- re-building ‘RobPer_vignette.Rnw’ using Sweave
Loading required package: robustbase
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: splines
Loading required package: BB
Loading required package: rgenoud
##  rgenoud (Version 5.9-0.3, Build Date: 2022-04-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

Error: processing vignette 'RobPer_vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'RobPer_vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 97.5Mb
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    libs  96.7Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘ivgets’
Package unavailable to check Rd xrefs: ‘ivgets’
installed size is 22.9Mb
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    libs  22.3Mb
Specified C++11: please drop specification unless essential
installed size is 27.1Mb
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installed size is  7.0Mb
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    data   1.5Mb
    libs   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  9.2Mb
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    doc               1.7Mb
    libs              5.1Mb
    simulationStudy   1.5Mb
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'car', 'HH'
Package unavailable to check Rd xrefs: ‘HH’
'LazyData' is specified without a 'data' directory
'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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.5Mb
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    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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GNU make is a SystemRequirements.
installed size is  6.5Mb
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    R         3.7Mb
    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
sh: cmake: command not found
------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - installr::install.cmake()  (Windows; inside the R console)
 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal)
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not 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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/ROracle.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘MBESS’
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
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    R      2.0Mb
    data   2.7Mb
    libs   5.3Mb
'LazyData' is specified without a 'data' directory
installed size is 14.6Mb
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    R      5.0Mb
    libs   8.3Mb
Package suggested but not available for checking: ‘RandomFields’
installed size is 61.1Mb
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GNU make is a SystemRequirements.
installed size is  6.8Mb
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    libs   6.4Mb
installed size is 21.1Mb
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    libs  20.2Mb
installed size is  5.7Mb
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    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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    libs   4.8Mb
installed size is  9.9Mb
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    data   2.3Mb
    libs   5.9Mb
'LazyData' is specified without a 'data' directory
installed size is 53.1Mb
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    libs  53.0Mb
installed size is  8.4Mb
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    libs   7.9Mb
installed size is  5.4Mb
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    extdata   4.5Mb
'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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
'LazyData' is specified without a 'data' directory
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 102.8Mb
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    libs  102.2Mb
installed size is  5.6Mb
  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
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
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    doc   3.3Mb
Errors in running code in vignettes:
when running code in ‘Using.RRPP.Rmd’
  ...
> fit.par <- lm(fit$call$f1, data = fit$LM$data)

> all.equal(fit$LM$coefficients, fit.par$coefficients)
[1] TRUE

> summary(manova(fit.par))

  When sourcing ‘Using.RRPP.R’:
Error: residuals have rank 49 < 112
Execution halted

  ‘ANOVA.vs.MANOVA.Rmd’ using ‘UTF-8’... [28s/42s] OK
  ‘Using.RRPP.Rmd’ using ‘UTF-8’... failed
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'fields', 'qgraph'
installed size is  5.5Mb
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    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘getInputHandler’, ‘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
installed size is 25.2Mb
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installed size is 27.4Mb
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    R      2.0Mb
    libs  24.9Mb
'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: ‘gurobi’
installed size is  7.3Mb
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    libs   6.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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    libs   9.0Mb
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Package suggested but not available for checking: ‘INLA’
installed size is  5.9Mb
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    R      4.2Mb
    help   1.5Mb
Specified C++11: please drop specification unless essential
installed size is 47.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 12.3Mb
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    libs  11.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 299.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    doc     4.7Mb
    libs  291.8Mb
GNU make is a SystemRequirements.
installed size is 96.4Mb
  sub-directories of 1Mb or more:
    libs  96.1Mb
GNU make is a SystemRequirements.
installed size is 58.5Mb
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    libs  57.9Mb
GNU make is a SystemRequirements.
installed size is 49.8Mb
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    lib   34.7Mb
    libs  11.5Mb
GNU make is a SystemRequirements.
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Package suggested but not available for checking: ‘ggpubr’
installed size is  6.0Mb
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    libs       3.9Mb
installed size is 38.0Mb
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installed size is 28.0Mb
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installed size is 27.9Mb
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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
installed size is  5.3Mb
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installed size is 11.4Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘Gviz’
installed size is 18.0Mb
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    libs  17.9Mb
installed size is  5.7Mb
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    projects   2.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.3Mb
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installed size is 123.1Mb
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installed size is  8.5Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    R   5.1Mb
Specified C++11: please drop specification unless essential
installed size is 28.6Mb
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GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
installed size is 224.1Mb
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GNU make is a SystemRequirements.
Running examples in ‘RtsEva-Ex.R’ failed
The error most likely occurred in:

> ### Name: tsEstimateAverageSeasonality
> ### Title: Estimate Average Seasonality
> ### Aliases: tsEstimateAverageSeasonality
> 
> ### ** Examples
> 
> timeAndSeries <- ArdecheStMartin
> timeStamps <- ArdecheStMartin[,1]
> series  <- ArdecheStMartin[,2]
> timeWindow <- 30*365  # 30 years
> rs <- tsEvaDetrendTimeSeries(timeStamps, series, timeWindow)
> nRunMn <- rs@nRunMn
> cat("computing trend seasonality ...\n")
computing trend seasonality ...
> seasonalitySeries <- rs@detrendSeries
> result <- tsEstimateAverageSeasonality(timeStamps, seasonalitySeries, timeWindow=rs@nRunMn)
Warning in pracma::interp1(avgTmStamp, monthAvgVec, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
Warning in pracma::interp1(avgTmStamp, monthAvgVex, timeStampsN, method = "spline") :
  Points in argument in 'x' unsorted; will be sorted.
> plot(result$regime, type = "l", xlab = "Day", ylab = "Regime", main = "Estimated Regime")
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is  6.2Mb
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    libs      4.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  7.7Mb
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    R      3.0Mb
    libs   2.5Mb
installed size is 11.7Mb
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    data   4.6Mb
    libs   6.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Non-standard license specification:
  CECILL-2.1
Standardizable: FALSE
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘glmmADMB’
Package required but not available: ‘GSVAdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 48.6Mb
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Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
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installed size is 59.2Mb
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    libs     53.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
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Package suggested but not available for checking: ‘rWCVPdata’
installed size is  5.9Mb
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installed size is 10.8Mb
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Package suggested but not available for checking: ‘partykit’
Package unavailable to check Rd xrefs: ‘partykit’
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'LazyData' is specified without a 'data' directory
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installed size is  6.4Mb
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    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
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    data   5.0Mb
Malformed Title field: should not end in a period.
installed size is  5.5Mb
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    data   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is 15.2Mb
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installed size is 11.3Mb
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    R         2.0Mb
    include   1.1Mb
    libs      6.4Mb
installed size is  9.0Mb
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    libs   8.6Mb
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
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    yacas   1.3Mb
Specified C++14: please drop specification unless essential
installed size is 10.3Mb
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    yacas   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.8Mb
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installed size is 12.3Mb
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Specified C++14: please drop specification unless essential
installed size is 38.0Mb
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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
installed size is  7.7Mb
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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  8.7Mb
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'LazyData' is specified without a 'data' directory
installed size is 16.6Mb
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    libs  15.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘lme4’
Note: skipping ‘my-vignette.Rnw’ due to unavailable dependencies: 'lme4'
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Specified C++11: please drop specification unless essential
installed size is 20.5Mb
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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: \$
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checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
installed size is 54.3Mb
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Specified C++11: please drop specification unless essential
installed size is 10.0Mb
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    help   3.4Mb
    libs   3.8Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'car', 'ergm', 'networkTomography',
  'org.Sc.sgd.db'
'LazyData' is specified without a 'data' directory
installed size is 47.7Mb
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    libs  47.6Mb
'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:
    libs   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
'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.
installed size is  5.3Mb
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    bin   4.5Mb
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
'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:
    Updated help pages with examples
    Updated conjugate model sampler
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    libs   3.6Mb
'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
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    doc    2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Packages suggested but not available for checking:
  'dittoSeq', 'DropletUtils', 'Nebulosa'
Packages unavailable to check Rd xrefs: ‘DropletUtils’, ‘Nebulosa’
Package required but not available: ‘glmGamPoi’

Package suggested but not available for checking: ‘Linnorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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    libs   2.9Mb
Packages suggested but not available for checking:
  'ontoProc', 'rrvgo', 'SingleCellSignalR'
'LazyData' is specified without a 'data' directory
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Package required and available but unsuitable version: ‘UCell’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package required but not available: ‘batchelor’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘simplifyEnrichment’
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 32.1Mb
  sub-directories of 1Mb or more:
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    include   4.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Package unavailable to check Rd xrefs: ‘infercnv’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘glmGamPoi’
installed size is 21.2Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘oligoClasses’
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
'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
Package which this enhances but not available for checking: ‘glmGamPoi’
Error(s) in re-building vignettes:
--- re-building ‘intro.Rnw’ using Sweave
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’
scuba 1.11-1 
Type ‘help(scuba)’ for an introduction 
Read the warnings in ‘help(scuba.disclaimer)’ 
For news about changes to the package, type ‘news(package='scuba')’

Attaching package: ‘scuba’

The following objects are masked _by_ ‘.GlobalEnv’:

    pedro902, pedro903, pedro904, pedro922, pedro943, pedro944,
    pedro945, pedro946, pedro948, pedro949, pedro950

Error: processing vignette 'intro.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \marginsize
               {2cm}{2cm}{2cm}{2cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdcSpatial.Rmd’ using rmarkdown
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
Quitting from lines 190-192 (sdcSpatial.Rmd) 
Error: processing vignette 'sdcSpatial.Rmd' failed with diagnostics:
different crs
--- failed re-building ‘sdcSpatial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R          3.0Mb
    external   1.2Mb
installed size is 89.3Mb
  sub-directories of 1Mb or more:
    libs  87.4Mb
Error(s) in re-building vignettes:
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/Builds/packages/big-sur-x86_64/results/4.3/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sealasso.Rnw’ using Sweave
Loading required package: lars
Loaded lars 1.3

Error: processing vignette 'sealasso.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'sealasso.tex' failed.
LaTeX errors:
! LaTeX Error: File `anysize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \marginsize
               {2.5cm}{2.5cm}{2.5cm}{2.5cm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘sealasso.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R   8.6Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs  15.4Mb
GNU make is a SystemRequirements.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
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    libs   8.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
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    libs   7.8Mb
Packages required but not available: 'ggmsa', 'msa'

Package suggested but not available for checking: ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rsbml’
Packages suggested but not available for checking:
  'ArrayExpress', 'org.Mm.eg.db'
Package unavailable to check Rd xrefs: ‘ArrayExpress’
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
'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
Package suggested but not available for checking: ‘Rmpfr’
Package suggested but not available for checking: ‘Ecdat’
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Problems with news in ‘NEWS.md’:
No news entries found.
Packages suggested but not available for checking: 'blavaan', 'emmeans'
Package unavailable to check Rd xrefs: ‘blavaan’
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
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Specified C++11: please drop specification unless essential
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs    21.1Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   4.5Mb
Specified C++14: please drop specification unless essential
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Package suggested but not available for checking: ‘airway’
Packages suggested but not available for checking:
  'FactoMineR', 'descriptio'
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs  10.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
GNU make is a SystemRequirements.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pwalign’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  54.5Mb
GNU make is a SystemRequirements.
installed size is 16.0Mb
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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
Packages suggested but not available for checking: 'HDF5Array', 'BPCells'
Packages suggested but not available for checking:
  'BPCells', 'glmGamPoi', 'monocle', 'presto'
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   8.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   5.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggraph’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 272.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
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    sqlite    1.5Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package unavailable to check Rd xrefs: ‘tripack’
'LazyData' is specified without a 'data' directory
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
'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’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
'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 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
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    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
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'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.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
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    www  10.3Mb
'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
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
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: ‘edgeR’
Note: skipping ‘SIBER.Rnw’ due to unavailable dependencies: 'edgeR'
'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: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  5.9Mb
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Packages suggested but not available for checking:
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installed size is  5.1Mb
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Packages unavailable to check Rd xrefs: ‘motifmatchr’, ‘TFBSTools’, ‘chromVAR’
Package suggested but not available for checking: ‘rhdf5’
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'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 required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
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installed size is 18.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  8.2Mb
  sub-directories of 1Mb or more:
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    doc    1.0Mb
    libs   3.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
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    libs  12.4Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
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
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Packages suggested but not available for checking:
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Package unavailable to check Rd xrefs: ‘copula’
installed size is  5.1Mb
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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
installed size is 22.7Mb
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installed size is  5.4Mb
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    libs   2.7Mb
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   6.8Mb
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'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
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R         2.1Mb
    extdata   1.2Mb
    libs      6.4Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
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Package which this enhances but not available for checking: ‘kmndirs’
installed size is  7.1Mb
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GNU make is a SystemRequirements.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
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Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 33.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.9Mb
  sub-directories of 1Mb or more:
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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  9.1Mb
  sub-directories of 1Mb or more:
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checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
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: \$ \$
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checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
installed size is  7.2Mb
  sub-directories of 1Mb or more:
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Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.2Mb
'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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
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installed size is 16.7Mb
  sub-directories of 1Mb or more:
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'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’
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
Package which this enhances but not available for checking: ‘Rmpi’
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
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    extdata   3.1Mb
    libs      2.8Mb
Package required but not available: ‘GWASTools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/soilassessment.Rcheck/00install.out’ for details.
installed size is  5.9Mb
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    R     4.0Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'raster', 'rasterVis', 'meteoForecast'
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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    data      3.8Mb
    extdata   1.1Mb
installed size is 14.2Mb
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installed size is  7.7Mb
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    libs   7.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘SciencesPo’
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Package suggested but not available for checking: ‘DropletUtils’
installed size is  6.7Mb
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Package suggested but not available for checking: ‘gridlayout’
installed size is  5.4Mb
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installed size is 16.8Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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installed size is  8.2Mb
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installed size is  5.6Mb
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installed size is  5.1Mb
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    data   2.4Mb
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installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
installed size is  6.8Mb
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    R   5.0Mb
Package suggested but not available for checking: ‘NLMR’
'LazyData' is specified without a 'data' directory
installed size is 39.9Mb
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    R      3.1Mb
    libs  35.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    java   1.8Mb
'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:
    libs   4.2Mb
'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
installed size is 15.1Mb
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'LazyData' is specified without a 'data' directory
S3 methods shown with full name in documentation object 'SparseM.ontology':
  ‘as.matrix.csr’ ‘is.matrix.csr’ ‘is.matrix.csc’ ‘is.matrix.ssr’
  ‘is.matrix.ssc’ ‘is.matrix.coo’

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.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 35.1Mb
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    libs  34.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/spaths.Rcheck/00install.out’ for details.
Package required but not available: ‘SpatialExperiment’

Package suggested but not available for checking: ‘HDF5Array’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘INLA’
installed size is 95.0Mb
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Specified C++11: please drop specification unless essential
installed size is  5.8Mb
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installed size is  5.5Mb
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    data   2.6Mb
    help   1.7Mb
    libs   1.2Mb
Specified C++14: please drop specification unless essential
installed size is 14.1Mb
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    doc    1.2Mb
    libs  12.5Mb
GNU make is a SystemRequirements.
installed size is  6.1Mb
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    libs   4.2Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
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    R      2.0Mb
    help   2.2Mb
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', '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.univar',
  '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.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
installed size is  5.2Mb
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    doc   4.5Mb
installed size is 23.1Mb
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    libs  22.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   9.5Mb
installed size is  6.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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    libs   8.0Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.6Mb
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    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
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    data   4.3Mb
    help   1.5Mb
installed size is  9.7Mb
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    doc   6.0Mb
    etc   2.1Mb
Package suggested but not available for checking: ‘scRNAseq’
Running examples in ‘speaq-Ex.R’ failed
The error most likely occurred in:

> ### 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
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:34.091 R[19637:2290508776] XType: Using static font registry.

Quitting from lines 111-120 [Spectral_alignment] (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
Pandoc is required to build R Markdown vignettes but not available. Please make sure it is installed.
2023-07-10 23:48:40.223 R[20964:2290511430] XType: Using static font registry.

Quitting from lines 71-83 [detect winepeaks] (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
installed size is  5.5Mb
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    data   4.8Mb
installed size is  6.0Mb
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    doc   4.6Mb
Undocumented S4 methods:
  generic '[' and siglist 'SpectraInTime,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTime,missing,ANY,ANY'
  generic '[' and siglist 'SpectraInTime,missing,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,ANY,ANY'
  generic '[' and siglist 'SpectraInTimeComp,ANY,missing,ANY'
  generic '[' and siglist 'SpectraInTimeComp,missing,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.8Mb
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'LazyData' is specified without a 'data' directory
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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Specified C++11: please drop specification unless essential
installed size is 22.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
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installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
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    doc    1.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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    libs   5.1Mb
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
installed size is  5.9Mb
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    R      2.0Mb
    data   1.8Mb
    doc    1.5Mb
installed size is 17.3Mb
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    doc       1.1Mb
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    libs     12.1Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
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    R      2.0Mb
    libs   3.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggraph’
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
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.1Mb
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installed size is 50.2Mb
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    doc    1.5Mb
    libs  48.3Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Running examples in ‘spsurv-Ex.R’ failed
The error most likely occurred in:

> ### Name: bppo
> ### Title: Bernstein Polynomial Based Proportional Odds Model
> ### Aliases: bppo
> 
> ### ** Examples
> 
> 
> library("spsurv")
> data("veteran")
Warning in data("veteran") : data set ‘veteran’ not found
> 
> fit <- bppo(Surv(time, status) ~ karno + celltype,
+ data = veteran)
Error in optimHess(theta, fn, gr, control = list(fnscale = -1)) : 
  non-finite value supplied by optim
Calls: bppo ... spbp.mle -> <Anonymous> -> <Anonymous> -> .local -> optimHess
Execution halted
Running ‘testthat.R’ [17s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── Error ('test.R:33:1'): (code run outside of `test_that()`) ──────────────────
  Error in `optimHess(theta, fn, gr, control = list(fnscale = -1))`: non-finite value supplied by optim
  Backtrace:
      ▆
   1. └─spsurv::bppo(Surv(time, status) ~ karno + factor(celltype), data = veteran) at test.R:33:0
   2.   └─spsurv:::spbp.default(...)
   3.     └─spsurv:::spbp.mle(standata = standata, ...)
   4.       ├─rstan::optimizing(...)
   5.       └─rstan::optimizing(...)
   6.         └─rstan (local) .local(object, ...)
   7.           └─stats::optimHess(theta, fn, gr, control = list(fnscale = -1))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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installed size is 13.3Mb
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    help   1.1Mb
    libs  10.8Mb
installed size is  8.7Mb
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Package suggested but not available for checking: ‘ecpc’
installed size is  5.6Mb
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    shiny-squid   5.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: ‘GSVA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'LazyData' is specified without a 'data' directory
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
'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 99.2Mb
  sub-directories of 1Mb or more:
    libs  98.7Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘SSsimple.Snw’ using Sweave
Loading required package: mvtnorm
Error: processing vignette 'SSsimple.Snw' failed with diagnostics:
Running 'texi2dvi' on 'SSsimple.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SSsimple.Snw’

SUMMARY: processing the following file failed:
  ‘SSsimple.Snw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    libs  35.8Mb
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.8Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    include  11.7Mb
    lib       3.7Mb
GNU make is a SystemRequirements.
installed size is 92.5Mb
  sub-directories of 1Mb or more:
    libs  91.7Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘starsdata’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   2.4Mb
    libs      4.2Mb
installed size is  7.5Mb
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    libs   6.5Mb
Package suggested but not available for checking: ‘asreml’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tweedie’
Package unavailable to check Rd xrefs: ‘tweedie’
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’
unable to reach CRAN

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
Packages suggested but not available for checking:
  'semPlot', 'FactoMineR', 'FactoInvestigate', 'factoextra'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.2Mb
installed size is  7.0Mb
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    data   2.3Mb
    libs   4.4Mb
installed size is 25.4Mb
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    libs  25.1Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs  62.2Mb
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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 ‘StMoMoVignette.Rnw’ using Sweave
Loading required package: gnm
Loading required package: forecast
Error: processing vignette 'StMoMoVignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'StMoMoVignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `ctable.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [caption = false]{subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'StMoMoVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.5Mb
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.9Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 10.5Mb
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    libs  10.3Mb
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
'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:
    libs   5.0Mb
Package unavailable to check Rd xrefs: ‘HDoutliers’
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/streamDAG.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.0Mb
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    7.1Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  6.8Mb
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GNU make is a SystemRequirements.
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Problems with news in ‘NEWS.md’:
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    pre-release switchboard (2020 - 2021)
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GNU make is a SystemRequirements.
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installed size is 10.3Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
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LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
Package required but not available: ‘microbiome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Package unavailable to check Rd xrefs: ‘dearseq’
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Malformed Description field: should contain one or more complete sentences.
installed size is  7.5Mb
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installed size is 10.5Mb
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installed size is 35.0Mb
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Package which this enhances but not available for checking: ‘R2wd’
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installed size is  7.0Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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installed size is  8.9Mb
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Package required and available but unsuitable version: ‘worcs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
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checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
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checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
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checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
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installed size is 84.5Mb
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GNU make is a SystemRequirements.
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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’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggplot2’
Package suggested but not available for checking: ‘lme4’
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    Minor changes:
Package suggested but not available for checking: ‘SingleR’
installed size is 47.2Mb
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Running ‘testthat.R’ [14s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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installed size is  6.4Mb
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Package suggested but not available for checking: ‘rrelaxiv’
installed size is 58.4Mb
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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
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installed size is 98.9Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
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Specified C++14: please drop specification unless essential
installed size is  9.9Mb
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installed size is 16.7Mb
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installed size is 30.3Mb
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GNU make is a SystemRequirements.
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
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Package suggested but not available for checking: ‘stm’
Package unavailable to check Rd xrefs: ‘stm’
Packages suggested but not available for checking:
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Package suggested but not available for checking: ‘gurobi’
installed size is  7.4Mb
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installed size is 200.1Mb
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Package suggested but not available for checking: ‘toscaData’
installed size is  5.1Mb
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Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 13.0Mb
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installed size is  5.3Mb
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installed size is  6.3Mb
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Package suggested but not available for checking: ‘competitiontoolbox’
Package unavailable to check Rd xrefs: ‘competitiontoolbox’
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installed size is  7.6Mb
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installed size is  9.0Mb
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Package suggested but not available for checking: ‘fwelnet’
installed size is  5.1Mb
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Packages required but not available: 'csaw', 'HiCDOC'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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installed size is  8.7Mb
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Package suggested but not available for checking: ‘Seurat’
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Specified C++11: please drop specification unless essential
installed size is 10.4Mb
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installed size is  5.9Mb
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installed size is  8.4Mb
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installed size is  5.7Mb
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Package suggested but not available for checking: ‘brms’
Package unavailable to check Rd xrefs: ‘brms’
installed size is 18.7Mb
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Problems with news in ‘NEWS.md’:
No news entries found.
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GNU make is a SystemRequirements.
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Specified C++11: please drop specification unless essential
installed size is 39.5Mb
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GNU make is a SystemRequirements.
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Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
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'LazyData' is specified without a 'data' directory
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/triptych.Rcheck/00install.out’ for details.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
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installed size is 34.1Mb
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GNU make is a SystemRequirements.
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
installed size is  8.3Mb
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There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Package unavailable to check Rd xrefs: ‘fpc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathabx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {microtype}^^M
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  9.8Mb
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checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 44.9Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 133.9Mb
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'LazyData' is specified without a 'data' directory
installed size is 15.1Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 96.9Mb
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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 Description field: should contain one or more complete sentences.
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package unavailable to check Rd xrefs: ‘twang’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 19.8Mb
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Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘sl3’
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Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
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installed size is 132.0Mb
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GNU make is a SystemRequirements.
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installed size is  8.0Mb
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Specified C++11: please drop specification unless essential
installed size is 27.2Mb
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'LazyData' is specified without a 'data' directory
Running examples in ‘UKFE-Ex.R’ failed
The error most likely occurred in:

> ### Name: MonthlyStats
> ### Title: Monthly Statistics
> ### Aliases: MonthlyStats
> 
> ### ** Examples
> 
> # Get the mean flows for each month for the Thames at Kingston
> QMonThames <- MonthlyStats(ThamesPQ[,c(1,3)], Stat = mean,
+ ylab = "Discharge (m3/s)", main = "Thames at Kingston monthly mean flow", Plot = TRUE)
Error in MonthlyStats(ThamesPQ[, c(1, 3)], Stat = mean, ylab = "Discharge (m3/s)",  : 
  At least one month does not have the same number of years available as the others. This may be because you have at least one whole month missing (as opposed to a month of NA values for example). You need at least one time step within each month
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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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
installed size is  5.9Mb
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installed size is  5.4Mb
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'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
installed size is 14.0Mb
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Specified C++14: please drop specification unless essential
installed size is 16.3Mb
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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
installed size is 64.0Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.1Mb
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘adespatial’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘USA.state.boundaries.data’
installed size is  7.2Mb
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'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:
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'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
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installed size is  7.3Mb
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'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
installed size is 14.1Mb
  sub-directories of 1Mb or more:
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installed size is 39.3Mb
  sub-directories of 1Mb or more:
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    libs  37.3Mb
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
installed size is 24.5Mb
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installed size is  9.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
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installed size is 257.5Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
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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
installed size is  8.3Mb
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checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
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'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 15.2Mb
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installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  8.6Mb
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GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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installed size is  8.6Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ggtern’
Specified C++11: please drop specification unless essential
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installed size is  5.2Mb
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installed size is  5.1Mb
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'LazyData' is specified without a 'data' directory
installed size is  9.5Mb
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Missing link or links in documentation object 'amlbinomial.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlexponential.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlnormal.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'amlpoisson.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'extlogF.UC.Rd':
  ‘[VGAMdata]{dalap}’

Missing link or links in documentation object 'extlogF1.Rd':
  ‘[VGAMdata]{alaplace1}’ ‘[VGAMdata]{dalap}’

Missing link or links in documentation object 'grc.Rd':
  ‘[VGAMdata]{alaplace2}’

Missing link or links in documentation object 'laplace.Rd':
  ‘[VGAMdata]{alaplace2}’

Missing link or links in documentation object 'lms.bcn.Rd':
  ‘[VGAMdata]{alaplace1}’

Missing link or links in documentation object 'simulate.vlm.Rd':
  ‘[VGAMdata]{alaplace1}’ ‘[VGAMdata]{alaplace2}’
  ‘[VGAMdata]{triangle}’

Missing link or links in documentation object 'triangleUC.Rd':
  ‘[VGAMdata]{triangle}’

Missing link or links in documentation object 'wald.stat.Rd':
  ‘[VGAMdata]{alaplace1}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
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installed size is  5.2Mb
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'LazyData' is specified without a 'data' directory
installed size is 55.7Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
installed size is 33.0Mb
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GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
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    htmlwidgets   6.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
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installed size is  6.4Mb
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installed size is  6.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
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    extdata   1.1Mb
'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:
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Package suggested but not available for checking: ‘INLA’
Package unavailable to check Rd xrefs: ‘INLA’
installed size is 33.8Mb
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GNU make is a SystemRequirements.
installed size is 63.9Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
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    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: \&
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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  9.8Mb
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installed size is  9.9Mb
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'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 117.8Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
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'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
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
installed size is 10.5Mb
  sub-directories of 1Mb or more:
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Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 27.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 12.8Mb
  sub-directories of 1Mb or more:
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    libs  10.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is 94.2Mb
  sub-directories of 1Mb or more:
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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
installed size is 58.8Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘classInt’
installed size is  8.8Mb
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installed size is  5.2Mb
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installed size is  5.3Mb
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Package suggested but not available for checking: ‘wordnetDicts’
installed size is  7.2Mb
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'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
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Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
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installed size is 11.5Mb
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installed size is 11.4Mb
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Package suggested but not available for checking: ‘wmtsa’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.9Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
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Package suggested but not available for checking: ‘preprocessCore’
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  7.4Mb
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installed size is 14.9Mb
  sub-directories of 1Mb or more:
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 54.4Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 32.6Mb
  sub-directories of 1Mb or more:
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Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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Package suggested but not available for checking: ‘nlmixr2’
installed size is  7.5Mb
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installed size is 25.4Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
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installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
GNU make is a SystemRequirements.
installed size is 40.3Mb
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  8.7Mb
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Packages suggested but not available for checking: 'RNRCS', 'metScanR'
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Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 41.2Mb
  sub-directories of 1Mb or more:
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GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/getting-started.Rmd’
   ‘vignettes/project-owners.Rmd’
(Is a VignetteBuilder field missing?)
Package suggested but not available for checking: ‘rJava’
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
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Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.3/zoomerjoin.Rcheck/00install.out’ for details.
Specified C++11: please drop specification unless essential
installed size is  7.8Mb
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Package suggested but not available for checking: ‘partitions’
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
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Package suggested but not available for checking: 'INLA'
installed size is  7.0Mb
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'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
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'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 11.7Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.6Mb
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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
'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  7.5Mb
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checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.6Mb
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installed size is  7.2Mb
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installed size is  6.9Mb
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installed size is  9.4Mb
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  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  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'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
Package suggested but not available for checking: 'INLA'
Package which this enhances but not available for checking: 'asreml'
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
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
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) 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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
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
Error(s) in re-building vignettes:
--- re-building 'ascariasis.Rmd' using rmarkdown
File figure/asc_plot_mixt-1.png not found in resource path
Error: processing vignette 'ascariasis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'ascariasis.Rmd'

--- re-building 'simulation_study.Rmd' using rmarkdown
File figure/sim_plot_true_data-1.png not found in resource path
Error: processing vignette 'simulation_study.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'simulation_study.Rmd'

SUMMARY: processing the following files failed:
  'ascariasis.Rmd' 'simulation_study.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
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
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
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: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' 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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.4Mb
    screenshots   1.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   2.1Mb
    doc    1.8Mb
sort_asap: no visible global function definition for 'sort_by'
Undefined global functions or variables:
  sort_by
Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
Found the following significant warnings:
  Warning: read_bcal.Rd:27: unknown macro '\abbr'
  Warning: read_chronomodel.Rd:36: unknown macro '\abbr'
  Warning: read_oxcal.Rd:27: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/ArchaeoPhases.Rcheck/00install.out' for details.
prepare_Rd: read_bcal.Rd:27: unknown macro '\abbr'
prepare_Rd: read_chronomodel.Rd:36: unknown macro '\abbr'
prepare_Rd: read_oxcal.Rd:27: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(arcpullr)
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  > 
  > test_check("arcpullr")
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 51 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_layer_properties.R:21:3'): legend values and colors are correct ──
  legend$color not equal to `legend_colors`.
  14/16 mismatches
  x[1]: "#C84141"
  y[1]: "#C94242"
  
  x[3]: "#F2EE86"
  y[3]: "#F2EF87"
  
  x[5]: "#E6AC2E"
  y[5]: "#E6AC2B"
  
  x[6]: "#9C7209"
  y[6]: "#9D7207"
  
  x[7]: "#016400"
  y[7]: "#006300"
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 51 ]
  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
'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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 44.7Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  39.7Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
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
'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
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'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
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'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    4.9Mb
    libs   3.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.5Mb
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
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/bapred.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    4.4Mb
    help   2.2Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.1Mb
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) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
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: \$
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.4Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Package suggested but not available for checking: 'INLA'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
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: \$
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
'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
Package suggested but not available for checking: 'BRugs'
'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  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.6Mb
'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
'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
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.6Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
installed size is 150.3Mb
  sub-directories of 1Mb or more:
    include  149.3Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
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: 'rrelaxiv'
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'asreml'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    help   2.6Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.0Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
'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
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
  Warning: 'blandr.output.text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Packages suggested but not available for checking: 'cmdstanr', 'blavsam'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.2Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   1.2Mb
'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
Specified C++11: please drop specification unless essential
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
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  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.2Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.9Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
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) bp_rats.Rd:41: 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.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'brea.Rmd' using rmarkdown

Quitting from lines 303-305 [unnamed-chunk-18] (brea.Rmd)
Error: processing vignette 'brea.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'brea.Rmd'

SUMMARY: processing the following file failed:
  'brea.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Running examples in 'bskyr-Ex.R' failed
The error most likely occurred in:

> ### Name: bs_uri_to_url
> ### Title: Convert Universal Resource Identifiers to Hypertext Transfer
> ###   Protocol Secure URLs
> ### Aliases: bs_uri_to_url
> 
> ### ** Examples
> 
> bs_uri_to_url('at://did:plc:ic6zqvuw5ulmfpjiwnhsr2ns/app.bsky.feed.post/3k7qmjev5lr2s')
Error in curl::curl_parse_url(url, baseurl = base_url, decode = FALSE) : 
  Failed to parse URL: Port number was not a decimal number between 0 and 65535
Calls: bs_uri_to_url -> <Anonymous> -> <Anonymous>
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [12s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bskyr)
  > 
  > test_check("bskyr")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 53 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-url_uri.R:2:3'): uri to urls works ─────────────────────────────
  Error in `curl::curl_parse_url(url, baseurl = base_url, decode = FALSE)`: Failed to parse URL: Port number was not a decimal number between 0 and 65535
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-url_uri.R:2:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─bskyr::bs_uri_to_url("at://did:plc:ic6zqvuw5ulmfpjiwnhsr2ns/app.bsky.feed.post/3k7qmjev5lr2s")
   5.   └─httr2::url_parse(uri)
   6.     └─curl::curl_parse_url(url, baseurl = base_url, decode = FALSE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 53 ]
  Error: Test failures
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.4Mb
    lib          5.0Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
GNU make is a SystemRequirements.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/btb.Rcheck/00install.out' for details.
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > test_check("btergm")
  Loading required package: btergm
  Registered S3 methods overwritten by 'btergm':
    method    from
    plot.gof  ergm
    print.gof ergm
  Package:  btergm
  Version:  1.10.12
  Date:     2024-03-31
  Authors:  Philip Leifeld (University of Manchester)
            Skyler J. Cranmer (The Ohio State University)
            Bruce A. Desmarais (Pennsylvania State University)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  
  ══ Skipped tests (8) ═══════════════════════════════════════════════════════════
  • On CRAN (8): 'test-btergm.R:82:3', 'test-btergm.R:180:3',
    'test-btergm.R:197:3', 'test-data.R:4:3', 'test-interpret.R:4:3',
    'test-interpret.R:32:3', 'test-interpret.R:59:3', 'test-interpret.R:87:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-btergm.R:73:3'): offset argument in btergm works without composition change ──
  Error in `ergm::ergm.pl(nw, Clist.miss, model, theta.offset = c(rep(FALSE, 
      length(l$rhs.terms) - 1), TRUE), verbose = FALSE, control = control.ergm)`: VECTOR_ELT() can only be applied to a 'list', not a 'NULL'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-btergm.R:73:3
   2. │ └─base::withCallingHandlers(...)
   3. └─btergm::btergm(...)
   4.   └─ergm::ergm.pl(...)
  
  [ FAIL 1 | WARN 2 | SKIP 8 | PASS 51 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'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  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) kink_estimator.Rd:60: 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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
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
GNU make is a SystemRequirements.
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
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   9.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
'LazyData' is specified without a 'data' directory
'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
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    entry_level                 1.7Mb
    virtual_patient_simulator   3.1Mb
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  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
'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: 'rnaturalearthhires'
Running examples in 'casabourse-Ex.R' failed
The error most likely occurred in:

> ### Name: bySector
> ### Title: bySector
> ### Aliases: bySector
> 
> ### ** Examples
> 
> {R.utils::withTimeout(bySector(),timeout = 4)}
Error in .Call(R_curl_fetch_memory, enc2utf8(url), handle, nonblocking) : 
  reached elapsed time limit

Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
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
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
Specified C++14: 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
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
Package suggested but not available for checking: 'rkeops'
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
GNU make is a SystemRequirements.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc   16.4Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'atp_calculation.Rmd' using rmarkdown
File mito_glyco_tests.png not found in resource path
Error: processing vignette 'atp_calculation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'atp_calculation.Rmd'

--- re-building 'ceas.Rmd' using rmarkdown
--- finished re-building 'ceas.Rmd'

SUMMARY: processing the following file failed:
  'atp_calculation.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
'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
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'chain_glm.Rmd' using rmarkdown

Quitting from lines 173-174 [glm1_3] (chain_glm.Rmd)
Error: processing vignette 'chain_glm.Rmd' failed with diagnostics:
package 'MASS' must be installed
--- failed re-building 'chain_glm.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

SUMMARY: processing the following file failed:
  'chain_glm.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R     5.0Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'darts'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:

  Warning: 'process_marker_data' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Package suggested but not available for checking: 'countreg'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'README.Rmd'

SUMMARY: processing the following file failed:
  'README.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'entab'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'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:
    R         1.8Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
'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  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
    libs      1.0Mb
'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
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
checkRd: (-1) clme.Rd:84: Escaped LaTeX specials: \&
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
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
'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:
    data   5.2Mb
'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
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'tobit1'
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
.stop_not_number: no visible global function definition for '%||%'
Undefined global functions or variables:
  %||%
Package which this enhances but not available for checking: 'rkward'
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    help   1.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
'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:
    R      1.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
'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  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.1Mb
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
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
Specified C++11: please drop specification unless essential
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
'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
checkRd: (-1) babies.Rd:35: 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
'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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
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
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc             2.0Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.2Mb
'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
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
'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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.8Mb
'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
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.9Mb
'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
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BSgenome.Scerevisiae.UCSC.sacCer3'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'EnsDb.Hsapiens.v86'
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Package suggested but not available for checking: 'INLA'
'LazyData' is specified without a 'data' directory
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc   11.7Mb
    help   1.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.5Mb
'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  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.5Mb
File 'curl/libs/x64/curl.dll':
  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.
Packages required and available but unsuitable versions:
  'stats', 'tools', 'utils'

See section 'The DESCRIPTION file' 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
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'using_cvdprevent.Rmd' using rmarkdown

Quitting from lines 176-178 [unnamed-chunk-16] (using_cvdprevent.Rmd)
Error: processing vignette 'using_cvdprevent.Rmd' failed with diagnostics:
no applicable method for 'group_vars' applied to an object of class "NULL"
--- failed re-building 'using_cvdprevent.Rmd'

SUMMARY: processing the following file failed:
  'using_cvdprevent.Rmd'

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'RGtk2'
'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
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.3Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
'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:
  Warning: jpegReport.Rd:22: unknown macro '\abbr'
  Warning: jpegReport.Rd:50: unknown macro '\abbr'
  Warning: jpegReport.Rd:53: unknown macro '\abbr'
  Warning: jpegReport.Rd:56: unknown macro '\abbr'
  Warning: jpegReport.Rd:58: unknown macro '\abbr'
  Warning: jpegReport.Rd:62: unknown macro '\abbr'
  Warning: pdfReport.Rd:101: unknown macro '\abbr'
  Warning: pngReport.Rd:22: unknown macro '\abbr'
  Warning: pngReport.Rd:50: unknown macro '\abbr'
  Warning: pngReport.Rd:53: unknown macro '\abbr'
  Warning: pngReport.Rd:55: unknown macro '\abbr'
  Warning: pngReport.Rd:59: unknown macro '\abbr'
  Warning: readReportTable.Rd:35: unknown macro '\abbr'
  Warning: readReportTable.Rd:167: unknown macro '\abbr'
  Warning: scanReport.Rd:45: unknown macro '\abbr'
  Warning: scanReport.Rd:60: unknown macro '\abbr'
  Warning: scanReport.Rd:61: unknown macro '\abbr'
  Warning: scanReport.Rd:162: unknown macro '\abbr'
See 'd:/Rcompile/CRANpkg/local/4.3/D4TAlink.light.Rcheck/00install.out' for details.
prepare_Rd: jpegReport.Rd:22: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:50: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:53: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:56: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:58: unknown macro '\abbr'
prepare_Rd: jpegReport.Rd:62: unknown macro '\abbr'
prepare_Rd: pdfReport.Rd:101: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:22: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:50: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:53: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:55: unknown macro '\abbr'
prepare_Rd: pngReport.Rd:59: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:35: unknown macro '\abbr'
prepare_Rd: readReportTable.Rd:167: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:45: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:60: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:61: unknown macro '\abbr'
prepare_Rd: scanReport.Rd:162: unknown macro '\abbr'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'doMC'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
'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
Package suggested but not available for checking: 'SASxport'
'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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
'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: 'BRugs'
Package suggested but not available for checking: 'INLA'
'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.
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
'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
'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 'testthat.R' [25s]
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(defineR)
  Loading required package: common
  Loading required package: glue
  > 
  > test_check("defineR")
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
'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  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'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:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.6Mb
    libs   1.2Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
Error(s) in re-building vignettes:
--- re-building 'custom.Rmd' using rmarkdown
--- finished re-building 'custom.Rmd'

--- re-building 'documentation.Rmd' using rmarkdown
--- finished re-building 'documentation.Rmd'

--- re-building 'engine.Rmd' using rmarkdown
Warning in gsub(this, knitr::sew(tmp), code) :
  TRE pattern compilation error 'Invalid back reference'

Quitting from lines 170-171 [unnamed-chunk-11] (engine.Rmd)
Error: processing vignette 'engine.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2025_01_31_01_50_00_7169\RtmpcfZaVV\file333942e8c297b.png', reason 'Invalid back reference'
--- failed re-building 'engine.Rmd'

--- re-building 'objects.Rmd' using rmarkdown

Quitting from lines 56-62 [unnamed-chunk-5] (objects.Rmd)
Error: processing vignette 'objects.Rmd' failed with diagnostics:
invalid regular expression 'D:\temp\2025_01_31_01_50_00_7169\Rtmp8cAoBX\file31980f612ca1.png', reason 'Invalid back reference'
--- failed re-building 'objects.Rmd'

--- re-building 'sessioninfo.Rmd' using rmarkdown
--- finished re-building 'sessioninfo.Rmd'

--- re-building 'tests_and_coverage.Rmd' using rmarkdown
--- finished re-building 'tests_and_coverage.Rmd'

SUMMARY: processing the following files failed:
  'engine.Rmd' 'objects.Rmd'

Error: Vignette re-building failed.
Execution halted
'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:
    data          1.8Mb
    htmlwidgets   3.6Mb
GNU make is a SystemRequirements.
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 required but not available: 'signatureSearchData'

See section 'The DESCRIPTION file' 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
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
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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
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: \&
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
Package which this enhances but not available for checking: 'INLA'
'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.
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
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
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: \&
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
GNU make is a SystemRequirements.
'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  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
'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  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R         2.0Mb
    data      2.0Mb
    extdata   2.3Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Package suggested but not available for checking: 'gurobi'
'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:
    assets   2.9Mb
    doc      2.2Mb
Package suggested but not available for checking: 'pwalign'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'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: \&
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
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Running examples in 'dsem-Ex.R' failed
The error most likely occurred in:

> ### Name: dsemRTMB
> ### Title: Fit dynamic structural equation model
> ### Aliases: dsemRTMB
> 
> ### ** Examples
> 
> # Define model
> sem = "
+   # Link, lag, param_name
+   cprofits -> consumption, 0, a1
+   cprofits -> consumption, 1, a2
+   pwage -> consumption, 0, a3
+   gwage -> consumption, 0, a3
+   cprofits -> invest, 0, b1
+   cprofits -> invest, 1, b2
+   capital -> invest, 0, b3
+   gnp -> pwage, 0, c2
+   gnp -> pwage, 1, c3
+   time -> pwage, 0, c1
+ "
> 
> # Load data
> data(KleinI, package="AER")
> TS = ts(data.frame(KleinI, "time"=time(KleinI) - 1931))
> tsdata = TS[,c("time","gnp","pwage","cprofits",'consumption',
+                "gwage","invest","capital")]
> 
> # Fit model
> fit = dsemRTMB( sem=sem,
+             tsdata = tsdata,
+             estimate_delta0 = TRUE,
+             control = dsem_control(quiet=TRUE) )
Read 10 records
Error in advector(e1) : 
  Invalid argument to 'advector' (lost class attribute?)
Calls: dsemRTMB ... dgmrf -> as.vector -> Ops.advector -> Arith2 -> advector
Execution halted
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
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'dsBase', 'dsBaseClient'
Packages suggested but not available for checking: 'dsBaseClient', 'dsBase'
'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  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    data   7.3Mb
    doc    1.1Mb
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: 'lle'
'LazyData' is specified without a 'data' directory
'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: \&
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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: \&
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.1Mb
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    libs  11.0Mb
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The following files should probably not be installed:
  'econet.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
GNU make is a SystemRequirements.
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
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GNU make is a SystemRequirements.
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Package unavailable to check Rd xrefs: 'cmdstanr'
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No news entries found.
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CCRR: no visible global function definition for '%||%'
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PhiCoefficient: no visible global function definition for '%||%'
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createBinaryFunction : <anonymous>: no visible global function
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crr: no visible global function definition for '%||%'
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passage: no visible global function definition for '%||%'
percentile: no visible global function definition for '%||%'
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stanine: no visible global function definition for '%||%'
Undefined global functions or variables:
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/exceedProb.Rcheck/00install.out' for details.
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  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
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GNU make is a SystemRequirements.
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    doc    3.0Mb
    help   1.2Mb
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GNU make is a SystemRequirements.
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installed size is  6.4Mb
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.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
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Running 'testthat.R' [100s]
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(fdicdata)
  > 
  > test_check("fdicdata")
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-getInstitution.R:4:3'): getInstitutionsAll returns a data frame with expected columns ──
  is.data.frame(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-getInstitution.R:5:3'): getInstitutionsAll returns a data frame with expected columns ──
  "CERT" %in% colnames(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-getInstitution.R:6:3'): getInstitutionsAll returns a data frame with expected columns ──
  "NAME" %in% colnames(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-getInstitution.R:7:3'): getInstitutionsAll returns a data frame with expected columns ──
  "CITY" %in% colnames(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-getInstitution.R:8:3'): getInstitutionsAll returns a data frame with expected columns ──
  "STALP" %in% colnames(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-getInstitution.R:9:3'): getInstitutionsAll returns a data frame with expected columns ──
  "ZIP" %in% colnames(df) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 6 | WARN 1 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
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installed size is  5.3Mb
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installed size is  5.8Mb
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installed size is 10.7Mb
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    R         4.7Mb
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installed size is  5.6Mb
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    doc   4.9Mb
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checkRd: (-1) bitspec.Rd:8: Escaped LaTeX specials: \&
search_finna : <anonymous>: no visible global function definition for
  '%||%'
search_finna : <anonymous> : <anonymous>: no visible global function
  definition for '%||%'
search_publisher : <anonymous>: no visible global function definition
  for '%||%'
Undefined global functions or variables:
  %||%
Running examples in 'finna-Ex.R' failed
The error most likely occurred in:

> ### Name: analyze_metadata
> ### Title: Analyze Refined Finna Metadata
> ### Aliases: analyze_metadata
> 
> ### ** Examples
> 
> library(finna)
> sibelius_data <- search_finna("sibelius")
Warning in search_finna("sibelius") :
  Default limit of 100 records is being used. Specify 'limit' argument for more records.
Error in record$id %||% NA : could not find function "%||%"
Calls: search_finna -> lapply -> FUN
Execution halted
Running 'testthat.R' [7s]
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/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(finna)
  > 
  > test_check("finna")
  Total results found: 2062419
  Data fetching completed in 1.24 seconds.
  Total results found: 3
  Data fetching completed in 0.22 seconds.
  Total results found: 2062419
  Data fetching completed in 0.80 seconds.
  No encoding supplied: defaulting to UTF-8.
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-search_publisher.R:3:3'): search_publisher performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_publisher("sibelius", limit = 10)) at test-search_publisher.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_publisher("sibelius", limit = 10)
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  ── Error ('test_search_finna.R:3:3'): search_finna performs a basic search correctly ──
  Error in `record$id %||% NA`: could not find function "%||%"
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(search_finna("sibelius", type = "Author")) at test_search_finna.R:3:3
   2. │ └─base::withCallingHandlers(...)
   3. └─finna::search_finna("sibelius", type = "Author")
   4.   └─base::lapply(...)
   5.     └─finna (local) FUN(X[[i]], ...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 61 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown

Quitting from lines 23-26 [unnamed-chunk-1] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
could not find function "%||%"
--- failed re-building 'vignette.Rmd'

SUMMARY: processing the following file failed:
  'vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
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checkRd: (-1) fitmixEM.Rd:51: Escaped LaTeX specials: \&
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Package unavailable to check Rd xrefs: 'fivethirtyeightdata'
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Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) flashClust.Rd:92: Escaped LaTeX specials: \&
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GNU make is a SystemRequirements.
installed size is  6.9Mb
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Error(s) in re-building vignettes:
--- re-building 'geoAr_geofacet.Rmd' using rmarkdown
File figure/tucmap-1.png not found in resource path
Error: processing vignette 'geoAr_geofacet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_geofacet.Rmd'

--- re-building 'geoAr_leaflet.Rmd' using rmarkdown
File figure/map-1.png not found in resource path
Error: processing vignette 'geoAr_leaflet.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'geoAr_leaflet.Rmd'

--- re-building 'georefar.Rmd' using rmarkdown
--- finished re-building 'georefar.Rmd'

SUMMARY: processing the following files failed:
  'geoAr_geofacet.Rmd' 'geoAr_leaflet.Rmd'

Error: Vignette re-building failed.
Execution halted
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/GeoModels.Rcheck/00install.out' for details.
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accrualReport: multiple local function definitions for 'gg' with
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Package required but not available: 'EnsDb.Hsapiens.v75'

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

> ### Name: gw_nsprcomp
> ### Title: Geographically Weighted non-negative Principal Component
> ###   Analysis
> ### Aliases: gw_nsprcomp
> ### Keywords: "SPATIAL" "MULTIVALIATE"
> 
> ### ** Examples
> 
> 
> ### This example is for demonstrating GWnnegPCA only.
> ### The application does not imply any reasonable meanings.
> 
> library(sp)
> library(spData)
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source')`
> library(sf)
Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
> 
> boston <- as(st_read(system.file("shapes/boston_tracts.shp",
+                                  package="spData")[1]), "Spatial")
Error: `dsn` must point to a source, not an empty string.
Execution halted
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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'
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    data   1.5Mb
    doc    3.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
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
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.5Mb
'LazyData' is specified without a 'data' directory
'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: \&
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
'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 suggested but not available for checking: 'INLA'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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
GNU make is a SystemRequirements.
Package which this enhances but not available for checking: 'HadoopStreaming'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.3Mb
html_describe_con: multiple local function definitions for 'g' with
  different formal arguments
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: \&
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    4.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'glmmADMB'
Package suggested but not available for checking: 'microViz'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    app   1.7Mb
    doc   3.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
'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  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.3Mb
    help   1.1Mb
Specified C++14: please drop specification unless essential
checkRd: (-1) simplePostToHost.Rd:14: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'hubExamples', 'hubVis'
'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
Package suggested but not available for checking: 'hurricaneexposuredata'
'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: 'microViz'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
'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 suggested but not available for checking: 'SparkR'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
'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: 'icd'
checkRd: (-1) ICEscale.Rd:53: Escaped LaTeX specials: \^
checkRd: (-1) dpwdg.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) dpwdg.Rd:15: 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
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rggobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'IFCdata'
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:196:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:197:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/minwindef.h:198:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/processthreadsapi.h:130:47: warning: ISO C does not allow extra ';' outside of a function [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:451:3: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1333:24: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/urlmon.h:1745:25: warning: ISO C restricts enumerator values to range of 'int' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winioctl.h:359:11: warning: ISO C forbids zero-size array 'SerialNumber' [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/igraph.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.2Mb
    help   2.0Mb
    libs   6.4Mb
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8404:37: warning: ISO C++ forbids flexible array member 'Elements' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8667:22: warning: ISO C++ forbids flexible array member 'pEventLogRecords' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/winnt.h:8673:13: warning: ISO C++ forbids flexible array member 'ulOffsets' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/rpcndr.h:447:19: warning: ISO C++ forbids flexible array member 'Format' [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:548:37: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/rtools43/usr/lib/mxe/usr/x86_64-w64-mingw32.static.posix/include/oaidl.h:499:29: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.3/imager.Rcheck/00install.out' for details.
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.7Mb
    extdata   1.0Mb
    include   3.3Mb
    libs     10.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs   10.5Mb
    share  10.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
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  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
    libs   1.0Mb
'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
'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  5.2Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.1Mb
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++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) school23.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) school23.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
Package which this enhances but not available for checking: 'gurobi'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'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:
    INSPECTumours (development version)
Malformed Title field: should not end in a period.
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
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc   9.7Mb
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
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'surveyspec'
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/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
checkRd: (-1) constrained.Rd:49: 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
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: \&
'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  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.3Mb
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
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'iucnrdata'
Package suggested but not available for checking: 'gurobi'
Package suggested but not available for checking: 'locClass'
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
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
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          11.0Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
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'.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   4.0Mb
    help      1.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
    libs      1.1Mb
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
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    i18n   6.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'remMap'
'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  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
'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:
    pre-release juicr (2017 - 2021)
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kanjistat.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
'LazyData' is specified without a 'data' directory
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   7.8Mb
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:
    Minor Changes
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'rkward'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'RGeostats'
'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 required but not available: 'pwalign'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'kadmin'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
':::' calls which should be '::':
  'xfun:::find_globals' 'xfun:::find_locals'
  See the note in ?`:::` about the use of this operator.
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:
  '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
'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
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   1.7Mb
'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
'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'using_latent2likert.Rmd' using rmarkdown
File man/figures/courses-grouped-min.png not found in resource path
Error: processing vignette 'using_latent2likert.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'using_latent2likert.Rmd'

SUMMARY: processing the following file failed:
  'using_latent2likert.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
'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
'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':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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    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
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    Author
    Maintainer
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Malformed Description field: should contain one or more complete sentences.
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/manifold.Rcheck/00install.out' for details.
installed size is  5.3Mb
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Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Bug Fixes
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mapping_tmap: warning in tm_credits(srcAuth, size =
  options$credits.size, col = options$credits.color, fontface =
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mapping_tmap_US: warning in tm_credits(srcAuth, size =
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GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
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GNU make is a SystemRequirements.
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Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MazamaSpatialUtils)
  Loading required package: sf
  Linking to GEOS 3.11.2, GDAL 3.8.2, PROJ 9.3.1; sf_use_s2() is TRUE
  > library(MazamaSpatialPlots)
  > 
  > test_check("MazamaSpatialPlots")
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 35 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-countyMap.R:62:3'): subsets by stateCode correctly ───────────
  length(plottedStates) not equal to nrow(countyList).
  1/1 mismatches
  [1] 0 - 75 == -75
  ── Failure ('test-countyMap.R:63:3'): subsets by stateCode correctly ───────────
  "WA" %in% plottedStates is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-countyMap.R:64:3'): subsets by stateCode correctly ───────────
  "OR" %in% plottedStates is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-stateMap.R:59:3'): subsets by stateCode correctly ────────────
  length(plottedStates) not equal to length(stateCodeList).
  1/1 mismatches
  [1] 0 - 2 == -2
  ── Failure ('test-stateMap.R:60:3'): subsets by stateCode correctly ────────────
  "WA" %in% plottedStates is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-stateMap.R:61:3'): subsets by stateCode correctly ────────────
  "OR" %in% plottedStates is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 35 ]
  Error: Test failures
  Execution halted
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Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
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Adding so many packages to the search path is excessive and importing
selectively is preferable.
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Missing link or links in documentation object 'dat.baker2009.Rd':
  '[netmeta]{pairwise}'

Missing link or links in documentation object 'dat.dogliotti2014.Rd':
  '[netmeta]{pairwise}'

Missing link or links in documentation object 'dat.dong2013.Rd':
  '[netmeta]{pairwise}'

Missing link or links in documentation object 'dat.gurusamy2011.Rd':
  '[netmeta]{pairwise}'

Missing link or links in documentation object 'dat.linde2015.Rd':
  '[netmeta]{pairwise}'

Missing link or links in documentation object 'dat.stowe2010.Rd':
  '[netmeta]{pairwise}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
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    Bug Fix
    Update Vignettes
    Function Optimizing
    New Functions
    Vignette
    Optimization
    Fix Bugs
    Add New Function
    Update Description Files
    Fix bugs
    New .R files
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Found the following significant warnings:

  Warning: 'maximization_to_minimization' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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installed size is 13.7Mb
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'alstructure'

Packages which this enhances but not available for checking:
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Packages suggested but not available for checking:
  'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene'
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checkRd: (-1) modeest-package.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) vieu.Rd:56: Escaped LaTeX specials: \&
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installed size is 14.7Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) genotype_data.Rd:7: Escaped LaTeX specials: \_
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GNU make is a SystemRequirements.
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installed size is  5.3Mb
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checkRd: (-1) ml_g.Rd:47: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
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Problems with news in 'NEWS.md':
No news entries found.
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Package suggested but not available for checking: 'cmdstanr'
installed size is  7.9Mb
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installed size is 17.5Mb
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GNU make is a SystemRequirements.
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checkRd: (-1) mPhen.defineOptions.Rd:4: Escaped LaTeX specials: \$
GNU make is a SystemRequirements.
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    libs   1.1Mb
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installed size is  5.9Mb
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Package unavailable to check Rd xrefs: 'cmdstanr'
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Package unavailable to check Rd xrefs: 'rTubeDB'
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installed size is 16.2Mb
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Package suggested but not available for checking: 'spatialClust'
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
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GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/nbfar.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  9.5Mb
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installed size is 15.7Mb
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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
Specified C++14: please drop specification unless essential
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installed size is  6.2Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'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
Specified C++11: please drop specification unless essential
installed size is  5.9Mb
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Package suggested but not available for checking: 'fastshp'
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
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installed size is 14.7Mb
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    libs  13.9Mb
GNU make is a SystemRequirements.
installed size is  7.9Mb
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    data   7.8Mb
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Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
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installed size is  6.5Mb
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checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
installed size is  5.1Mb
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installed size is  6.8Mb
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Package which this enhances but not available for checking: 'jpndistrict'
Malformed Description field: should contain one or more complete sentences.
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Specified C++11: please drop specification unless essential
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    extdata   3.7Mb
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
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Package suggested but not available for checking: 'INLA'
Running examples in 'NMAoutlier-Ex.R' failed
The error most likely occurred in:

> ### Name: NMAoutlier.measures
> ### Title: Outlier and influential detection measures in network
> ###   meta-analysis.
> ### Aliases: NMAoutlier.measures
> 
> ### ** Examples
> 
> data(smokingcessation, package = "netmeta")
> smokingcessation$id <- 1:nrow(smokingcessation)
> 
> study912 <- subset(smokingcessation, id %in% 9:12)
> p1 <- netmeta::pairwise(list(treat1, treat2, treat3),
+                         list(event1, event2, event3),
+                         list(n1, n2, n3),
+                         data = study912,
+                         sm = "OR")
Error: 'pairwise' is not an exported object from 'namespace:netmeta'
Execution halted
installed size is  5.7Mb
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Package suggested but not available for checking: 'simpar'
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NMsim)
  NMsim 0.1.5. Browse NMsim documentation at
  https://nmautoverse.github.io/NMsim/
  > 
  > test_check("NMsim")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_NMsim_NWPRI.R:30:5'): NMsim_NWPRI ──────────────────────────────
  Error in `while (i <= blocksize) {
      idx.start = sum(sapply(X = 1:i, FUN = function(x) length(1:x))) - 
          i + 1
      idx.end = idx.start + i - 1
      row[[i]] = block_values[idx.start:idx.end]
      i = i + 1
  }`: argument is of length zero
  Backtrace:
      ▆
   1. ├─NMsim::NMsim(...) at test_NMsim_NWPRI.R:30:5
   2. │ ├─...[]
   3. │ └─data.table:::`[.data.table`(...)
   4. └─NMsim (local) method.sim(...)
   5.   └─NMsim:::prettyMatLines(lines.thetapv)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 63 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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Package suggested but not available for checking: 'hurricaneexposuredata'
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'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
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checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
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'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
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.0Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.6Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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installed size is  9.4Mb
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    R         1.5Mb
    doc       5.7Mb
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installed size is  6.2Mb
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    R            1.6Mb
    test_files   4.2Mb
installed size is 10.7Mb
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    R      2.7Mb
    data   1.0Mb
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    help   3.1Mb
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installed size is  5.1Mb
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    libs   1.2Mb
'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  6.8Mb
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'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
GNU make is a SystemRequirements.
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
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'unix'
GNU make is a SystemRequirements.
installed size is 30.3Mb
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installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
installed size is 16.5Mb
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    R        2.6Mb
    data     1.4Mb
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    models   4.8Mb
GNU make is a SystemRequirements.
installed size is  7.2Mb
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    java     1.2Mb
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Package suggested but not available for checking: 'openNLPmodels.en'
installed size is  5.6Mb
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installed size is  7.8Mb
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    doc    2.6Mb
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installed size is  5.1Mb
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    R      1.0Mb
    libs   1.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      1.4Mb
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
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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
Error(s) in re-building vignettes:
--- re-building 'OptimModel_vignette.Rmd' using rmarkdown

Quitting from lines 393-408 [unnamed-chunk-10] (OptimModel_vignette.Rmd)
Error: processing vignette 'OptimModel_vignette.Rmd' failed with diagnostics:
<text>:11:1: unexpected '<'
10: attr(f.model,"srcref") <- 
11: <
    ^
--- failed re-building 'OptimModel_vignette.Rmd'

SUMMARY: processing the following file failed:
  'OptimModel_vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
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
installed size is  5.2Mb
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    data   4.7Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
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    R       1.0Mb
    nifti   3.8Mb
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'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  6.9Mb
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    doc    5.0Mb
    libs   1.4Mb
installed size is  5.2Mb
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    data   3.5Mb
    help   1.1Mb
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Package suggested but not available for checking: 'Rcplex'
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'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
installed size is  7.0Mb
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    doc       1.9Mb
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installed size is 15.2Mb
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Package suggested but not available for checking: 'CorShrink'
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checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
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'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.
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:
    doc    3.1Mb
    libs   2.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Aliases: ybp2date date2ybp
> 
> ### ** Examples
> 
> ybp2date(-10000)
[1] "-8050-01-01 UTC"
> ybp2date(0)
[1] "1950-01-01 UTC"
> # back and forth
> date2ybp(ybp2date(-10000))
[1] -10000
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  9.87 0.34 10.25 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.1Mb
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installed size is  5.6Mb
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GNU make is a SystemRequirements.
installed size is  9.9Mb
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    R      7.1Mb
    help   2.6Mb
installed size is  6.6Mb
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    R      3.1Mb
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installed size is  5.5Mb
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    R      2.7Mb
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installed size is  6.3Mb
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    help   3.5Mb
installed size is  6.5Mb
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    R      2.9Mb
    help   3.4Mb
installed size is  5.3Mb
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    libs   2.3Mb
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'LazyData' is specified without a 'data' directory
installed size is  6.3Mb
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    data   2.7Mb
    doc    1.2Mb
installed size is  5.1Mb
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    doc        1.4Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.5Mb
'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
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.4Mb
GNU make is a SystemRequirements.
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  Cannot extract version info from the following section titles:
    Fixed issues
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installed size is  6.8Mb
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Package suggested but not available for checking: 'pollimetrydata'
Running examples in 'pollimetry-Ex.R' failed
The error most likely occurred in:

> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  'there is no package called 'pollimetrydata''
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Loading required package: rstan
Loading required package: StanHeaders
Error: package or namespace load failed for 'rstan' in .doLoadActions(where, attach):
 error in load action .__A__.1 for package rstan: Rcpp::loadModule(module = "class_model_base", what = TRUE, env = ns, : Unable to load module "class_model_base": attempt to apply non-function
Error in .requirePackage(package) : 
  unable to find required package 'rstan'
Calls: bodysize ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
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installed size is  5.4Mb
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installed size is 11.0Mb
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    doc  10.5Mb
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checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
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Running 'testthat.R' [77s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("OMP_THREAD_LIMIT" = 2)
  > 
  > library(testthat)
  > library(profoc)
  > 
  > 
  > test_check("profoc")
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 159 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • debug_mode is not TRUE (1): 'test-zzz_debug.R:6:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-save_predictions_grid.R:88:1'): (code run outside of `test_that()`) ──
  <std::logic_error/C++Error/error/condition>
  Error: sort(): detected NaN
  Backtrace:
      ▆
   1. └─profoc::online(...) at test-save_predictions_grid.R:88:1
   2.   └─model_instance$learn()
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 159 ]
  Error: Test failures
  In addition: Warning messages:
  1: In .Internal(gc(verbose, reset, full)) : Timer "core" not stopped yet. 
  Use toc("core") to stop the timer.
  2: In .Internal(gc(verbose, reset, full)) : Timer "loss" not stopped yet. 
  Use toc("loss") to stop the timer.
  3: In .Internal(gc(verbose, reset, full)) :
    Timer "init update" not stopped yet. 
  Use toc("init update") to stop the timer.
  Execution halted
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'LazyData' is specified without a 'data' directory
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installed size is 10.9Mb
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GNU make is a SystemRequirements.
installed size is 12.6Mb
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'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
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    doc    4.4Mb
    libs   1.0Mb
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    libs      2.9Mb
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'library' or 'require' call to 'RDCOMClient' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
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installed size is 11.5Mb
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    htmlwidgets   1.8Mb
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    htmlwidgets   1.8Mb
    libs          2.2Mb
installed size is  5.6Mb
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'LazyData' is specified without a 'data' directory
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    data   4.6Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.1Mb
    libs      1.4Mb
'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  5.6Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
'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       2.6Mb
    rstudio   1.5Mb
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
installed size is  9.5Mb
  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  6.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
'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: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    cont  20.1Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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
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  8.8Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.5Mb
    po    2.4Mb
Package suggested but not available for checking: 'conics'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Package suggested but not available for checking: 'pd.hg.u133.plus.2'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rcplex.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      1.2Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    include  38.1Mb
    libs      1.4Mb
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    include  47.2Mb
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    include   9.6Mb
    libs      1.2Mb
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
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.1Mb
GNU make is a SystemRequirements.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.3Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    include        7.2Mb
    jsonexamples   3.8Mb
    libs           2.0Mb
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.2Mb
'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  6.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   1.5Mb
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
'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
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.8Mb
'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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.1Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    redengine  16.6Mb
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.1Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
'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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'Rcplex'
'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  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.4Mb
'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
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: \_
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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: \_ \_
Package suggested but not available for checking: 'resourcecodedata'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.3Mb
    java      2.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs      1.7Mb
    models    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/revert.Rcheck/00install.out' for details.
'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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rfast2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rfast.Rcheck/00install.out' for details.
Problems with news in 'NEWS.md':
No news entries found.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    data  13.1Mb
'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  5.4Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.2Mb
    extdata   1.9Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
'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
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc     7.1Mb
    fonts   1.5Mb
    libs    2.7Mb
'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 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
'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:
  'mimic.demo', 'eicu.demo'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Riemann.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/RiemBase.Rcheck/00install.out' for details.
'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  7.9Mb
  sub-directories of 1Mb or more:
    lib    3.3Mb
    libs   4.1Mb
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    'run_Rmainloop'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLinit', 'R_RunExitFinalizers', 'R_SetParams', 'R_TempDir',
    'Rf_endEmbeddedR', 'Rf_initEmbeddedR', 'getRUser', 'get_R_HOME',
    '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
'LazyData' is specified without a 'data' directory
Running examples in 'RISCA-Ex.R' failed
The error most likely occurred in:

> ### Name: markov.3states.rsadd
> ### Title: 3-state Relative Survival Markov Model with Additive Risks
> ### Aliases: markov.3states.rsadd
> ### Keywords: Markov
> 
> ### ** Examples
> 
> # import the observed data
> # (X=1 corresponds to initial state with a functioning graft, X=2 to acute rejection episode, 
> # X=3 to return to dialysis, X=4 to death with a functioning graft)
> 
> data(dataDIVAT1)
> 
> # A subgroup analysis to reduce the time needed for this example
> 
> dataDIVAT1$id<-c(1:nrow(dataDIVAT1))
> set.seed(2)
> d3<-dataDIVAT1[dataDIVAT1$id %in% sample(dataDIVAT1$id, 200, replace = FALSE),]
> 
> # Individuals with trajectory 13 and 123 are 
> # censored at the time of transition into state X=3
> 
> d3$trajectory[d3$trajectory==13]<-1
> d3$trajectory[d3$trajectory==123]<-12
> d3$trajectory[d3$trajectory==14]<-13
> d3$trajectory[d3$trajectory==124]<-123
> 
> # import the expected mortality rates
> 
> data(fr.ratetable)
> 
> # 3-state Markov model with additive risks including one explicative variable 
> # (z is the delayed graft function) on all transitions. We only reduced
> # the precision and the number of iteration to save time in this example,
> # prefer the default values.
> 
> markov.3states.rsadd(times1=d3$time1, times2=d3$time2, sequences=d3$trajectory,
+   dist=c("E","E","E"), ini.dist.12=c(8.34),
+   ini.dist.13=c(10.70), ini.dist.23=c(11.10),
+   cov.12=d3$z, init.cov.12=c(0.04), names.12=c("beta12_z"),
+   cov.13=d3$z, init.cov.13=c(1.04), names.13=c("beta1E_z"),
+   cov.23=d3$z, init.cov.23=c(0.29), names.23=c("beta2E_z"),
+   p.age=d3$ageR*365.24, p.sex=d3$sexR,
+   p.year=as.date(paste("01","01",d3$year.tx), order = "mdy"),
+   p.rate.table=fr.ratetable,  conf.int=TRUE,
+   silent=FALSE, precision=0.001)
Error in as.date(paste("01", "01", d3$year.tx), order = "mdy") : 
  could not find function "as.date"
Calls: markov.3states.rsadd
Execution halted
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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 for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

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
'LazyData' is specified without a 'data' directory
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      3.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  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 50.2Mb
  sub-directories of 1Mb or more:
    R     4.0Mb
    exe  45.7Mb
'LazyData' is specified without a 'data' directory
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.8Mb
'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: \$
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lemon   2.9Mb
    libs    2.1Mb
Error(s) in re-building vignettes:
--- re-building 'RLescalation.Rmd' using rmarkdown
File man/figures/logo.png not found in resource path
Error: processing vignette 'RLescalation.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'RLescalation.Rmd'

SUMMARY: processing the following file failed:
  'RLescalation.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
GNU make is a SystemRequirements.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include   7.4Mb
    lib       3.0Mb
    libs      5.7Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Running examples in 'rllama-Ex.R' failed
The error most likely occurred in:

> ### Name: get_defillama_stablecoin_data
> ### Title: Stablecoins Data
> ### Aliases: get_defillama_stablecoin_data
> 
> ### ** Examples
> 
> stablecoin_data = get_defillama_stablecoin_data()
Error in circulating * price : non-numeric argument to binary operator
Calls: get_defillama_stablecoin_data -> [ -> [.data.table -> eval -> eval
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
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rnaturalearthhires'
'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  7.0Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
GNU make is a SystemRequirements.
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  5.6Mb
  sub-directories of 1Mb or more:
    libs       1.0Mb
    minizinc   2.3Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Package unavailable to check Rd xrefs: 'cmdstanr'
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.
Error(s) in re-building vignettes:
--- re-building 'rnaCrosslinkOO.Rmd' using rmarkdown
File rnaCrosslinkProtocol.jpg not found in resource path
Error: processing vignette 'rnaCrosslinkOO.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'rnaCrosslinkOO.Rmd'

SUMMARY: processing the following file failed:
  'rnaCrosslinkOO.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rnaturalearthhires'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.3Mb
'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:
    data   2.8Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Specified C++11: please drop specification unless essential
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  d:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.3.0\include\emmintrin.h:134:24: 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 'd:/Rcompile/CRANpkg/local/4.3/RobustGaSP.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
* used C++ compiler: 'g++.exe (GCC) 12.3.0'
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc               1.7Mb
    libs              1.3Mb
    simulationStudy   1.6Mb
'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) 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
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc  15.2Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.4Mb
  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
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
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/ROracle.Rcheck/00install.out' for details.
'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      2.0Mb
    data   2.7Mb
    libs   1.5Mb
'LazyData' is specified without a 'data' directory
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.7Mb
    libs   1.7Mb
Package suggested but not available for checking: 'RandomFields'
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/Rpoppler.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
'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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  5.5Mb
  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
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
'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  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
GNU make is a SystemRequirements.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.3/Rserve/libs/x64/Rserve.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'R_Visible',
    'Rf_initialize_R', 'setup_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. 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
'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: 'gurobi'
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: 'INLA'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   1.5Mb
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
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    4.7Mb
    libs  11.6Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    exec   1.7Mb
    lib    1.9Mb
    libs   1.5Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
Specified C++11: please drop specification unless essential
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    libs    1.1Mb
    swipl  40.5Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    rmarkdown  11.0Mb
GNU make is a SystemRequirements.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Specified C++11: please drop specification unless essential
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   7.7Mb
'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:
    R   5.0Mb
Specified C++11: please drop specification unless essential
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   9.8Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  'nimble' 'nimbleAPT'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'glmmADMB'
Found the following significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      5.3Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rWCVPdata'
Specified C++11: please drop specification unless essential
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
'LazyData' is specified without a 'data' directory
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    include   1.1Mb
    libs      4.8Mb
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'unix'
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
Specified C++14: please drop specification unless essential
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
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
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
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 15.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.6Mb
Specified C++11: please drop specification unless essential
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   1.3Mb
Package suggested but not available for checking: 'networkTomography'
'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
GNU make is a SystemRequirements.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.0Mb
GNU make is a SystemRequirements.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   1.2Mb
'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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
'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
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/scDHA.Rcheck/00install.out' for details.
'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
'LazyData' is specified without a 'data' directory
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    cppad     9.5Mb
    include   4.7Mb
    libs      2.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'ScottKnott-Ex.R' failed
The error most likely occurred in:

> ### Name: SK
> ### Title: The SK Test for Single Experiments
> ### Aliases: SK SK.default SK.aov SK.lm SK.formula SK.aovlist SK.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='SK')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> sk1 <- with(RCBD,
+             SK(y ~ blk + tra,
+                data=dfm,
+                which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... eval -> SK -> SK.formula -> SK -> SK.lm -> data.frame
Execution halted
'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
'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
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'MuSiC', 'seAMLessData'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   8.1Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    extdata  18.0Mb
'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:
    R      1.6Mb
    libs   2.1Mb
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
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
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    www  34.4Mb
'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
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs     3.3Mb
    models   1.6Mb
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++14: please drop specification unless essential
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    libs   1.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: 'doMC'
GNU make is a SystemRequirements.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'pwalign'
GNU make is a SystemRequirements.
'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:
    doc    1.2Mb
    libs   3.2Mb
GNU make is a SystemRequirements.
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: \&
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sessioninfo)
  > 
  > test_check("sessioninfo")
  Starting 2 test processes
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 115 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (14): 'test-dependent-packages.R:84:3',
    'test-dependent-packages.R:92:3', 'test-warnings.R:4:3',
    'test-warnings.R:37:3', 'test-warnings.R:63:3', 'test-warnings.R:101:3',
    'test-diff.R:15:3', 'test-diff.R:27:3', 'test-diff.R:168:3',
    'test-diff.R:235:3', 'test-diff.R:243:3', 'test-diff.R:300:3',
    'test-diff.R:342:3', 'test-diff.R:356:3'
  • On Windows (1): 'test-diff.R:126:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-diff.R:114:3'): get_session_info_url ───────────────────────────
  Error in `find_session_info_in_html(url, html)`: Cannot parse session info from 'https://github.com/r-lib/sessioninfo/issues/6'.
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-diff.R:114:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─sessioninfo:::get_session_info_url(url)
   5.   └─sessioninfo:::find_session_info_in_html(url, html)
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 115 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'BPCells'
Packages suggested but not available for checking: 'BPCells', 'presto'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.2Mb
'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  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is 107.6Mb
  sub-directories of 1Mb or more:
    doc      1.8Mb
    gdal     3.0Mb
    libs    89.8Mb
    proj     8.4Mb
    sqlite   1.5Mb
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  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
'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'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.4Mb
'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 20.5Mb
  sub-directories of 1Mb or more:
    www  19.7Mb
'LazyData' is specified without a 'data' directory
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
'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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    shinymgr    1.4Mb
    tutorials   3.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
'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.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www  10.1Mb
'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
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
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    help      1.7Mb
    libs      1.0Mb
'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 significant warnings:

  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
  Warning: 'adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error(s) in re-building vignettes:
--- re-building 'sim.BA.Rmd' using rmarkdown
File images/dag.png not found in resource path
Error: processing vignette 'sim.BA.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sim.BA.Rmd'

SUMMARY: processing the following file failed:
  'sim.BA.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    extdata  13.0Mb
    libs      1.5Mb
'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.
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
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++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
Problems with news in 'NEWS.md':
No news entries found.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   1.8Mb
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
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(sjtable2df)
  > 
  > test_check("sjtable2df")
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  boundary (singular) fit: see help('isSingular')
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-mtab2df.R:48:5', 'test-mtab2df.R:136:5',
    'test-xtab2df.R:36:5', 'test-xtab2df.R:206:5', 'test-xtab2df.R:253:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-mtab2df.R:134:5'): correct functioning of mtab2df: glmer ─────
  nrow(final_tab) == 10 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 5 | SKIP 5 | PASS 18 ]
  Error: Test failures
  Execution halted
Package which this enhances but not available for checking: 'kmndirs'
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'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:
    doc   4.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
GNU make is a SystemRequirements.
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 significant warnings:

  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
  Warning: 'vegan::adonis' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/SmartSVA.Rcheck/00install.out' for details.
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.1Mb
'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
Package suggested but not available for checking: 'doMC'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    3.4Mb
    libs   1.7Mb
'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'
'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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   1.1Mb
checkRd: (-1) llwrPTF.Rd:7: 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:
    data   1.3Mb
    doc    1.3Mb
    libs   1.7Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'SciencesPo'
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.0Mb
Package suggested but not available for checking: 'gridlayout'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
    libs      1.1Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'NLMR'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   4.8Mb
Package suggested but not available for checking: 'NLMR'
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs   1.9Mb
'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
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
S3 methods shown with full name in documentation object 'SparseM.ontology':
  'as.matrix.csr' 'is.matrix.csr' 'is.matrix.csc' 'is.matrix.ssr'
  'is.matrix.ssc' 'is.matrix.coo'

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.
'LazyData' is specified without a 'data' directory
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
Package suggested but not available for checking: 'INLA'
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    help   1.7Mb
    libs   1.1Mb
Specified C++14: please drop specification unless essential
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', '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.univar',
  '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.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', '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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'spDataLarge'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
    etc   2.1Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(spectralGraphTopology)
  
  Attaching package: 'spectralGraphTopology'
  
  The following object is masked from 'package:stats':
  
      D
  
  > 
  > test_check("spectralGraphTopology")
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-learnGraphTopology.R:21:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-learnSmoothSignalGraph.R:9:1'): (code run outside of `test_that()`) ──
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  ── Error ('test-operators.R:122:1'): (code run outside of `test_that()`) ───────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::pmap(all_pars, build_and_run_test, desc = desc_stub, code = captured, 
      .interpret_glue = .interpret_glue)`: ℹ In index: 1.
  Caused by error:
  ! Failed to parse glue component
  Caused by error in `parse()`:
  ! <text>:1:1: unexpected ','
  1: ,
      ^
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 43 ]
  Error: Test failures
  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
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
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
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.8Mb
    doc    1.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   2.6Mb
    libs      1.7Mb
Specified C++11: please drop specification unless essential
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   1.8Mb
'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 of 10th May 2021
Specified C++11: please drop specification unless essential
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running examples in 'squat-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.qtsclust
> ### Title: Plot for 'qtsclust' objects
> ### Aliases: autoplot.qtsclust
> 
> ### ** Examples
> 
> ## Don't show: 
> if (requireNamespace("ggplot2", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
+ ggplot2::autoplot(out)
+ ## Don't show: 
+ }) # examplesIf
> out <- kmeans(vespa64$igp[1:10], n_clusters = 2)
Error in `check_option_compatibility()`:
! The L2 metric is neither dilation-invariant nor affine-invariant.
Backtrace:
     ▆
  1. ├─(if (getRversion() >= "3.4") withAutoprint else force)(...)
  2. │ └─base::source(...)
  3. │   ├─base::withVisible(eval(ei, envir))
  4. │   └─base::eval(ei, envir)
  5. │     └─base::eval(ei, envir)
  6. ├─squat::kmeans(vespa64$igp[1:10], n_clusters = 2)
  7. └─squat:::kmeans.qts_sample(vespa64$igp[1:10], n_clusters = 2)
  8.   └─fdacluster::fdakmeans(...)
  9.     └─fdacluster:::check_option_compatibility(...)
 10.       └─cli::cli_abort("The L2 metric is neither dilation-invariant nor affine-invariant.")
 11.         └─rlang::abort(...)
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    shiny-squid   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
'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  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running examples in 'ssifs-Ex.R' failed
The error most likely occurred in:

> ### Name: smokingcessation
> ### Title: Stochastic Search Inconsistency Factor Selection of
> ###   interventions for smoking cessation
> ### Aliases: smokingcessation
> 
> ### ** Examples
> 
> data(smokingcessation)
> 
> # Transform data from arm-based format to contrast-based format
> 
> smokingcessation$id <- 1:dim(smokingcessation)[1]
> smoking.pair <- netmeta::pairwise(
+   treat = list(treat1, treat2, treat3),
+   event = list(event1, event2, event3),
+   n = list(n1, n2, n3),
+   studlab = id,
+   data = smokingcessation,
+   sm = "OR"
+ )
Error: 'pairwise' is not an exported object from 'namespace:netmeta'
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include  11.3Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'starsdata'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    nc    1.7Mb
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.4Mb
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
Package suggested but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'
unable to reach CRAN

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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    shiny-apps   6.1Mb
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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
'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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
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++14: please drop specification unless essential
Package suggested but not available for checking: 'StrathE2E2examples'
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
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'LazyData' is specified without a 'data' directory
Error(s) in re-building vignettes:
--- re-building 'stratifyR-vignette.Rmd' using rmarkdown

Quitting from lines 636-641 [unnamed-chunk-9] (stratifyR-vignette.Rmd)
Error: processing vignette 'stratifyR-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'stratifyR-vignette.Rmd'

SUMMARY: processing the following file failed:
  'stratifyR-vignette.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Malformed Title field: should not end in a period.
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
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
installed size is  9.1Mb
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    doc    7.1Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'STRaitRazoR'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.1Mb
    help   1.0Mb
installed size is  5.4Mb
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    lib    2.8Mb
    libs   1.6Mb
Package suggested but not available for checking: 'velocyto.R'
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'extraTrees'
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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: 'INLA'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.3Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'INLA'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    doc    2.5Mb
Package suggested but not available for checking: 'gurobi'
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc', 'INLA'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    5.3Mb
Specified C++11: please drop specification unless essential
'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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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    dist3   2.0Mb
    dist4   1.7Mb
    dist5   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'swephRdata'
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
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
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Error(s) in re-building vignettes:
--- re-building 'odesystem.Rmd' using rmarkdown

Quitting from lines 77-83 [unnamed-chunk-5] (odesystem.Rmd)
Error: processing vignette 'odesystem.Rmd' failed with diagnostics:
Error 1 occurred building shared library.
--- failed re-building 'odesystem.Rmd'

--- re-building 'quick_start.Rmd' using rmarkdown
--- finished re-building 'quick_start.Rmd'

SUMMARY: processing the following file failed:
  'odesystem.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
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'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'unix'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    libs   1.4Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.1Mb
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installed size is 13.6Mb
  sub-directories of 1Mb or more:
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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
'LazyData' is specified without a 'data' directory
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
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Package suggested but not available for checking: 'tashudata'
'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
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    8.2Mb
    libs   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.3/TDA.Rcheck/00install.out' for details.
Specified C++11: please drop specification unless essential
Running examples in 'teal.modules.clinical-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_gee
> ### Title: teal Module: Generalized Estimating Equations (GEE) analysis
> ### Aliases: tm_a_gee
> 
> ### ** 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 <- teal_data()
> data <- within(data, {
+   ADSL <- tmc_ex_adsl
+   ADQS <- tmc_ex_adqs %>%
+     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+     mutate(
+       AVISIT = as.factor(AVISIT),
+       AVISITN = rank(AVISITN) %>%
+         as.factor() %>%
+         as.numeric() %>%
+         as.factor(),
+       AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
+     ) %>%
+     droplevels()
+ })
> datanames <- c("ADSL", "ADQS")
> datanames(data) <- datanames
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> join_keys(data) <- default_cdisc_join_keys[datanames]
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_gee(
+       label = "GEE",
+       dataname = "ADQS",
+       aval_var = choices_selected("AVALBIN", fixed = TRUE),
+       id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+       arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
+       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+       paramcd = choices_selected(
+         choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
+         selected = "FKSI-FWB"
+       ),
+       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
+     )
+   )
+ )
Initializing tm_a_gee (prototype)
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in 'teal.modules.general-Ex.R' failed
The error most likely occurred in:

> ### Name: tm_a_pca
> ### Title: 'teal' module: Principal component analysis
> ### Aliases: tm_a_pca
> 
> ### ** Examples
> 
> library(teal.widgets)
> 
> # general data example
> data <- teal_data()
> data <- within(data, {
+   require(nestcolor)
+   USArrests <- USArrests
+ })
> 
> datanames(data) <- "USArrests"
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
> 
> app <- init(
+   data = data,
+   modules = modules(
+     tm_a_pca(
+       "PCA",
+       dat = data_extract_spec(
+         dataname = "USArrests",
+         select = select_spec(
+           choices = variable_choices(
+             data = data[["USArrests"]], c("Murder", "Assault", "UrbanPop", "Rape")
+           ),
+           selected = c("Murder", "Assault"),
+           multiple = TRUE
+         ),
+         filter = NULL
+       ),
+       ggplot2_args = ggplot2_args(
+         labs = list(subtitle = "Plot generated by PCA Module")
+       )
+     )
+   )
+ )
[INFO] 2025-01-31 18:09:27.0909 pid:37208 token:[] teal.modules.general Initializing tm_a_pca
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Running examples in 'teal-Ex.R' failed
The error most likely occurred in:

> ### Name: example_module
> ### Title: An example 'teal' module
> ### Aliases: example_module
> 
> ### ** Examples
> 
> app <- init(
+   data = teal_data(IRIS = iris, MTCARS = mtcars),
+   modules = example_module()
+ )
Error in as.list(data@env) : 
  no slot of name "env" for this object of class "teal_data"
Calls: init -> create_app_id -> as.list
Execution halted
Error(s) in re-building vignettes:
--- re-building 'adding-support-for-reporting.Rmd' using rmarkdown

Quitting from lines 106-112 [unnamed-chunk-4] (adding-support-for-reporting.Rmd)
Error: processing vignette 'adding-support-for-reporting.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'adding-support-for-reporting.Rmd'

--- re-building 'bootstrap-themes-in-teal.Rmd' using rmarkdown
--- finished re-building 'bootstrap-themes-in-teal.Rmd'

--- re-building 'creating-custom-modules.Rmd' using rmarkdown

Quitting from lines 174-183 [unnamed-chunk-4] (creating-custom-modules.Rmd)
Error: processing vignette 'creating-custom-modules.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'creating-custom-modules.Rmd'

--- re-building 'data-as-shiny-module.Rmd' using rmarkdown
--- finished re-building 'data-as-shiny-module.Rmd'

--- re-building 'filter-panel.Rmd' using rmarkdown
--- finished re-building 'filter-panel.Rmd'

--- re-building 'getting-started-with-teal.Rmd' using rmarkdown

Quitting from lines 33-52 [unnamed-chunk-1] (getting-started-with-teal.Rmd)
Error: processing vignette 'getting-started-with-teal.Rmd' failed with diagnostics:
no slot of name "env" for this object of class "teal_data"
--- failed re-building 'getting-started-with-teal.Rmd'

--- re-building 'including-data-in-teal-applications.Rmd' using rmarkdown
--- finished re-building 'including-data-in-teal-applications.Rmd'

--- re-building 'teal-options.Rmd' using rmarkdown
--- finished re-building 'teal-options.Rmd'

SUMMARY: processing the following files failed:
  'adding-support-for-reporting.Rmd' 'creating-custom-modules.Rmd'
  'getting-started-with-teal.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
Package suggested but not available for checking: 'INLA'
'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:
    doc   5.9Mb
installed size is  9.5Mb
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    doc    5.5Mb
    help   2.7Mb
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installed size is 108.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    gdal   3.0Mb
    libs  92.9Mb
    proj   8.4Mb
installed size is 23.3Mb
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    libs       8.1Mb
    tessdata  14.0Mb
Package suggested but not available for checking: 'gurobi'
'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:
    data   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
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
'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
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installed size is  8.8Mb
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    data   1.1Mb
    rda    7.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
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    R      4.1Mb
    data   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
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    R              1.2Mb
    threeBrainJS   2.9Mb
'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
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
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Minor changes:
Error(s) in re-building vignettes:
--- re-building 'creating_prompt_wraps.Rmd' using rmarkdown
--- finished re-building 'creating_prompt_wraps.Rmd'

--- re-building 'getting_started.Rmd' using rmarkdown
File ../man/figures/answer_using_r1-1.png not found in resource path
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'getting_started.Rmd'

--- re-building 'sentiment_analysis.Rmd' using rmarkdown
File ../man/figures/plot_sentiment_analysis-1.png not found in resource path
Error: processing vignette 'sentiment_analysis.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'sentiment_analysis.Rmd'

SUMMARY: processing the following files failed:
  'getting_started.Rmd' 'sentiment_analysis.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tidystats)
  This version of tidystats uses a new and improved way of structuring statistics. This breaks previous (major) versions of tidystats.
  > 
  > test_check("tidystats")
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_glm.R:118:3'): glm anova works ───────────────────────────────
  `tidy_model` not equal to `expected_tidy_model`.
  Component "groups": Component 1: Component 2: Component 2: Component 2: Length mismatch: comparison on first 4 components
  Component "groups": Component 1: Component 2: Component 3: Component 2: Length mismatch: comparison on first 4 components
  Backtrace:
      ▆
   1. └─tidystats:::expect_equal_models(model = model, expected_tidy_model = expected_statistics$anova_glm) at test_glm.R:118:3
   2.   └─testthat::expect_equal(tidy_model, expected_tidy_model, tolerance = tolerance)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 183 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'rrelaxiv'
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
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
'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  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:131:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:334:16: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:453:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:471:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:496:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:497:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:509:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:522:9: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  D:/RCompile/recent/R-4.3.3/Tcl/include/X11/Xlib.h:1053:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:93:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
  tcltkimg.c:94:1: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/tkrplot.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    examples  12.7Mb
    include    3.6Mb
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:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
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'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: 'gurobi'
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    R         5.8Mb
    help      1.7Mb
    include   1.9Mb
    libs     18.3Mb
Package suggested but not available for checking: 'toscaData'
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.8Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'taxidata'
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  13.4Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Packages suggested but not available for checking: 'fwelnet', 'doMC'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'Capr'
Package suggested but not available for checking: 'TreeDistData'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.3Mb
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    datasets   1.6Mb
    doc        1.3Mb
    libs       1.1Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    doc       1.3Mb
    extdata  14.8Mb
Problems with news in 'NEWS.md':
No news entries found.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   7.3Mb
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.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'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
GNU make is a SystemRequirements.
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'
'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: \&
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
'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  7.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
'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 Description field: should contain one or more complete sentences.
Running examples in 'TukeyC-Ex.R' failed
The error most likely occurred in:

> ### Name: TukeyC
> ### Title: The TukeyC Test for Single Experiments
> ### Aliases: TukeyC TukeyC.default TukeyC.lm TukeyC.formula TukeyC.aovlist
> ###   TukeyC.lmerMod
> ### Keywords: package
> 
> ### ** Examples
> 
> ##
> ## Examples:Randomized Complete Block Design (RCBD)
> ## More details: demo(package='TukeyC')
> ##
> 
> ## The parameters can be: formula, aov, lm, aovlist and lmerMod
> 
> data(RCBD)
> 
> ## From: formula
> tk1 <- with(RCBD,
+             TukeyC(y ~ blk + tra,
+                    data=dfm,
+                    which='tra'))
Error in data.frame(means = aux_mt1, reps = reps) : 
  arguments imply differing number of rows: 0, 5
Calls: with ... TukeyC.formula -> TukeyC -> TukeyC.lm -> data.frame
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
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 which this enhances but not available for checking: 'sl3'
'LazyData' is specified without a 'data' directory
'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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc     4.5Mb
    ubinc   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   4.4Mb
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data       1.1Mb
    doc        1.4Mb
    shinyapp   4.9Mb
Specified C++11: please drop specification unless essential
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.6Mb
'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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   2.6Mb
'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
Specified C++14: please drop specification unless essential
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
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
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.1Mb
    libs  14.9Mb
GNU make is a SystemRequirements.
'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   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'USA.state.boundaries.data'
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
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
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: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
'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:
  randutils.c:60:12: warning: function declaration isn't a prototype [-Wstrict-prototypes]
See 'd:/Rcompile/CRANpkg/local/4.3/uuid.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.0Mb
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
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 104.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    gdal      3.0Mb
    libs     88.9Mb
    proj      8.4Mb
'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
'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
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
'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) 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: \&
'LazyData' is specified without a 'data' directory
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.0Mb
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   5.2Mb
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc           2.0Mb
    htmlwidgets   6.8Mb
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       5.4Mb
    extdata   1.1Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'INLA'
Package unavailable to check Rd xrefs: 'INLA'
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     19.9Mb
GNU make is a SystemRequirements.
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
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   8.5Mb
'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  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'LazyData' is specified without a 'data' directory
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   1.0Mb
'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
Package suggested but not available for checking: 'prepr'
Problems with news in 'NEWS.md':
No news entries found.
Error(s) in re-building vignettes:
--- re-building 'use_case.Rmd' using rmarkdown
--- finished re-building 'use_case.Rmd'

--- re-building 'weatherOz.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz.Rmd'

--- re-building 'weatherOz_for_BOM.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz_for_BOM.Rmd'

--- re-building 'weatherOz_for_DPIRD.Rmd' using rmarkdown_notangle
File vignettes/view_sw_ag_region-1.png not found in resource path
Error: processing vignette 'weatherOz_for_DPIRD.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building 'weatherOz_for_DPIRD.Rmd'

--- re-building 'weatherOz_for_SILO.Rmd' using rmarkdown_notangle
--- finished re-building 'weatherOz_for_SILO.Rmd'

SUMMARY: processing the following file failed:
  'weatherOz_for_DPIRD.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    client   9.1Mb
    doc      1.0Mb
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
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
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   3.6Mb
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 'WindCurves_Info.Rmd' using rmarkdown

Quitting from lines 66-77 [unnamed-chunk-3] (WindCurves_Info.Rmd)
Error: processing vignette 'WindCurves_Info.Rmd' failed with diagnostics:
dumpdata.R:2:1: unexpected '<'
1: random <-
2: <
   ^
--- failed re-building 'WindCurves_Info.Rmd'

SUMMARY: processing the following file failed:
  'WindCurves_Info.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
Package suggested but not available for checking: 'wordnetDicts'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.1Mb
'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:
    data   6.5Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
Package suggested but not available for checking: 'wmtsa'
Malformed Title field: should not end in a period.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.5Mb
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    help   1.9Mb
    libs   1.0Mb
'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:
    bin   5.6Mb
'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:
    libs   4.6Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    java  26.1Mb
Problems with news in 'NEWS.md':
No news entries found.
'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
Found the following significant warnings:
  DocParse.c:1334:5: warning: 'xmlKeepBlanksDefault' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:134:7: warning: 'xmlSkipBlankChars' is deprecated [-Wdeprecated-declarations]
  RSDTD.c:135:7: warning: 'xmlParseMarkupDecl' is deprecated [-Wdeprecated-declarations]
  RUtils.c:142:5: warning: 'xmlSubstituteEntitiesDefault' is deprecated [-Wdeprecated-declarations]
See 'd:/Rcompile/CRANpkg/local/4.3/XML.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.3.0'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running examples in 'Xplortext-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.LexChar
> ### Title: Plot LexChar objects
> ### Aliases: plot.LexChar
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), var.agg="Gen_Edu", Fmin=10, Dmin=10,
+         remov.number=TRUE, stop.word.tm=TRUE)
> LD<-LexChar(res.TD,maxCharDoc = 0)
> plot(LD)
Error in `gtable_add_grob()`:
! `grobs` must be a single grob or a list of grobs, not a list.
Backtrace:
     ▆
  1. ├─base::plot(LD)
  2. └─Xplortext:::plot.LexChar(LD)
  3.   ├─base::suppressWarnings(...)
  4.   │ └─base::withCallingHandlers(...)
  5.   └─Xplortext (local) marrangeGrob2(grobs = pword, nrow = numr, ncol = numc, top = top)
  6.     ├─base::do.call(gridExtra::arrangeGrob, c(grobs[groups[[g]]], params))
  7.     └─gridExtra (local) `<fn>`(...)
  8.       └─gtable::gtable_add_grob(grobs = grobs)
  9.         └─gtable:::stop_input_type(grobs, "a single grob or a list of grobs")
 10.           └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.4Mb
'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
Error(s) in re-building vignettes:
--- re-building 'a01_introduction.Rmd' using rmarkdown
--- finished re-building 'a01_introduction.Rmd'

--- re-building 'a02_workflow-tidycensus.Rmd' using rmarkdown

Quitting from lines 29-35 [unnamed-chunk-2] (a02_workflow-tidycensus.Rmd)
Error: processing vignette 'a02_workflow-tidycensus.Rmd' failed with diagnostics:
Failure when receiving data from the peer [api.census.gov]: Recv failure: Connection was reset
--- failed re-building 'a02_workflow-tidycensus.Rmd'

--- re-building 'a03_developer-notes.Rmd' using rmarkdown
--- finished re-building 'a03_developer-notes.Rmd'

SUMMARY: processing the following file failed:
  'a02_workflow-tidycensus.Rmd'

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
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: \_
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory