File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
Running examples in ‘Hmisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: summaryP
> ### Title: Multi-way Summary of Proportions
> ### Aliases: summaryP plot.summaryP ggplot.summaryP latex.summaryP
> ### Keywords: hplot category manip
> 
> ### ** Examples
> 
> n <- 100
> f <- function(na=FALSE) {
+   x <- sample(c('N', 'Y'), n, TRUE)
+   if(na) x[runif(100) < .1] <- NA
+   x
+ }
> set.seed(1)
> d <- data.frame(x1=f(), x2=f(), x3=f(), x4=f(), x5=f(), x6=f(), x7=f(TRUE),
+                 age=rnorm(n, 50, 10),
+                 race=sample(c('Asian', 'Black/AA', 'White'), n, TRUE),
+                 sex=sample(c('Female', 'Male'), n, TRUE),
+                 treat=sample(c('A', 'B'), n, TRUE),
+                 region=sample(c('North America','Europe'), n, TRUE))
> d <- upData(d, labels=c(x1='MI', x2='Stroke', x3='AKI', x4='Migraines',
+                  x5='Pregnant', x6='Other event', x7='MD withdrawal',
+                  race='Race', sex='Sex'))
Input object size:	 13016 bytes;	 12 variables	 100 observations
New object size:	17800 bytes;	12 variables	100 observations
> dasna <- subset(d, region=='North America')
> with(dasna, table(race, treat))
          treat
race        A  B
  Asian     8 10
  Black/AA 13  6
  White     4 10
> s <- summaryP(race + sex + ynbind(x1, x2, x3, x4, x5, x6, x7, label='Exclusions') ~
+               region + treat, data=d)
> # add exclude1=FALSE below to include female category
> plot(s, groups='treat')
Warning in matrix(0, n.row, n.col) :
  NAs introduced by coercion to integer range
Error in matrix(0, n.row, n.col) : invalid 'nrow' value (too large or NA)
Calls: <Anonymous> ... evaluate.legend -> do.call -> fun -> draw.key -> matrix
Execution halted
Running examples in ‘Hmsc-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotGradient
> ### Title: plotGradient
> ### Aliases: plotGradient
> 
> ### ** Examples
> 
> # Plot response of species 2 over the gradient of environmental variable x1
> Gradient = constructGradient(TD$m, focalVariable="x1")
# weights:  3 (2 variable)
initial  value 34.657359 
final  value 34.655390 
converged
> predY = predict(TD$m, Gradient=Gradient)
Error in PiNew[, r] <- sapply(dfPiNew[, r], function(s) which(rowNames ==  : 
  incorrect number of subscripts on matrix
Calls: predict -> predict.Hmsc
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
File ‘HotDeckImputation/libs/HotDeckImputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
File ‘hpa/libs/hpa.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.7Mb
  sub-directories of 1Mb or more:
    libs  67.1Mb
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
    doc    2.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.9Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Mmusculus.UCSC.mm10'
Packages unavailable to check Rd xrefs: ‘BSgenome.Hsapiens.1000genomes.hs37d5’, ‘BSgenome.Mmusculus.UCSC.mm10’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/icd.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   8.1Mb
Running ‘testthat.R’ [45s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # this is common code to all the tests, each of which runs test_check with a
  > # different filter:
  > library("icd")
  > library("testthat", warn.conflicts = FALSE, quietly = TRUE)
  > icd:::.show_options()
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > # Definitely don't download data on CRAN
  > if (!icd:::.env_var_is_true("NOT_CRAN")) {
  +   old_offline <- options("icd.data.offline" = TRUE)
  +   on.exit(options(old_offline), add = TRUE)
  + } else {
  +   old_offline <- options("icd.data.offline" = FALSE)
  +   on.exit(options(old_offline), add = TRUE)
  + }
  > if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
  +   old_test_slow <- options("icd.test_slow" = TRUE)
  +   on.exit(options(old_test_slow), add = TRUE)
  + }
  > old_interact <- options("icd.data.interact" = FALSE)
  > on.exit(options(old_interact), add = TRUE)
  > icd:::.show_options()
  $icd.data.interact
  [1] FALSE
  
  $icd.data.offline
  [1] TRUE
  
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > testthat::test_check("icd")
  loading helper-base.R
  loading helper-icd10.R
  ── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333)  ───
  van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
  Component "id": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: van_walraven comodbidity index and score (@test-score.R#333) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
File ‘icemelt/libs/icemelt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
File ‘icensmis/libs/icensmis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  25.2Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     43.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Running ‘testthat.R’ [79s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(iml)
  > 
  > test_check("iml")
  ── 1. Failure: probs.to.labels (@test-utils.R#20)  ─────────────────────────────
  probs.to.labels(probs) not equal to `labels`.
  Component "..class": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 510 | SKIPPED: 0 | WARNINGS: 48 | FAILED: 1 ]
  1. Failure: probs.to.labels (@test-utils.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Immigrate.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
File ‘IndependenceTests/libs/IndependenceTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.6Mb
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘infoDecompuTE-Ex.R’ failed
The error most likely occurred in:

> ### Name: summaryAovOnePhase
> ### Title: Summarize an Theoretical Analysis of Variance Model of
> ###   Single-Phase Experiments
> ### Aliases: summaryAovOnePhase
> ### Keywords: design
> 
> ### ** Examples
> 
> 
> design1 <- local({ 
+   Ani = as.factor(LETTERS[c(1,2,3,4,
+                             5,6,7,8)])
+   Trt = as.factor(letters[c(1,1,1,1,
+                             2,2,2,2)])
+   data.frame(Ani, Trt)
+ })
> 
> summaryAovOnePhase(design1, blk.str = "Ani", trt.str = "Trt") 
Error in eigen(t(T) %*% t(N) %*% C %*% N %*% T) : 0 x 0 matrix
Calls: summaryAovOnePhase ... lapply -> FUN -> getEffFactor -> invInfMat -> eigen
Execution halted
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Running ‘testthat.R’ [165s/432s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
File ‘intervals/libs/intervals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EValue’ ‘tidyverse’
  All declared Imports should be used.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Namespaces in Imports field not imported from:
  ‘chron’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘reshape2’
  ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘dplyr’ ‘testthat’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:492:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/iRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.0Mb
Error(s) in re-building vignettes:
--- re-building ‘isocat.Rmd’ using rmarkdown
Quitting from lines 206-214 (isocat.Rmd) 
Error: processing vignette 'isocat.Rmd' failed with diagnostics:
indivIDs must be of class 'vector' or 'factor'.
--- failed re-building ‘isocat.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘pangaear’ ‘rcrossref’ ‘rgdal’ ‘stringr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘acf.Rmd’ using rmarkdown
--- finished re-building ‘acf.Rmd’

--- re-building ‘inspect.Rmd’ using rmarkdown
Quitting from lines 101-106 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘inspect.Rmd’

--- re-building ‘test.Rmd’ using rmarkdown
Quitting from lines 187-200 (test.Rmd) 
Error: processing vignette 'test.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘test.Rmd’

SUMMARY: processing the following files failed:
  ‘inspect.Rmd’ ‘test.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          20.6Mb
Running ‘testthat.R’ [14s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  
  Attaching package: 'janitor'
  
  The following objects are masked from 'package:stats':
  
      chisq.test, fisher.test
  
  > 
  > test_check("janitor")
  ── 1. Failure: totals col is correct (@test-add-totals.R#33)  ──────────────────
  untabyl(adorn_totals(ct, "col")) not equal to data.frame(...).
  Component "a": Modes: character, numeric
  Component "a": Attributes: < target is NULL, current is list >
  Component "a": target is character, current is factor
  
  ── 2. Failure: values are converted to NAs at the data.frame level (@test-clean-
  cleaned_df[[2]] not equal to factor(c(NA, NA, "b"), levels = c("a", "b")).
  Types not compatible: character is not integer
  
  Reading layer `nc' from data source `/data/gannet/ripley/R/test-clang/sf/shape/nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  ── 3. Failure: show_missing_levels parameter works (@test-tabyl.R#216)  ────────
  z %>% tabyl(a, b, new, show_missing_levels = TRUE) not equal to list(...).
  Component "lvl1": Attributes: < Component "core": Component "a": 'current' is not a factor >
  Component "lvl1": Component "a": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 554 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: totals col is correct (@test-add-totals.R#33) 
  2. Failure: values are converted to NAs at the data.frame level (@test-clean-NAs.R#31) 
  3. Failure: show_missing_levels parameter works (@test-tabyl.R#216) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/JavaGD.Rcheck/00install.out’ for details.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.7Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/jomo.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘survC1’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.8Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jsonify)
  > 
  > test_check("jsonify")
  ── 1. Failure: column factors return levels and characters (@test-to_json_datafr
  as.character(js) not equal to "{\"id\":[1,2,3,4,5],\"val\":[1,2,3,4,5]}".
  1/1 mismatches
  x[1]: "{\"id\":[1,2,3,4,5],\"val\":[\"a\",\"b\",\"c\",\"d\",\"e\"]}"
  y[1]: "{\"id\":[1,2,3,4,5],\"val\":[1,2,3,4,5]}"
  
  ── 2. Failure: factors work as expected (@test-to_json_vectors.R#99)  ──────────
  as.character(to_json(df, factors_as_string = FALSE)) not equal to "[{\"x\":1},{\"x\":1},{\"x\":1}]".
  1/1 mismatches
  x[1]: "[{\"x\":\"a\"},{\"x\":\"a\"},{\"x\":\"a\"}]"
  y[1]: "[{\"x\":1},{\"x\":1},{\"x\":1}]"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 381 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: column factors return levels and characters (@test-to_json_dataframe.R#119) 
  2. Failure: factors work as expected (@test-to_json_vectors.R#99) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Running examples in ‘kamila-Ex.R’ failed
The error most likely occurred in:

> ### Name: classifyKamila
> ### Title: Classify new data into existing KAMILA clusters
> ### Aliases: classifyKamila
> 
> ### ** Examples
> 
> # Generate toy data set
> set.seed(1234)
> dat1 <- genMixedData(400, nConVar = 2, nCatVar = 2, nCatLevels = 4,
+   nConWithErr = 2, nCatWithErr = 2, popProportions = c(.5,.5),
+   conErrLev = 0.2, catErrLev = 0.2)
> # Partition the data into training/test set
> trainingIds <- sample(nrow(dat1$conVars), size = 300, replace = FALSE)
> catTrain <- data.frame(apply(dat1$catVars[trainingIds,], 2, factor))
> conTrain <- data.frame(scale(dat1$conVars)[trainingIds,])
> catTest <- data.frame(apply(dat1$catVars[-trainingIds,], 2, factor))
> conTest <- data.frame(scale(dat1$conVars)[-trainingIds,])
> # Run the kamila clustering procedure on the training set
> kamilaObj <- kamila(conTrain, catTrain, numClust = 2, numInit = 10)
Error in matrix(data = log(gtools::rdirichlet(n = numClust, alpha = rep(1,  : 
  length of 'dimnames' [2] not equal to array extent
Calls: kamila -> lapply -> FUN -> matrix
Execution halted
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.4Mb
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mice’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.3Mb
File ‘ktspair/libs/ktspair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  17.6Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("LaF")
  Loading required package: LaF
  ── 1. Failure: detect_dm_csv works (@test_meta.R#74)  ──────────────────────────
  `x` not equal to `expected`.
  target is NULL, current is character
  
  ── 2. Failure: detect_dm_csv works (@test_meta.R#75)  ──────────────────────────
  `x` not equal to `expected`.
  1/8 mismatches
  x[3]: ""
  y[3]: NA
  
  ── 3. Failure: detect_dm_csv works (@test_meta.R#79)  ──────────────────────────
  `x` isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 168 | SKIPPED: 0 | WARNINGS: 42 | FAILED: 3 ]
  1. Failure: detect_dm_csv works (@test_meta.R#74) 
  2. Failure: detect_dm_csv works (@test_meta.R#75) 
  3. Failure: detect_dm_csv works (@test_meta.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
Package suggested but not available for checking: ‘zipcode’

Suggests orphaned packages:
  ‘car’ ‘data.table’ ‘ggplot2’ ‘googleVis’ ‘knitr’ ‘lattice’ ‘reshape2’
  ‘rmarkdown’ ‘tidyr’ ‘vcd’ ‘zipcode’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘run_tests.R’
Running the tests in ‘tests/run_tests.R’ failed.
Complete output:
  > library(testthat)
  > library(lambda.r)
  
  Attaching package: 'lambda.r'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > library(lambda.tools)
  > test_package('lambda.tools')
  ── 1. Failure: A named data.frame has the correct types (@test_any.R#47)  ──────
  `ts` not equal to c("numeric", "factor", "logical").
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ── 2. Failure: An unnamed data.frame has the correct types (@test_any.R#56)  ───
  `ts` not equal to c("numeric", "factor", "logical").
  1/3 mismatches
  x[2]: "character"
  y[2]: "factor"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 110 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: A named data.frame has the correct types (@test_any.R#47) 
  2. Failure: An unnamed data.frame has the correct types (@test_any.R#56) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
File ‘LambertW/libs/LambertW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.0Mb
    help   1.1Mb
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in ‘lavaSearch2-Ex.R’ failed
The error most likely occurred in:

> ### Name: iid2
> ### Title: Extract corrected i.i.d. decomposition
> ### Aliases: iid2 iid2.lm iid2.gls iid2.lme iid2.lvmfit iid2.lm2 iid2.gls2
> ###   iid2.lme2 iid2.lvmfit2
> 
> ### ** Examples
> 
> n <- 5e1
> p <- 3
> X.name <- paste0("X",1:p)
> link.lvm <- paste0("Y~",X.name)
> formula.lvm <- as.formula(paste0("Y~",paste0(X.name,collapse="+")))
> 
> m <- lvm(formula.lvm)
> distribution(m,~Id) <- sequence.lvm(0)
Error in sequence.lvm(0) : could not find function "sequence.lvm"
Execution halted
Running ‘test-all.R’ [135s/158s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library(lavaSearch2)
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("lavaSearch2")
  Loading required package: lavaSearch2
  Loading required package: ggplot2
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  lavaSearch2 version 1.5.4
  ── 1. Error: (unknown) (@test1-sCorrect-validObjects.R#48)  ────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(lvm(G ~ X1), data = d)
   2. lava:::estimate.lvm(lvm(G ~ X1), data = d)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 2. Error: (unknown) (@test2-modelsearch2.R#37)  ─────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m, data = df.sim)
   2. lava:::estimate.lvm(m, data = df.sim)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 3. Error: (unknown) (@test3-multcomp.R#149)  ────────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m.lvm, df.data)
   2. lava:::estimate.lvm(m.lvm, df.data)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 464 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: (unknown) (@test1-sCorrect-validObjects.R#48) 
  2. Error: (unknown) (@test2-modelsearch2.R#37) 
  3. Error: (unknown) (@test3-multcomp.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘ReinforcementLearning’ ‘ggplot2’ ‘grDevices’ ‘h2o’ ‘lubridate’
  ‘magrittr’ ‘openssl’ ‘readr’ ‘stringr’
  All declared Imports should be used.
File ‘lbfgsb3/libs/lbfgsb3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/lda.svi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘tm’
  All declared Imports should be used.
Running ‘tests.R’
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > library(ldat)
  Loading required package: lvec
  
  Attaching package: 'lvec'
  
  The following object is masked from 'package:base':
  
      order
  
  Loading required package: Rcpp
  
  Attaching package: 'ldat'
  
  The following objects are masked from 'package:base':
  
      append, match, table, which
  
  > library(testthat)
  > 
  > test_check("ldat")
  ── 1. Failure: as_ldat works (@test_ldat.R#26)  ────────────────────────────────
  lvec_type(x$b) not equal to "integer".
  1/1 mismatches
  x[1]: "character"
  y[1]: "integer"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 386 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: as_ldat works (@test_ldat.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘lemon-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)

Attaching package: ‘ggplot2’

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

    element_render

> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in upgradeUnit.default(list(0, NULL, 1L)) : Not a unit object
Calls: <Anonymous> ... <Anonymous> -> pSummary -> <Anonymous> -> upgradeUnit.default
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lemon)
  > 
  > 
  > if (TRUE) {
  +   test_check("lemon")
  + } #else {
  ── 1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_
  `l + 1` threw an error with unexpected message.
  Expected match: "Don't know how to add 1 to a plot"
  Actual message: "Can't add `1` to a ggplot object."
  Backtrace:
   1. testthat::expect_error(...)
   6. ggplot2:::`+.gg`(l, 1)
   7. ggplot2:::add_ggplot(e1, e2, e2name)
   9. ggplot2:::ggplot_add.default(object, p, objectname)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 137 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: ggplot2 does not break lemon_plot by altering class (@test_lemon_plot.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘capped-axes.Rmd’ using rmarkdown
--- finished re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
--- finished re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
Quitting from lines 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
invalid line type
--- failed re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
Quitting from lines 42-61 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘gtable_show_lemonade.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘geoms.Rmd’ ‘gtable_show_lemonade.Rmd’

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘liayson.Rnw’ using Sweave

Error: processing vignette 'liayson.Rnw' failed with diagnostics:
 chunk 1 
Error in bmRequest(request = request, verbose = verbose) : 
  Service Unavailable (HTTP 503).

--- failed re-building ‘liayson.Rnw’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    extdata   1.2Mb
    libs      7.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
  All declared Imports should be used.
Running examples in ‘lilikoi-Ex.R’ failed
The error most likely occurred in:

> ### Name: lilikoi.get_pd_scores
> ### Title: A lilikoi.get_pd_scores Function
> ### Aliases: lilikoi.get_pd_scores
> 
> ### ** Examples
> 
> filename <- system.file("extdata", "plasma_breast_cancer.csv", package = "lilikoi")
> data <- read.csv(file = filename, check.names = FALSE, row.names = 1)[, 1:20]
> metaboliteNames <- colnames(data)[-1]
> matches <- lilikoi.metab_to_pathway(metaboliteNames, "name")
[1] "18 out of 19 Matched metabolites 90 %"
[1] "1 out of 19 UnMatched metabolites 0 %"
> PDSmatrix <- lilikoi.get_pd_scores(data, matches, lilikoi::data.smpdb[1:23,], maxit = 1)
Warning in function_list[[i]](value) : NAs introduced by coercion
robust_score_bydist. min_exp= 0 , min_std= 0 
Error in matrix(0, attempts, m) : invalid 'ncol' value (too large or NA)
Calls: lilikoi.get_pd_scores -> .quantify_pathways_deregulation -> matrix
Execution halted
Running ‘testthat.R’ [16s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lilikoi)
  > 
  > test_check("lilikoi")
  [1] "18 out of 19 Matched metabolites 90 %"
  [1] "1 out of 19 UnMatched metabolites 0 %"
  robust_score_bydist. min_exp= 0 , min_std= 0 
  ── 1. Error: full pipeline works (@test-all.r#12)  ─────────────────────────────
  invalid 'ncol' value (too large or NA)
  Backtrace:
   1. lilikoi::lilikoi.get_pd_scores(...)
   2. lilikoi:::.quantify_pathways_deregulation(...)
   3. base::matrix(0, attempts, m)
  
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
  [1] "1 out of 4 Matched metabolites 60 %"
  [1] "3 out of 4 UnMatched metabolites 40 %"
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "4 out of 5 Matched metabolites 80 %"
  [1] "1 out of 5 UnMatched metabolites 20 %"
  [1] "1 out of 1 Matched metabolites 100 %"
  [1] "0 out of 1 UnMatched metabolites 0 %"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: full pipeline works (@test-all.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  10.4Mb
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs      20.4Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘logisticRR.Rmd’ using rmarkdown
Quitting from lines 162-169 (logisticRR.Rmd) 
Error: processing vignette 'logisticRR.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘logisticRR.Rmd’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Namespace in Imports field not imported from: ‘futile.options’
  All declared Imports should be used.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 51.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.1Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   1.8Mb
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘etm’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   6.9Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.3Mb
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.5Mb
    libs         47.1Mb
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘brew’ ‘svglite’ ‘uuid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  10.4Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs  11.3Mb
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.4Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 52.1Mb
  sub-directories of 1Mb or more:
    libs  51.1Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘methods’ ‘purrr’
  All declared Imports should be used.
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘mds’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.1Mb
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘coxphw’ ‘gmodels’
  All declared Imports should be used.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.9Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.1Mb
installed size is 122.9Mb
  sub-directories of 1Mb or more:
    libs  122.3Mb
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘foreign’ ‘gplots’ ‘httr’ ‘jsonlite’ ‘knitr’ ‘lmerTest’
  ‘magrittr’ ‘mgcv’ ‘repmis’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 123.5Mb
  sub-directories of 1Mb or more:
    libs  123.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘metricTester-Ex.R’ failed
The error most likely occurred in:

> ### Name: killSomeBig
> ### Title: Remove most closely related individuals for large arenas
> ### Aliases: killSomeBig
> 
> ### ** Examples
> 
> #simulate tree with birth-death process
> tree <- geiger::sim.bdtree(b=0.1, d=0, stop="taxa", n=50)
> 
> #prep the data for the simulation
> prepped <- prepSimulations(tree, arena.length=300, mean.log.individuals=1, 
+ length.parameter=5000, sd.parameter=50, max.distance=20, proportion.killed=0.2,
+ competition.iterations=5)
> 
> #use the random simulation to generate a starting arena
> random <- randomArena(prepped)
> 
> #in normal use, these parameters will be carried down from the simulations.input object
> new.arena <- killSomeBig(tree, arena.output=random, max.distance=50, 
+ proportion.killed=0.2)
Error in dis[sppInSample, sppInSample] : subscript out of bounds
Calls: killSomeBig -> modifiedMPD
Execution halted
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  24.7Mb
    misc   1.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Running examples in ‘mfbvar-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot-mfbvar
> ### Title: Plotting methods for posterior mfbvar objects
> ### Aliases: plot-mfbvar plot.mfbvar_ss plot.mfbvar_ssng plot.mfbvar_minn
> ###   plot.mfbvar_dl varplot
> 
> ### ** Examples
> 
> prior_obj <- set_prior(Y = mf_sweden[, 4:5], d = "intercept",
+                        freq = c("m", "q"), n_lags = 4, n_burnin = 20, n_reps = 20,
+                        n_fcst = 4, n_fac = 1)
> 
> prior_intervals <- matrix(c(-0.1, 0.1,
+                             0.4, 0.6), ncol = 2, byrow = TRUE)
> psi_moments <- interval_to_moments(prior_intervals)
> prior_psi_mean <- psi_moments$prior_psi_mean
> prior_psi_Omega <- psi_moments$prior_psi_Omega
> prior_obj <- update_prior(prior_obj,
+                           prior_psi_mean = prior_psi_mean,
+                           prior_psi_Omega = prior_psi_Omega)
> 
> mod_ss <- estimate_mfbvar(prior_obj, prior = "ss", variance = "fsv")
> plot(mod_ss)
Error in vapply(guides, function(guide) identical(guide$position, position),  : 
  argument "panel_params" is missing, with no default
Calls: plot ... panel_guide_label -> %||% -> guide_for_position -> vapply
Execution halted
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
Running examples in ‘mfe-Ex.R’ failed
The error most likely occurred in:

> ### Name: infotheo
> ### Title: Information-theoretic meta-features
> ### Aliases: infotheo infotheo.default infotheo.formula
> 
> ### ** Examples
> 
> ## Extract all metafeatures
> infotheo(Species ~ ., iris)
Error in `[.data.frame`(x, , j) : undefined columns selected
Calls: infotheo ... concentration.coefficient -> table -> [ -> [.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘mfe-vignette.Rmd’ using rmarkdown
Quitting from lines 55-66 (mfe-vignette.Rmd) 
Error: processing vignette 'mfe-vignette.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘mfe-vignette.Rmd’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.6Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Running ‘testthat.R’ [29s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores── 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  ── 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  start Ranking Schemes on cluster with  2 cores── 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘mipfp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   7.7Mb
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [291s/552s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  ── 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  ───────────
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  ── 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘classiFunc’

Suggests orphaned packages:
  ‘clValid’ ‘flare’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.4Mb
Running examples in ‘mlr-Ex.R’ failed
The error most likely occurred in:

> ### Name: generateLearningCurveData
> ### Title: Generates a learning curve.
> ### Aliases: generateLearningCurveData LearningCurveData
> 
> ### ** Examples
> 
> r = generateLearningCurveData(list("classif.rpart", "classif.knn"),
+   task = sonar.task, percs = seq(0.2, 1, by = 0.2),
+   measures = list(tp, fp, tn, fn), resampling = makeResampleDesc(method = "Subsample", iters = 5),
+   show.info = FALSE)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 0, 10
Calls: generateLearningCurveData -> cbind -> cbind -> data.frame
Execution halted
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘modelStudio-Ex.R’ failed
The error most likely occurred in:

> ### Name: modelStudio
> ### Title: Generate Interactive Studio for Explanatory Model Analysis
> ### Aliases: modelStudio modelStudio.explainer
> 
> ### ** Examples
> 
> library("DALEX")
Welcome to DALEX (version: 1.0.1).
Find examples and detailed introduction at: https://pbiecek.github.io/ema/

> library("modelStudio")
> 
> #:# ex1 classification on 'titanic_imputed' dataset
> 
> # Create a model
> model_titanic <- glm(survived ~.,
+                      data = titanic_imputed,
+                      family = "binomial")
> 
> # Wrap it into an explainer
> explain_titanic <- explain(model_titanic,
+                            data = titanic_imputed[,-8],
+                            y = titanic_imputed[,8],
+                            label = "glm",
+                            verbose = FALSE)
> 
> # Pick some data points
> new_observations <- titanic_imputed[1:2,]
> rownames(new_observations) <- c("Lucas","James")
> 
> # Make a studio for the model
> modelStudio(explain_titanic, new_observations,
+             N = 100, B = 10, show_info = FALSE)
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: modelStudio ... modelStudio.explainer -> prepare_partial_dependence -> droplevels
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [19s/65s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("modelStudio")
  > library("DALEX")
  Welcome to DALEX (version: 1.0.1).
  Find examples and detailed introduction at: https://pbiecek.github.io/ema/
  
  > library("randomForest")
  randomForest 4.6-14
  Type rfNews() to see new features/changes/bug fixes.
  > 
  > test_check("modelStudio")
  ── 1. Error: (unknown) (@test_modelStudio.R#5)  ────────────────────────────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
    1. testthat::expect_silent(...)
   10. modelStudio:::modelStudio.explainer(...)
   11. modelStudio:::prepare_partial_dependence(pd_n, pd_c, variables = variable_names)
   12. base::droplevels(aggregated_profiles$`_vname_`)
  
  ── 2. Error: (unknown) (@test_modelStudioOptions.R#76)  ────────────────────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. modelStudio::modelStudio(...)
   2. modelStudio:::modelStudio.explainer(...)
   3. modelStudio:::prepare_partial_dependence(pd_n, pd_c, variables = variable_names)
   4. base::droplevels(aggregated_profiles$`_vname_`)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test_modelStudio.R#5) 
  2. Error: (unknown) (@test_modelStudioOptions.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘BioStatR’ ‘ggplot2’
  All declared Imports should be used.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   9.0Mb
Running ‘testthat.R’ [113s/162s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.4Mb
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 79.4Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         75.5Mb
    mathematica   1.5Mb
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  15.2Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  26.6Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  18.5Mb
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
Running examples in ‘MST-Ex.R’ failed
The error most likely occurred in:

> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
Error in plot.window(...) : need finite 'ylim' values
Calls: MST -> plot -> plot.default -> localWindow -> plot.window
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
Execution halted
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
installed size is 83.3Mb
  sub-directories of 1Mb or more:
    libs  83.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (!requireNamespace("testthat", quietly=TRUE)) install.packages("testthat", dependencies=TRUE, repos="http://cran.rstudio.com/")
  > library(nbc4va)
  To view the 'nbc4va' package description see: 
  help(nbc4va) 
  
  To view the 'nbc4va' package documentation, see: 
  https://rrwen.github.io/nbc4va 
  
  To cite the original method used in the 'nbc4va' package see: 
  citation("nbc4va")
  > 
  > testthat::test_check("nbc4va")
  ── 1. Failure: (unknown) (@test_nbc4va.R#29)  ──────────────────────────────────
  `results <- nbc(train, test)` did not produce any warnings.
  
  ── 2. Failure: (unknown) (@test_nbc4va.R#32)  ──────────────────────────────────
  `resultsNoCauses <- nbc(train, noCauses, known = FALSE)` did not produce any warnings.
  
  ── 3. Failure: nbc() sets the out$test.known to correctly indicate whether or no
  `expect_equal(...)` did not produce any warnings.
  
  ── 4. Error: nbc() can handle incorrect column data types in the correct positio
  The train data IDs are not unique (duplicates found:)
  Backtrace:
   1. testthat::expect_warning(...)
   6. nbc4va:::internalCheckNBC(trainTypes, testTypes)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 68 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 4 ]
  1. Failure: (unknown) (@test_nbc4va.R#29) 
  2. Failure: (unknown) (@test_nbc4va.R#32) 
  3. Failure: nbc() sets the out$test.known to correctly indicate whether or not the test causes are known (@test_nbc4va.R#46) 
  4. Error: nbc() can handle incorrect column data types in the correct positions (@test_nbc4va.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(neighbr)
  > 
  > test_check("neighbr")
  ── 1. Failure: knn with jaccard object contains expected items - 1 (@test_knn.R#
  fit$categorical_levels not equal to c("green", "orange", "red").
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 92 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: knn with jaccard object contains expected items - 1 (@test_knn.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.8Mb
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Running examples in ‘nFactors-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              6.1Mb
    classic-bugs   1.6Mb
    include        5.7Mb
    libs          17.2Mb
    tests          1.6Mb
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘KernelKnn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘multicool’ ‘mvnfast’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stars’
  All declared Imports should be used.
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘arrow’
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘nonlinearTseries_quickstart.Rmd’ using rmarkdown
Quitting from lines 91-94 (nonlinearTseries_quickstart.Rmd) 
Error: processing vignette 'nonlinearTseries_quickstart.Rmd' failed with diagnostics:
need finite 'ylim' values
--- failed re-building ‘nonlinearTseries_quickstart.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  20.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.3Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readODS’ ‘xlsx’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   3.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
Running examples in ‘ODEnetwork-Ex.R’ failed
The error most likely occurred in:

> ### Name: setEvents
> ### Title: Setting Events
> ### Aliases: setEvents
> 
> ### ** Examples
> 
> masses <- 1
> dampers <- as.matrix(1.5)
> springs <- as.matrix(4)
> odenet <- ODEnetwork(masses, dampers, springs)
> eventdat <- data.frame(  var = c("x.1", "x.1")
+                        , time = c(1, 3)
+                        , value = c(1, 3)
+                        )
> odenet <- setState(odenet, 0, 0)
> odenet <- setEvents(odenet, eventdat)
Error: Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ODEnetwork.Rmd’ using rmarkdown
Quitting from lines 168-175 (ODEnetwork.Rmd) 
Error: processing vignette 'ODEnetwork.Rmd' failed with diagnostics:
Assertion failed. One of the following must apply:
 * checkDataFrame(events): May only contain the following types:
 * {factor,numeric,numeric}, but element 1 has type 'character'
 * checkDataFrame(events): Must have exactly 4 cols, but has 3 cols
--- failed re-building ‘ODEnetwork.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.1Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Running examples in ‘opencastR-Ex.R’ failed
The error most likely occurred in:

> ### Name: oc_group
> ### Title: Query Opencast for a specific group
> ### Aliases: oc_group
> 
> ### ** Examples
> 
> Sys.setenv(OPENCAST_HOST = "https://legacy.opencast.org")
> Sys.setenv(OPENCAST_USERNAME = "admin")
> Sys.setenv(OPENCAST_PASSWORD = "opencast")
> 
> oc_group("MH_DEFAULT_ORG_EXTERNAL_APPLICATIONS")
Error: lexical error: invalid char in json text.
                                       Cannot find a group with id 'MH
                     (right here) ------^
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.2Mb
installed size is 211.6Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    201.5Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
  possible bashism in configure line 79 ($(OS|MACH)TYPE):
  case "$OSTYPE" in
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      6.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.8Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’
File ‘OriGen/libs/OriGen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   7.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Running examples in ‘OTE-Ex.R’ failed
The error most likely occurred in:

> ### Name: OTClass
> ### Title: Train the ensemble of optimal trees for classification.
> ### Aliases: OTClass
> ### Keywords: OTClass OptTreesEns
> 
> ### ** Examples
> 
> #load the data
> 
>   data(Body)
>   data <- Body
>   
> #Divide the data into training and test parts
> 
>   set.seed(9123) 
>   n <- nrow(data)
>   training <- sample(1:n,round(2*n/3))
>   testing <- (1:n)[-training]
>   X <- data[,1:24]
>   Y <- data[,25]
>   
> #Train OTClass on the training data
> 
>   Opt.Trees <- OTClass(XTraining=X[training,],YTraining = Y[training],t.initial=200)
Assessing trees for individual performance..............
Error in order(er) : unimplemented type 'list' in 'orderVector1'
Calls: OTClass -> order
Execution halted
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Running examples in ‘packMBPLSDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_pred_mbplsda
> ### Title: Plot the results of the fonction pred_mbplsda in a pdf file
> ### Aliases: plot_pred_mbplsda
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(status)
> data(medical)
> data(omics)
> data(nutrition)
> ktabX <- ktab.list.df(list(medical = medical, nutrition = nutrition, omics = omics))
> disjonctif <- (disjunctive(status))
> dudiY   <- dudi.pca(disjonctif , center = FALSE, scale = FALSE, scannf = FALSE)
> bloYobs <- 2
> ncpopt <- 1
> modelembplsQ <- mbplsda(dudiY, ktabX, scale = TRUE, option = "uniform", scannf = FALSE, nf = 2)
> predictions <- pred_mbplsda(modelembplsQ, optdim = ncpopt, threshold = 0.5, 
+ bloY=bloYobs, algo = c("max", "gravity", "threshold"))
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
> plot_pred_mbplsda(predictions,"plotPred_nf1", propbestvar=0.20)
Error in as.graphicsAnnot(legend) : 
  argument "legend" is missing, with no default
Calls: plot_pred_mbplsda -> legend -> as.graphicsAnnot
Execution halted
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Quitting from lines 77-79 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘GenomicAlignments’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘network’ ‘scales’ ‘sna’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [11s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PANICr)
  > 
  > test_check("PANICr")
  ── 1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25)  ────────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = TRUE) not equal to `test_10_dm`.
  Component "MP.tests": Component "pool_test": Modes: character, numeric
  Component "MP.tests": Component "pool_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "pool_test": target is character, current is factor
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ── 2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40)  ────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = FALSE) not equal to `test_10_ndm`.
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25) 
  2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘M3C’
Running ‘run-all.R’ [22s/29s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  ── 1. Failure: requires works (@test_OptPath.R#198)  ───────────────────────────
  d[, 1:4] not equal to data.frame(...).
  Component "x": 'current' is not a factor
  
  ── 2. Error: plotEAF works (@test_plotEAF.R#27)  ───────────────────────────────
  groups must be a factor
  Backtrace:
   1. ParamHelpers::plotEAF(opt.paths)
   4. eaf:::eafplot.formula(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1050 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: requires works (@test_OptPath.R#198) 
  2. Error: plotEAF works (@test_plotEAF.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘patchDVI/libs/patchDVI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Running examples in ‘patternplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: imagebar_s
> ### Title: Plot a stacked bar chart with bars filled with png and jpeg
> ###   images.
> ### Aliases: imagebar_s
> 
> ### ** Examples
> 
> library(patternplot)
> library(jpeg)
> library(ggplot2)
> 
> childcare<-readJPEG(system.file("img", "childcare.jpg", package="patternplot"))
> food<-readJPEG(system.file("img", "food.jpg", package="patternplot"))
> housing <-readJPEG(system.file("img", "housing.jpg", package="patternplot"))
> 
> data <- read.csv(system.file("extdata", "monthlyexp.csv", package="patternplot"))
> x<-data$Location
> y<-data$Amount
> group<-data$Type
> pattern.type<-list(childcare, food, housing)
> 
> imagebar_s(data,x, y, group, xlab='', ylab='Monthly Expenses, Dollar',
+ pattern.type=pattern.type, label.size=3.5, frame.size=1, frame.color='black',
+ legend.type='h', legend.h=6, legend.y.pos=0.49, legend.pixel=20, legend.w=0.2,
+  legend.x.pos=1.1)+scale_y_continuous(limits = c(0, 6800))
Error: geom_text requires the following missing aesthetics: label
Backtrace:
    █
 1. ├─(function (x, ...) ...
 2. └─ggplot2:::print.ggplot(x)
 3.   ├─ggplot2::ggplot_build(x)
 4.   └─ggplot2:::ggplot_build.ggplot(x)
 5.     └─ggplot2:::by_layer(function(l, d) l$compute_geom_1(d))
 6.       └─ggplot2:::f(l = layers[[i]], d = data[[i]])
 7.         └─l$compute_geom_1(d)
 8.           └─ggplot2:::f(..., self = self)
 9.             └─ggplot2:::check_required_aesthetics(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘patternplot-intro.Rmd’ using docco_linear
Quitting from lines 271-281 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
geom_text requires the following missing aesthetics: label
--- failed re-building ‘patternplot-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘animation’ ‘c060’
  ‘cluster’ ‘gplots’ ‘grid’ ‘jetset’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdNCDF4/libs/pbdNCDF4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib  10.0Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      3.2Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is 156.1Mb
  sub-directories of 1Mb or more:
    doc     2.7Mb
    libs  152.9Mb
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.8Mb
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘peperr/libs/peperr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Running ‘testthat.R’ [13s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_phrasemachine.Rmd’ using rmarkdown
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_phrasemachine.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  14.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_pifpaf_package.Rmd’ using rmarkdown
Loading required package: pifpaf
Loading required package: ggplot2
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-async.R’ [22s/28s]
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgmaker)
  Loading required package: registry
  
  Attaching package: 'pkgmaker'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > 
  > test_check("pkgmaker")
  ── 1. Failure: ldata (@test-utils.r#154)  ──────────────────────────────────────
  e[["iris"]] not identical to `a`.
  Component "Species": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 92 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 1 ]
  1. Failure: ldata (@test-utils.r#154) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘PK-Ex.R’ failed
The error most likely occurred in:

> ### Name: nca
> ### Title: Estimation of various PK parameters
> ### Aliases: nca nca.ssd nca.batch nca.complete
> ### Keywords: htest
> 
> ### ** Examples
> 
> #### serial sampling designs
> ## example for a serial sampling data design from Wolfsegger and Jaki (2009)
> conc <- c(0, 0, 0, 2.01, 2.85, 2.43, 0.85, 1.00, 0.91, 0.46, 0.35, 0.63, 0.39, 0.32, 
+           0.45, 0.11, 0.18, 0.19, 0.08, 0.09, 0.06)
> time <- c(rep(0,3), rep(5/60,3), rep(3,3), rep(6,3), rep(9,3), rep(16,3), rep(24,3))
> 
> # Direct call of the function
> # CAUTION: this might take a few minutes
> # Note: 1E4 bootstrap replications were used in the example given 
> # in Wolfsegger and Jaki (2009)
> set.seed(34534)
> nca.ssd(conc=conc, time=time, n.tail=4, dose=200, method=c("z","boott"), 
+          conf.level=0.95, nsample=500)
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: nca.ssd ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.5Mb
Running examples in ‘pla-Ex.R’ failed
The error most likely occurred in:

> ### Name: AgarDiffusionAssay
> ### Title: Antibiotic agar diffusion assay using a rectangular tray
> ### Aliases: AgarDiffusionAssay
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgarDiffusionAssay); Agar <- AgarDiffusionAssay
> Agar <- read.table(paste(system.file(package = "pla"),
+                    "vignettes/PhEur/data/AntibioticAgarDiffusionAssay.txt",
+                    sep = "/"), header = TRUE)
> select   <- c("Row", "Column", "Sample", "Dilution", "Response")
> PHframe  <- data2assayFrame(Agar[, select])
Warning in data2assayFrame(Agar[, select]) : NAs introduced by coercion
> plaModel <- pla(Agar, design = "lsd",
+                 assayTitle = "PhEur: Antibiotic agar diffusion assay")
Warning in data2assayFrame(data[, select], dr = dilutionRatio, design = design) :
  NAs introduced by coercion
Error in if ((indexOfReference == 1) & (indexOfReference != iOR)) indexOfReference <- iOR : 
  argument is of length zero
Calls: pla
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinythemes’
  ‘sqldf’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plethem)
  You are now using PLETHEM.
                          If you have installed PLETHEM for the first time or have just updated it, please run setUserDb() to select an existing database or createUserDb() to create a new one.
  > 
  > test_check("plethem")
  ── 1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19)
  invalid 'type' (list) of argument
  Backtrace:
   1. plethem::getLifecourseTissueVolumes(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.9Mb
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
Running ‘testthat.R’ [107s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotly")
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  ── 1. Error: (unknown) (@test-cookbook-lines.R#192)  ───────────────────────────
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  ── 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  ── 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1395 | SKIPPED: 48 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘pmml-Ex.R’ failed
The error most likely occurred in:

> ### Name: xform_function
> ### Title: Add a function transformation to a xform_wrap object.
> ### Aliases: xform_function
> 
> ### ** Examples
> 
> # Load the standard iris dataset:
> data(iris)
> 
> # Wrap the data:
> iris_box <- xform_wrap(iris)
> 
> # Perform a transform on the Sepal.Length field:
> # the value is squared and then divided by 100
> iris_box <- xform_function(iris_box,
+   orig_field_name = "Sepal.Length",
+   new_field_name = "Sepal.Length.Transformed",
+   expression = "(Sepal.Length^2)/100"
+ )
> 
> # Combine two fields to create another new feature:
> iris_box <- xform_function(iris_box,
+   orig_field_name = "Sepal.Width, Petal.Width",
+   new_field_name = "Width.Sum",
+   expression = "Sepal.Width + Sepal.Length"
+ )
Warning in `[<-.factor`(`*tmp*`, ri, value = c("original", "original", "original",  :
  invalid factor level, NA generated
> 
> # Create linear model using the derived features:
> fit <- lm(Petal.Length ~
+ Sepal.Length.Transformed + Width.Sum, data = iris_box$data)
> 
> # Create pmml from the fit:
> fit_pmml <- pmml(fit, transform = iris_box)
Error in if (transformed$field_data[field$name[i], "type"] == "original") { : 
  missing value where TRUE/FALSE needed
Calls: pmml -> pmml.lm -> append.XMLNode -> .pmmlDataDictionary
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘packages_and_functions.Rmd’ using rmarkdown
--- finished re-building ‘packages_and_functions.Rmd’

--- re-building ‘xform_function.Rmd’ using rmarkdown
Loading required package: XML
Quitting from lines 155-158 (xform_function.Rmd) 
Error: processing vignette 'xform_function.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘xform_function.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘ggthemes’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘memisc’ ‘shinyWidgets’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc  11.8Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘here’ ‘tidyr’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Running examples in ‘preprocomb-Ex.R’ failed
The error most likely occurred in:

> ### Name: setgrid
> ### Title: constructor function for creating the combinations
> ### Aliases: setgrid
> 
> ### ** Examples
> 
> grid <- setgrid(phases=c("outliers", "selection"), data=iris)
[1] "Running diagnostics on single preprocessors:"
Error in initializedataclassobject(data) : 
  Argument 'data' must have one and only one factor column.
Calls: setgrid -> testpreprocessors -> initializedataclassobject
Execution halted
Running ‘testthat.R’ [9s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preprocomb)
  > 
  > test_check("preprocomb")
  [1] "Running diagnostics on single preprocessors:"
  ── 1. Error: (unknown) (@tests.R#23)  ──────────────────────────────────────────
  Argument 'data' must have one and only one factor column.
  Backtrace:
   1. preprocomb::setgrid(phases = c("outliers"), data = modifiediris)
   2. preprocomb::testpreprocessors(unique(unlist(gridclassobject@grid)))
   3. preprocomb::initializedataclassobject(data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@tests.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preproviz)
  > 
  > test_check("preproviz")
  ── 1. Error: (unknown) (@test.R#5)  ────────────────────────────────────────────
  Argument to initializedataobject must have one and only one factor column.
  Backtrace:
   1. preproviz::initializedataobject(testdata)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Running ‘testthat.R’ [6s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  ── 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ──────────
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_preText.Rmd’ using rmarkdown
Quitting from lines 60-69 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building ‘getting_started_with_preText.Rmd’

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

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

> ### Name: prewas
> ### Title: Preprocess SNPs before bGWAS
> ### Aliases: prewas
> 
> ### ** Examples
> 
> vcf = prewas::vcf
> gff = prewas::gff
> tree = prewas::tree
> outgroup = prewas::outgroup
> output <- prewas(dna = vcf,
+                  tree = tree,
+                  outgroup = outgroup,
+                  gff = gff,
+                  anc = FALSE)
Loading required package: vcfR

   *****       ***   vcfR   ***       *****
   This is vcfR 1.10.0 
     browseVignettes('vcfR') # Documentation
     citation('vcfR') # Citation
   *****       *****      *****       *****

Error in check_is_this_class(alleles, "factor") : Input must be a factor
Calls: prewas -> remove_unknown_alleles -> check_is_this_class
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting_started_with_prewas.Rmd’ using rmarkdown
Quitting from lines 98-100 (getting_started_with_prewas.Rmd) 
Error: processing vignette 'getting_started_with_prewas.Rmd' failed with diagnostics:
Input must be a factor
--- failed re-building ‘getting_started_with_prewas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘prim-2d.Rnw’ using Sweave
--- finished re-building ‘prim-2d.Rnw’

--- re-building ‘prim-3d.Rnw’ using Sweave

Error: processing vignette 'prim-3d.Rnw' failed with diagnostics:
 chunk 8 
Error in summ.mat[, 1] * summ.mat[, 2] : 
  non-numeric argument to binary operator

--- failed re-building ‘prim-3d.Rnw’

SUMMARY: processing the following file failed:
  ‘prim-3d.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
File ‘ProbitSpatial/libs/ProbitSpatial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
Running examples in ‘processanimateR-Ex.R’ failed
The error most likely occurred in:

> ### Name: renderer_leaflet
> ### Title: Render as graph on a geographical map
> ### Aliases: renderer_leaflet
> 
> ### ** Examples
> 
> data(example_log)
> 
> # Animate the example process with activities placed in some locations
> animate_process(example_log,
+   renderer = renderer_leaflet(
+     node_coordinates = data.frame(
+        act = c("A", "B", "C", "D", "Start", "End"),
+        lat = c(63.443680, 63.426925, 63.409207, 63.422336, 63.450950, 63.419706),
+        lng = c(10.383625, 10.396972, 10.406418, 10.432119, 10.383368, 10.252347),
+        stringsAsFactors = FALSE),
+     edge_coordinates = data.frame(
+        act_from = c("B"),
+        act_to = c("C"),
+        lat = c(63.419207),
+        lng = c(10.386418),
+        stringsAsFactors = FALSE),
+     options = list(center = c(63.412273, 10.399590), zoom = 12)),
+   duration = 5, repeat_count = Inf)
Error in renderer(processmap, width, height) : 
  Missing coordinates for activitiesARTIFICIAL_ENDMissing coordinates for activitiesARTIFICIAL_START
Calls: animate_process -> renderer
Execution halted
Namespaces in Imports field not imported from:
  ‘expm’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.3Mb
Package suggested but not available for checking: ‘qtbase’
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   3.0Mb
Running examples in ‘PROSPER-Ex.R’ failed
The error most likely occurred in:

> ### Name: gen_diploid
> ### Title: Diploid genetics: recombination of alleles
> ### Aliases: gen_diploid
> 
> ### ** Examples
> 
> # generate a 'dfgenotype' data.frame:
> struc_preparation(Rmx=10, n_loci=2, epis=0, dom=1)
struc_preparation starts...Error in matrix(ncol = n_loci, as.numeric(unlist(strsplit(as.character(dfgenotype[,  : 
  invalid 'ncol' value (too large or NA)
Calls: struc_preparation -> sel_resist -> data.frame -> matrix
Execution halted
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘barebones_correlation.Rmd’ using rmarkdown
--- finished re-building ‘barebones_correlation.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 97-103 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespace in Imports field not imported from: ‘pbv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘performance’ ‘tidyr’
  All declared Imports should be used.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.1Mb
    examples   2.6Mb
Running examples in ‘PTXQC-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_CalibratedMSErr
> ### Title: Plot bargraph of uncalibrated mass errors for each Raw file.
> ### Aliases: plot_CalibratedMSErr
> 
> ### ** Examples
> 
>   n = c(150, 1000, 1000, 1000)
>   data = data.frame(fc.raw.file = repEach(letters[4:1], n),
+                     mass.error..ppm. = c(rnorm(n[1], 1, 2.4),
+                                          rnorm(n[2], 0.5, 0.5),
+                                          rnorm(n[3], 0.1, 0.7),
+                                          rnorm(n[4], 0.3, 0.8)))
>   stats = data.frame(fc.raw.file = letters[4:1],
+                      sd = c(2.4, 0.5, 0.7, 0.8),
+                      outOfCal = c(TRUE, FALSE, FALSE, FALSE))           
>   plot_CalibratedMSErr(data, MQBug_raw_files = letters[1], stats, y_lim = c(-20,20), 15, "subtitle")
Error in scale_x_discrete_reverse(data$fc.raw.file) : 
  Cannot use scale_x_discrete_reverse() on non-factor()
Calls: plot_CalibratedMSErr -> scale_x_discrete_reverse
Execution halted
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘dplyr’
  All declared Imports should be used.
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘FSA’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘fractal’ ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘hms’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    gui          1.7Mb
    staticdocs   3.4Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(qfasar)
  > 
  > test_check("qfasar")
  ── 1. Failure: Prey partitioning is correct (@test_make_prey_part.R#24)  ───────
  round(test_obj$pool_pre, 1) not equivalent to matrix(c(1, 0, 0, 0.4, 0, 0.6), nrow = 2).
  Lengths differ: 1 is not 6
  
  ── 2. Failure: Prey partitioning is correct (@test_make_prey_part.R#26)  ───────
  test_obj$pool_post not equivalent to matrix(c(1, 0, 0, 0, 1, 1), nrow = 3).
  target is logical, current is matrix
  
  ── 3. Error: Replacements of zero and NA are correct (@test_prep_sig.R#19)  ────
  incorrect number of dimensions
  Backtrace:
   1. testthat::expect_equivalent(...)
   2. testthat::quasi_label(enquo(object), label, arg = "object")
   3. rlang::eval_bare(expr, quo_get_env(quo))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 36 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Prey partitioning is correct (@test_make_prey_part.R#24) 
  2. Failure: Prey partitioning is correct (@test_make_prey_part.R#26) 
  3. Error: Replacements of zero and NA are correct (@test_prep_sig.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘orthography_processing.Rmd’ using rmarkdown
--- finished re-building ‘orthography_processing.Rmd’

--- re-building ‘recoding_nominal_data.Rmd’ using rmarkdown
Quitting from lines 49-60 (recoding_nominal_data.Rmd) 
Error: processing vignette 'recoding_nominal_data.Rmd' failed with diagnostics:
factor level [3] is duplicated
--- failed re-building ‘recoding_nominal_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 92.7Mb
  sub-directories of 1Mb or more:
    libs  92.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Error(s) in re-building vignettes:
--- re-building ‘qtlnet.Rnw’ using Sweave
Loading required package: qtl
Loading required package: igraph

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: sem
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    normalize, path, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: ‘graph’

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

    degree, edges, intersection

Loading required package: pcalg

Error: processing vignette 'qtlnet.Rnw' failed with diagnostics:
 chunk 2 
Error in igraph::graph.data.frame(edges, TRUE, vertices = vertices) : 
  Some vertex names in edge list are not listed in vertex data frame

--- failed re-building ‘qtlnet.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.6Mb
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs  13.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  rf.c:454:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/quantregForest.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   5.8Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘R2DT-Ex.R’ failed
The error most likely occurred in:

> ### Name: setRefLevelDT
> ### Title: Setting the reference level of all or a selected set of the
> ###   factor columns of a data.table object
> ### Aliases: setRefLevelDT
> 
> ### ** Examples
> 
> library(data.table)
> inputDT <- as.data.table(data.frame(x = LETTERS[11:20], y = LETTERS[1:10]))
> 
> 
> levels(inputDT$x)[1]
NULL
> levels(inputDT$y)[1]
NULL
> setRefLevelDT(inputDT, c('x', 'y'), c('L', 'C'))
Error in setRefLevelDT(inputDT, c("x", "y"), c("L", "C")) : 
  The variables x, y of the "inputDT" argument are not factors.
Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Package suggested but not available for checking: ‘batchelor’

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.1Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Matrix’ ‘PharmacoGx’ ‘cluster’
  All declared Imports should be used.
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(radjust)
  > test_check("radjust")
  ── 1. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_adaptive` not equivalent to eo$mice_rv_adaptive.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 2. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt_sel` not equivalent to eo$mice_rv_non_adpt_sel.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 3. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt` not equivalent to eo$mice_rv_non_adpt.
  Component "results_table": Component "name": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#9) 
  2. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#10) 
  3. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.2Mb
Found the following significant warnings:
  rf.c:460:17: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/randomForest.Rcheck/00install.out’ for details.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
File ‘rappdirs/libs/rappdirs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  12.6Mb
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   7.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘progress’ ‘rayshader’ ‘scales’
  All declared Imports should be used.
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  30.0Mb
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   8.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.0Mb
    libs      1.8Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    lib    5.0Mb
    libs   1.6Mb
‘configure’: /bin/bash is not portable
  possible bashism in cleanup line 1 (brace expansion):
  rm -f src/*.{o,so}
  possible bashism in cleanup line 2 (brace expansion):
  rm -f src/cwb/cl/*.{a,o}
  possible bashism in cleanup line 4 (brace expansion):
  rm -f src/cwb/cqp/*.{a,o}
  possible bashism in cleanup line 8 (brace expansion):
  rm -r src/cwb/utils/*.{a,o}
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     24.0Mb
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      42.4Mb
    libs     12.9Mb
File ‘RcppMLPACK/libs/RcppMLPACK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       3.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.4Mb
    libs      5.5Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    jsonexamples   3.8Mb
    libs           1.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
Running examples in ‘RCrypto-Ex.R’ failed
The error most likely occurred in:

> ### Name: CoinMarketCap_Ticker
> ### Title: 'Coinmarketcap' Select Ticker Symbol
> ### Aliases: CoinMarketCap_Ticker
> 
> ### ** Examples
> 
> MyData <- CoinMarketCap_Ticker(currency = "CAD",ticker = "ETH")
Error in symbol %in% c(ticker) : object 'symbol' not found
Calls: CoinMarketCap_Ticker ... as.data.frame -> filter -> filter.tbl_df -> filter_impl -> %in%
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Running examples in ‘rCUR-Ex.R’ failed
The error most likely occurred in:

> ### Name: rCUR-package
> ### Title: CUR matrix decomposition package
> ### Aliases: rCUR-package rCUR
> ### Keywords: svd prcomp
> 
> ### ** Examples
> 
> library(rCUR)
> library(lattice)
> 
> data(STTm)
> data(STTa)
> 
> n = 27
> res = CUR(STTm, 31, n, 4)
> 
> plotLeverage(res, C=FALSE, top.n=n, xlab='Gene ID', las=1, top.col='black', 
+   top.pch=16, ul.col='black', ul.lty=2, col='grey')
> 
> PCA01 = prcomp(STTm, scale=TRUE)
> 
> top.idx = topLeverage(res, C=FALSE, top.n=n, sort=FALSE)
> top.STTm = STTm[top.idx,]
> PCA02 = prcomp(top.STTm, scale=TRUE)
> 
> t.top.STTm = t(top.STTm)
> x = 1:dim(t.top.STTm)[1]
> y = 1:dim(t.top.STTm)[2]
> 
> ann.tab = STTa[top.idx,]
> genes = as.character(ann.tab$Gene)
> genes[genes==''] = as.character(ann.tab[genes=='','Hs'])
> 
> op = par(mar=c(3.5, 0, 0, 5) + 0.1)
> image(x, y, t.top.STTm, col=rev(gray(0:256/300)), axes=FALSE, xlab='', 
+   ylab='')
> axis(1, at=c(10,22,31), labels=c('GIST','LEIO','SARC'), tick=FALSE, 
+   las=2, cex=0.6, line=-0.8)
> axis(4, at=1:length(genes), labels=genes, tick=FALSE, las=1, cex=0.6, 
+   line=-0.8)
> par(op)
> 
> PCAs = rbind(PCA01$rotation[,c(1,2)], PCA02$rotation[,c(1,2)])
> group = rownames(PCAs)
> pchs = ifelse(group=='GIST', 16, 0)
> pchs = ifelse(group=='LEIO', 17, pchs)
> pchs = ifelse(group=='SARC', 18, pchs)
> PCAs = data.frame(PC1=PCAs[,1], PC2=PCAs[,2], 
+   lab=c(rep('all',31),rep('selected',31)), group, pchs)
> 
> xyplot(PC2 ~ PC1 | lab, data = PCAs, pch=pchs, cex=1.0, col='black', 
+   fill='black', key = list(space = "bottom", text = list(levels(PCAs$group)), 
+   points=TRUE, pch=c(16, 17, 18), fill='black', columns=3, just=1))
Error in fun(key = base::quote(list(space = "bottom", text = list(NULL),  : 
  first component of text must be vector of labels
Calls: <Anonymous> ... print.trellis -> printFunction -> evaluate.legend -> do.call -> fun
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # library(AER)
  > # library(sandwich)
  > # library(lmtest)
  > # library(Formula)
  > library(rddapp)
  > library(rdd)
  Loading required package: sandwich
  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: AER
  Loading required package: car
  Loading required package: carData
  Loading required package: survival
  Loading required package: Formula
  > library(rddtools)
  Error in library(rddtools) : there is no package called 'rddtools'
  Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rdsdp.Rcheck/00install.out’ for details.
File ‘Rdsdp/libs/Rdsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.3Mb
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.5Mb
Running ‘testthat.R’ [72s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(recipes)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("recipes", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("recipes")
  + }
  Loading required namespace: xml2
  ── 1. Failure: add appropriate column with default settings (@test_intercept.R#2
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 2. Failure: adds arbitrary numeric column (@test_intercept.R#33)  ───────────
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 3. Failure: check_new_values works on factors (@test_newvalues.R#135)  ──────
  `res` not equal to `x1`.
  Incompatible type for column `a`: x factor, y character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1431 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: add appropriate column with default settings (@test_intercept.R#21) 
  2. Failure: adds arbitrary numeric column (@test_intercept.R#33) 
  3. Failure: check_new_values works on factors (@test_newvalues.R#135) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.4Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   5.7Mb
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  17.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘ROCR’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’ ‘gbm’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘rattle’ ‘rpart’ ‘shinyWidgets’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetstcltk’
  All declared Imports should be used.
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/resemble.Rcheck/00install.out’ for details.
File ‘resemble/libs/resemble.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘resemble-Ex.R’ failed
The error most likely occurred in:

> ### Name: fDiss
> ### Title: Euclidean, Mahalanobis and cosine dissimilarity measurements
> ### Aliases: fDiss
> 
> ### ** Examples
> 
> require(prospectr)
Loading required package: prospectr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘prospectr’
> 
> data(NIRsoil)
Warning in data(NIRsoil) : data set ‘NIRsoil’ not found
> 
> Xu <- NIRsoil$spc[!as.logical(NIRsoil$train),]
Error: object 'NIRsoil' not found
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(reshape2)
  > 
  > test_check("reshape2")
  ── 1. Failure: labels are correct when missing combinations dropped/kept (@test-
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 16 == -12
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 126 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: labels are correct when missing combinations dropped/kept (@test-cast.r#126) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs      3.9Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
Running ‘spelling.R’
  Running ‘testthat.R’ [23s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  ── 1. Error: IDT format is read correctly (@test-format-idt.R#9)  ──────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  ── 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  ───────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  ── 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ───────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  57.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       1.4Mb
    extdata   1.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.9Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.7Mb
Packages suggested but not available for checking: 'playwith', 'pmg'
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/data/gannet/ripley/R/packages/tests-clang/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   9.1Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
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_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’
File ‘RInside/libs/RInside.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘RISCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: expect.utility2
> ### Title: Cut-Off Estimation Of A Prognostic Marker (Two Groups Are
> ###   observed).
> ### Aliases: expect.utility2
> ### Keywords: Utility
> 
> ### ** Examples
> 
> 
> # import and attach the data example
> 
> data(dataCSL)
> dataCSL <- dataCSL[order(dataCSL$id, dataCSL$time),]
> dataCSL$ordre <-0
> for (i in unique(dataCSL$id))
+  {dataCSL$ordre[dataCSL$id==i] <- 1:sum(dataCSL$id==i)}
> 
> dataCSL$ttt[dataCSL$treat==0]<-"A"
> dataCSL$ttt[dataCSL$treat==1]<-"B"
> 
> dataCSL0 <- dataCSL[dataCSL$ordre==1,]
> dataCSL0<-dataCSL0[,c(1,4,5,14,9)]
> 
> # the expected utility function for a prognostic up to 8 years
> 
> EUt.obj <- expect.utility2(dataCSL0$eventT, dataCSL0$dc,
+  dataCSL0$prot.base, treatment= dataCSL0$ttt,
+  pro.time=8, u.A0=0.75*0.95, u.A1=0, u.B0=0.75, u.B1=0)
Warning in expect.utility2(dataCSL0$eventT, dataCSL0$dc, dataCSL0$prot.base,  :
  NAs introduced by coercion
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(event[who2]) :
  no non-missing arguments to max; returning -Inf
Error in rep(1:nstrat, x$strata) : invalid 'times' argument
Calls: expect.utility2 -> meanALL -> summary -> summary.survfit -> survmean
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rjstat)
  > 
  > test_check("rjstat")
  ── 1. Failure: value objects give correct output (@test-output.R#33)  ──────────
  fromJSONstat(txt1, use_factors = TRUE) not equal to data.frame(V1 = letters, value = c(1, rep(NA, 25))).
  Component "V1": 'current' is not a factor
  
  ── 2. Failure: value objects give correct output (@test-output.R#38)  ──────────
  fromJSONstat(txt2, use_factors = TRUE) not equal to data.frame(V1 = letters, value = c(1:2, rep(NA, 24))).
  Component "V1": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 57 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: value objects give correct output (@test-output.R#33) 
  2. Failure: value objects give correct output (@test-output.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’ ‘magrittr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: FPgrowth_A
> ### Title: FPgrowth_A KEEL Association Rules Algorithm
> ### Aliases: FPgrowth_A R6_FPgrowth_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/data/gannet/ripley/R/test-clang/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- FPgrowth_A(dat)
> 
> #Run algorithm
> algorithm$run()
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 59.1Mb
  sub-directories of 1Mb or more:
    libs  58.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.7Mb
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.8Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘statmod’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Running examples in ‘rmutil-Ex.R’ failed
The error most likely occurred in:

> ### Name: tvctomat
> ### Title: Create a Time-varying, Intra-individual Covariate (tvcov) Object
> ### Aliases: tvctomat
> ### Keywords: manip
> 
> ### ** Examples
> 
> z <- matrix(rpois(20,5),ncol=5)
> print(tvc <- tvctomat(z, units="days"))
           
Names: z   
Units: days
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc)
 [1]  4  3  6  6  6  4  8  2  4 11  5  9  3  7  4  8  6  3  5  7
> names(tvc)
[1] "z"
> v <- data.frame(matrix(rep(c("a","b","c","d","e"),4),ncol=5))
> print(tvc2 <- tvctomat(v, oldtvc=tvc, units=NA))
                
Names: z    v   
Units: days <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc2)
    z v
1   4 a
2   3 e
3   6 d
4   6 c
5   6 b
6   4 b
7   8 a
8   2 e
9   4 d
10 11 c
11  5 c
12  9 b
13  3 a
14  7 e
15  4 d
16  8 d
17  6 c
18  3 b
19  5 a
20  7 e
> print(tvc3 <- tvctomat(v, oldtvc=tvc, dataframe=FALSE, units=NA))
                               
Names: z    vb   vc   vd   ve  
Units: days <NA> <NA> <NA> <NA>
Number of individuals:                4 
Number of observations:               20 
Number of observations per individual:
 5 5 5 5 
> covariates(tvc3)
    z vb vc vd ve
1   4  0  0  0  0
2   3  0  0  0  1
3   6  0  0  1  0
4   6  0  1  0  0
5   6  1  0  0  0
6   4  1  0  0  0
7   8  0  0  0  0
8   2  0  0  0  1
9   4  0  0  1  0
10 11  0  1  0  0
11  5  0  1  0  0
12  9  1  0  0  0
13  3  0  0  0  0
14  7  0  0  0  1
15  4  0  0  1  0
16  8  0  0  1  0
17  6  0  1  0  0
18  3  1  0  0  0
19  5  0  0  0  0
20  7  0  0  0  1
> print(tvc4 <- tvctomat(tvc2, interaction=c("z","v")))
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: print -> tvctomat -> colnames<-
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.6Mb
    libs      3.5Mb
installed size is 92.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     90.4Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘abind’ ‘foreach’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  16.0Mb
File ‘robcp/libs/robcp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
File ‘robustloggamma/libs/robustloggamma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘ROCt-Ex.R’ failed
The error most likely occurred in:

> ### Name: EUt2
> ### Title: Optimal Cut-Off Estimation Of A Prognostic Marker (The Two
> ###   Groups Are observed).
> ### Aliases: EUt2
> ### Keywords: utility
> 
> ### ** Examples
> 
> 
> # import and attach the data example
> 
> data(csl)
> csl <- csl[order(csl$id, csl$time),]
> csl$ordre <-0
> for (i in unique(csl$id)) {csl$ordre[csl$id==i] <- 1:sum(csl$id==i)}
> 
> csl$ttt[csl$treat==0]<-"A"
> csl$ttt[csl$treat==1]<-"B"
> 
> csl0 <- csl[csl$ordre==1,]
> csl0<-csl0[,c(1,4,5,14,9)]
> 
> # the expected utility function for a prognostic up to 8 years
> 
> EUt.obj <- EUt2(csl0$eventT, csl0$dc, csl0$prot.base, treatment= csl0$ttt,
+  pro.time=8, u.A0=0.75*0.95, u.A1=0, u.B0=0.75, u.B1=0)
Warning in EUt2(csl0$eventT, csl0$dc, csl0$prot.base, treatment = csl0$ttt,  :
  NAs introduced by coercion
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(tab.res$utility, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
Warning in max(event[who2]) :
  no non-missing arguments to max; returning -Inf
Error in rep(1:nstrat, x$strata) : invalid 'times' argument
Calls: EUt2 -> meanALL -> summary -> summary.survfit -> survmean
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Running examples in ‘roughrf-Ex.R’ failed
The error most likely occurred in:

> ### Name: mfix
> ### Title: Four single imputation methods
> ### Aliases: mfix
> 
> ### ** Examples
> 
> dat=data.frame(continuous=c(1,2,3,4,5),categorical=c('a','a','a','a','b'))
> dat[2,]=NA
> dat
  continuous categorical
1          1           a
2         NA        <NA>
3          3           a
4          4           a
5          5           b
> summary(dat)
   continuous   categorical       
 Min.   :1.00   Length:5          
 1st Qu.:2.50   Class :character  
 Median :3.50   Mode  :character  
 Mean   :3.25                     
 3rd Qu.:4.25                     
 Max.   :5.00                     
 NA's   :1                        
> mfix(dat,1)[2,]  #median/mode imputation
Error in mmfix.data.frame(x) : mfix only works for numeric or factor
Calls: mfix -> mmfix -> mmfix.data.frame
Execution halted
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.4Mb
    tests   1.3Mb
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Error(s) in re-building vignettes:
--- re-building ‘diagnostics.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'dplyr'

The following objects are masked from 'package:Hmisc':

    src, summarize

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 202-204 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
contrasts can be applied only to factors with 2 or more levels
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘user_guide.Rmd’ using rmarkdown
Loading required package: survival
--- finished re-building ‘user_guide.Rmd’

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

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

> ### Name: ScorecardProfet
> ### Title: Scorecard Builder
> ### Aliases: ScorecardProfet
> 
> ### ** Examples
> 
> mydata <- ISLR::Default
> 
> mydata$ID = seq(1:nrow(mydata)) ## make the ID variable
> mydata$default<-ifelse(mydata$default=="Yes",1,0) ## Creating numeric binary target variable
> 
> binned <- BinProfet(mydata, id= "ID", target= "default", num.bins = 5) ## Binning variables
> 
> WOE_dat <- WOEProfet(binned, "ID","default", 3:5) ## WOE transformation of bins
Error in aggregate.data.frame(lhs, mf[-1L], FUN = FUN, ...) : 
  no rows to aggregate
Calls: WOEProfet ... aggregate -> aggregate.formula -> aggregate.data.frame
Execution halted
Found the following significant warnings:
  wrapper_Message.cpp:149:25: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
  wrapper_Message.cpp:253:49: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RProtoBuf.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rf.c:485:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mvMORPH’
  All declared Imports should be used.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running examples in ‘RScelestial-Ex.R’ failed
The error most likely occurred in:

> ### Name: distance.matrix.scelestial
> ### Title: Calculates distance matrix for result of scelestial
> ### Aliases: distance.matrix.scelestial
> 
> ### ** Examples
> 
> ## Synthesise an evolution
> S = synthesis(10, 5, 20, seed=7)
> ## Run Scelestial
> SC = scelestial(as.ten.state.matrix(S$seqeunce))
Error in .scelestial(seq, mink, maxk) : 
  Not compatible with requested type: [type=character; target=integer].
Calls: scelestial -> .scelestial
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘RScelestial-vignette.Rmd’ using rmarkdown
Quitting from lines 45-48 (RScelestial-vignette.Rmd) 
Error: processing vignette 'RScelestial-vignette.Rmd' failed with diagnostics:
Not compatible with requested type: [type=character; target=integer].
--- failed re-building ‘RScelestial-vignette.Rmd’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
installed size is 217.1Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  210.4Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 191.4Mb
  sub-directories of 1Mb or more:
    libs  188.6Mb
installed size is 101.9Mb
  sub-directories of 1Mb or more:
    libs  100.5Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.7Mb
    projects   2.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘quantmod’
  All declared Imports should be used.
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/RTransProb.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Quitting from lines 171-172 (Skylark_example.Rmd) 
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’

--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Quitting from lines 261-264 (rtrim_2_extensions.Rmd) 
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’

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

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

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

--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’

SUMMARY: processing the following files failed:
  ‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  21.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
--- re-building ‘apply_any_r_function.Rmd’ using rmarkdown
--- finished re-building ‘apply_any_r_function.Rmd’

--- re-building ‘built-in_functions.Rmd’ using rmarkdown
--- finished re-building ‘built-in_functions.Rmd’

--- re-building ‘runner_examples.Rmd’ using rmarkdown

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

Quitting from lines 80-103 (runner_examples.Rmd) 
Error: processing vignette 'runner_examples.Rmd' failed with diagnostics:
Not compatible with requested type: [type=character; target=integer].
--- failed re-building ‘runner_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  57.1Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 57.6Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     53.3Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs    8.5Mb
    yacas   1.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs    9.2Mb
    yacas   1.6Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  13.0Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.7Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    extdata  62.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘spData’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  16.9Mb
Namespaces in Imports field not imported from:
  ‘ForeCA’ ‘Mcomp’ ‘repmis’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SemNetCleaner’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.1Mb
Running examples in ‘sEparaTe-Ex.R’ failed
The error most likely occurred in:

> ### Name: lrt2d_svc
> ### Title: Unbiased modified likelihood ratio test for simple separability
> ###   of a variance-covariance matrix.
> ### Aliases: lrt2d_svc
> 
> ### ** Examples
> 
> #To reduce the time elapsed, this example uses only 160 simulations.
> #8000 simulations or more are recommended in an example like this.
> output <- lrt2d_svc(value2d~Id1+Id2, rep = "K", data = data2d, n.simul = 160)
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  'x' must be atomic
Calls: lrt2d_svc ... quantile.default -> sort -> sort.default -> sort.int
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  14.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'

Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   7.9Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    libs     9.4Mb
    sqlite   1.5Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Running examples in ‘sgRSEA-Ex.R’ failed
The error most likely occurred in:

> ### Name: sgRSEA
> ### Title: Perform a permutation test which computes gene scores and their
> ###   significance
> ### Aliases: sgRSEA
> 
> ### ** Examples
> 
> data(melanoma808)
> dat = UQnormalize(melanoma808, trt=c('PLX7_R1','PLX7_R2'), ctrl=c('D7_R1','D7_R2'))
> results = sgRSEA(dat=dat, multiplier=30)
Error in sum(ifelse(zj >= 0, zj, 0)) : 
  invalid 'type' (character) of argument
Calls: sgRSEA ... Tmaxmean.Null.Tss2 -> T.maxmean -> tapply -> lapply -> FUN
Execution halted
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
Running examples in ‘ShapeSelectForest-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotshape
> ### Title: The Plot Routine for an Object of the Shape Routine
> ### Aliases: plotshape
> ### Keywords: graphic routine
> 
> ### ** Examples
> 
> 	# import the matrix of Landsat signals 
> 	data("ymat")	
> 
> 	# define the predictor vector: the year 1985 to the year 2010
> 	x <- 1985:2010
> 
> 	# make a fit by the shape routine using "CIC" 
> 	# and not allow a double jump shape.
> 	ans <- shape(x, ymat, "CIC", db = FALSE)
> 
> 	# make a plot for the 1st column of ymat 
> 	plotshape(ans, ids = 1, both = TRUE, form = TRUE, tt = "Pixel 420")
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'plot' not found
Calls: plotshape -> ::: -> get
Execution halted
File ‘sharpData/libs/sharpData.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘getPass’ ‘svglite’ ‘websocket’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.3Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘ellipse’ ‘viridis’
  All declared Imports should be used.
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  12.9Mb
Running examples in ‘SIMMS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SIMMS-package
> ### Title: SIMMS - Subnetwork Integration for Multi-Modal Signatures
> ### Aliases: SIMMS-package SIMMS
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> options("warn" = -1);
> 
> # get data directory 
> data.directory <- get.program.defaults(networks.database = "test")[["test.data.dir"]];
> 
> # initialise params
> output.directory <- ".";
> data.types <- c("mRNA");
> feature.selection.datasets <- c("Breastdata1");
> training.datasets <- c("Breastdata1");
> validation.datasets <- c("Breastdata2");
> feature.selection.p.thresholds <- c(0.5);
> feature.selection.p.threshold <- 0.5;
> learning.algorithms <- c("backward", "forward", "glm");
> top.n.features <- 5;
> 
> # compute network HRs for all the subnet features
> derive.network.features(
+   data.directory = data.directory,
+   output.directory = output.directory,
+   data.types = data.types,
+   feature.selection.datasets = feature.selection.datasets,
+   feature.selection.p.thresholds = feature.selection.p.thresholds,
+   networks.database = "test"
+   );
Error in order(x[, 1], decreasing = TRUE) : 
  unimplemented type 'list' in 'orderVector1'
Calls: derive.network.features -> as.matrix -> order
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Using-SIMMS.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: MASS
Loading required package: glmnet
Loading required package: Matrix
Loaded glmnet 3.0-2

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Quitting from lines 125-232 (Using-SIMMS.Rmd) 
Error: processing vignette 'Using-SIMMS.Rmd' failed with diagnostics:
unimplemented type 'list' in 'orderVector1'

--- failed re-building ‘Using-SIMMS.Rmd’

SUMMARY: processing the following file failed:
  ‘Using-SIMMS.Rmd’

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  23.0Mb
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   8.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘het.test’ ‘lmtest’ ‘lubridate’ ‘magrittr’ ‘tibble’ ‘tseries’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/skeleSim.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.8Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘clues’
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  11.2Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/smoothSurv.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.8Mb
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   6.5Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  33.9Mb
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fasterize’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.1Mb
Note: found 25 marked Latin-1 strings
  Note: found 658 marked UTF-8 strings
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/data/gannet/ripley/R/packages/tests-clang/spatial.tools.Rcheck/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  19.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.2Mb
    libs   2.1Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  11.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘spm12r-Ex.R’ failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> in_ci <- function() {
+ nzchar(Sys.getenv("CI"))
+ }
> if (.Platform$OS.type == "unix" | in_ci()) { # windows problem
+ res = install_spm12(install_dir = tdir)
+ res = install_spm12(install_dir = tdir)
+ }
cloning into '/tmp/RtmphYImzF/working_dir/RtmpQQJWTQ/file2a4769d4c26f/spm12'...

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",     local_path = out_path, progress = verbose)
 2: install_spm12(install_dir = tdir)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs  10.0Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
possible bashism in configure line 19 ('command' with option other than -p):
  if [ $(command -v pkg-config) ]; then
  possible bashism in configure line 33 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 34 ('command' with option other than -p):
    if [ $(command -v brew) ]; then
  possible bashism in configure line 38 (should be '.', not 'source'):
      source autobrew
installed size is 79.8Mb
  sub-directories of 1Mb or more:
    libs  79.4Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    include  10.3Mb
    lib       3.0Mb
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.9Mb
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Running examples in ‘StepReg-Ex.R’ failed
The error most likely occurred in:

> ### Name: bestsubset
> ### Title: Best subset selection
> ### Aliases: bestsubset
> ### Keywords: best subset selection
> 
> ### ** Examples
> 
> set.seed(4)
> dfY <- data.frame(matrix(c(rnorm(20,0,2),c(rep(1,10),rep(2,10)),rnorm(20,2,3)),20,3))
> colnames(dfY) <- paste("Y",1:3,sep="")
> dfX <- data.frame(matrix(c(rnorm(100,0,2),rnorm(100,2,1)),20,10))
> colnames(dfX) <- paste("X",1:10,sep="")
> yx <- cbind(dfY,dfX)
> bestsubset(yx,y="Y1",exclude="Y3",include="Y2",Class="Y2",
+ weights=c(rep(0.5,2),rep(1,18)),select="SBC",tolerance=1e-7,best=5)
Error in `colnames<-`(`*tmp*`, value = colnames(tempresult)) : 
  attempt to set 'colnames' on an object with less than two dimensions
Calls: bestsubset -> colnames<-
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
Running examples in ‘strandCet-Ex.R’ failed
The error most likely occurred in:

> ### Name: HP.pred
> ### Title: Prediction of Heligman-Pollard model.
> ### Aliases: HP.pred
> ### Keywords: Heligman-Pollard mortality prediction
> 
> ### ** Examples
> 
> 
> lifeN <- life.tab(cetaceans)
Error in life$Sx/d : non-numeric argument to binary operator
Calls: life.tab
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘RColorBrewer’ ‘Rcpp’ ‘readr’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Running examples in ‘stylo-Ex.R’ failed
The error most likely occurred in:

> ### Name: perform.svm
> ### Title: Support Vector Machines classifier
> ### Aliases: perform.svm
> 
> ### ** Examples
> 
> ## Not run: 
> ##D perform.svm(training.set, test.set)
> ## End(Not run)
> 
> # classifying the standard 'iris' dataset:
> data(iris)
> x = subset(iris, select = -Species)
> train = rbind(x[1:25,], x[51:75,], x[101:125,])
> test = rbind(x[26:50,], x[76:100,], x[126:150,])
> train.classes = c(rep("s",25), rep("c",25), rep("v",25))
> test.classes = c(rep("s",25), rep("c",25), rep("v",25))
> 
> perform.svm(train, test, train.classes, test.classes)
Error in svm.default(x, y, scale = scale, ..., na.action = na.action) : 
  Need numeric dependent variable for regression.
Calls: perform.svm -> svm -> svm.formula -> svm.default
Execution halted
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.4Mb
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
aggtrees: no visible global function definition for ‘predict’
coef.pelora: no visible global function definition for ‘fitted’
dlda: no visible binding for global variable ‘var’
logreg: no visible global function definition for ‘glm’
logreg: no visible binding for global variable ‘binomial’
logreg: no visible global function definition for ‘predict’
plot.pelora: no visible global function definition for ‘text’
plot.wilma: no visible global function definition for ‘fitted’
plot.wilma: no visible global function definition for ‘text’
predict.pelora: no visible global function definition for ‘fitted’
predict.pelora: no visible global function definition for ‘coef’
predict.wilma: no visible global function definition for ‘fitted’
print.wilma: no visible global function definition for ‘fitted’
ridge.coef: no visible binding for global variable ‘var’
sign.change: no visible binding for global variable ‘cov’
standardize.genes: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  binomial coef cov fitted glm predict sd text var
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "binomial", "coef", "cov", "fitted", "glm",
             "predict", "sd", "var")
to your NAMESPACE file.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   1.8Mb
Running examples in ‘surveillance-Ex.R’ failed
The error most likely occurred in:

> ### Name: epidata_plot
> ### Title: Plotting the Evolution of an Epidemic
> ### Aliases: plot.epidata plot.summary.epidata stateplot
> ### Keywords: hplot methods spatial
> 
> ### ** Examples
> 
> data("hagelloch")
> (s <- summary(hagelloch))

AN SIR EPIDEMIC
  Time range: 0 -- 92.5452383686788 
  Number of individuals: 188 
  1 initially infected individuals:
    "184"
  0 never infected individuals
  Size of the epidemic: 187 

$ counters ('data.frame', 376 x 6 ): evolution of the epidemic:
         time type  id nSusceptible nInfectious nRemoved
1    0.000000                   187           1        0
2    1.136356    I 173          186           2        0
3    7.197762    R 173          186           1        1
       [....]                                           
375 85.688298    I 141            0           1      187
376 92.545238    R 141            0           0      188

> 
> # rudimentary stateplot
> stateplot(s, id = "187")
Warning in xy.coords(x, y, setLab = FALSE) : NAs introduced by coercion
Error in approxfun(x, y[-if (right) n1 else 1], method = "constant", yleft = y[1L],  : 
  zero non-NA points
Calls: stateplot -> stepfun -> approxfun
Execution halted
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 156.8Mb
  sub-directories of 1Mb or more:
    libs  155.2Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘stats’ ‘survival’ ‘utils’
  All declared Imports should be used.
Running examples in ‘survsup-Ex.R’ failed
The error most likely occurred in:

> ### Name: nar
> ### Title: Add a numbers at risk table to a Kaplan-Meier plot
> ### Aliases: nar
> 
> ### ** Examples
> 
> library(survsup); library(ggplot2); library(dplyr); library(survival)

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

> 
> retinopathy %>%
+     survfit(Surv(futime, status) ~ trt, data = .) %>%
+    plot_survfit() %>%
+ 	   nar()
Error in `$<-.data.frame`(`*tmp*`, "y", value = NA_real_) : 
  replacement has 1 row, data has 0
Calls: %>% ... withVisible -> <Anonymous> -> nar -> $<- -> $<-.data.frame
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘survsup_intro.Rmd’ using rmarkdown
Quitting from lines 92-96 (survsup_intro.Rmd) 
Error: processing vignette 'survsup_intro.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘survsup_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.8Mb
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘magrittr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘bibliography.Rmd’ using rmarkdown
--- finished re-building ‘bibliography.Rmd’

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

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

--- re-building ‘seriation.Rmd’ using rmarkdown
Quitting from lines 230-276 (seriation.Rmd) 
Error: processing vignette 'seriation.Rmd' failed with diagnostics:
<BootCA> instance initialization:
* 'rows[[1]]' must be integer; not character.
* 'columns[[1]]' must be integer; not character.
--- failed re-building ‘seriation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.3Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘example.Rmd’ using rmarkdown
--- finished re-building ‘example.Rmd’

--- re-building ‘fda-example.Rmd’ using rmarkdown
Quitting from lines 242-244 (fda-example.Rmd) 
Error: processing vignette 'fda-example.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘fda-example.Rmd’

--- re-building ‘single-style.Rmd’ using rmarkdown
--- finished re-building ‘single-style.Rmd’

--- re-building ‘summary-example.Rmd’ using rmarkdown
--- finished re-building ‘summary-example.Rmd’

SUMMARY: processing the following file failed:
  ‘fda-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘glmnet’ ‘quadprog’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.0Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

Requires orphaned package: ‘d3heatmap’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.4Mb
Running examples in ‘TeachingDemos-Ex.R’ failed
The error most likely occurred in:

> ### Name: simfun
> ### Title: Create a function to simulate data
> ### Aliases: simfun
> ### Keywords: datagen design
> 
> ### ** Examples
> 
> # Create a function to simulate heights for a given dataset
> 
> simheight <- simfun( {h <- c(64,69); height<-h[sex]+ rnorm(10,0,3)}, drop='h' )
> 
> my.df <- data.frame(sex=rep(c('Male','Female'),each=5))
> simdat <- simheight(my.df)
> t.test(height~sex, data=simdat)
Error in t.test.formula(height ~ sex, data = simdat) : 
  grouping factor must have exactly 2 levels
Calls: t.test -> t.test.formula
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.9Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 42 (should be '.', not 'source'):
      source autobrew
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘par-7269706c6579’
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.9Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Running ‘testthat.R’ [40s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(themetagenomics)
  Loading required package: Rcpp
  > 
  > test_check("themetagenomics")
  ── 1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92)  ─
  `prepare_data(...)` did not produce any warnings.
  
  ── 2. Error: prepare_data works with multiclass factor and continuous (@test-pre
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ── 3. Error: prepare_data works with multiclass factor and spline (@test-prepare
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 45 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92) 
  2. Error: prepare_data works with multiclass factor and continuous (@test-prepare.R#139) 
  3. Error: prepare_data works with multiclass factor and spline (@test-prepare.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’ [18s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(theseus)
  > 
  > test_check("theseus")
  ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
  attempting to coerce non-factor
  Backtrace:
   1. base::table(...)
   2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
   3. base::as.character.factor(df[[tax_level]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Running examples in ‘tidymv-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_difference
> ### Title: Plot difference smooth from a GAM.
> ### Aliases: plot_difference
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
> set.seed(10)
> data <- gamSim(4)
Factor `by' variable example
> model <- gam(y ~ fac + s(x2) + s(x2, by = fac) + s(x0), data = data)
> 
> plot_difference(model, x2, list(fac = c("1", "2")))
Error in table(predictors$Terms) - table(predictors[predictors$Label %in%  : 
  non-conformable arrays
Calls: plot_difference -> %>% -> eval -> eval
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

--- re-building ‘predict-gam.Rmd’ using rmarkdown
--- finished re-building ‘predict-gam.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’ ‘usethis’
  All declared Imports should be used.
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyxl.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.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.

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    examples  15.0Mb
    include    3.0Mb
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Running examples in ‘traitdataform-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbind.traitdata
> ### Title: Combine trait datasets
> ### Aliases: rbind.traitdata
> 
> ### ** Examples
> 
> 
> pulldata("carabids")
The dataset 'carabids' is now available for use! 

> 
> dataset1 <- as.traitdata(carabids,
+   taxa = "name_correct",
+   traits = c("body_length", "antenna_length", "metafemur_length"),
+   units = "mm",
+   keep = c(datasetID = "source_measurement", measurementRemarks = "note"),
+   metadata = as.metadata(
+     bibliographicCitation = c(
+         "van der Plas et al. (2017) Methods in Ecol. & Evol., doi: 10.1111/2041-210x.12728"
+        ),
+     author = "Fons van der Plas",
+     license = "http://creativecommons.org/publicdomain/zero/1.0/"
+     )
+ )
Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!
> 
> 
> traits1 <- as.thesaurus(
+  body_length = as.trait("body_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
+  antenna_length = as.trait("antenna_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
+  metafemur_length = as.trait("metafemur_length",
+    expectedUnit = "mm", valueType = "numeric",
+    identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
+ )
> 
> dataset1Std <- standardize.traits(dataset1, thesaurus = traits1)
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: standardize.traits -> droplevels
Execution halted
Running ‘testthat.R’ [8s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  ── 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ─────────
  Value hashes to 2448e3596a, not bc9f97d273
  
  ── 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ─────────
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  ── 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  ── 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ─────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 64 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘traitdataform.Rmd’ using rmarkdown
Quitting from lines 310-312 (traitdataform.Rmd) 
Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
no applicable method for 'droplevels' applied to an object of class "character"
--- failed re-building ‘traitdataform.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.3Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 126.8Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    libs  121.8Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  rfmod.c:467:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/trimTrees.Rcheck/00install.out’ for details.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘htmltools’ ‘scales’ ‘stringr’
  All declared Imports should be used.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.6Mb
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/tsmp.Rcheck/00install.out’ for details.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.5Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    libs      2.9Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   9.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘upm-primer.Rmd’ using rmarkdown
Quitting from lines 70-71 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
A variable(s) is listed by user as factors but data type in design matrix is not actually a factor. Reformat.
--- failed re-building ‘upm-primer.Rmd’

SUMMARY: processing the following file failed:
  ‘upm-primer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘rstudioapi’ ‘testthat’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘saemix’
  All declared Imports should be used.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘utils’
  All declared Imports should be used.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 50.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.2Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘diptest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ingredients’
  All declared Imports should be used.
installed size is 46.2Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Error(s) in re-building vignettes:
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
Quitting from lines 284-288 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘vortexRguide.Rmd’

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

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

> ### Name: project
> ### Title: Projection of voxels within a plan
> ### Aliases: project
> ### Keywords: 3d points cloud 2d points cloud projection
> 
> ### ** Examples
> 
> data(treecloud_vox)
> 
> #-projection in "xy" plan
> 
> proj <- project(treecloud_vox,dim="xy")
> 
> #-creating vectors with interests variables
> 
> npts <- c(proj[,4])
> nvox <- c(proj[,3])
> ratio <- c(proj[,5])
> 
> #-discretisation level
> 
> 	 # by quantiles (20% quantiles or 25% quantiles)
> lev_vox <- level(nvox,by="quantiles",levels=c(0.2))
> lev_ratio <- level(ratio,by="quantiles",levels=c(0.25))
> 	# by percents
> lev_pts <- level(npts,by="percents",levels=c(0.2,0.4,0.6,0.8)) 
> 
> 
> #- computing surfaces
> 
> 	# surface in proportion
> surf_nvox <- surface(proj,method="nvox",levels=lev_vox,res=0.02,proportion=TRUE)
> 	# surface in absolute
> surf_ratio <- surface(proj,method="ratio",levels=lev_ratio,res=1,proportion=FALSE)
> 	# surface in absolute
> surf_npts <- surface(proj,method="npts",levels=lev_pts,res=0.02,proportion=FALSE)
> 
> #- ploting raster images
> 
> par(mfrow=c(1,1),mai=c(1,0,1,0),omi=c(0,1,0,0))
> 
> raster.proj(proj,title="nvox",res=0.02,method="nvox",levels=lev_vox,
+ 			colors=c("lightblue","green","yellow","red","purple"),
+             contour=TRUE,surf=surf_nvox,dim="xy")
Loading required package: raster
Loading required package: sp
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: raster.proj -> plot -> plot.default -> xy.coords
Execution halted
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 63.0Mb
  sub-directories of 1Mb or more:
    libs  61.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.4Mb
Namespaces in Imports field not imported from:
  ‘raster’ ‘reshape2’
  All declared Imports should be used.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘zoo’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘later’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
possible bashism in configure line 49 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Package suggested but not available for checking: ‘ROTS’
Packages unavailable to check Rd xrefs: ‘cleaver’, ‘ROTS’
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.9Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/x13binary.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggdendro’
  All declared Imports should be used.
Running examples in ‘Xplortext-Ex.R’ failed
The error most likely occurred in:

> ### Name: LexHCca
> ### Title: Hierarchical Clustering of Documents on Textual Correspondence
> ###   Analysis Coordinates (LexHCca)
> ### Aliases: LexHCca
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(open.question)
> res.TD<-TextData(open.question, var.text=c(9,10), Fmin=10, Dmin=10, stop.word.tm=TRUE,
+         context.quali=c("Gender","Age_Group","Education"), context.quanti=c("Age"))
> res.LexCA<-LexCA(res.TD, graph=FALSE, ncp=8)
Error in which(unlist(lapply(listModa, is.numeric))) : 
  argument to 'which' is not logical
Calls: LexCA -> as.matrix -> t -> tab.disjonctif -> which
Execution halted
Running examples in ‘xpose-Ex.R’ failed
The error most likely occurred in:

> ### Name: amt_vs_idv
> ### Title: Compartment kinetics
> ### Aliases: amt_vs_idv
> 
> ### ** Examples
> 
> amt_vs_idv(xpdb_ex_pk)
Using data from $prob no.1
Tidying data by ID, SEX, MED1, MED2, AMT ... and 20 more variables
Error: Cannot create zero-length unit vector ("unit" subsetting)
Execution halted
Running ‘testthat.R’ [59s/145s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  ── 1. Failure: parial xp_themes are properly added (@test-update_themes.R#39)  ─
  update_themes(xpdb = xpdb_ex_pk, xp_theme = c(point_color = "green"))$xp_theme not equivalent to `theme_xp_custom`.
  Component "labeller": target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 521 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: parial xp_themes are properly added (@test-update_themes.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   3.5Mb
    libs      1.8Mb
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [15s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(yardstick)
  For binary classification, the first factor level is assumed to be the event.
  Set the global option `yardstick.event_first` to `FALSE` to change this.
  
  > 
  > test_check("yardstick")
  ── 1. Error: Three class (@test-prob-mn_log_loss.R#14)  ────────────────────────
  `truth` should be a factor but a character was supplied.
  Backtrace:
    1. testthat::expect_equal(...)
   13. yardstick:::metric_fn(...)
   14. yardstick::metric_vec_template(...)
   15. yardstick:::validate_truth_estimate_checks(...)
   16. yardstick:::validate_class(truth, "truth", cls[1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 511 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Three class (@test-prob-mn_log_loss.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    libs  41.1Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.3Mb
Running ‘testthat.R’ [5s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(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
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:car':
  
      recode
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(geepack)
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(zeligverse)
  Error in library(zeligverse) : there is no package called 'zeligverse'
  Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  ── 1. Error: (unknown) (@test_export.R#8)  ─────────────────────────────────────
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [16s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ARTool)
  > 
  > test_check("ARTool")
  ── 1. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ── 2. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to ref[-2].
  Component "Term": 'current' is not a factor
  
  ── 3. Failure: anova.art of Higgins1990Table1 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  
  ── 4. Failure: anova.art of HigginsABC matches results of the original ARTool (@
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 108 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#45) 
  2. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#50) 
  3. Failure: anova.art of Higgins1990Table1 matches results of the original ARTool (@test.anova.art.R#69) 
  4. Failure: anova.art of HigginsABC matches results of the original ARTool (@test.anova.art.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(attachment)
  > 
  > test_check("attachment")
  ── 1. Error: (unknown) (@test-to-description.R#8)  ─────────────────────────────
  object 'na.omit' is not exported by 'namespace:utils'
  Backtrace:
    1. attachment::att_to_description(path = dummypackage)
    3. attachment::att_from_namespace(path.n, document = document)
    4. devtools::document(dirname(path))
    7. roxygen2::roxygenise(pkg$path, roclets, load_code = load_code)
    8. roxygen2:::load_code(base_path)
    9. pkgload::load_all(path, helpers = FALSE, attach_testthat = FALSE)
   10. pkgload:::load_imports(path)
   11. pkgload:::process_imports(path)
   12. base::tryCatch(...)
   13. base:::tryCatchList(expr, classes, parentenv, handlers)
   14. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-to-description.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/augmentedRCBD.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  ── 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ─────────────────────
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [92s/195s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(batchtools)
  > 
  > test_check("batchtools")
  ### [bt]: Setting seed to 18526 ...
  ── 1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ── 2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ### [bt]: Setting seed to 3080 ...
  ### [bt]: Setting seed to 3082 ...
  ### [bt]: Setting seed to 3081 ...
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1459 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64) 
  2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [16s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesPostEst)
  > 
  > test_check("BayesPostEst")
  ── 1. Failure: pars subsetting works (@test_mcmcTab.R#61)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:3))).
  Types not compatible: character is not integer
  
  ── 2. Failure: pars subsetting works (@test_mcmcTab.R#83)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:2))).
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: pars subsetting works (@test_mcmcTab.R#61) 
  2. Failure: pars subsetting works (@test_mcmcTab.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘bestglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneSDRule
> ### Title: Utility function. Implements the 1-sd rule.
> ### Aliases: oneSDRule
> 
> ### ** Examples
> 
> CV<-c(1.4637799,0.7036285,0.6242480,0.6069406,0.6006877,0.6005472,0.5707958,
+       0.5907897,0.5895489)
> CVsd<-c(0.24878992,0.14160499,0.08714908,0.11376041,0.08522291,
+  0.11897327,0.07960879,0.09235052,0.12860983)
> CVout <- matrix(c(CV,CVsd), ncol=2)
> oneSDRule(CVout)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
bestglm
 --- call from context --- 
oneSDRule(CVout)
 --- call from argument --- 
if (class(CVout) == "train") {
    ans <- CVout
    CVout <- with(ans$results, cbind(RMSE, RMSESD))
}
 --- R stacktrace ---
where 1: oneSDRule(CVout)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (CVout) 
{
    stopifnot(is.matrix(CVout) || is.data.frame(CVout) || class(CVout) == 
        "train")
    if (class(CVout) == "train") {
        ans <- CVout
        CVout <- with(ans$results, cbind(RMSE, RMSESD))
    }
    cverrs <- CVout[, 1]
    indMin <- which.min(cverrs)
    fmin <- CVout[indMin, 2]
    cutOff <- fmin + cverrs[indMin]
    min(which(cverrs < cutOff))
}
<bytecode: 0xd3b15c8>
<environment: namespace:bestglm>
 --- function search by body ---
Function oneSDRule in namespace bestglm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(CVout) == "train") { : the condition has length > 1
Calls: oneSDRule
Execution halted
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Running ‘testthat.R’ [6s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BisqueRNA)
  > 
  > test_check("BisqueRNA")
  ── 1. Error: Catches data where zero variance in training data (@test_ref_based.
  incorrect number of dimensions
  Backtrace:
   1. testthat::expect_equal(...)
   4. BisqueRNA::ReferenceBasedDecomposition(bulk.eset, sc.eset, use.overlap = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 49 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 1 ]
  1. Error: Catches data where zero variance in training data (@test_ref_based.R#125) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [36s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bnclassify)
  > 
  > test_check("bnclassify")
  -1.54485 -1.50696 -1.31785 -1.2128 -1.4612 -1.20742 -1.26966 -1.67055 -0.440312 -1.11241 -4.29046 -4.29046 -0.545227 -0.93827 -4.23411 -4.23411
  ── 1. Error: aode str (@test-learn-aode.r#15)  ─────────────────────────────────
  are_factors(dataset) is not TRUE
  Backtrace:
   1. bnclassify::aode(class = "a", alphadb[, 1:2, drop = FALSE])
   2. bnclassify:::get_features(class = class, dataset = dataset)
   3. bnclassify:::check_class_in_dataset(class, dataset)
   4. bnclassify:::check_dataset(dataset)
   5. base::stopifnot(are_factors(dataset))
  
  ── 2. Error: aode bnc funs (@test-learn-aode.r#35)  ────────────────────────────
  are_factors(dataset) is not TRUE
  Backtrace:
   1. bnclassify::aode(class = "a", lets)
   2. bnclassify:::get_features(class = class, dataset = dataset)
   3. bnclassify:::check_class_in_dataset(class, dataset)
   4. bnclassify:::check_dataset(dataset)
   5. base::stopifnot(are_factors(dataset))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 587 | SKIPPED: 33 | WARNINGS: 3 | FAILED: 2 ]
  1. Error: aode str (@test-learn-aode.r#15) 
  2. Error: aode bnc funs (@test-learn-aode.r#35) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [6m/17m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  ── 1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#
  all(exp_names_lvls %in% res_names_lvls) isn't true.
  
  ── 2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12)  
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1, classes)
  
  ── 3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38)  ──
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1.b, classes.b)
  
  ── 4. Failure: handles situation when there's a single column per transformation
  `preprocessed` not equal to data.frame(x = c("a", "a"), y = c(-0.5, 0.5)).
  Component "x": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#126) 
  2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12) 
  3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38) 
  4. Failure: handles situation when there's a single column per transformation (@test_preProcess_internals.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [77s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CHNOSZ)
  CHNOSZ version 1.3.5 (2020-02-16)
  reset: creating "thermo" object
  obigt: loading default database with 1849 aqueous, 3374 total species
  > 
  > # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
  > # (since we use makeCluster() etc via palply)
  > Sys.setenv("R_TESTS" = "") 
  > 
  > test_check("CHNOSZ")
  ── 1. Failure: add.protein works as expected (@test-add.protein.R#13)  ─────────
  `ip <- add.protein(aa)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 568 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: add.protein works as expected (@test-add.protein.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘clam-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.dates
> ### Title: Add dates to age-depth plots
> ### Aliases: add.dates
> 
> ### ** Examples
> 
>   clam(coredir=tempfile())
The run's files will be put in this folder: /tmp/RtmpFHG7mc/working_dir/Rtmp2frz67/file9df03b78c9a8/Example

 Warning, dates spanning beyond the calibration curve will be truncated! 
 Calibrating dates... Error in smp[i, (1:its) + 1, ] <- calibs[[i]][sample(1:length(calibs[[i]][,  : 
  incorrect number of subscripts
Calls: clam -> .smpl
Execution halted
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/clv.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [79s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) 
  > library(codyn)
  > test_check("codyn")
  ── 1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#1
  result[, 1] inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 359 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [13s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 612 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [6s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DoE.multi.response)
  Loading required package: DoE.wrapper
  Loading required package: FrF2
  Loading required package: DoE.base
  Loading required package: grid
  Loading required package: conf.design
  
  Attaching package: 'DoE.base'
  
  The following objects are masked from 'package:stats':
  
      aov, lm
  
  The following object is masked from 'package:graphics':
  
      plot.design
  
  The following object is masked from 'package:base':
  
      lengths
  
  Loading required package: rsm
  
  Attaching package: 'DoE.wrapper'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("DoE.multi.response")
  ── 1. Error: (unknown) (@testufccd.R#8)  ───────────────────────────────────────
  non-numeric argument to binary operator
  Backtrace:
   1. DoE.multi.response::ufccd(x)
   2. DoE.wrapper::ccd.design(...)
   3. DoE.wrapper::ccd.augment(...)
   4. FrF2::add.center(cube, ncenter[1])
   7. base::substr(rostdrplev, punkt1 + 1, 999)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@testufccd.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  fintegrate.c:350:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  gibbsEM.c:417:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/eco.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [18s/20s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘sleep.R’ [3s/12s]
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [53s/202s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528)  ──
  contrasts can be applied only to factors with 2 or more levels
  Backtrace:
   1. estimatr::lm_robust(...)
   2. estimatr::lm_robust_fit(...)
   3. estimatr:::prep_data(...)
   5. stats::model.matrix.default(~0 + ., data = fe_dat)
   6. stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1309 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [45s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fgeo.analyze)
  > 
  > test_check("fgeo.analyze")
  ── 1. Failure: as.data.frame.tt_lst takes arguments via `...` (@test-as_tibble.R
  as.data.frame(tt_lst)[["sp"]] inherits from `character` not `factor`.
  
  ── 2. Failure: as.data.frame.demography_ctfs takes arguments via `...` (@test-as
  as.data.frame(result)[["groups"]] inherits from `character` not `factor`.
  
  $N2
  [1] 29
  
  $R
  [1] 3
  
  $rate
  [1] 0.02413113
  
  $lower
  [1] 0.0084585
  
  $upper
  [1] 0.06812388
  
  $time
  [1] 4.525246
  
  $date1
  [1] 18937.96
  
  $date2
  [1] 20600.72
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: as.data.frame.tt_lst takes arguments via `...` (@test-as_tibble.R#31) 
  2. Failure: as.data.frame.demography_ctfs takes arguments via `...` (@test-as_tibble.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [20s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genBaRcode)
  > 
  > test_check("genBaRcode")
  ── 1. Failure: helper functions - com_pair (@test_helper_functions.R#72)  ──────
  test_dat$shared not equal to res$shared.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 2. Failure: helper functions - com_pair (@test_helper_functions.R#73)  ──────
  test_dat$unique_sample1 not equal to res$unique_sample1.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ── 3. Failure: helper functions - com_pair (@test_helper_functions.R#74)  ──────
  test_dat$unique_sample2 not equal to res$unique_sample2.
  Component "barcode": Modes: character, numeric
  Component "barcode": Attributes: < target is NULL, current is list >
  Component "barcode": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 47 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 3 ]
  1. Failure: helper functions - com_pair (@test_helper_functions.R#72) 
  2. Failure: helper functions - com_pair (@test_helper_functions.R#73) 
  3. Failure: helper functions - com_pair (@test_helper_functions.R#74) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [100s/120s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojsonio")
  
  Attaching package: 'geojsonio'
  
  The following object is masked from 'package:base':
  
      pretty
  
  > test_check("geojsonio")
  ── 1. Failure: topojson_read works with file inputs (@test-topojson_read.R#11)  
  df$id inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 408 | SKIPPED: 23 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: topojson_read works with file inputs (@test-topojson_read.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/gglasso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/ggtern.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(glmdisc)
  > 
  > test_check("glmdisc")
  # weights:  9 (4 variable)
  initial  value 109.861229 
  iter  10 value 12.701739
  iter  20 value 5.686166
  iter  30 value 5.061799
  iter  40 value 4.906182
  iter  50 value 4.731498
  final  value 4.731498 
  stopped after 50 iterations
  # weights:  9 (4 variable)
  initial  value 109.861229 
  iter  10 value 12.701739
  iter  20 value 5.686166
  iter  30 value 5.061799
  iter  40 value 4.906182
  iter  50 value 4.731498
  final  value 4.731498 
  stopped after 50 iterations
  ── 1. Error: cutpoints works with continuous data (@test-method_cutpoints.R#10) 
  subscript out of bounds
  Backtrace:
   1. glmdisc::glmdisc(...)
  
  ── 2. Error: predict works with continuous data (@test-method_predict.R#11)  ───
  subscript out of bounds
  Backtrace:
   1. glmdisc::glmdisc(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: cutpoints works with continuous data (@test-method_cutpoints.R#10) 
  2. Error: predict works with continuous data (@test-method_predict.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘glmdisc.Rmd’ using rmarkdown
Iteration 1 ended with a performance of aic = -Inf
Iteration 2 ended with a performance of aic = -125.558105892201
Iteration 3 ended with a performance of aic = -130.284539045592
Iteration 4 ended with a performance of aic = -114.554112436357
Iteration 5 ended with a performance of aic = -120.490787432135
Iteration 6 ended with a performance of aic = -125.359063416885
Iteration 7 ended with a performance of aic = -149.617341567942
Iteration 8 ended with a performance of aic = -131.083149038966
Iteration 9 ended with a performance of aic = -116.835650746318
Iteration 10 ended with a performance of aic = -119.078237910777
Iteration 11 ended with a performance of aic = -125.491371748376
Iteration 12 ended with a performance of aic = -131.427665239927
Iteration 13 ended with a performance of aic = -135.45824579743
Iteration 14 ended with a performance of aic = -127.541070532663
Iteration 15 ended with a performance of aic = -130.664611594568
Quitting from lines 298-301 (glmdisc.Rmd) 
Error: processing vignette 'glmdisc.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘glmdisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [62s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > all.pkgs <- c("testthat", "dplyr", "dtplyr", "data.table", "magrittr", "survey", "zoo")
  > 
  > 
  > if (all(vapply(all.pkgs, requireNamespace, logical(1L), quietly = TRUE))) {
  +   
  +   library(testthat)
  +   library(grattan)
  +   library(hutils)
  +   library(data.table)
  +   library(magrittr)
  +   
  +   if (identical(Sys.getenv("CIRCLECI"), "true")) {
  +     test_check("grattan",
  +                reporter = JunitReporter$new(file = "junit_result.xml"))
  +   } else {
  +     test_check("grattan")
  +   }
  + }
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  ── 1. Error: Multiple People (@test_pension_supplement.R#59)  ──────────────────
  arguments imply differing number of rows: 1, 2
  Backtrace:
   1. testthat::expect_equal(...)
   4. grattan::pension_supplement(...)
   8. base::data.frame(..., check.names = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 833 | SKIPPED: 106 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Multiple People (@test_pension_supplement.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/icd.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [42s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # this is common code to all the tests, each of which runs test_check with a
  > # different filter:
  > library("icd")
  > library("testthat", warn.conflicts = FALSE, quietly = TRUE)
  > icd:::.show_options()
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > # Definitely don't download data on CRAN
  > if (!icd:::.env_var_is_true("NOT_CRAN")) {
  +   old_offline <- options("icd.data.offline" = TRUE)
  +   on.exit(options(old_offline), add = TRUE)
  + } else {
  +   old_offline <- options("icd.data.offline" = FALSE)
  +   on.exit(options(old_offline), add = TRUE)
  + }
  > if (icd:::.env_var_is_true("ICD_TEST_SLOW")) {
  +   old_test_slow <- options("icd.test_slow" = TRUE)
  +   on.exit(options(old_test_slow), add = TRUE)
  + }
  > old_interact <- options("icd.data.interact" = FALSE)
  > on.exit(options(old_interact), add = TRUE)
  > icd:::.show_options()
  $icd.data.interact
  [1] FALSE
  
  $icd.data.offline
  [1] TRUE
  
  $icd.data.who_url
  [1] "https://icd.who.int/browse10"
  
  > testthat::test_check("icd")
  loading helper-base.R
  loading helper-icd10.R
  ── 1. Failure: van_walraven comodbidity index and score (@test-score.R#333)  ───
  van_walraven(mydf, visit_name = "id", icd_name = "value", return_df = TRUE) not equivalent to data.frame(id = factor(c(1, 2, 3)), vanWalraven = c(10, 12, -2)).
  Component "id": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6000 | SKIPPED: 35 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: van_walraven comodbidity index and score (@test-score.R#333) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [103s/193s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(iml)
  > 
  > test_check("iml")
  ── 1. Failure: probs.to.labels (@test-utils.R#20)  ─────────────────────────────
  probs.to.labels(probs) not equal to `labels`.
  Component "..class": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 510 | SKIPPED: 0 | WARNINGS: 48 | FAILED: 1 ]
  1. Failure: probs.to.labels (@test-utils.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [168s/425s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  
  Attaching package: 'janitor'
  
  The following objects are masked from 'package:stats':
  
      chisq.test, fisher.test
  
  > 
  > test_check("janitor")
  ── 1. Failure: totals col is correct (@test-add-totals.R#33)  ──────────────────
  untabyl(adorn_totals(ct, "col")) not equal to data.frame(...).
  Component "a": Modes: character, numeric
  Component "a": Attributes: < target is NULL, current is list >
  Component "a": target is character, current is factor
  
  ── 2. Failure: values are converted to NAs at the data.frame level (@test-clean-
  cleaned_df[[2]] not equal to factor(c(NA, NA, "b"), levels = c("a", "b")).
  Types not compatible: character is not integer
  
  Reading layer `nc' from data source `/data/gannet/ripley/R/test-4.0/sf/shape/nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  ── 3. Failure: show_missing_levels parameter works (@test-tabyl.R#216)  ────────
  z %>% tabyl(a, b, new, show_missing_levels = TRUE) not equal to list(...).
  Component "lvl1": Attributes: < Component "core": Component "a": 'current' is not a factor >
  Component "lvl1": Component "a": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 554 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: totals col is correct (@test-add-totals.R#33) 
  2. Failure: values are converted to NAs at the data.frame level (@test-clean-NAs.R#31) 
  3. Failure: show_missing_levels parameter works (@test-tabyl.R#216) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Running ‘test-all.R’ [133s/160s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > #library(lavaSearch2)
  > suppressPackageStartupMessages(library("testthat"))
  > test_check("lavaSearch2")
  Loading required package: lavaSearch2
  Loading required package: ggplot2
  Loading required package: lava
  
  Attaching package: 'lava'
  
  The following object is masked from 'package:ggplot2':
  
      vars
  
  The following object is masked from 'package:testthat':
  
      compare
  
  lavaSearch2 version 1.5.4
  ── 1. Error: (unknown) (@test1-sCorrect-validObjects.R#48)  ────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(lvm(G ~ X1), data = d)
   2. lava:::estimate.lvm(lvm(G ~ X1), data = d)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 2. Error: (unknown) (@test2-modelsearch2.R#37)  ─────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m, data = df.sim)
   2. lava:::estimate.lvm(m, data = df.sim)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ── 3. Error: (unknown) (@test3-multcomp.R#149)  ────────────────────────────────
  cannot coerce type 'closure' to vector of type 'any'
  Backtrace:
   1. lava::estimate(m.lvm, df.data)
   2. lava:::estimate.lvm(m.lvm, df.data)
   4. lava:::ordinal.estimate.hook(...)
   5. base::setdiff(lava::endogenous(x), bin)
   6. base::as.vector(y)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 464 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 3 ]
  1. Error: (unknown) (@test1-sCorrect-validObjects.R#48) 
  2. Error: (unknown) (@test2-modelsearch2.R#37) 
  3. Error: (unknown) (@test3-multcomp.R#149) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lilikoi)
  > 
  > test_check("lilikoi")
  [1] "18 out of 19 Matched metabolites 90 %"
  [1] "1 out of 19 UnMatched metabolites 0 %"
  robust_score_bydist. min_exp= 0 , min_std= 0 
  ── 1. Error: full pipeline works (@test-all.r#12)  ─────────────────────────────
  invalid 'ncol' value (too large or NA)
  Backtrace:
   1. lilikoi::lilikoi.get_pd_scores(...)
   2. lilikoi:::.quantify_pathways_deregulation(...)
   3. base::matrix(0, attempts, m)
  
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "Over half of the compound IDs could not be matched to our database. Please make sure that correct compound IDs or common compound names are used."
  [1] "1 out of 4 Matched metabolites 60 %"
  [1] "3 out of 4 UnMatched metabolites 40 %"
  [1] "5 out of 5 Matched metabolites 100 %"
  [1] "0 out of 5 UnMatched metabolites 0 %"
  [1] "4 out of 5 Matched metabolites 80 %"
  [1] "1 out of 5 UnMatched metabolites 20 %"
  [1] "1 out of 1 Matched metabolites 100 %"
  [1] "0 out of 1 UnMatched metabolites 0 %"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: full pipeline works (@test-all.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [25s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > #library(microsamplingDesign)
  > 
  > #source("generateTestData.R")
  > 
  > #test_check("microsamplingDesign")
  > 
  > testthat::test_check("microsamplingDesign")
  Loading required package: microsamplingDesign
  Loading required package: Rcpp
  start Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 coresstart Ranking Schemes on cluster with  1 cores── 1. Failure: fastRank schemes , default fixed options identcal results  (@test
  all.equal(getRanking(origExample), getRanking(fastExample)) isn't true.
  
  ── 2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@t
  rankedSetOfSchemesOrig@ranking not equal to rankedSetOfSchemesNew@ranking.
  Component "name": 'current' is not a factor
  
  start Ranking Schemes on cluster with  2 cores── 3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47)  ────────────
  rankTimePointsOrig@ranking not equal to rankedTimePointsNew@ranking.
  Component "name": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: fastRank schemes , default fixed options identcal results  (@testRankSetOfSchemes.R#87) 
  2. Failure: Equal ranking SetOfSchemes (consistent with original ranking) (@testRankSetOfSchemes.R#95) 
  3. Failure: Equal ranking timePoints (@testRankTimePoints.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Running ‘testthat.R’ [5m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("checkmate")
  > library("testthat")
  > library("mlr3")
  > library("paradox")
  > library("mlr3pipelines")
  > 
  > test_check("mlr3pipelines")
  Training debug.multi with input list(input_1 = 1, input_2 = 1)
  ── 1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12)  ───────────
  <TaskClassif:tsk> has the following unsupported feature types: character
  Backtrace:
   1. lrn$train(tsk)
   2. mlr3::assert_learnable(task, self)
   3. mlr3misc::stopf(...)
  
  ── 2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removecon
  Target column 'target' must have at least two levels
  Backtrace:
   1. mlr3pipelines:::test_dropping(iris, iris, list())
   2. TaskClassif$new(...)
   3. .subset2(public_bind_env, "initialize")(...)
   4. private$.update_class_property()
   5. mlr3misc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7497 | SKIPPED: 44 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: LearnerClassifAvg (@test_learner_weightedaverage.R#12) 
  2. Error: PipeOpRemoveConstants removes expected cols (@test_pipeop_removeconstants.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [19s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("modelStudio")
  > library("DALEX")
  Welcome to DALEX (version: 1.0.1).
  Find examples and detailed introduction at: https://pbiecek.github.io/ema/
  
  > library("randomForest")
  randomForest 4.6-14
  Type rfNews() to see new features/changes/bug fixes.
  > 
  > test_check("modelStudio")
  ── 1. Error: (unknown) (@test_modelStudio.R#5)  ────────────────────────────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
    1. testthat::expect_silent(...)
   10. modelStudio:::modelStudio.explainer(...)
   11. modelStudio:::prepare_partial_dependence(pd_n, pd_c, variables = variable_names)
   12. base::droplevels(aggregated_profiles$`_vname_`)
  
  ── 2. Error: (unknown) (@test_modelStudioOptions.R#76)  ────────────────────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. modelStudio::modelStudio(...)
   2. modelStudio:::modelStudio.explainer(...)
   3. modelStudio:::prepare_partial_dependence(pd_n, pd_c, variables = variable_names)
   4. base::droplevels(aggregated_profiles$`_vname_`)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test_modelStudio.R#5) 
  2. Error: (unknown) (@test_modelStudioOptions.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [109s/288s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  rcpp_segBreedComp.cpp:42:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segBreedComp.cpp:45:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segN.cpp:48:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_nativecont.cpp:30:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_nativecont.cpp:34:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/optiSel.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 77-79 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PANICr)
  > 
  > test_check("PANICr")
  ── 1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25)  ────────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = TRUE) not equal to `test_10_dm`.
  Component "MP.tests": Component "pool_test": Modes: character, numeric
  Component "MP.tests": Component "pool_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "pool_test": target is character, current is factor
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ── 2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40)  ────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = FALSE) not equal to `test_10_ndm`.
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25) 
  2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘run-all.R’ [22s/24s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > library(BBmisc)
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > library(ParamHelpers)
  > 
  > test_check("ParamHelpers")
  ── 1. Failure: requires works (@test_OptPath.R#198)  ───────────────────────────
  d[, 1:4] not equal to data.frame(...).
  Component "x": 'current' is not a factor
  
  ── 2. Error: plotEAF works (@test_plotEAF.R#27)  ───────────────────────────────
  groups must be a factor
  Backtrace:
   1. ParamHelpers::plotEAF(opt.paths)
   4. eaf:::eafplot.formula(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1050 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: requires works (@test_OptPath.R#198) 
  2. Error: plotEAF works (@test_plotEAF.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [11s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#7)  ───────────────
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-async.R’ [22s/27s]
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plethem)
  You are now using PLETHEM.
                          If you have installed PLETHEM for the first time or have just updated it, please run setUserDb() to select an existing database or createUserDb() to create a new one.
  > 
  > test_check("plethem")
  ── 1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19)
  invalid 'type' (list) of argument
  Backtrace:
   1. plethem::getLifecourseTissueVolumes(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Tissue volumes are less than 85% of body weight (@test_physio.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [120s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotly")
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  ── 1. Error: (unknown) (@test-cookbook-lines.R#192)  ───────────────────────────
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  ── 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  ── 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1395 | SKIPPED: 48 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [8s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(preprocomb)
  > 
  > test_check("preprocomb")
  [1] "Running diagnostics on single preprocessors:"
  ── 1. Error: (unknown) (@tests.R#23)  ──────────────────────────────────────────
  Argument 'data' must have one and only one factor column.
  Backtrace:
   1. preprocomb::setgrid(phases = c("outliers"), data = modifiediris)
   2. preprocomb::testpreprocessors(unique(unlist(gridclassobject@grid)))
   3. preprocomb::initializedataclassobject(data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@tests.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:103:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:92:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/qtbase.Rcheck/00install.out’ for details.
Found the following file(s) containing GNU extensions:
  src-build/Makefile
  tools/kdebindings-build/Makefile
  tools/kdebindings-build/generator/Makefile
  tools/kdebindings-build/generator/generators/Makefile
  tools/kdebindings-build/generator/generators/dump/Makefile
  tools/kdebindings-build/generator/generators/smoke/Makefile
  tools/kdebindings-build/generator/parser/Makefile
  tools/kdebindings-build/smoke/Makefile
  tools/kdebindings-build/smoke/qt/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.so’:
  Found no call to: ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘batchelor’
Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(radjust)
  > test_check("radjust")
  ── 1. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_adaptive` not equivalent to eo$mice_rv_adaptive.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 2. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt_sel` not equivalent to eo$mice_rv_non_adpt_sel.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 3. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt` not equivalent to eo$mice_rv_non_adpt.
  Component "results_table": Component "name": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#9) 
  2. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#10) 
  3. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RDieHarder.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  Rreadsdpa.c:496:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:504:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:528:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:540:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:549:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:554:55: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:560:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:602:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:607:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:1028:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  dsdpsetoptions.c:161:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/re2r.Rcheck/00install.out’ for details.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [71s/183s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(recipes)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("recipes", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("recipes")
  + }
  Loading required namespace: xml2
  ── 1. Failure: add appropriate column with default settings (@test_intercept.R#2
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 2. Failure: adds arbitrary numeric column (@test_intercept.R#33)  ───────────
  `rec_trans` not equal to `exp_res`.
  Incompatible type for column `cat`: x factor, y character
  
  ── 3. Failure: check_new_values works on factors (@test_newvalues.R#135)  ──────
  `res` not equal to `x1`.
  Incompatible type for column `a`: x factor, y character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1431 | SKIPPED: 8 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: add appropriate column with default settings (@test_intercept.R#21) 
  2. Failure: adds arbitrary numeric column (@test_intercept.R#33) 
  3. Failure: check_new_values works on factors (@test_newvalues.R#135) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [22s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  ── 1. Error: IDT format is read correctly (@test-format-idt.R#9)  ──────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  ── 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  ───────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  ── 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ───────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/data/gannet/ripley/R/packages/tests-devel/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: FPgrowth_A
> ### Title: FPgrowth_A KEEL Association Rules Algorithm
> ### Aliases: FPgrowth_A R6_FPgrowth_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/data/gannet/ripley/R/test-4.0/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- FPgrowth_A(dat)
> 
> #Run algorithm
> algorithm$run()
Found the following significant warnings:
  graph_io_chac.c:106:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:179:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  graph_io_chac.c:208:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/rmumps.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’, declared with attribute warn_unused_result [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’, declared with attribute warn_unused_result [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'MAST', 'monocle'
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/graph/detail/adjacency_list.hpp:2239:43: warning: ‘p.Edge::color’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SimilaR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/skeleSim.Rcheck/00install.out’ for details.
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.3.2, released 2018/09/21
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/data/gannet/ripley/R/packages/tests-devel/spatial.tools.Rcheck/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
Running examples in ‘spm12r-Ex.R’ failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> in_ci <- function() {
+ nzchar(Sys.getenv("CI"))
+ }
> if (.Platform$OS.type == "unix" | in_ci()) { # windows problem
+ res = install_spm12(install_dir = tdir)
+ res = install_spm12(install_dir = tdir)
+ }
cloning into '/tmp/Rtmpyb3o7K/working_dir/RtmppnG9Zh/file24f9540e7314/spm12'...

 *** caught segfault ***
address 0xc800010009, cause 'memory not mapped'

Traceback:
 1: git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",     local_path = out_path, progress = verbose)
 2: install_spm12(install_dir = tdir)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [39s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(themetagenomics)
  Loading required package: Rcpp
  > 
  > test_check("themetagenomics")
  ── 1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92)  ─
  `prepare_data(...)` did not produce any warnings.
  
  ── 2. Error: prepare_data works with multiclass factor and continuous (@test-pre
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ── 3. Error: prepare_data works with multiclass factor and spline (@test-prepare
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 45 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92) 
  2. Error: prepare_data works with multiclass factor and continuous (@test-prepare.R#139) 
  3. Error: prepare_data works with multiclass factor and spline (@test-prepare.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [17s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(theseus)
  > 
  > test_check("theseus")
  ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
  attempting to coerce non-factor
  Backtrace:
   1. base::table(...)
   2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
   3. base::as.character.factor(df[[tax_level]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [7s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  ── 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ─────────
  Value hashes to 2448e3596a, not bc9f97d273
  
  ── 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ─────────
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  ── 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  ── 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ─────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 64 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/tsmp.Rcheck/00install.out’ for details.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [55s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  ── 1. Failure: parial xp_themes are properly added (@test-update_themes.R#39)  ─
  update_themes(xpdb = xpdb_ex_pk, xp_theme = c(point_color = "green"))$xp_theme not equivalent to `theme_xp_custom`.
  Component "labeller": target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 521 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: parial xp_themes are properly added (@test-update_themes.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(yardstick)
  For binary classification, the first factor level is assumed to be the event.
  Set the global option `yardstick.event_first` to `FALSE` to change this.
  
  > 
  > test_check("yardstick")
  ── 1. Error: Three class (@test-prob-mn_log_loss.R#14)  ────────────────────────
  `truth` should be a factor but a character was supplied.
  Backtrace:
    1. testthat::expect_equal(...)
   13. yardstick:::metric_fn(...)
   14. yardstick::metric_vec_template(...)
   15. yardstick:::validate_truth_estimate_checks(...)
   16. yardstick:::validate_class(truth, "truth", cls[1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 511 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Three class (@test-prob-mn_log_loss.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(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
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:car':
  
      recode
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(geepack)
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(zeligverse)
  Error in library(zeligverse) : there is no package called 'zeligverse'
  Execution halted
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AcuityView.Rcheck/00install.out' for details.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AFM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/AIG.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/airqualityES.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/alphashape3d.Rcheck/00install.out' for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/anipaths.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.2Mb
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.8Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/archiDART.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Arothron.Rcheck/00install.out' for details.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/atakrig.Rcheck/00install.out' for details.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rPython'
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2020-01-28 r77738) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.0Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BAT.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BayesARIMAX.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
NeedsCompilation field should likely be 'yes'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.7Mb
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/bdl.Rcheck/00install.out' for details.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 133.1Mb
  sub-directories of 1Mb or more:
    include  132.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/BIEN.Rcheck/00install.out' for details.
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/biganalytics.Rcheck/00install.out' for details.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.7Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigmemory.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [245s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigsnpr)
  Loading required package: bigstatsr
  > 
  > test_check("bigsnpr", filter = "7-")
  == testthat results  ===========================================================
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "1-")
  -- 1. Error: same sign as PLINK (no switch 0 <-> 2) (@test-1-readBed.R#58)  ----
  File 'D:\temp\RtmpeqiVR3\file1fb1c1e7a77b1.assoc' does not exist or is non-readable. getwd()=='d:/Rcompile/CRANpkg/local/4.0/bigsnpr.Rcheck/tests_i386/testthat'
  Backtrace:
   1. bigreadr::fread2(paste0(tmp, ".assoc"))
   2. data.table::fread(input, ..., data.table = data.table, nThread = nThread)
  
  == testthat results  ===========================================================
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: same sign as PLINK (no switch 0 <-> 2) (@test-1-readBed.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [216s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigsnpr)
  Loading required package: bigstatsr
  > 
  > test_check("bigsnpr", filter = "7-")
  == testthat results  ===========================================================
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "1-")
  -- 1. Error: same sign as PLINK (no switch 0 <-> 2) (@test-1-readBed.R#58)  ----
  File 'D:\temp\RtmpUvzX7i\file2e210367fc84.assoc' does not exist or is non-readable. getwd()=='d:/Rcompile/CRANpkg/local/4.0/bigsnpr.Rcheck/tests_x64/testthat'
  Backtrace:
   1. bigreadr::fread2(paste0(tmp, ".assoc"))
   2. data.table::fread(input, ..., data.table = data.table, nThread = nThread)
  
  == testthat results  ===========================================================
  [ OK: 165 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: same sign as PLINK (no switch 0 <-> 2) (@test-1-readBed.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.0Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigtabulate.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.3Mb
    extdata   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BMA.Rcheck/00install.out' for details.
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BonEV.Rcheck/00install.out' for details.
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      50.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/BPEC.Rcheck/00install.out' for details.
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Brundle.Rcheck/00install.out' for details.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.0Mb
plot.bursts: no visible global function definition for 'plot'
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/CARBayesST.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/car.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/cati.Rcheck/00install.out' for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for 'cor'
img.estim.regul: no visible global function definition for 'par'
img.estim.regul: no visible global function definition for 'image'
img.estim.regul: no visible global function definition for
  'heat.colors'
img.estim.regul: no visible global function definition for 'axis'
img.estim.regul: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'par'
img.matcor: no visible global function definition for 'image'
img.matcor: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'abline'
img.matcor: no visible global function definition for 'layout'
loo: no visible global function definition for 'cor'
matcor: no visible global function definition for 'cor'
plt.cc: no visible global function definition for 'par'
plt.cc: no visible global function definition for 'layout'
plt.indiv: no visible global function definition for 'plot'
plt.indiv: no visible global function definition for 'text'
plt.indiv: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'plot'
plt.var: no visible global function definition for 'points'
plt.var: no visible global function definition for 'text'
plt.var: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'lines'
rcc: no visible global function definition for 'var'
rcc: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for 'qchisq'
dominate.random.sample: no visible global function definition for
  'runif'
draw.circle: no visible global function definition for 'polygon'
juggle2: no visible global function definition for 'rbinom'
plot.cccd: no visible global function definition for 'gray'
plot.cccd: no visible global function definition for 'plot'
plot.cccd: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'plot'
plot.ccd: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'plot'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
CM: no visible global function definition for 'sd'
Erf: no visible global function definition for 'pnorm'
Erfc: no visible global function definition for 'pnorm'
boot.Cenarma: no visible global function definition for 'coef'
boot.Cenarma: no visible global function definition for 'arima.sim'
cenarma: no visible global function definition for 'arima'
cenarma: no visible global function definition for 'coef'
cenarma: no visible global function definition for 'ARMAacf'
cenarma: no visible global function definition for 'var'
plot.cents: no visible global function definition for 'plot'
plot.cents: no visible global function definition for 'segments'
plot.cents: no visible global function definition for 'rgb'
plot.cents: no visible global function definition for 'points'
rcarma: no visible global function definition for 'arima.sim'
rcarma: no visible global function definition for 'quantile'
scenNID: no visible global function definition for 'sd'
se.Cenarma: no visible global function definition for 'coef'
se.Cenarma: no visible global function definition for 'sd'
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
sw.plot : <anonymous>: no visible global function definition for
  'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
  'lines'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
  'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
  'median'
sw.threshold : <anonymous>: no visible global function definition for
  'mad'
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'plot'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/clustrd.Rcheck/00install.out' for details.
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/clv.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/cmaesr.Rcheck/00install.out' for details.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'plot'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'plot'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'plot'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Running examples in 'cobalt-Ex.R' failed
The error most likely occurred in:

> ### Name: bal.tab.mimids
> ### Title: Balance Statistics for MatchThem Objects
> ### Aliases: bal.tab.mimids bal.tab.wimids
> ### Keywords: tables
> 
> ### ** Examples
> 
> library(MatchThem)
Loading required package: MatchIt

Attaching package: 'MatchIt'

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

    lalonde

Loading required package: WeightIt
> library(mice)

Attaching package: 'mice'

The following objects are masked from 'package:MatchThem':

    complete, pool

The following objects are masked from 'package:base':

    cbind, rbind

> data("lalonde_mis", package = "cobalt")
> 
> #Imputing the missing data
> imp <- mice(lalonde_mis, m = 5)

 iter imp variable
  1   1  married  re74  re75
  1   2  married  re74  re75
  1   3  married  re74  re75
  1   4  married  re74  re75
  1   5  married  re74  re75
  2   1  married  re74  re75
  2   2  married  re74  re75
  2   3  married  re74  re75
  2   4  married  re74  re75
  2   5  married  re74  re75
  3   1  married  re74  re75
  3   2  married  re74  re75
  3   3  married  re74  re75
  3   4  married  re74  re75
  3   5  married  re74  re75
  4   1  married  re74  re75
  4   2  married  re74  re75
  4   3  married  re74  re75
  4   4  married  re74  re75
  4   5  married  re74  re75
  5   1  married  re74  re75
  5   2  married  re74  re75
  5   3  married  re74  re75
  5   4  married  re74  re75
  5   5  married  re74  re75
> 
> #Matching using within-imputation propensity scores
> mt.out1 <- matchthem(treat ~ age + educ + race + 
+                        married + nodegree + re74 + re75, 
+                        data = imp, approach = "within")
Error in mice::is.mids(object) : 
  argument "object" is missing, with no default
Calls: matchthem ... complete.mids -> <Anonymous> -> complete.mids -> <Anonymous>
Execution halted
Running examples in 'colorspace-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_colour_continuous_diverging
> ### Title: HCL-Based Continuous Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_continuous_diverging
> ###   scale_color_continuous_diverging scale_fill_continuous_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
> 
> # generate dataset and base plot
> set.seed(100)
> df <- data.frame(country = LETTERS, V = runif(26, -40, 40))
> df$country = factor(LETTERS, LETTERS[order(df$V)]) # reorder factors
> gg <- ggplot(df, aes(x = country, y = V, fill = V)) +
+   geom_bar(stat = "identity") +
+   labs(y = "Under/over valuation in %", x = "Country") +
+   coord_flip() + theme_minimal()
>   
> # plot with default diverging scale
> gg + scale_fill_continuous_diverging()
Error in if (!alpha || all(lab_in[, 4] == 1)) { : 
  missing value where TRUE/FALSE needed
Calls: scale_fill_continuous_diverging ... <Anonymous> -> ggproto -> <Anonymous> -> colour_ramp
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
addxaxis: no visible global function definition for 'par'
addxaxis: no visible global function definition for 'axis'
addxaxis: no visible global function definition for 'mtext'
eplot: no visible global function definition for 'plot'
eplot: no visible global function definition for 'par'
eplot: no visible global function definition for 'axis'
eplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
conicPlot: no visible global function definition for 'palette'
conicPlotAsymptotes: no visible global function definition for
  'palette'
conicPlotAsymptotes: no visible global function definition for 'abline'
conicPlotAxes: no visible global function definition for 'palette'
conicPlotAxes: no visible global function definition for 'abline'
plotDegenerateConic: no visible global function definition for 'plot'
plotDegenerateConic: no visible global function definition for 'points'
plotDegenerateConic: no visible global function definition for 'abline'
plotEllipsis: no visible global function definition for 'lines'
plotEllipsis: no visible global function definition for 'plot'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'plot'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
plotParabola: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
maCooperative: no visible global function definition for 'points'
maCooperative: no visible global function definition for 'legend'
maPessimistic: no visible global function definition for 'combn'
maRules: no visible global function definition for 'capture.output'
mstCooperative: no visible global function definition for 'points'
mstCooperative: no visible global function definition for 'legend'
mstOptimistic: no visible global function definition for 'combn'
mstPessimistic: no visible global function definition for 'combn'
mstRules: no visible global function definition for 'capture.output'
plotCoreSet: no visible global function definition for 'points'
plotCoreSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'par'
plotImputationSet: no visible global function definition for 'plot'
plotImputationSet: no visible global function definition for 'box'
plotImputationSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'text'
shapleyValue: no visible global function definition for 'combn'
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      1.5Mb
Package suggested but not available for checking: 'ProData'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/covatest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/CovTools.Rcheck/00install.out' for details.
CoxBoost: no visible global function definition for 'Matrix'
CoxBoost: no visible binding for global variable 'sd'
CoxBoost: no visible global function definition for 'predict'
cv.CoxBoost : eval.fold: no visible global function definition for
  'predict'
cv.CoxBoost: no visible global function definition for 'mclapply'
cv.CoxBoost: no visible binding for global variable 'sd'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'terms'
iCoxBoost: no visible global function definition for 'model.response'
iCoxBoost: no visible global function definition for 'model.frame'
iCoxBoost: no visible global function definition for 'model.matrix'
iCoxBoost: no visible global function definition for 'Matrix'
plot.CoxBoost: no visible global function definition for 'plot'
plot.CoxBoost: no visible global function definition for 'lines'
plot.CoxBoost: no visible global function definition for 'text'
predict.iCoxBoost: no visible global function definition for
  'model.response'
predict.iCoxBoost: no visible global function definition for
  'model.frame'
predict.iCoxBoost: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
comp.graph: no visible global function definition for 'qnorm'
comp.graph: no visible global function definition for 'plot'
comp.graph: no visible global function definition for 'polygon'
comp.graph: no visible global function definition for 'lines'
cox.ridge: no visible global function definition for 'terms'
cox.ridge: no visible global function definition for 'model.extract'
cox.ridge: no visible global function definition for 'model.matrix'
cox.ridge: no visible binding for global variable 'hat'
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'plot'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/cplexAPI.Rcheck/00install.out' for details.
Running examples in 'cptec-Ex.R' failed
The error most likely occurred in:

> ### Name: condicoes_tempo
> ### Title: Data frame containing "tempo" descriptions
> ### Aliases: condicoes_tempo
> ### Keywords: brazil forecast weather
> 
> ### ** Examples
> 
> condicoes_tempo()
Error in open.connection(x, "rb") : 
  Timeout was reached: [servicos.cptec.inpe.br] Resolving timed out after 10000 milliseconds
Calls: condicoes_tempo -> <Anonymous> -> read_html.default
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.8Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/cruts.Rcheck/00install.out' for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
Error(s) in re-building vignettes:
--- re-building 'quick_start_guide.Rmd' using rmarkdown
trying URL 'http://census.cso.ie/censusasp/saps/boundaries/Census2011_NUTS3_generalised20m.zip'
Content type 'application/x-zip-compressed' length 841102 bytes (821 KB)
=========================================
downloaded 680 KB

Quitting from lines 57-58 (quick_start_guide.Rmd) 
Error: processing vignette 'quick_start_guide.Rmd' failed with diagnostics:
Cannot open "D:\temp\RtmpyWS2Zv/Census2011_NUTS3_generalised20m.shp"; The file doesn't seem to exist.
--- failed re-building 'quick_start_guide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'plot'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Running examples in 'ctDNAtools-Ex.R' failed
The error most likely occurred in:

> ### Name: get_mutations_read_counts
> ### Title: Counts ref and alt reads for a set of mutations
> ### Aliases: get_mutations_read_counts
> 
> ### ** Examples
> 
> data("mutations", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
Error: .onLoad failed in loadNamespace() for 'S4Vectors', details:
  call: validObject(.Object)
  error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ctDNAtools)
  > 
  > test_check("ctDNAtools")
  -- 1. Error: (unknown) (@test-ctDNAtest.R#3)  ----------------------------------
  package 'S4Vectors' could not be loaded
  Backtrace:
   1. base::suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
   3. base::library(BSgenome.Hsapiens.UCSC.hg19)
   4. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
   5. base::library(...)
   6. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  -- 2. Error: (unknown) (@test-fragment_size.R#13)  -----------------------------
  .onLoad failed in loadNamespace() for 'S4Vectors', details:
    call: validObject(.Object)
    error: invalid class "LLint" object: superclass "integer_OR_LLint" not defined in the environment of the object's class
  Backtrace:
   1. ctDNAtools::get_fragment_size(bamN3)
   2. Rsamtools::scanBamFlag
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   8. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   9. base:::runHook(".onLoad", env, package.lib, package)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctDNAtest.R#3) 
  2. Error: (unknown) (@test-fragment_size.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'ctDNAtools.Rmd' using rmarkdown
Quitting from lines 42-69 (ctDNAtools.Rmd) 
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
package 'S4Vectors' could not be loaded
--- failed re-building 'ctDNAtools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/curl.Rcheck/00install.out' for details.
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'plot'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'plot'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'plot'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'plot'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'cutpointr.Rmd' using rmarkdown
Quitting from lines 181-184 (cutpointr.Rmd) 
Error: processing vignette 'cutpointr.Rmd' failed with diagnostics:
there is no package called 'registry'
--- failed re-building 'cutpointr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.9Mb
allCombs: no visible global function definition for 'combn'
brute.search: no visible global function definition for 'na.omit'
dag.draw: no visible global function definition for 'plot'
dag.draw: no visible global function definition for 'text'
dag.init: no visible global function definition for
  'installed.packages'
dag.legend: no visible global function definition for 'text'
dag.letter: no visible global function definition for 'text'
dag.move: no visible global function definition for 'identify'
dag.move: no visible global function definition for 'locator'
dag.sim: no visible global function definition for 'rnorm'
dag.sim: no visible global function definition for 'rbinom'
dag.sim : <anonymous>: no visible global function definition for
  'rbinom'
garrows: no visible global function definition for 'arrows'
smoothArc: no visible global function definition for 'points'
summary_dagRdag: no visible global function definition for 'na.omit'
viv: no visible global function definition for 'na.omit'
write.paths: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DandEFA.Rcheck/00install.out' for details.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'plot'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.9Mb
datadict.profile: no visible global function definition for
  'txtProgressBar'
datadict.profile: no visible global function definition for
  'setTxtProgressBar'
datadict_profile: no visible global function definition for
  'txtProgressBar'
datadict_profile: no visible global function definition for
  'setTxtProgressBar'
heatmap.quality: no visible global function definition for
  'colorRampPalette'
heatmap.quality: no visible global function definition for 'heatmap'
heatmap_quality: no visible global function definition for
  'colorRampPalette'
heatmap_quality: no visible global function definition for 'heatmap'
is.oneOf: no visible global function definition for 'read.csv'
is_one_of: no visible global function definition for 'read.csv'
pkg.version: no visible global function definition for 'citation'
pkg_version: no visible global function definition for 'citation'
ruleCoverage: no visible global function definition for 'dotchart'
ruleCoverage: no visible global function definition for 'abline'
rule_coverage: no visible global function definition for 'dotchart'
rule_coverage: no visible global function definition for 'abline'
scoreSum: no visible global function definition for 'plot'
score_sum: no visible global function definition for 'plot'
shortSummary: no visible global function definition for 'sd'
short_summary: no visible global function definition for 'sd'
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11828 (sockconn)
Execution halted
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
plot.deamer: no visible global function definition for 'plot'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for 'qchisq'
compare.relimp: no visible global function definition for 'pchisq'
plot_transition: no visible global function definition for 'dnorm'
plot_transition: no visible global function definition for 'par'
plot_transition: no visible global function definition for 'plot'
plot_transition: no visible global function definition for 'lines'
plot_transition: no visible global function definition for 'plogis'
plot_transition: no visible global function definition for 'axis'
plot_transition: no visible global function definition for 'mtext'
relative.importance: no visible global function definition for 'glm'
relative.importance: no visible global function definition for 'sd'
relative.importance : tr.pr: no visible global function definition for
  'pnorm'
relative.importance: no visible global function definition for 'vcov'
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
bootbagg: no visible global function definition for 'runif'
bootworpl: no visible global function definition for 'runif'
des12: no visible global function definition for 'rnorm'
des12: no visible global function definition for 'runif'
eval.stage.gauss: no visible global function definition for 'var'
plotparti: no visible global function definition for 'plot'
plotparti: no visible global function definition for 'lines'
plotpartilev: no visible global function definition for 'plot'
plotpartilev: no visible global function definition for 'polygon'
plotpartilev: no visible global function definition for 'points'
simesi: no visible global function definition for 'runif'
simesi3d: no visible global function definition for 'runif'
simfssk: no visible global function definition for 'rnorm'
simfssk: no visible global function definition for 'runif'
simmix.delt: no visible global function definition for 'rnorm'
simmix.delt: no visible global function definition for 'runif'
simpp: no visible global function definition for 'rnorm'
simpp: no visible global function definition for 'runif'
simutree: no visible global function definition for 'runif'
stage.gaussR: no visible global function definition for 'var'
unidis: no visible global function definition for 'runif'
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
MBD: no visible global function definition for 'par'
MBD: no visible global function definition for 'gray'
MBD: no visible global function definition for 'matplot'
MBD: no visible global function definition for 'polygon'
MBD: no visible global function definition for 'lines'
MBD: no visible global function definition for 'legend'
MBD: no visible global function definition for 'matlines'
R.test: no visible global function definition for 'runif'
R.test: no visible global function definition for 'wilcox.test'
centralPlot: no visible global function definition for 'par'
centralPlot: no visible global function definition for
  'colorRampPalette'
centralPlot: no visible global function definition for 'matplot'
centralPlot: no visible global function definition for 'matlines'
centralPlot: no visible global function definition for 'legend'
scalecurve: no visible global function definition for 'plot'
scalecurve: no visible global function definition for 'lines'
scalecurve: no visible global function definition for 'legend'
tmean: no visible global function definition for 'matplot'
tmean: no visible global function definition for 'matlines'
tmean: no visible global function definition for 'lines'
tmean: no visible global function definition for 'legend'
tmean: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.9Mb
arrayUpdate : pairUpdate: no visible global function definition for
  'runif'
conditionUpdate: no visible global function definition for 'runif'
designGG: no visible global function definition for 'runif'
experimentDesignTable: no visible global function definition for
  'write.csv'
plotAllScores: no visible global function definition for 'png'
plotAllScores: no visible global function definition for 'par'
plotAllScores: no visible global function definition for 'plot'
plotAllScores: no visible global function definition for 'text'
plotAllScores: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
fs.agreement.part: no visible global function definition for 'as.dist'
fs.agreement.part: no visible global function definition for 'cor'
fs.leave.k.out.combn: no visible global function definition for 'sd'
fs.leave.k.out.sample: no visible global function definition for 'sd'
fs.rd: no visible global function definition for 'pchisq'
fs.selection: no visible global function definition for 'p.adjust'
plot.FIT: no visible global function definition for 'qchisq'
plot.FIT: no visible global function definition for 'ppoints'
plot.FIT: no visible global function definition for 'plot'
plot.FIT: no visible global function definition for 'points'
plot.FIT: no visible global function definition for 'abline'
plotJn: no visible global function definition for 'plot'
plotJn: no visible global function definition for 'points'
robust.distance.signed: no visible global function definition for
  'mahalanobis'
snowball: no visible global function definition for 'is'
snowball: no visible global function definition for 'median'
weight.sd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
makeAdjMatrix: no visible global function definition for 'combn'
plotPosteriorN: no visible global function definition for 'plot'
plotPosteriorN: no visible global function definition for 'title'
plotPosteriorN: no visible global function definition for 'lines'
plotPosteriorN: no visible global function definition for 'legend'
venn3: no visible global function definition for 'plot'
venn3: no visible global function definition for 'runif'
venn3: no visible global function definition for 'points'
venn3: no visible global function definition for 'lines'
venn3: no visible global function definition for 'text'
venn4: no visible global function definition for 'plot'
venn4: no visible global function definition for 'lines'
venn4: no visible global function definition for 'runif'
venn4: no visible global function definition for 'points'
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11724 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11724 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11768 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11768 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'plot'
fAssocplot: no visible global function definition for 'coordinates'
fAssocplot: no visible global function definition for 'text'
fAssocplot: no visible global function definition for 'box'
fDrawfigure: no visible global function definition for 'slot'
fDrawfigure : <anonymous>: no visible global function definition for
  'slot'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fDrawfigure: no visible global function definition for 'plot'
fDrawfigure: no visible global function definition for 'image'
fDrawfigure: no visible global function definition for
  'colorRampPalette'
fDrawfigure: no visible global function definition for 'points'
fRanXY : <anonymous>: no visible global function definition for 'slot'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
aLine: no visible global function definition for 'lines'
aLine: no visible global function definition for 'ecdf'
dip.test: no visible global function definition for 'complete.cases'
dip.test: no visible global function definition for 'runif'
dip.test: no visible global function definition for 'approx'
plot.dip: no visible global function definition for 'par'
plot.dip: no visible global function definition for 'ecdf'
plot.dip: no visible global function definition for 'plot'
plot.dip: no visible global function definition for 'title'
plot.dip: no visible global function definition for 'abline'
plot.dip: no visible global function definition for 'axis'
plot.dip: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
dist.multiPhylo: no visible global function definition for 'as.dist'
gromov.hyperbolicity: no visible global function definition for
  'as.dist'
mcmc.target.seq: no visible global function definition for 'runif'
phylo.diff: no visible global function definition for 'par'
phylo.diff: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/distrMod.Rcheck/00install.out' for details.
Warning: multiple methods tables found for 'plot'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Running examples in 'distrMod-Ex.R' failed
The error most likely occurred in:

> ### Name: BinomFamily
> ### Title: Generating function for Binomial families
> ### Aliases: BinomFamily
> ### Keywords: models
> 
> ### ** Examples
> 
> (B1 <- BinomFamily(size = 25, prob = 0.25))
An object of class "BinomFamily"
### name:	Binomial family

### distribution:	Distribution Object of Class: Binom
 size: 25
 prob: 0.25

### param:	An object of class "ParamFamParameter"
name:	probability of success
prob:	0.25
fixed part of param.:
	size:	25
trafo:
     prob
prob    1

### props:
[1] "The Binomial family is symmetric with respect to prob = 0.5;"
[2] "i.e., d(Binom(size, prob))(k)=d(Binom(size,1-prob))(size-k)" 
> plot(B1)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.0Mb
Package suggested but not available for checking: 'rPython'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dplyr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/DSsim.Rcheck/00install.out' for details.
DStree: no visible global function definition for 'model.frame'
DStree: no visible global function definition for 'model.matrix'
DStree: no visible global function definition for 'model.response'
DStree: no visible global function definition for 'as.formula'
bag: no visible global function definition for 'model.frame'
bag: no visible global function definition for 'model.response'
plot.DStree: no visible global function definition for 'par'
plot.DStree: no visible global function definition for 'plot'
plot.DStree: no visible global function definition for 'rainbow'
plot.DStree: no visible global function definition for 'lines'
plot.DStree: no visible global function definition for 'legend'
predict.DStree: no visible global function definition for 'predict'
print.DStree: no visible global function definition for 'naprint'
prune.DStree: no visible global function definition for 'median'
prune.DStree: no visible global function definition for 'predict'
prune.DStree: no visible binding for global variable 'var'
summ.MAE: no visible global function definition for 'predict'
summary.DStree: no visible global function definition for 'naprint'
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'pdf'
DS: no visible global function definition for 'plot'
DS: no visible global function definition for 'dev.off'
LFC: no visible global function definition for 'glm'
LFC: no visible global function definition for 'predict'
PartialCor: no visible global function definition for 'na.omit'
comDCGLplot: no visible global function definition for 'pdf'
comDCGLplot: no visible global function definition for 'plot'
comDCGLplot: no visible global function definition for 'dev.off'
percentLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'pt'
qLinkfilter: no visible global function definition for 'p.adjust'
rLinkfilter: no visible global function definition for 'cor'
varianceBasedfilter: no visible binding for global variable 'var'
varianceBasedfilter: no visible global function definition for 'median'
varianceBasedfilter: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
Package required and available but unsuitable version: 'aws'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
DTK.plot: no visible global function definition for 'plot'
DTK.plot: no visible global function definition for 'axis'
DTK.plot: no visible global function definition for 'title'
DTK.plot: no visible global function definition for 'lines'
DTK.plot: no visible global function definition for 'points'
DTK.test: no visible binding for global variable 'sd'
DTK.test: no visible global function definition for 'qtukey'
TK.test: no visible global function definition for 'TukeyHSD'
TK.test: no visible global function definition for 'aov'
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for 'runif'
DTMC: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/dtwSat.Rcheck/00install.out' for details.
prepare_Rd: multiple methods tables found for 'plot'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.0Mb
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dyndimred)
  > library(dynutils)
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  > 
  > test_check("dyndimred")
  -- 1. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(expr)
   2. dynutils::install_packages("destiny")
  
  -- 2. Error: Perform dimred dm_destiny  ----------------------------------------
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  == testthat results  ===========================================================
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ecr.Rcheck/00install.out' for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
comPlot: no visible global function definition for 'plot'
comPlot: no visible global function definition for 'lines'
convertEiData: no visible global function definition for 'model.frame'
plot.eiwild: no visible global function definition for 'plot'
plot.eiwild: no visible global function definition for 'par'
plotResult: no visible global function definition for 'grey'
plotResult: no visible global function definition for
  'colorRampPalette'
plotResult: no visible global function definition for 'plot.new'
plotResult: no visible global function definition for 'plot.window'
prioriPlot: no visible global function definition for 'par'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rgamma'
prioriPlot : <anonymous>: no visible global function definition for
  'rbeta'
prioriPlot: no visible global function definition for 'hist'
prioriPlot : <anonymous>: no visible global function definition for
  'rgamma'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rexp'
prioriPlot : <anonymous>: no visible global function definition for
  'rexp'
runMBayes: no visible global function definition for 'runif'
runMBayes: no visible global function definition for 'rgamma'
runMBayes: no visible global function definition for 'rexp'
str0: no visible global function definition for 'str'
tuneVars: no visible global function definition for 'sd'
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
empiricalFDR: no visible global function definition for 'axis'
empiricalFDR: no visible global function definition for 'loess'
empiricalFDR: no visible global function definition for 'predict'
empiricalFDR: no visible global function definition for 'lines'
empiricalFDR: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'plot'
fdrBiCurve: no visible global function definition for 'axis'
fdrBiCurve: no visible global function definition for 'lines'
fdrBiCurve: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'legend'
simulateCounts: no visible global function definition for
  'txtProgressBar'
simulateCounts: no visible global function definition for
  'setTxtProgressBar'
simulateCounts: no visible global function definition for 'rnorm'
simulateCounts: no visible global function definition for 'hist'
simulateCounts: no visible global function definition for 'colData'
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
plot.episplineDensity: no visible global function definition for 'plot'
plot.episplineDensity: no visible global function definition for
  'points'
postproc: no visible global function definition for 'plot'
postproc: no visible global function definition for 'points'
preprocess.data: no visible global function definition for 'sd'
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
FCIplot: no visible global function definition for 'na.omit'
FCIplot: no visible global function definition for 'plot'
FCIplot: no visible global function definition for 'tail'
FCIplot: no visible global function definition for 'grid'
FCIplot: no visible global function definition for 'polygon'
FCIplot: no visible global function definition for 'rgb'
linpred: no visible global function definition for 'lm'
mplott: no visible global function definition for 'par'
mplott: no visible global function definition for 'plot'
mplott: no visible global function definition for 'na.omit'
mplott: no visible global function definition for 'lines'
mplott: no visible global function definition for 'legend'
mplott: no visible global function definition for 'grid'
plott: no visible global function definition for 'lines'
plott: no visible global function definition for 'par'
plott: no visible global function definition for 'plot'
plott: no visible global function definition for 'grid'
tsideplot: no visible global function definition for 'par'
tsideplot: no visible global function definition for 'plot'
tsideplot: no visible global function definition for 'axis'
tsideplot: no visible global function definition for 'grid'
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in 'eqn2svg-Ex.R' failed
The error most likely occurred in:

> ### Name: eqn2svg
> ### Title: Convert a LaTeX math formula to an SVG object
> ### Aliases: eqn2svg
> 
> ### ** Examples
> 
> # Take LaTeX code for the Heaviside
> # Function and convert that to SVG
> heaviside <-
+   eqn2svg(
+     eqn = l_time_domain[25],
+     preview = FALSE
+   )
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: eqn2svg -> readLines -> file
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
ESA: no visible binding for global variable 'var'
plot.esabcv: no visible global function definition for 'plot'
plot.esabcv: no visible global function definition for 'points'
plot.esabcv: no visible global function definition for 'axis'
plot.esabcv: no visible global function definition for 'title'
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for 'rnorm'
ESEA.Main: no visible global function definition for 'sd'
ESEA.Main: no visible global function definition for 'p.adjust'
PlotGlobEdgeCorProfile: no visible global function definition for
  'plot'
PlotGlobEdgeCorProfile: no visible global function definition for
  'lines'
PlotGlobEdgeCorProfile: no visible global function definition for
  'colors'
PlotGlobEdgeCorProfile: no visible global function definition for
  'points'
PlotGlobEdgeCorProfile: no visible global function definition for
  'legend'
PlotGlobEdgeCorProfile: no visible global function definition for
  'text'
PlotPathwayGraph: no visible global function definition for 'par'
PlotPathwayGraph: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'lines'
PlotRunEnrichment: no visible global function definition for 'colors'
PlotRunEnrichment: no visible global function definition for 'text'
SavePathway2File: no visible global function definition for 'is'
calEdgeCorScore: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
rAllRisksFactors: no visible global function definition for 'new'
rAssetDistribution: no visible global function definition for 'new'
rDefaultSpread: no visible global function definition for 'new'
rLiquiditySpread: no visible global function definition for 'new'
rRealEstate: no visible global function definition for 'new'
rShortRate: no visible global function definition for 'new'
rStock: no visible global function definition for 'new'
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
MartingaleTest,Scenarios: no visible global function definition for
  'plot'
MartingaleTest,Scenarios: no visible global function definition for
  'lines'
MartingaleTest,Scenarios: no visible global function definition for
  'title'
customPathsGeneration,Scenarios: no visible global function definition
  for 'rnorm'
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ESTER.Rcheck/00install.out' for details.
.Transition: no visible global function definition for 'rnorm'
.Transition.DC: no visible global function definition for 'runif'
CondPdf.CC.interval: no visible global function definition for 'plot'
CondPdf.DC.interval: no visible global function definition for 'plot'
Simu.Cond.HR: no visible global function definition for 'rpois'
Simu.Cond.HR: no visible global function definition for 'runif'
Simu.Cond.HR: no visible global function definition for 'hist'
Simu.Cond.HR: no visible global function definition for 'var'
Simu.HR: no visible global function definition for 'rpois'
Simu.HR: no visible global function definition for 'runif'
Simu.HR: no visible global function definition for 'hist'
Simu.HR: no visible global function definition for 'var'
Simu.PDMP: no visible global function definition for 'plot'
Simu.PDMP.DC: no visible global function definition for 'plot'
plotCHR: no visible global function definition for 'plot'
plotHR: no visible global function definition for 'plot'
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
EW : PhiP : Phi: no visible global function definition for 'pnorm'
EWplot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
extfunnel: no visible global function definition for 'qnorm'
extfunnel: no visible global function definition for 'meta.summaries'
extfunnel: no visible global function definition for 'flush.console'
extfunnel: no visible global function definition for 'qt'
extfunnel: no visible global function definition for 'dev.new'
extfunnel: no visible global function definition for 'par'
extfunnel: no visible global function definition for 'plot'
extfunnel: no visible global function definition for 'polygon'
extfunnel: no visible global function definition for 'segments'
extfunnel: no visible global function definition for 'abline'
extfunnel: no visible global function definition for 'axis'
extfunnel: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
createFormula: no visible global function definition for 'tail'
createFormula: no visible global function definition for 'head'
createFormula: no visible global function definition for 'as.formula'
ezsim: no visible global function definition for 'runif'
plot.ezsim: no visible global function definition for 'quantile'
plot.ezsim: no visible global function definition for 'head'
plot.ezsim: no visible global function definition for 'tail'
plot.ezsim: no visible global function definition for 'plot'
plot.ezsim: no visible binding for global variable 'dnorm'
plot.ezsim: no visible binding for global variable 'pdf'
plot.ezsim: no visible global function definition for 'dev.off'
plot.ezsim : <anonymous>: no visible global function definition for
  'dev.new'
plot.summary.ezsim: no visible global function definition for 'head'
plot.summary.ezsim: no visible global function definition for 'tail'
plot.summary.ezsim: no visible binding for global variable 'pdf'
plot.summary.ezsim: no visible global function definition for 'dev.off'
plot.summary.ezsim : <anonymous>: no visible global function definition
  for 'dev.new'
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
PTSingleAssetBarrierOption2: no visible global function definition for
  'new'
newton: no visible global function definition for 'plot'
newton: no visible global function definition for 'abline'
probInRange: no visible global function definition for 'pnorm'
shortfall_risk: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fdANOVA.Rcheck/00install.out' for details.
FDRreg: no visible global function definition for 'dnorm'
colnormalize: no visible global function definition for 'sd'
efron: no visible global function definition for 'median'
efron: no visible global function definition for 'hist'
efron: no visible global function definition for 'glm'
efron: no visible binding for global variable 'poisson'
efron: no visible global function definition for 'qchisq'
efron: no visible global function definition for 'predict'
efron: no visible global function definition for 'quantile'
efron: no visible global function definition for 'lm'
efron: no visible global function definition for 'coef'
make.bspline.matrix: no visible global function definition for
  'quantile'
plotFDR: no visible global function definition for 'hist'
plotFDR: no visible global function definition for 'par'
plotFDR: no visible global function definition for 'plot'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'lines'
plotFDR: no visible global function definition for 'legend'
plotFDR: no visible global function definition for 'rug'
plotFDR: no visible global function definition for 'title'
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/fGarch.Rcheck/00install.out' for details.
fgeasy: no visible global function definition for 'dist'
fgeasy : cor.est: no visible global function definition for 'cor.test'
fgeasy: no visible binding for global variable 'var'
fgperm : runrand: no visible global function definition for 'runif'
fgperm : runrand: no visible global function definition for 'ave'
fgploc : runrand: no visible global function definition for 'runif'
fgploc : runrand: no visible global function definition for 'ave'
fyshuffle: no visible global function definition for 'runif'
plot.fg: no visible global function definition for 'par'
plot.fg: no visible global function definition for 'plot'
plot.fg: no visible global function definition for 'segments'
plot.fg: no visible binding for global variable 'quantile'
plot.fg: no visible global function definition for 'abline'
plot.fg: no visible global function definition for 'axis'
summary.fg: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
lsmacof: no visible global function definition for 'cmdscale'
plotInc: no visible global function definition for 'rainbow'
plotInc: no visible global function definition for 'plot'
prepareCalib: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/float.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
GCV: no visible global function definition for 'lm'
GCV: no visible global function definition for 'resid'
ffplot: no visible global function definition for 'par'
ffplot: no visible global function definition for 'plot'
ffplot: no visible global function definition for 'points'
ffplot: no visible global function definition for 'legend'
flowfield: no visible global function definition for 'write.table'
gpr: no visible global function definition for 'quantile'
gpr: no visible global function definition for 'var'
smoothp: no visible global function definition for 'lm'
smoothp: no visible global function definition for 'predict'
smoothp: no visible global function definition for 'resid'
smoothp: no visible global function definition for 'optimize'
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/fPortfolio.Rcheck/00install.out' for details.
ComputeDCT2FFT: no visible global function definition for 'fft'
ComputeSemipgramFFT: no visible global function definition for 'fft'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
do.fd.estimate2d.simple: no visible global function definition for
  'median'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fd.plot.legend: no visible global function definition for 'legend'
fd.plot.loglog: no visible global function definition for 'plot'
fd.plot.loglog: no visible global function definition for 'points'
fd.plot.loglog: no visible global function definition for 'abline'
summary.FractalDim: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.5Mb
custom.draw.circle: no visible global function definition for 'lines'
frcc: no visible binding for global variable 'sd'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'cor'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible binding for global variable 'sd'
plot_units: no visible global function definition for 'plot'
plot_units: no visible global function definition for 'points'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'plot'
plot_variables: no visible global function definition for 'points'
plot_variables: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'segments'
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(freetypeharfbuzz)
  > 
  > test_check("freetypeharfbuzz")
  -- 1. Failure: string metrics are computed for various edge cases (@test-string-
  `metrics` not equal to c(width = w, height = h, ascent = a, descent = d).
  2/4 mismatches (average diff: 1e-04)
  [2] 1.28 - 1.28 == 1e-04
  [3] 1.28 - 1.28 == 1e-04
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: string metrics are computed for various edge cases (@test-string-info.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: 'dggrids'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
.FunFEM.main: no visible global function definition for 'kmeans'
.FunFEM.main: no visible global function definition for 'rmultinom'
.FunFEM.main: no visible global function definition for 'cutree'
.FunFEM.main: no visible global function definition for 'hclust'
.FunFEM.main: no visible global function definition for 'dist'
.FunFEM.main: no visible global function definition for 'par'
.FunFEM.main: no visible global function definition for 'plot'
.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
FPTsimul: no visible global function definition for 'runif'
histplot: no visible global function definition for 'dev.new'
histplot: no visible global function definition for 'hist'
histplot: no visible global function definition for 'par'
histplot: no visible global function definition for 'plot'
histplot: no visible global function definition for 'legend'
mdt: no visible binding for global variable 'deltat'
plot.FPTdensity: no visible global function definition for 'dev.new'
plot.FPTdensity: no visible global function definition for 'plot'
res_summary: no visible global function definition for 'write.table'
res_summary: no visible global function definition for 'sd'
res_summary: no visible global function definition for 'median'
vdt: no visible binding for global variable 'deltat'
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/GADMTools.Rcheck/00install.out' for details.
CI.RMSEA: no visible global function definition for 'qchisq'
CI.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'par'
GAIPE.RMSEA: no visible global function definition for 'plot'
GAIPE.RMSEA: no visible global function definition for 'abline'
GAIPE.RMSEA: no visible global function definition for 'colors'
GAIPE.RMSEA: no visible global function definition for 'text'
GAIPE.RMSEA: no visible global function definition for 'arrows'
GAIPE.RMSEA: no visible global function definition for 'points'
GAIPE.RMSEA: no visible global function definition for 'axis'
GAIPE.RMSEA: no visible global function definition for 'lines'
GAIPE.RMSEA: no visible global function definition for 'legend'
GAIPE.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'qchisq'
GAIPE.RMSEA: no visible global function definition for 'mtext'
GAIPE.RMSEA: no visible global function definition for 'title'
PA.RMSEA: no visible global function definition for 'pchisq'
PA.RMSEA: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
cvriskMSM: no visible global function definition for 'predict'
plotcvriskMSM: no visible global function definition for 'plot'
plotcvriskMSM: no visible binding for global variable 'lines'
plotcvriskMSM: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
GAMBoost: no visible global function definition for 'binomial'
GAMBoost: no visible global function definition for 'gaussian'
GAMBoost: no visible global function definition for 'poisson'
GAMBoost: no visible binding for global variable 'sd'
GAMBoost: no visible global function definition for 'Matrix'
calc.confidence.bands: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'binomial'
cv.GAMBoost : eval.fold: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'mclapply'
cv.GAMBoost: no visible binding for global variable 'var'
estimPVal: no visible global function definition for 'mclapply'
plot.GAMBoost: no visible global function definition for 'plot'
plot.GAMBoost: no visible global function definition for 'lines'
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
contindic.gb2: no visible global function definition for 'contour'
contindic.gb2: no visible global function definition for 'box'
contindic.gb2: no visible global function definition for 'mtext'
contprof.gb2: no visible global function definition for 'image'
contprof.gb2: no visible global function definition for 'heat.colors'
contprof.gb2: no visible global function definition for 'contour'
contprof.gb2: no visible global function definition for 'text'
contprof.gb2: no visible global function definition for 'box'
dplot.cavgb2: no visible global function definition for 'par'
dplot.cavgb2: no visible global function definition for 'curve'
dplot.cavgb2: no visible global function definition for 'legend'
dplot.cavgb2: no visible global function definition for 'plot'
dplot.cavgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'curve'
dplot.cgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'legend'
plotsML.gb2: no visible global function definition for 'par'
plotsML.gb2: no visible global function definition for 'plot'
plotsML.gb2: no visible global function definition for 'abline'
plotsML.gb2: no visible global function definition for 'curve'
plotsML.gb2: no visible global function definition for 'legend'
saveplot : <local>: no visible global function definition for 'dev.set'
saveplot : <local>: no visible global function definition for
  'dev.print'
saveplot : <local>: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
coeplot: no visible global function definition for 'plot'
coeplot: no visible global function definition for 'axis'
coeplot: no visible global function definition for 'lines'
coeplot: no visible global function definition for 'title'
coeplot: no visible global function definition for 'legend'
corplot: no visible global function definition for 'par'
corplot: no visible global function definition for 'pairs'
corplot: no visible global function definition for 'strwidth'
lm.estimate: no visible global function definition for 'as.formula'
lm.estimate: no visible global function definition for 'glm'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
panel.smooth.r: no visible global function definition for 'par'
panel.smooth.r: no visible global function definition for 'points'
panel.smooth.r: no visible global function definition for 'lines'
posplot: no visible global function definition for 'par'
posplot: no visible global function definition for 'barplot'
posplot: no visible global function definition for 'plot'
posplot: no visible global function definition for 'points'
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.1Mb
    proj     5.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gdistance.Rcheck/00install.out' for details.
Running examples in 'gdistance-Ex.R' failed
The error most likely occurred in:

> ### Name: accCost
> ### Title: Accumulated Cost Surface
> ### Aliases: accCost accCost,TransitionLayer,RasterLayer-method
> ###   accCost,TransitionLayer,Coords-method
> ### Keywords: spatial
> 
> ### ** Examples
> 
> library("raster")
> # example equivalent to that in the documentation on r.cost in GRASS
> r <- raster(nrows=6, ncols=7, 
+             xmn=0, xmx=7, 
+             ymn=0, ymx=6, 
+             crs="+proj=utm +units=m")
> 
> r[] <- c(2, 2, 1, 1, 5, 5, 5,
+          2, 2, 8, 8, 5, 2, 1,
+          7, 1, 1, 8, 2, 2, 2,
+          8, 7, 8, 8, 8, 8, 5,
+          8, 8, 1, 1, 5, 3, 9,
+          8, 1, 1, 2, 5, 3, 9)
> 
> # 1/mean: reciprocal to get permeability
> tr <- transition(r, function(x) 1/mean(x), 8) 
> tr <- geoCorrection(tr)
> 
> c1 <- c(5.5,1.5) 
> c2 <- c(1.5,5.5)
> 
> A <- accCost(tr, c1)
> plot(A)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Overview.Rmd' using knitr
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

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

    union

The following objects are masked from 'package:stats':

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: 'gdistance'

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

    normalize

Quitting from lines 137-139 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
plot.rbga: no visible global function definition for 'par'
plot.rbga: no visible global function definition for 'hist'
plot.rbga: no visible global function definition for 'plot'
plot.rbga: no visible global function definition for 'lines'
rbga: no visible global function definition for 'runif'
rbga: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gensphere.Rcheck/00install.out' for details.
splineAnalyze: no visible global function definition for 'var'
splineAnalyze: no visible global function definition for 'par'
splineAnalyze: no visible global function definition for 'plot'
splineAnalyze: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  'integrate'
PAEAAnalysis: no visible global function definition for
  'txtProgressBar'
PAEAAnalysis : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
PAEAAnalysis: no visible global function definition for 'par'
PAEAAnalysis: no visible global function definition for 'barplot'
chdirSig: no visible global function definition for 'prcomp'
chdirSig: no visible global function definition for 'rchisq'
chdirSig: no visible global function definition for 'txtProgressBar'
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
chdirplots : <anonymous>: no visible global function definition for
  'par'
chdirplots : <anonymous>: no visible global function definition for
  'plot'
chdirplots : <anonymous>: no visible global function definition for
  'arrows'
chdirplots : <anonymous>: no visible global function definition for
  'barplot'
multigmtPAEAAnalysis: no visible global function definition for
  'txtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'data'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'write.table'
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         8.9Mb
    extdata   1.5Mb
geoscaleBox: no visible global function definition for 'boxplot'
geoscaleBox: no visible global function definition for 'par'
geoscaleBox: no visible global function definition for 'plot'
geoscaleBox: no visible global function definition for 'text'
geoscaleBox: no visible global function definition for 'segments'
geoscaleBox: no visible global function definition for 'rect'
geoscaleBox: no visible global function definition for 'rgb'
geoscaleBox: no visible global function definition for 'polygon'
geoscaleBox: no visible global function definition for 'points'
geoscaleBox: no visible global function definition for 'axis'
geoscalePlot: no visible global function definition for 'par'
geoscalePlot: no visible global function definition for 'plot'
geoscalePlot: no visible global function definition for 'text'
geoscalePlot: no visible global function definition for 'segments'
geoscalePlot: no visible global function definition for 'rect'
geoscalePlot: no visible global function definition for 'rgb'
geoscalePlot: no visible global function definition for 'points'
geoscalePlot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   3.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/geoTS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/geouy.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/GET.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
acovamcmc: no visible global function definition for 'rnorm'
acovamcmc: no visible global function definition for 'rgamma'
acovamcmc: no visible binding for global variable 'quantile'
acovamcmc: no visible global function definition for 'quantile'
acovamcmc: no visible global function definition for 'var'
plot.acovamcmc: no visible global function definition for 'dev.new'
plot.acovamcmc: no visible global function definition for 'par'
plot.acovamcmc: no visible global function definition for 'plot'
plot.acovamcmc: no visible global function definition for 'density'
plot.acovamcmc: no visible global function definition for 'acf'
plot.acovamcmc: no visible global function definition for 'contour'
plot.acovamcmc: no visible global function definition for 'image'
plot.acovamcmc: no visible global function definition for 'persp'
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       21.2Mb
    test_data   1.2Mb
plot.glmulti: no visible global function definition for 'windows'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
Undefined global functions or variables:
  regsubsets windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
Package suggested but not available for checking: 'cplexAPI'
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.0/GMMAT.Rcheck/00install.out' for details.
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/gnn.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GPareto.Rcheck/00install.out' for details.
CumulativeVarPlot: no visible global function definition for 'plot'
CumulativeVarPlot: no visible global function definition for 'axis'
PCplot: no visible global function definition for 'par'
PCplot: no visible global function definition for 'plot'
PCplot: no visible global function definition for 'rainbow'
PCplot: no visible global function definition for 'density'
gDist: no visible global function definition for 'plot'
gDist: no visible global function definition for 'density'
gDist: no visible global function definition for 'abline'
gPCA.batchdetect: no visible global function definition for 'var'
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for 'dev.new'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca : Build3d: no visible global function definition for 'text'
gpca : Build3d: no visible global function definition for 'plot'
gpca : Build3d: no visible global function definition for 'abline'
gpca : Build3d: no visible global function definition for 'rect'
gpca: no visible global function definition for 'cor'
gpca: no visible global function definition for 'dev.new'
gpca: no visible global function definition for 'plot'
gpca: no visible global function definition for 'text'
gpca: no visible global function definition for 'abline'
gpca: no visible global function definition for 'rect'
gpca: no visible global function definition for 'scatterplot3d'
gpca: no visible global function definition for 'segments'
gpca: no visible global function definition for 'points'
gpca: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
gpfr: no visible global function definition for 'rnorm'
gpfr: no visible global function definition for 'runif'
gpfrpred : <anonymous>: no visible global function definition for
  'predict'
gpfrtrain: no visible global function definition for 'nlminb'
gppredict: no visible global function definition for 'predict'
gpr: no visible global function definition for 'rnorm'
gpr: no visible global function definition for 'runif'
gpr: no visible global function definition for 'lm'
gpr: no visible global function definition for 'resid'
gpr: no visible global function definition for 'nlminb'
main1: no visible global function definition for 'lm'
main1: no visible global function definition for 'resid'
main2 : <anonymous>: no visible global function definition for
  'predict'
main2: no visible global function definition for 'predict'
main3: no visible global function definition for 'lm'
main3: no visible global function definition for 'resid'
plot.gpfr: no visible global function definition for 'polygon'
plot.gpfr: no visible global function definition for 'rgb'
plot.gpfr: no visible global function definition for 'matpoints'
plot.gpfr: no visible global function definition for 'matlines'
plot.gpfr: no visible global function definition for 'lines'
plot.gpr: no visible global function definition for 'plot'
plot.gpr: no visible global function definition for 'polygon'
plot.gpr: no visible global function definition for 'rgb'
plot.gpr: no visible global function definition for 'points'
plot.gpr: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/gpuR.Rcheck/00install.out' for details.
GriegSmith: no visible global function definition for 'is.ppp'
envelopes: no visible binding for global variable 'quantile'
plot.GriegSmith: no visible global function definition for 'plot'
plot.GriegSmith: no visible global function definition for 'lines'
plot.GriegSmith: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: 'dse1'
gte: no visible global function definition for 'model.extract'
gte: no visible global function definition for 'model.matrix'
gte: no visible binding for global variable 'sd'
gte: no visible global function definition for 'dnorm'
plot.gte: no visible global function definition for 'plot'
plot.gte: no visible global function definition for 'par'
plot.gte: no visible global function definition for 'polygon'
plot.gte: no visible global function definition for 'gray'
plot.gte: no visible global function definition for 'lines'
plot.gte: no visible global function definition for 'legend'
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
PoincarePlot: no visible global function definition for 'plot'
PoincarePlot: no visible global function definition for 'lines'
PoincarePlot: no visible global function definition for 'lowess'
hctest: no visible global function definition for 'cor.test'
rdplot: no visible global function definition for 'plot'
rdplot: no visible global function definition for 'lines'
rdplot: no visible global function definition for 'lowess'
rdplot: no visible global function definition for 'rgb'
simer: no visible global function definition for 'runif'
simer: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.5Mb
    CWrappers_1.10.3   2.4Mb
    libs               6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
heatmap.plus: no visible binding for global variable 'dist'
heatmap.plus: no visible binding for global variable 'hclust'
heatmap.plus : <anonymous>: no visible global function definition for
  'reorder'
heatmap.plus: no visible global function definition for 'as.dendrogram'
heatmap.plus: no visible global function definition for
  'order.dendrogram'
heatmap.plus: no visible binding for global variable 'sd'
heatmap.plus: no visible global function definition for 'par'
heatmap.plus: no visible global function definition for 'layout'
heatmap.plus: no visible global function definition for 'image'
heatmap.plus: no visible global function definition for 'axis'
heatmap.plus: no visible global function definition for 'mtext'
heatmap.plus: no visible global function definition for 'plot'
heatmap.plus: no visible global function definition for 'frame'
heatmap.plus: no visible global function definition for 'title'
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.0Mb
Undocumented S4 classes:
  'otherornull'
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.
HubNetwork: no visible global function definition for 'rbinom'
HubNetwork: no visible global function definition for 'runif'
HubNetwork: no visible global function definition for 'cov2cor'
binaryMCMC: no visible global function definition for 'rbinom'
image.hbn: no visible global function definition for 'col2rgb'
image.hbn: no visible global function definition for 'rgb'
image.hbn: no visible global function definition for 'dev.new'
image.hbn: no visible global function definition for 'par'
image.hbn: no visible global function definition for 'image'
image.hcov: no visible global function definition for 'col2rgb'
image.hcov: no visible global function definition for 'rgb'
image.hcov: no visible global function definition for 'dev.new'
image.hcov: no visible global function definition for 'par'
image.hcov: no visible global function definition for 'image'
image.hglasso: no visible global function definition for 'col2rgb'
image.hglasso: no visible global function definition for 'rgb'
image.hglasso: no visible global function definition for 'dev.new'
image.hglasso: no visible global function definition for 'par'
image.hglasso: no visible global function definition for 'image'
plot.hbn: no visible global function definition for 'rgb'
plot.hbn: no visible global function definition for 'plot'
plot.hcov: no visible global function definition for 'rgb'
plot.hcov: no visible global function definition for 'plot'
plot.hglasso: no visible global function definition for 'rgb'
plot.hglasso: no visible global function definition for 'plot'
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  'ggplot2:::build_guides' 'ggplot2:::guide_axis'
  'ggplot2:::scales_list'
  See the note in ?`:::` about the use of this operator.
compute.contrasts: no visible binding for global variable 'sd'
compute.contrasts: no visible global function definition for 'cor'
compute.contrasts: no visible global function definition for 'sd'
plot.estfdr: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'legend'
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.5Mb
overlay.sim: no visible global function definition for 'points'
plotDistr: no visible global function definition for 'dev.hold'
plotDistr: no visible global function definition for 'dev.flush'
plotDistr: no visible global function definition for 'plot'
plotDistr: no visible global function definition for 'segments'
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
baumwelchcont: no visible global function definition for 'dnorm'
hmmcontSimul: no visible global function definition for 'rnorm'
hmmcontSimul: no visible global function definition for 'rbinom'
plot.ContObservHMM: no visible global function definition for 'plot'
plot.ContObservHMM: no visible global function definition for 'lines'
statesDistributionsPlot: no visible global function definition for
  'dnorm'
statesDistributionsPlot: no visible global function definition for 'sd'
statesDistributionsPlot: no visible global function definition for
  'plot'
statesDistributionsPlot: no visible global function definition for
  'lines'
statesDistributionsPlot: no visible global function definition for
  'legend'
summary.ContObservHMM: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for 'plot'
dishonestCasino: no visible global function definition for 'axis'
dishonestCasino: no visible global function definition for 'text'
dishonestCasino: no visible global function definition for 'rect'
dishonestCasino: no visible global function definition for 'rgb'
dishonestCasino: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for 'par'
hpbayes.plot: no visible global function definition for 'plot'
hpbayes.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'par'
postpri.plot: no visible global function definition for 'plot'
postpri.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'segments'
postpri.plot: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/HRM.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'plot'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/hydroTSM.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
ibdhap.barplot: no visible global function definition for 'plot'
ibdhap.barplot: no visible global function definition for 'rect'
ibdhap.compare.loci: no visible global function definition for 'hist'
ibdhap.compare.segs: no visible global function definition for 'tail'
ibdhap.make.calls: no visible global function definition for
  'count.fields'
ibdhap.make.calls: no visible global function definition for
  'read.table'
ibdhap.make.true: no visible global function definition for
  'read.table'
ibdhap.names: no visible global function definition for 'count.fields'
ibdhap.names: no visible global function definition for 'read.table'
ibdhap.reduce.states: no visible global function definition for
  'read.table'
ibdhap.reduce.states: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
create.ibd.dat: no visible global function definition for 'read.table'
create.pairs.frame: no visible global function definition for 'terms'
ibd.moments: no visible global function definition for 'var'
ibdreg: no visible global function definition for 'terms'
ibdreg: no visible global function definition for 'as.formula'
linkage.tests: no visible global function definition for 'pchisq'
pchibar: no visible global function definition for 'pchisq'
plot.linkage.all: no visible global function definition for 'plot'
plot.linkage.all: no visible global function definition for 'title'
plotpval: no visible global function definition for 'plot'
plotpval: no visible global function definition for 'lines'
sim.ibd.var: no visible global function definition for 'read.table'
sim.mark.prop: no visible global function definition for 'runif'
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
ICA: no visible global function definition for 'runif'
plot.ICA: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for 'na.omit'
ICCbare: no visible global function definition for 'formula'
ICCbare: no visible global function definition for 'replications'
ICCbare: no visible global function definition for 'aggregate'
ICCbare: no visible global function definition for 'anova'
ICCbare: no visible global function definition for 'aov'
ICCbareF: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'na.omit'
ICCest: no visible global function definition for 'anova'
ICCest: no visible global function definition for 'aov'
ICCest: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'qf'
ICCest: no visible global function definition for 'qnorm'
Nest: no visible global function definition for 'qnorm'
effort : CIW: no visible global function definition for 'qf'
effort: no visible global function definition for 'plot'
effort: no visible global function definition for 'axis'
effort: no visible global function definition for 'lines'
effort: no visible global function definition for 'legend'
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.4Mb
INCAncinner : dian: no visible global function definition for 'cutree'
INCAncinner : bestela: no visible global function definition for
  'cutree'
center: no visible global function definition for 'var'
dbhatta: no visible global function definition for 'as.dist'
dcor: no visible global function definition for 'cor'
dcor: no visible global function definition for 'as.dist'
dgower: no visible global function definition for 'as.dist'
dmahal: no visible global function definition for 'as.dist'
dproc2: no visible global function definition for 'as.dist'
plot.incaix: no visible global function definition for 'barplot'
plot.incanc: no visible global function definition for 'plot'
plot.incanc: no visible global function definition for 'lines'
plot.incanc: no visible global function definition for 'legend'
selectioncluster : dian: no visible global function definition for
  'cutree'
selectioncluster : bestela: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Running examples in 'icrf-Ex.R' failed
The error most likely occurred in:

> ### Name: plot
> ### Title: icrf IMSE rate plot
> ### Aliases: plot plot.icrf
> 
> ### ** Examples
> 
> # rats data example
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> data(rat2)
> set.seed(1)
> samp <- sample(1:dim(rat2)[1], 200)
> rats.train <- rat2[samp, ]
> rats.test <- rat2[-samp, ]
> L = ifelse(rats.train$tumor, 0, rats.train$survtime)
> R = ifelse(rats.train$tumor, rats.train$survtime, Inf)
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> set.seed(2)
> ## Don't show: 
> # 1. formula (currentstatus)
>  rats.icrf.small <-
+    icrf(~ dose.lvl + weight + male + cage.no, data = rat2,
+         data.type = "currentstatus", currentstatus.label = c("survtime", "tumor"),
+         returnBest = TRUE, ntree=2, nfold=1)
Error in icrf.default(m, L, R, ...) : 
  NA/NaN/Inf in foreign function call (arg 50)
Calls: icrf -> icrf.formula -> icrf.default
Execution halted
Found the following significant warnings:
  uuid/gen_uuid.c:321:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/igraph.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.4Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     15.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
A.dep.tests: no visible global function definition for 'combn'
A.dep.tests: no visible global function definition for 'pchisq'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
dependogram: no visible global function definition for 'combn'
dependogram: no visible global function definition for 'plot'
dependogram: no visible global function definition for 'points'
dependogram: no visible global function definition for 'segments'
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
interact: no visible global function definition for 'cor'
plot.interact: no visible global function definition for 'plot'
standardize.matrix: no visible binding for global variable 'var'
standardize.matrix: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Mo.Th.Ra.: no visible global function definition for 'aggregate'
daily_mean: no visible global function definition for 'aggregate'
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
par_calibration: no visible global function definition for 'aggregate'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
plot_meas_sim: no visible global function definition for 'plot'
plot_meas_sim: no visible global function definition for 'par'
plot_meas_sim: no visible global function definition for 'legend'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
shape_calibration: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for 'pnorm'
icScoreTest: no visible global function definition for 'pchisq'
icfit.formula: no visible global function definition for 'terms'
icfit.formula: no visible global function definition for
  'model.extract'
icfitBootCI: no visible global function definition for 'binom.test'
ictest.formula: no visible global function definition for
  'model.extract'
plot.icfit: no visible global function definition for 'gray'
plot.icfit: no visible global function definition for 'plot'
plot.icfit: no visible global function definition for 'axis'
plot.icfit : polygon.icfit: no visible global function definition for
  'polygon'
scoresFromFit: no visible global function definition for 'dnorm'
scoresFromFit: no visible global function definition for 'qnorm'
wsrHLYpclt: no visible global function definition for 'model.matrix'
wsrHLYpclt: no visible global function definition for 'pchisq'
wsrHLYpclt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable 'sd'
interventionEffects: no visible global function definition for 'pt'
interventionEffects: no visible global function definition for 'sd'
interventionalInference: no visible global function definition for 'sd'
interventionalInferenceAdvanced: no visible global function definition
  for 'sd'
linesROC: no visible global function definition for 'segments'
plotMaxML: no visible global function definition for 'plot'
plotMaxML: no visible global function definition for 'segments'
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
ILik : rbern: no visible global function definition for 'runif'
ILik : q: no visible global function definition for 'dnorm'
ILik : SlambdaG: no visible global function definition for 'rnorm'
ILik : Pi_hat: no visible global function definition for 'rnorm'
ILik : q: no visible global function definition for 'dgamma'
ILik : SlambdaG: no visible global function definition for 'rgamma'
ILik : Pi_hat: no visible global function definition for 'rgamma'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'coef'
ILik: no visible global function definition for 'hessian'
ILik: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
f.B: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'dnorm'
f.grovest3 : f.est: no visible global function definition for 'survfit'
f.grovest3 : f.est: no visible global function definition for 'plot'
f.grovest3 : f.est: no visible global function definition for 'lines'
f.grovest3: no visible global function definition for 'model.frame'
f.grovest3: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.frame'
invGauss: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.matrix'
predict.invGauss: no visible global function definition for
  'model.frame'
predict.invGauss: no visible global function definition for
  'model.extract'
predict.invGauss: no visible global function definition for
  'model.matrix'
predict.invGauss: no visible binding for global variable 'formula'
predict.invGauss: no visible binding for global variable 'data'
summary.invGauss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
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.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11132 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11132 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11031 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11031 (sockconn)
Execution halted
residualplot: no visible global function definition for 'predict'
residualplot: no visible global function definition for 'rstandard'
residualplot: no visible global function definition for
  'complete.cases'
residualplot: no visible global function definition for 'plot'
residualplot: no visible global function definition for 'points'
residualplot: no visible global function definition for 'lines'
residualplot: no visible global function definition for 'smooth.spline'
residualplot: no visible global function definition for 'sd'
residualplot: no visible global function definition for 'rgb'
residualplot: no visible global function definition for 'polygon'
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           8.6Mb
getSysinfo: no visible global function definition for 'sessionInfo'
getVecInfo: no visible global function definition for 'sd'
isSeriesConstant: no visible global function definition for 'median'
labelMargins: no visible global function definition for 'mtext'
plotBG: no visible global function definition for 'plot'
plotBG: no visible global function definition for 'polygon'
plotBG: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'text'
plotImageRotated: no visible global function definition for
  'heat.colors'
plotImageRotated: no visible global function definition for 'par'
plotImageRotated: no visible global function definition for 'plot'
plotImageRotated: no visible global function definition for 'image'
plotImageRotated: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'par'
plotNLines: no visible global function definition for 'plot'
plotNLines: no visible global function definition for 'mtext'
plotNLines: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'points'
plotNLines: no visible global function definition for 'sd'
userCoords: no visible global function definition for 'par'
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'doMC'
binteg: no visible global function definition for 'contourLines'
binteg: no visible global function definition for 'approx'
binteg: no visible global function definition for 'par'
plot1: no visible global function definition for 'plot'
plot1: no visible global function definition for 'par'
plot1: no visible global function definition for 'rect'
plot1: no visible global function definition for 'axis'
plot1: no visible global function definition for 'contour'
plot1: no visible global function definition for 'contourLines'
plot1: no visible binding for global variable 'approx'
plot1: no visible global function definition for 'lines'
plot1: no visible global function definition for 'text'
plot2: no visible global function definition for 'plot'
plot2: no visible global function definition for 'abline'
plot2: no visible global function definition for 'lines'
plot2: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
expression_up : <anonymous>: no visible global function definition for
  'quantile'
expression_up : <anonymous>: no visible global function definition for
  'IQR'
expression_up : <anonymous>: no visible global function definition for
  'median'
expression_up : <anonymous>: no visible global function definition for
  'sd'
plot_up: no visible global function definition for 'plot'
plot_up: no visible global function definition for 'text'
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for 'cophenetic'
bw.nn : <anonymous>: no visible global function definition for
  'quantile'
dist.diss: no visible binding for global variable 'median'
dist.diss: no visible global function definition for 'dist'
hist.kdetrees: no visible binding for global variable 'density'
kdetrees : cutoff: no visible global function definition for 'quantile'
kdetrees.complete: no visible global function definition for 'plot'
kdetrees.complete: no visible global function definition for 'hist'
kdetrees.complete: no visible global function definition for
  'write.csv'
plot.kdetrees: no visible binding for global variable 'density'
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'rbeta'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'runif'
calculate.power : <anonymous>: no visible binding for global variable
  'quantile'
generate.benchmark.data: no visible global function definition for
  'runif'
generate.benchmark.data: no visible global function definition for
  'rnorm'
generate.benchmark.data: no visible global function definition for
  'rbinom'
generate.patchwork.copula: no visible global function definition for
  'rbeta'
generate.patchwork.copula: no visible global function definition for
  'runif'
novelTest.chisq: no visible global function definition for 'pchisq'
novelTest.chisq4nn: no visible global function definition for 'pchisq'
optimise.copula.mi : <anonymous>: no visible global function definition
  for 'optimize'
power.plot: no visible global function definition for 'plot'
power.plot: no visible global function definition for 'axis'
power.plot : <anonymous>: no visible global function definition for
  'points'
power.plot: no visible global function definition for 'legend'
roc.plot: no visible global function definition for 'colorRampPalette'
roc.plot : <anonymous>: no visible global function definition for
  'plot'
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
image.kriging: no visible global function definition for 'heat.colors'
image.kriging: no visible global function definition for 'image'
kriging: no visible global function definition for 'lm'
plot.kriging: no visible global function definition for 'plot'
plot.kriging: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'plot'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'plot'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/LabourMarketAreas.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.9Mb
    proj   5.0Mb
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'plot'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
plotCVLars: no visible global function definition for 'plot'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'plot'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
ARConfIntEst: no visible global function definition for 'sd'
PTLinkFunc: no visible global function definition for 'pnorm'
PTLinkFunc: no visible global function definition for 'qnorm'
PTMultiPeriodPD: no visible global function definition for 'uniroot'
PTOnePeriodPD : f: no visible global function definition for 'pbinom'
PTOnePeriodPD: no visible global function definition for 'uniroot'
QMMGetRLogitPD: no visible global function definition for 'ecdf'
QMMPDlinkFunc: no visible global function definition for 'qnorm'
QMMPlot: no visible global function definition for 'plot'
QMMPlot: no visible global function definition for 'lines'
QMMPlot: no visible global function definition for 'legend'
VDBCalibratePD: no visible global function definition for 'ecdf'
VDBGetK: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
AlternateSVD: no visible binding for global variable 'sd'
IPOD: no visible global function definition for 'mad'
IPOD: no visible global function definition for 'pnorm'
Pvalue: no visible global function definition for 'pf'
ROCplot: no visible global function definition for 'png'
ROCplot: no visible global function definition for 'matplot'
ROCplot: no visible global function definition for 'legend'
ROCplot: no visible global function definition for 'dev.off'
leapp: no visible global function definition for 'png'
leapp: no visible global function definition for 'plot'
leapp: no visible global function definition for 'dev.off'
ridge: no visible global function definition for 'sd'
ridge: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/lgcp.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/lidR.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
plotBox: no visible global function definition for 'sd'
plotBox: no visible global function definition for 'rect'
plotBox: no visible global function definition for 'qnorm'
plotBox: no visible global function definition for 'segments'
plotInit: no visible global function definition for 'plot'
plotInit: no visible global function definition for 'runif'
plotInit: no visible global function definition for 'mtext'
plotInit: no visible global function definition for 'segments'
plotStack: no visible global function definition for 'points'
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'plot'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'plot'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lmds.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
EstimateProbability: no visible global function definition for
  'predict'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'plot'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'plot'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'plot'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'plot'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'plot'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
learnPattern.default: no visible global function definition for 'runif'
plot.learnPattern: no visible global function definition for 'matplot'
plotMDS: no visible global function definition for 'par'
plotMDS: no visible global function definition for 'rainbow'
plotMDS: no visible global function definition for 'plot'
plotMDS: no visible global function definition for 'pairs'
visualizePattern: no visible global function definition for 'par'
visualizePattern: no visible global function definition for 'plot'
visualizePattern: no visible global function definition for 'points'
visualizePattern: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.6Mb
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:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
    proj   5.0Mb
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.7Mb
ageprofile: no visible global function definition for 'model.frame'
ageprofile: no visible binding for global variable 'poisson'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'as.formula'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'contrasts<-'
ageprofile: no visible global function definition for 'anova.gam'
plotap: no visible global function definition for 'dev.new'
plotap: no visible global function definition for 'plot'
plotap: no visible global function definition for 'lines'
plotap: no visible global function definition for 'points'
plotap: no visible global function definition for 'legend'
splitter: no visible global function definition for 'reshape'
tabm: no visible global function definition for 'coef'
tabm: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
MAT: no visible global function definition for 'dev.new'
MAT: no visible global function definition for 'plot'
MAT: no visible global function definition for 'points'
MAT: no visible global function definition for 'abline'
MAT: no visible global function definition for 'text'
MAT: no visible global function definition for 'legend'
MAT: no visible global function definition for 'lines'
MAT: no visible global function definition for 'par'
MAT: no visible global function definition for 'barplot'
MAT: no visible global function definition for 'cor'
print.MAT: no visible global function definition for 'sd'
print.MAT: no visible global function definition for 'cor'
simM3PL: no visible global function definition for 'rnorm'
simM3PL: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0/MatrixModels.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
GSTplot : <anonymous>: no visible global function definition for
  't.test'
GSTplot: no visible global function definition for 'rt'
GSTplot: no visible global function definition for 'layout'
GSTplot: no visible global function definition for 'par'
GSTplot: no visible global function definition for 'plot'
GSTplot: no visible global function definition for 'text'
GSTplot: no visible global function definition for 'lines'
GSTplot: no visible global function definition for 'polygon'
GSTplot: no visible global function definition for 'abline'
GSTplot: no visible global function definition for 'ecdf'
GSTplot: no visible global function definition for 'knots'
GSTplot : <anonymous>: no visible global function definition for 'aov'
GSTplot: no visible global function definition for 'qf'
MAVTn : <anonymous>: no visible global function definition for 'aov'
MAVTn: no visible global function definition for 'p.adjust'
MAVTn: no visible global function definition for 'plot'
MAVTn: no visible global function definition for 'par'
MAVTn: no visible global function definition for 'abline'
MAVTn: no visible global function definition for 'legend'
MAVTn: no visible global function definition for 'locator'
Tols : olsf: no visible global function definition for 't.test'
Tols: no visible global function definition for 'cor'
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'plot'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   2.6Mb
mcheatmaps : coscolorFun: no visible global function definition for
  'rgb'
mcheatmaps : halfcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : fullcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'hclust'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'as.dist'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'sd'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'cophenetic'
mcheatmaps : printDiag: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'strwidth'
mcheatmaps: no visible global function definition for 'pdf'
mcheatmaps: no visible global function definition for 'plot.new'
mcheatmaps: no visible global function definition for 'as.dendrogram'
mcheatmaps: no visible global function definition for 'reorder'
mcheatmaps: no visible global function definition for 'par'
mcheatmaps: no visible global function definition for 'plot'
mcheatmaps: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'heat.colors'
mcheatmaps: no visible global function definition for 'terrain.colors'
mcheatmaps: no visible global function definition for 'as.dist'
mcheatmaps: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/mcmcabn.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
plot.nsga2: no visible global function definition for 'plot'
plot.nsga2: no visible global function definition for 'lines'
plot.nsga2: no visible global function definition for 'pairs'
plot.nsga2.collection: no visible global function definition for
  'devAskNewPage'
plot.nsga2.collection: no visible binding for global variable 'plot'
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Mercator.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'plot'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Package suggested but not available for checking: 'unix'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.2Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
calc_z_var: no visible binding for global variable 'median'
diffScore: no visible global function definition for 'new'
diffScore: no visible global function definition for 'model.matrix'
logNORMcdf: no visible global function definition for 'pnorm'
mGSZ.adj.mean.std: no visible binding for global variable 'sd'
pick.data.cols: no visible binding for global variable 'var'
plotProfile: no visible binding for global variable 'quantile'
plotProfile: no visible global function definition for 'plot'
plotProfile: no visible global function definition for 'lines'
plotProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'plot'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
migration.cv.in : <anonymous>: no visible global function definition
  for 'sd'
migration.cv.out : <anonymous>: no visible global function definition
  for 'sd'
migration.field.diagram: no visible global function definition for
  'plot'
migration.field.diagram: no visible global function definition for
  'lines'
migration.field.diagram: no visible global function definition for
  'text'
migration.field.diagram: no visible global function definition for
  'polygon'
migration.field.diagram: no visible global function definition for 'lm'
migration.field.diagram: no visible global function definition for
  'predict'
migration.field.diagram: no visible global function definition for
  'points'
migration.field.diagram: no visible global function definition for
  'resid'
migration.field.diagram: no visible global function definition for
  'coef'
migration.field.diagram: no visible global function definition for
  'mtext'
migration.field.diagram: no visible global function definition for
  'density'
migration.field.diagram: no visible global function definition for
  'rug'
migration.gini.col : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.in : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.out : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.row : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.total: no visible global function definition for 'dist'
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
miney : plot.initial.matrix: no visible global function definition for
  'plot'
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'plot'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'plot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
confusionBarplot: no visible global function definition for 'par'
confusionBarplot: no visible global function definition for 'barplot'
confusionBarplot: no visible global function definition for 'lines'
confusionBarplot: no visible global function definition for 'text'
confusionBarplot: no visible global function definition for 'legend'
confusionBarplot: no visible global function definition for 'axis'
confusionDendrogram: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'par'
confusionImage: no visible global function definition for 'image'
confusionImage: no visible global function definition for 'text'
confusionImage: no visible global function definition for 'abline'
confusionImage: no visible global function definition for 'axis'
confusionImage: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'mtext'
confusionStars: no visible global function definition for 'par'
confusionStars: no visible global function definition for 'stars'
confusionStars: no visible global function definition for 'rect'
plot.mlearning: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.4Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/mob.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/MODISTools.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'modistools-vignette.Rmd' using rmarkdown
Quitting from lines 209-216 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'modistools-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/momentuHMM.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MomTrunc.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building 'Brief-Overview.Rmd' using rmarkdown
--- finished re-building 'Brief-Overview.Rmd'

--- re-building 'Example1.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://www4.stat.ncsu.edu/~boos/Monte.Carlo.se/table9_1.jpg
HttpExceptionRequest Request {
  host                 = "www4.stat.ncsu.edu"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/~boos/Monte.Carlo.se/table9_1.jpg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Example1.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Example1.Rmd'

--- re-building 'Example2.Rmd' using rmarkdown
--- finished re-building 'Example2.Rmd'

--- re-building 'Example3.Rmd' using rmarkdown
--- finished re-building 'Example3.Rmd'

SUMMARY: processing the following file failed:
  'Example1.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Mort1Dsmooth: no visible global function definition for 'time'
Mort1Dsmooth: no visible global function definition for 'glm'
Mort1Dsmooth: no visible binding for global variable 'poisson'
Mort1Dsmooth_optimize: no visible global function definition for
  'median'
Mort2Dsmooth: no visible global function definition for 'glm'
Mort2Dsmooth: no visible binding for global variable 'poisson'
Mort2Dsmooth: no visible global function definition for 'median'
Mort2Dsmooth_optimize: no visible global function definition for
  'median'
plot.HMDdata: no visible global function definition for 'plot'
plot.Mort1Dsmooth: no visible global function definition for 'matplot'
plot.Mort2Dsmooth: no visible global function definition for 'quantile'
predict.Mort1Dsmooth: no visible global function definition for 'glm'
predict.Mort1Dsmooth: no visible binding for global variable 'poisson'
predict.Mort2Dsmooth: no visible global function definition for 'glm'
predict.Mort2Dsmooth: no visible binding for global variable 'poisson'
print.summary.Mort1Dsmooth: no visible global function definition for
  'quantile'
print.summary.Mort2Dsmooth: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   9.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.4Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

diagram.mpa: no visible global function definition for 'plot'
diagram.mpa: no visible global function definition for 'abline'
diagram.mpa: no visible global function definition for 'text'
plotmpa: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable 'median'
mpcv: no visible global function definition for 'cov'
mpcv: no visible global function definition for 'dist'
plot.mpcv: no visible binding for global variable 'median'
plot.mpcv: no visible global function definition for 'par'
plot.mpcv: no visible global function definition for 'plot'
plot.mpcv: no visible global function definition for 'rect'
plot.mpcv: no visible global function definition for 'lines'
plot.mpcv: no visible global function definition for 'points'
plot.mpcv: no visible global function definition for 'legend'
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/mpMap2.Rcheck/00install.out' for details.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs         13.9Mb
    mathematica   1.5Mb
MRwarp: no visible global function definition for 'dev.new'
MRwarp: no visible global function definition for 'plot'
MRwarp: no visible global function definition for 'lines'
MRwarp: no visible global function definition for 'points'
MRwarp: no visible global function definition for 'hist'
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
msap: no visible global function definition for 'packageVersion'
msap: no visible global function definition for 'read.csv'
msap: no visible global function definition for 'write.csv'
msap: no visible global function definition for 'sd'
msap: no visible global function definition for 'wilcox.test'
msap: no visible global function definition for 'dist'
msap: no visible global function definition for 'rainbow'
msap: no visible global function definition for 'png'
msap: no visible global function definition for 'legend'
msap: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'cmdscale'
pcoa: no visible global function definition for 'png'
pcoa: no visible global function definition for 'par'
pcoa: no visible global function definition for 'plot'
pcoa: no visible global function definition for 'rainbow'
pcoa: no visible global function definition for 'points'
pcoa: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  20.9Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
compute.beta.hat: no visible global function definition for 'lm'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'new'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'model.matrix'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'validObject'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
kmCok: no visible global function definition for 'plot'
predict.kmCok: no visible global function definition for 'model.matrix'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'qnorm'
predict.kmCok: no visible global function definition for 'qt'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
--- re-building 'muHVT.Rmd' using rmarkdown
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'
Warning: package 'R.utils' is not available (for R Under development)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/4.0:
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/4.0/PACKAGES'
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
there is no package called 'R.utils'
--- failed re-building 'muHVT.Rmd'

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

Error: Vignette re-building failed.
Execution halted
plotOptionValues: no visible global function definition for 'plot'
plotOptionValues: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'lmer-vignette.Rmd' using rmarkdown
Quitting from lines 172-184 (lmer-vignette.Rmd) 
Error: processing vignette 'lmer-vignette.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x' and 'y'
--- failed re-building 'lmer-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
betas_plot: no visible global function definition for 'cov2cor'
betas_plot: no visible global function definition for
  'colorRampPalette'
betas_plot: no visible global function definition for 'pdf'
betas_plot: no visible global function definition for 'dev.off'
mhplot: no visible global function definition for 'read.table'
mhplot: no visible global function definition for 'pdf'
mhplot: no visible global function definition for 'plot'
mhplot: no visible global function definition for 'points'
mhplot: no visible global function definition for 'abline'
mhplot: no visible global function definition for 'axis'
mhplot: no visible global function definition for 'dev.off'
multi_meta: no visible global function definition for 'write.table'
multi_meta: no visible global function definition for 'read.table'
multi_meta: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'read.table'
qqplotter: no visible global function definition for 'qchisq'
qqplotter: no visible global function definition for 'ppoints'
qqplotter: no visible global function definition for 'median'
qqplotter: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'pdf'
qqplotter: no visible global function definition for 'plot'
qqplotter: no visible global function definition for 'abline'
qqplotter: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
.onAttach: no visible global function definition for
  'packageDescription'
genoudRob: no visible global function definition for 'genoud'
get.XYdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'model.matrix'
get.xy: no visible global function definition for 'terms'
get.xynames: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'model.response'
get.ydata: no visible global function definition for 'model.frame'
mt.dev: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'dt'
mt.mle: no visible global function definition for 'optim'
multinomRob: no visible global function definition for 'var'
plot.multinomRob: no visible global function definition for 'par'
plot.multinomRob: no visible global function definition for 'plot'
plot.multinomRob: no visible global function definition for 'title'
rdirich: no visible global function definition for 'rgamma'
residual.generator: no visible global function definition for 'median'
rmultinomial: no visible global function definition for 'runif'
rmultinomial: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'TwoModeNetworks.Rnw' using knitr
Quitting from lines 128-132 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'TwoModeNetworks.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
plotFID: no visible global function definition for 'plot'
plotFID: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   1.5Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [118s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nandb)
  > 
  > test_check("nandb")
  -- 1. Failure: median and smooth filters work (@test-filters.R#7)  -------------
  round(mean(median_filter(m, na_rm = TRUE), na.rm = TRUE), 3) not equal to 3.812.
  1/1 mismatches
  [1] 3.81 - 3.81 == 0.001
  
  == testthat results  ===========================================================
  [ OK: 153 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: median and smooth filters work (@test-filters.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
NAPPA: no visible binding for global variable 'sd'
NAPPA: no visible global function definition for 'sd'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'coef'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'lm'
calibrate.sigmoid.curve: no visible global function definition for
  'nls'
calibrate.sigmoid.curve: no visible binding for global variable
  'weights'
calibrate.sigmoid.curve: no visible global function definition for
  'coef'
calibrate.sigmoid.curve: no visible global function definition for
  'plot'
calibrate.sigmoid.curve: no visible global function definition for
  'rgb'
calibrate.sigmoid.curve: no visible global function definition for
  'box'
calibrate.sigmoid.curve: no visible global function definition for
  'axis'
calibrate.sigmoid.curve: no visible global function definition for
  'abline'
calibrate.sigmoid.curve: no visible global function definition for
  'lines'
calibrate.sigmoid.curve: no visible global function definition for
  'predict'
calibrate.sigmoid.curve: no visible global function definition for
  'smooth.spline'
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for 'nls'
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable 'weights'
calibrate.sigmoid.curve: no visible binding for global variable 'coef'
calibrate.sigmoid.curve: no visible global function definition for 'pf'
calibrate.sigmoid.curve: no visible global function definition for
  'legend'
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.9Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("nat.utils")
  Loading required package: nat.utils
  -- 1. Failure: common_path works (@test-fsutils.r#79)  -------------------------
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "d:/"
  y[1]: "D:/"
  
  == testthat results  ===========================================================
  [ OK: 73 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: common_path works (@test-fsutils.r#79) 
  
  Error: testthat unit tests failed
  Execution halted
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
NB.plot.likelihood: no visible global function definition for 'plot'
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
population: no visible global function definition for 'weighted.mean'
population: no visible global function definition for 'rpois'
population: no visible global function definition for 'lm'
population: no visible global function definition for 'coefficients'
population: no visible global function definition for 'sd'
population: no visible global function definition for 'par'
population: no visible global function definition for 'plot'
population: no visible global function definition for 'lines'
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/NestedCategBayesImpute.Rcheck/00install.out' for details.
clustConfigurations: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/NetLogoR.Rcheck/00install.out' for details.
Running examples in 'NetLogoR-Ex.R' failed
The error most likely occurred in:

> ### Name: NLwith
> ### Title: 'Agents' with
> ### Aliases: NLwith with NLwith,matrix,worldMatrix,missing-method
> ###   NLwith,matrix,worldArray,character-method
> ###   NLwith,agentMatrix,missing,character-method
> 
> ### ** Examples
> 
> # Patches
> w1 <- createWorld(minPxcor = 0, maxPxcor = 4, minPycor = 0, maxPycor = 4,
+                           data = sample(1:5, size = 25, replace = TRUE))
> plot(w1)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... plot.worldMatrix -> plot -> plot -> plot.default -> xy.coords
Execution halted
Running examples in 'nFactors-Ex.R' failed
The error most likely occurred in:

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/nichevol.Rcheck/00install.out' for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.2Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "D:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nomisr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nonlinearTseries.Rcheck/00install.out' for details.
NPHMC: no visible global function definition for 'integrate'
NPHMC: no visible global function definition for 'qnorm'
NPHMC: no visible global function definition for 'pnorm'
NPHMC: no visible global function definition for 'plot'
NPHMC: no visible global function definition for 'lines'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.0Mb
mapvar: no visible global function definition for 'data'
mapvar: no visible binding for global variable 'state.fips'
mapvar: no visible global function definition for 'rgb'
mapvar: no visible global function definition for 'rect'
mapvar: no visible global function definition for 'text'
rowScrape: no visible global function definition for 'tail'
rowScrape: no visible global function definition for 'head'
scrapeTable: no visible binding for global variable 'tail'
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/OpenCL.Rcheck/00install.out' for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs   20.0Mb
    share   9.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/openssl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/optBiomarker.Rcheck/00install.out' for details.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/Orcs.Rcheck/00install.out' for details.
Running examples in 'Orcs-Ex.R' failed
The error most likely occurred in:

> ### Name: merge
> ### Title: Merge Objects Stored in a List
> ### Aliases: merge merge,list,missing-method
> 
> ### ** Examples
> 
> ## Raster* input
> dms = list.files(system.file("extdata", package = "Orcs")
+                  , pattern = "ASTGTM2.*dem.tif$", full.names = TRUE)
> dms = lapply(dms, raster)
> 
> dem = merge(dms, tolerance = 1e4)                  
> plot(dem)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
genRidge: no visible global function definition for 'plogis'
ordGene: no visible global function definition for 'anova'
ordGene: no visible global function definition for 'lm'
ordSelect: no visible binding for global variable 'sd'
ordSmooth: no visible binding for global variable 'sd'
plot.ordPen: no visible global function definition for 'grey'
plot.ordPen: no visible global function definition for 'devAskNewPage'
plot.ordPen: no visible global function definition for 'plot'
plot.ordPen: no visible global function definition for 'lines'
predict.ordPen: no visible global function definition for 'plogis'
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'plot'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'plot'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
plot.osmar: no visible global function definition for 'gray'
plot_nodes: no visible global function definition for 'points'
plot_nodes: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'lines'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Electre3_AlphaBetaThresholds: no visible global function definition for
  'plot'
Electre3_SimpleThresholds: no visible global function definition for
  'plot'
Electre_1: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'plot'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Running 'test-pkgdepends.R' [52s]
  Running 'test-pkginstall.R' [0s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/test-pkgdepends.R' failed.
Complete output:
  > 
  > do <- function() {
  +   old <- Sys.getenv("R_PKG_CACHE_DIR", NA_character_)
  +   if (is.na(old)) {
  +     on.exit(Sys.unsetenv("R_PKG_CACHE_DIR"), add = TRUE)
  +   } else {
  +     on.exit(Sys.setenv("R_PKG_CACHE_DIR" = old), add = TRUE)
  +   }
  +   Sys.setenv("R_PKG_CACHE_DIR" = tempfile())
  + 
  +   if (file.exists("pkgdepends")) {
  +     library(testthat)
  +     library(pak)
  +     test <- function() {
  +       package <- "pak"
  +       env_test <- asNamespace("testthat")$env_test
  +       env_test$in_test <- TRUE
  +       env_test$package <- package
  +       on.exit({
  +         env_test$in_test <- FALSE
  +         env_test$package <- NULL
  +       }, add = TRUE)
  +       test_path <- "pkgdepends"
  +       asNamespace("testthat")$test_package_dir(
  +         package = package, test_path = test_path,
  +         filter = NULL, reporter = "check")
  +     }
  +     test()
  +   }
  + }
  > 
  > do()
  -- 1. Error: dependencies are honoured (@test-resolution.R#291)  ---------------
  Wrong entry types: `filesize (double, expected integer)`
  Backtrace:
   1. asNamespace("pkgcache")$synchronise(do("cran::dplyr", FALSE))
  
  == testthat results  ===========================================================
  [ OK: 675 | SKIPPED: 32 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: dependencies are honoured (@test-resolution.R#291) 
  
  Error: testthat unit tests failed
  Execution halted
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
ProteinCluster: no visible global function definition for 'plot'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
SignificantSubcluster: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
adalasso: no visible global function definition for 'predict'
lm.ridge.univariate: no visible global function definition for 'sd'
mylars: no visible global function definition for 'predict'
mylars: no visible binding for global variable 'var'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
performance.pcor: no visible global function definition for 'var'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/PathSelectMP.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pbdBASE.Rcheck/00install.out' for details.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pbdSLAP.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
draw.pcaBootPlot: no visible global function definition for 'plot'
draw.pcaBootPlot: no visible global function definition for 'grid'
draw.pcaBootPlot: no visible global function definition for 'points'
draw.pcaBootPlot: no visible global function definition for 'symbols'
draw.pcaBootPlot: no visible global function definition for 'legend'
pcaBootPlot: no visible global function definition for 'prcomp'
pcaBootPlot: no visible global function definition for 'cor'
pcaBootPlot: no visible global function definition for 'quantile'
pcaBootPlot: no visible global function definition for 'pdf'
pcaBootPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      1.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
peacf: no visible global function definition for 'is.ts'
peacf: no visible global function definition for 'cycle'
peacf: no visible global function definition for 'ts.intersect'
peacf: no visible global function definition for 'lag'
peacf: no visible global function definition for 'ts'
peacf: no visible global function definition for 'pchisq'
peacf.plot: no visible global function definition for 'plot'
peacf.plot: no visible global function definition for 'segments'
peacf.plot: no visible global function definition for 'title'
pear: no visible global function definition for 'cycle'
pear: no visible global function definition for 'pchisq'
peboxplot: no visible global function definition for 'cycle'
peboxplot: no visible global function definition for 'boxplot'
peboxplot: no visible global function definition for 'title'
peplot: no visible global function definition for 'par'
peplot: no visible global function definition for 'cycle'
peplot: no visible global function definition for 'plot'
peplot: no visible global function definition for 'identify'
peplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'plot'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/pegas.Rcheck/00install.out' for details.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11137 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11137 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/phateR.Rcheck/00install.out' for details.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
fox: no visible global function definition for 'plot'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in get_midday_list(site, direct = FALSE) :
  midday list file was not found on the Phenocam server!
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 202940 bytes (198 KB)
  ==================================================
  downloaded 198 KB
  
  Error in file(con, "r") : cannot open the connection
  -- 1. Error: (unknown) (@testphenocamapi.R#18)  --------------------------------
  a character vector argument expected
  Backtrace:
   1. base::basename(duke_middays[1])
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@testphenocamapi.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202940 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 202940 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 269042 bytes (262 KB)
==================================================
downloaded 262 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      1.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  -- 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  -- 2. Error: See if extractor works (@test_extract_phrases.R#7)  ---------------
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  == testthat results  ===========================================================
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_phrasemachine.Rmd' using rmarkdown
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building 'getting_started_with_phrasemachine.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
Warnings in file 'R/HT_IVIVE_InputModule.R':
  unable to translate '	<U+03BC>m' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/IVIVEGadget.R':
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/performIVIVEModule.R':
  unable to translate '<U+03BC>mol/min/10^6 hepatocytes' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
importHTTKData: no visible global function definition for
  'calc_hepatic_clearance'
Undefined global functions or variables:
  calc_hepatic_clearance
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/plotKML.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'plot'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pollimetry.Rcheck/00install.out' for details.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/PPRL.Rcheck/00install.out' for details.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
Running examples in 'PredictABEL-Ex.R' failed
The error most likely occurred in:

> ### Name: plotROC
> ### Title: Function for a receiver operating characteristic curve (ROC)
> ###   plot and area under the ROC curve (AUC) value.
> ### Aliases: plotROC
> ### Keywords: htest hplot
> 
> ### ** Examples
> # specify the arguments in the function to produce ROC plot
> # specify dataset with outcome and predictor variables
> data(ExampleData)
> # specify column number of the outcome variable
> cOutcome <- 2
> 
> # fit logistic regression models
> # all steps needed to construct a logistic regression model are written in a function
> # called 'ExampleModels', which is described on page 4-5
> riskmodel1 <- ExampleModels()$riskModel1
> riskmodel2 <- ExampleModels()$riskModel2
> 
> # obtain predicted risks
> predRisk1 <- predRisk(riskmodel1)
> predRisk2 <- predRisk(riskmodel2)
> 
> # specify label of the ROC curve
> labels <- c("without genetic factors", "with genetic factors")
> 
> # produce ROC curve
> plotROC(data=ExampleData, cOutcome=cOutcome, 
+ predrisk=cbind(predRisk1,predRisk2), labels=labels)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotROC -> plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'preputils.Rmd' using rmarkdown
Error: processing vignette 'preputils.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 3, column 7 found unknown escape character at line 10, column 4

--- failed re-building 'preputils.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  -- 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ----------
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_with_preText.Rmd' using rmarkdown
Quitting from lines 60-69 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
unused argument (alist())
--- failed re-building 'getting_started_with_preText.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
basisplot: no visible global function definition for 'plot'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
    proj   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.8Mb
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'plot'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'plot'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.6Mb
Warning: multiple methods tables found for 'plot'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'raceland-Ex.R' failed
The error most likely occurred in:

> ### Name: calculate_densities
> ### Title: Calculate Densities
> ### Aliases: calculate_densities
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
Warning: multiple methods tables found for 'plot'
> real_rasters = create_realizations(race_raster, n = 5)
> plot(real_rasters)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'raceland-intro1.Rmd' using rmarkdown
Loading required package: sp
Warning: multiple methods tables found for 'plot'
Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3

Attaching package: 'dplyr'

The following objects are masked from 'package:raster':

    intersect, select, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 115-116 (raceland-intro1.Rmd) 
Error: processing vignette 'raceland-intro1.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'raceland-intro1.Rmd'

--- re-building 'raceland-intro2.Rmd' using rmarkdown
Loading required package: sp
Warning: multiple methods tables found for 'plot'
Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3

Attaching package: 'dplyr'

The following objects are masked from 'package:raster':

    intersect, select, union

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building 'raceland-intro2.Rmd'

--- re-building 'raceland-intro3.Rmd' using rmarkdown
--- finished re-building 'raceland-intro3.Rmd'

SUMMARY: processing the following file failed:
  'raceland-intro1.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.0Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/randstr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/raptr.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
Running examples in 'raptr-Ex.R' failed
The error most likely occurred in:

> ### Name: randomPoints
> ### Title: Sample random points from a RasterLayer
> ### Aliases: randomPoints
> 
> ### ** Examples
> 
> # simulate data
> sim_pus <- sim.pus(225L)
> sim_spp <- sim.species(sim_pus, model = "normal", n = 1, res = 0.25)
> 
> # generate points
> pts1 <- randomPoints(sim_spp, n = 5)
> pts2 <- randomPoints(sim_spp, n = 5, prob = TRUE)
> 
> # plot points
> plot(sim_spp)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/rasterDT.Rcheck/00install.out' for details.
Running examples in 'rasterDT-Ex.R' failed
The error most likely occurred in:

> ### Name: fasterizeDT
> ### Title: Polygon Rasterization Using Numeric, Factor, or Character Fields
> ### Aliases: fasterizeDT
> 
> ### ** Examples
> 
> ## Load example polygons and prepare a template raster
> SPDF <- rgdal::readOGR(system.file("external", package = "raster"), "lux")
OGR data source with driver: ESRI Shapefile 
Source: "D:\RCompile\CRANpkg\lib\4.0\raster\external", layer: "lux"
with 12 features
It has 5 fields
> llratio <- 1/cos(pi * mean(coordinates(SPDF)[, 2])/180)
> rr <- raster(extent(SPDF),
+              resolution = c(llratio * 0.01, 0.01),
+              crs = proj4string(SPDF))
> 
> ## An integer-valued field produces a numeric raster
> rInt <- fasterizeDT(SPDF, rr, field = "ID_2")
> plot(rInt, col = colorRampPalette(blues9)(12))
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/Rcplex.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.0Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/rcrimeanalysis.Rcheck/00install.out' for details.
Running examples in 'rcrimeanalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: kde_int_comp
> ### Title: Comparison of KDE Maps Across Specified Time Intervals
> ### Aliases: kde_int_comp
> ### Keywords: dynamic hplot methods spatial
> 
> ### ** Examples
> 
> #Using provided dataset from Chicago Data Portal:
> data(crimes)
> int_out <- kde_int_comp(crimes, start1="1/1/2017", end1="3/1/2017",
+                                 start2="1/1/2018", end2="3/1/2018")
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: kde_int_comp ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Warnings in file 'R/crAddins.R':
  unable to translate '<U+25B2>' to native encoding
  unable to translate '<U+25BC>' to native encoding
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
CUR: no visible global function definition for 'runif'
CUR: no visible global function definition for 'new'
plotLeverage,CURobj: no visible global function definition for 'plot'
plotLeverage,CURobj: no visible global function definition for 'points'
plotLeverage,CURobj: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'readabs_vignette.Rmd' using rmarkdown
Quitting from lines 64-67 (readabs_vignette.Rmd) 
Error: processing vignette 'readabs_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://ausstats.abs.gov.au/servlet/TSSearchServlet?catno=6345.0&pg=1'
--- failed re-building 'readabs_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.3Mb
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
plot.REEMtree: no visible global function definition for 'plot'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'Rcplex'
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
colorDendClass: no visible global function definition for 'plot'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/reticulate.Rcheck/00install.out' for details.
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/rgbif.Rcheck/00install.out' for details.
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   5.0Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'plot'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.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/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
KM.plot: no visible global function definition for 'plot'
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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. 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.
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
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnBeg: no visible global function definition for 'plot'
plot.rknnBel: no visible global function definition for 'plot'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rmagic.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0/RobExtremes.Rcheck/00install.out' for details.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/ROracle.Rcheck/00install.out' for details.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    1.7Mb
    tests   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RPANDA.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rquake.Rcheck/00install.out' for details.
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/i386/Rserve.dll':
  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 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/x64/Rserve.dll':
  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/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', '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. 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.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.98 0.19 4.15 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  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RSpectra.Rcheck/00install.out' for details.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.8Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rstap.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2019-07-05 r76784)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.7.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   4.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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'.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'R-versus-CPP.Rmd' using rmarkdown
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'R-versus-CPP.Rmd'

SUMMARY: processing the following file failed:
  'R-versus-CPP.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/scMappR.Rcheck/00install.out' for details.
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
> 
> # execute script text
> output <- scriptexec::execute('echo command1\necho command2')
> expect_equal(output$status, 0)
> expect_equal(grepl('command1', output$output), TRUE)
Error: grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
--- failed re-building 'scriptexec.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/SDALGCP.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
Running examples in 'SDMPlay-Ex.R' failed
The error most likely occurred in:

> ### Name: brisaster.antarcticus
> ### Title: Records of _Brisaster antarcticus_ echinoid presences on the
> ###   Kerguelen Plateau
> ### Aliases: brisaster.antarcticus
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(brisaster.antarcticus)
> x <- brisaster.antarcticus
> 
> # plot of the occurrences:
> # selecting the species according to the campaigns
> brisaster7475 <- subset(x,x$year==1974 | x$year==1975)
> brisaster20102015 <- subset(x,x$campaign=='POKER II'| x$campaign=='PROTEKER')
> 
> # drawing the background (depth)
> library(grDevices)
> blue.palette <- colorRampPalette(c('blue','deepskyblue','azure'))(100)
> data('predictors1965_1974')
> depth <- raster :: subset(predictors1965_1974, 1)
> 
> raster::plot(depth, col=blue.palette,main= "Brisaster antarcticus occurrences")
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SDMPlay_vignette.Rmd' using knitr
Loading required package: sp
Warning: multiple methods tables found for 'plot'
Quitting from lines 51-54 (SDMPlay_vignette.Rmd) 
Error: processing vignette 'SDMPlay_vignette.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'SDMPlay_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/SDMtune.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
Package which this enhances but not available for checking: 'doMC'
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error in function (type, msg, asError = TRUE)  : 
  Unknown SSL protocol error in connection to seeclickfix.com:443 
Calls: list_places -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/sen2r.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.5Mb
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Package suggested but not available for checking: 'loomR'
Package unavailable to check Rd xrefs: 'loomR'
installed size is 95.1Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.1Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.1Mb
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.5Mb
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      1.7Mb
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.1Mb
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spatstat.Knet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/spatstat.local.Rcheck/00install.out' for details.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/spatsurv.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/SSDM.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'GUI.Rmd' using rmarkdown
--- finished re-building 'GUI.Rmd'

--- re-building 'SSDM.Rmd' using rmarkdown
Quitting from lines 75-78 (SSDM.Rmd) 
Error: processing vignette 'SSDM.Rmd' failed with diagnostics:
cannot coerce type 'S4' to vector of type 'double'
--- failed re-building 'SSDM.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/SSN.Rcheck/00install.out' for details.
Output for data("mf04", package = "SSN"):
  Warning message:
  multiple methods tables found for 'plot' 
Output for data("mf04p", package = "SSN"):
  Warning message:
  multiple methods tables found for 'plot' 
Output for data("modelFits", package = "SSN"):
  Warning message:
  multiple methods tables found for 'plot'
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   9.7Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.0Mb
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'plot'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
auc: no visible global function definition for 'plot'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'plot'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'plot'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'Details.Rmd' using rmarkdown

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


Attaching package: 'gridExtra'

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

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 rows containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Details.Rmd'

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

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

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

Attaching package: 'tigris'

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

    plot

Loading required package: sp
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 
 Linking to sp version: 1.4-0 
 Polygon checking: TRUE 

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: viridisLite
Warning: Removed 1 rows containing missing values (geom_path).
--- finished re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/stplanr.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'BSgenome.Ptroglodytes.UCSC.panTro5'
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/strataG.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/stringi.Rcheck/00install.out' for details.
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'plot'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    libs   1.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'plot'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs     5.7Mb
    mylibs   1.3Mb
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Package suggested but not available for checking: 'duckdb'
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   1.9Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/trackr.Rcheck/00install.out' for details.
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/TreeSimGM.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.5Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'plot'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tsmp.Rcheck/00install.out' for details.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.2Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/uFTIR.Rcheck/00install.out' for details.
installed size is 82.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.9Mb
    libs     69.1Mb
    proj      5.0Mb
Running examples in 'uFTIR-Ex.R' failed
The error most likely occurred in:

> ### Name: clipper
> ### Title: Clipper
> ### Aliases: clipper
> 
> ### ** Examples
> 
> x <- tile_read(base::system.file("extdata/tile.bsp", package = "uFTIR"))
> x <- tile_base_corr(x)
> x <- wavealign(x, primpke)
> x <- tile_sam(x)
> x <- smooth_sam(x, as.integer(length(primpke@clusternames)), window = 3, 1)
> 
> clip <- toClip(8,20,c(10,10))
> plot(x)
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... <Anonymous> -> <Anonymous> -> plot.default -> xy.coords
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/unmarked.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.3Mb
Running examples in 'unmarked-Ex.R' failed
The error most likely occurred in:

> ### Name: cruz
> ### Title: Landscape data for Santa Cruz Island
> ### Aliases: cruz
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(cruz)
> str(cruz)
'data.frame':	2787 obs. of  5 variables:
 $ x        : num  230737 231037 231337 230437 230737 ...
 $ y        : num  3774324 3774324 3774324 3774024 3774024 ...
 $ elevation: int  241 323 277 13 590 533 378 329 265 282 ...
 $ forest   : num  0 0 0 0 0 0 0 0 0 0 ...
 $ chaparral: num  0 0 0 0 0 0 0 0.02 0.01 0.02 ...
> 
> levelplot(elevation ~ x + y, cruz, aspect="iso",
+     col.regions=terrain.colors(100))
> 
> if(require(raster)) {
+ elev <- rasterFromXYZ(cruz[,1:3],
+      crs="+proj=utm +zone=11 +ellps=GRS80 +datum=NAD83 +units=m +no_defs")
+ elev
+ plot(elev)
+ }
Loading required package: raster
Loading required package: sp

Attaching package: 'sp'

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

    coordinates


Attaching package: 'raster'

The following objects are masked from 'package:unmarked':

    getData, projection

Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Running examples in 'upwaver-Ex.R' failed
The error most likely occurred in:

> ### Name: storypoints_and_status
> ### Title: Calculate storypoints ans status of the Cards of a specific
> ###   Board
> ### Aliases: storypoints_and_status
> 
> ### ** Examples
> 
> upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
No encoding supplied: defaulting to UTF-8.
Error in cards[[i]] : subscript out of bounds
Calls: <Anonymous>
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(upwaver)
  > 
  > test_check("upwaver")
  -- 1. Failure: list_cards() works (@test-upwaver.R#53)  ------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 1 - 4 == -3
  
  -- 2. Error: storypoints() works (@test-upwaver.R#71)  -------------------------
  subscript out of bounds
  Backtrace:
   1. upwaver::storypoints_and_status("4597", 14351, "807a0c3451c04602b4dbfdc0338a65f7")
  
  == testthat results  ===========================================================
  [ OK: 20 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: list_cards() works (@test-upwaver.R#53) 
  2. Error: storypoints() works (@test-upwaver.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'upwaver.Rmd' using rmarkdown
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 106-109 (upwaver.Rmd) 
Error: processing vignette 'upwaver.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building 'upwaver.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     68.8Mb
    proj      5.0Mb
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
level: no visible global function definition for 'quantile'
obj.rec: no visible global function definition for 'txtProgressBar'
obj.rec: no visible global function definition for 'setTxtProgressBar'
project: no visible global function definition for 'aggregate'
raster.proj: no visible global function definition for 'quantile'
raster.proj: no visible global function definition for 'rasterFromXYZ'
raster.proj: no visible global function definition for 'plot.new'
raster.proj: no visible global function definition for 'plot'
raster.proj: no visible global function definition for 'legend'
sub.obj: no visible global function definition for 'aggregate'
sub.obj: no visible global function definition for 'txtProgressBar'
sub.obj: no visible global function definition for 'setTxtProgressBar'
surface: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/WGCNA.Rcheck/00install.out' for details.
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.0Mb
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
wsvm.boost: no visible global function definition for 'plot'
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/x13binary.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    libs          4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Found the following significant warnings:
  Warning: multiple methods tables found for 'plot'
See 'd:/Rcompile/CRANpkg/local/4.0/zoon.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/adaptiveGPCA.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.3Mb
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    bin   22.9Mb
    misc   2.1Mb
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/audio.Rcheck/00install.out' for details.
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2020-01-27 r77730) -- "Unsuffered Consequences"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALD.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.5Mb
Running examples in 'BART-Ex.R' failed
The error most likely occurred in:

> ### Name: crisk2.bart
> ### Title: BART for competing risks
> ### Aliases: crisk2.bart mc.crisk2.bart
> ### Keywords: nonparametric survival model nonproportional hazards
> 
> ### ** Examples
> 
> 
> data(transplant)
> 
> pfit <- survfit(Surv(futime, event) ~ abo, transplant)
Error in if (flag["teleport"] > 0) { : 
  missing value where TRUE/FALSE needed
Calls: survfit -> survfit.formula -> survfitCI -> survcheck2
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Error(s) in re-building vignettes:
--- re-building 'adaptation_level.Rmd' using rmarkdown
Loading required package: Rcpp

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

Quitting from lines 85-87 (adaptation_level.Rmd) 
Error: processing vignette 'adaptation_level.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building 'adaptation_level.Rmd'

--- re-building 'afterimages.Rmd' using rmarkdown
Loading required package: Rcpp

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************


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

--- finished re-building 'afterimages.Rmd'

--- re-building 'flanker.Rmd' using rmarkdown
Loading required package: Rcpp

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

Warning in y1 - y2 :
  longer object length is not a multiple of shorter object length
Warning in y1 - y2 :
  longer object length is not a multiple of shorter object length
--- finished re-building 'flanker.Rmd'

--- re-building 'stroop.Rmd' using rmarkdown
Loading required package: Rcpp
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
--- finished re-building 'stroop.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.2Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BcDiag.Rcheck/00install.out' for details.
installed size is 132.5Mb
  sub-directories of 1Mb or more:
    include  131.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.1Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/biganalytics.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.2Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigmemory.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.3Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigtabulate.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bioRad.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BonEV.Rcheck/00install.out' for details.
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    include   8.6Mb
    lib      53.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Brundle.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
Package which this enhances but not available for checking: 'FastRWeb'
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Cairo.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/clv.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'Getting_Started.Rmd' using rmarkdown
Quitting from lines 44-47 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:

--- failed re-building 'Getting_Started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in 'compstatr-Ex.R' failed
The error most likely occurred in:

> ### Name: cs_create_index
> ### Title: Create Index of Available Months
> ### Aliases: cs_create_index
> 
> ### ** Examples
> 
> # create index
> i <- cs_create_index()
Warning in cs_request_POST(session, url, body = list(`__EVENTTARGET` = "GridView1",  :
  Internal Server Error (HTTP 500).
Error in read_xml.response(x$response, ..., as_html = as_html) : 
  Internal Server Error (HTTP 500).
Calls: cs_create_index ... html_nodes.session -> html_nodes -> <Anonymous> -> read_html.default
Execution halted
Package vignette with placeholder title 'Vignette Title':
  'condir-examples.Rmd'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.3Mb
Running examples in 'crypto-Ex.R' failed
The error most likely occurred in:

> ### Name: crypto_prices
> ### Title: Get current crypto currency prices
> ### Aliases: crypto_prices
> 
> ### ** Examples
> 
> {
+ kin_price <- crypto_prices('kin')
+ }
Error: 
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSFA.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.2Mb
Found the following significant warnings:
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [4294967292, 2147483647] [-Warray-bounds]
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cubature.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.1Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   2.4Mb
Package required but not available: 'flowDensity'

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

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0gcc8/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11702 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11220 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11220 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11608 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11608 (sockconn)
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   2.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    bin       6.1Mb
    extdata   2.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
nondominated_ordering: no visible binding for global variable 'par'
rsbxbeta: no visible global function definition for 'runif'
Undefined global functions or variables:
  par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in 'empiricalFDR.DESeq2-Ex.R' failed
The error most likely occurred in:

> ### Name: empiricalFDR.DESeq2-package
> ### Title: Simulation-Based False Discovery Rate in RNA-Seq
> ### Aliases: empiricalFDR.DESeq2-package empiricalFDR.DESeq2
> 
> ### ** Examples
> 
> 
> dds = makeExampleDESeqDataSet(betaSD=1, n=100)
> dds = DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> sims = simulateCounts(dds)
simulating...
================================================================================converting counts to integer mode
> sims = DESeq(sims)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> res = results(dds)
Error in .wrap_in_length_one_list_like_object(value, name, x) : 
  failed to coerce 'list(value)' to a DESeqResults object of length 1
Calls: results ... .append_list_element -> .wrap_in_length_one_list_like_object
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FGSG.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   2.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package required but not available: 'flowWorkspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fs.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.9Mb
    proj     5.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.1Mb
Running examples in 'GENLIB-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.find.Min.Distance.MRCA
> ### Title: Finds the minimum distances between pairs of individuals given a
> ###   set of ancestors.
> ### Aliases: gen.find.Min.Distance.MRCA
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(geneaJi) 
> genJi<-gen.genealogy(geneaJi) 
> matMRCA<-gen.findMRCA(genJi, individuals=c(1,29), NbProcess = 1)
[1] "warning"
converting NULL pointer to R NULL> gen.find.Min.Distance.MRCA(matMRCA)
Error in gen.find.Min.Distance.MRCA(matMRCA) : 
  genMatrix must be a matrix output from gen.findMRCA
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Running 'testthat.R' [90s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  -- 1. Failure: as_facets_list() coerces lists (@test-facet-.r#40)  -------------
  `out` not identical to `exp`.
  Component 3: Attributes: < Component "class": Lengths (2, 1) differ (string compare on first 1) >
  
  == testthat results  ===========================================================
  [ OK: 1097 | SKIPPED: 105 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: as_facets_list() coerces lists (@test-facet-.r#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       21.7Mb
    test_data   1.2Mb
Found the following significant warnings:
  kmppini.cpp:241:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
  kmppini.cpp:275:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMKMcharlie.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMMAT.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gpuR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/haven.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::.__C__GenomicRanges_OR_GenomicRangesList' by 'rtracklayer::.__C__GenomicRanges_OR_GenomicRangesList' when loading 'HiCfeat'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HiCfeat.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.8Mb
    libs          3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.9Mb
Found the following significant warnings:
  uuid/gen_uuid.c:321:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/igraph.Rcheck/00install.out' for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
Running 'testthat.R' [129s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(igraph)
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > suppressWarnings(RNGversion("3.5.0"))
  > test_check("igraph")
  -- 1. Failure:  (@test_layout.fr.R#13)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10.8 - 10.8 == 7.97e-05
  
  -- 2. Failure:  (@test_layout.fr.R#22)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 941 - 1004 == -62.5
  
  -- 3. Failure: SIR works (@test_sir.R#15)  ---------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "bc42d0cbe0bb3321e83979c0432f9cea"
  y[1]: "b73a8ad03b832b3543f2f03d07330398"
  
  == testthat results  =======================================================
  [ OK: 3308 | SKIPPED: 4 | WARNINGS: 1376 | FAILED: 3 ]
  1. Failure:  (@test_layout.fr.R#13) 
  2. Failure:  (@test_layout.fr.R#22) 
  3. Failure: SIR works (@test_sir.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     16.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'intePareto.Rmd' using rmarkdown
Loading required package: intePareto
get RNA counts
Cache found
get chip counts
use DESeq2 to calculate log2FoldChange of RNA-Seq
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Quitting from lines 118-126 (intePareto.Rmd) 
Error: processing vignette 'intePareto.Rmd' failed with diagnostics:
failed to coerce 'list(value)' to a DESeqResults object of length 1
--- failed re-building 'intePareto.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
Running examples in 'iotools-Ex.R' failed
The error most likely occurred in:

> ### Name: idstrsplit
> ### Title: Create an iterator for splitting binary or character input into
> ###   a dataframe
> ### Aliases: idstrsplit
> ### Keywords: iterator
> 
> ### ** Examples
> 
> col_names <- names(iris)
> write.csv(iris, file="iris.csv", row.names=FALSE)
> it <- idstrsplit("iris.csv", col_types=c(rep("numeric", 4), "character"), 
+                  sep=",")
> # Get the elements
> iris_read <- it$nextElem()[-1,]
> # or with the iterators package
> # nextElem(it)
> names(iris_read) <- col_names
> print(head(iris_read))
  Sepal.Length Sepal.Width Petal.Length Petal.Width  Species
2          5.1         3.5          1.4         0.2 "setosa"
3          4.9         3.0          1.4         0.2 "setosa"
4          4.7         3.2          1.3         0.2 "setosa"
5          4.6         3.1          1.5         0.2 "setosa"
6          5.0         3.6          1.4         0.2 "setosa"
7          5.4         3.9          1.7         0.4 "setosa"
> unlink("iris.csv")
> 
> 
> 
> cleanEx()
Error: connections left open:
	iris.csv (file)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11777 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11777 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11051 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11051 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.0Mb
Running examples in 'knor-Ex.R' failed
The error most likely occurred in:

> ### Name: test_centroids
> ### Title: A small example of centroids of dim: (8,5) used as for
> ###   micro-benchmarks of the knor package. The data are randomly
> ###   generated.
> ### Aliases: test_centroids
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(test_centroids)
> kms <- Kmeans(test_data, test_centroids)
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.4Mb
Found the following significant warnings:
  model_simul.cpp:838:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  model_simul.cpp:719:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:720:22: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 8 [-Wformat-overflow=]
  model_simul.cpp:721:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:722:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:723:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:724:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  printReadWrite.cpp:54:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:74:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:84:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:138:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:139:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:140:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:141:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:152:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/landsepi.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.5Mb
    proj   5.0Mb
sequence:
  function(nvec, ...)
sequence.lvm:
  function(a, b, integer)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  sequence.lvm
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.6Mb
    testdata   1.6Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
Found the following significant warnings:
  liblwgeom/lwgeom_topo.c:4305:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4357:38: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lwgeom.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
    proj   5.0Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lxb.Rcheck/00install.out' for details.
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.8Mb
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ManifoldOptim.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          8.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   3.2Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MatrixModels.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  -- 1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202)  --------
  package or namespace load failed for 'phyloseq' in library.dynam(lib, package, package.lib):
   DLL 'Rhdf5lib' not found: maybe not installed for this architecture?
  Backtrace:
   1. base::library(phyloseq)
   2. base::tryCatch(...)
   3. base:::tryCatchList(expr, classes, parentenv, handlers)
   4. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs   4.6Mb
    misc   1.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixKernel.Rcheck/00install.out' for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.5Mb
Found the following significant warnings:
  ./bson/bson-macros.h:180:19: warning: ISO C does not support '__FUNCTION__' predefined identifier [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mongolite.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    libs         14.0Mb
    mathematica   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  21.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  eclat/tract/src/tract.c:1399:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multinet.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   2.0Mb
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.6Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.2Mb
    include   5.6Mb
    libs      2.4Mb
    tests     1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Running 'testthat.R' [125s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("nlmixr_silent"="TRUE")
  > library(testthat)
  > library(nlmixr)
  > 
  > test_check("nlmixr")
  -- 1. Error: parsing functions fix drake compatibility (@test-drake.R#51)  -----
  object 'progress_bar' not found
  Backtrace:
    1. testthat::expect_equal(make(plan, cache = .cache), NULL)
    4. drake::make(plan, cache = .cache)
    6. drake::drake_config(...)
    7. drake:::logger(verbose = verbose, file = log_make)
    8. refclass_logger$new(verbose = verbose, file = file, progress_bar = progress_bar)
    9. methods::new(def, ...)
   11. methods::initialize(value, ...)
   12. methods::initRefFields(.Object, classDef, selfEnv, list(...))
  
  == testthat results  ===========================================================
  [ OK: 253 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parsing functions fix drake compatibility (@test-drake.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [115s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > Sys.setenv("nlmixr_silent"="TRUE")
  > library(testthat)
  > library(nlmixr)
  > 
  > test_check("nlmixr")
  -- 1. Error: parsing functions fix drake compatibility (@test-drake.R#51)  -----
  object 'progress_bar' not found
  Backtrace:
    1. testthat::expect_equal(make(plan, cache = .cache), NULL)
    4. drake::make(plan, cache = .cache)
    6. drake::drake_config(...)
    7. drake:::logger(verbose = verbose, file = log_make)
    8. refclass_logger$new(verbose = verbose, file = file, progress_bar = progress_bar)
    9. methods::new(def, ...)
   11. methods::initialize(value, ...)
   12. methods::initRefFields(.Object, classDef, selfEnv, list(...))
  
  == testthat results  ===========================================================
  [ OK: 253 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parsing functions fix drake compatibility (@test-drake.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenCL.Rcheck/00install.out' for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs   19.8Mb
    share   9.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.9Mb
    models   4.6Mb
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OpenMx)
  > 
  > test_check("OpenMx")
  -- 1. Failure: (unknown) (@test-wls-binary.R#43)  ------------------------------
  `mxRun(wlsTest4)` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 567 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-wls-binary.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
Running 'test-pkgdepends.R' [54s]
  Running 'test-pkginstall.R' [0s]
  Running 'testthat.R' [19s]
Running the tests in 'tests/test-pkgdepends.R' failed.
Complete output:
  > 
  > do <- function() {
  +   old <- Sys.getenv("R_PKG_CACHE_DIR", NA_character_)
  +   if (is.na(old)) {
  +     on.exit(Sys.unsetenv("R_PKG_CACHE_DIR"), add = TRUE)
  +   } else {
  +     on.exit(Sys.setenv("R_PKG_CACHE_DIR" = old), add = TRUE)
  +   }
  +   Sys.setenv("R_PKG_CACHE_DIR" = tempfile())
  + 
  +   if (file.exists("pkgdepends")) {
  +     library(testthat)
  +     library(pak)
  +     test <- function() {
  +       package <- "pak"
  +       env_test <- asNamespace("testthat")$env_test
  +       env_test$in_test <- TRUE
  +       env_test$package <- package
  +       on.exit({
  +         env_test$in_test <- FALSE
  +         env_test$package <- NULL
  +       }, add = TRUE)
  +       test_path <- "pkgdepends"
  +       asNamespace("testthat")$test_package_dir(
  +         package = package, test_path = test_path,
  +         filter = NULL, reporter = "check")
  +     }
  +     test()
  +   }
  + }
  > 
  > do()
  -- 1. Error: dependencies are honoured (@test-resolution.R#291)  ---------------
  Wrong entry types: `filesize (double, expected integer)`
  Backtrace:
   1. asNamespace("pkgcache")$synchronise(do("cran::dplyr", FALSE))
  
  == testthat results  ===========================================================
  [ OK: 675 | SKIPPED: 32 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: dependencies are honoured (@test-resolution.R#291) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [56s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(panelr)
  Loading required package: lme4
  Loading required package: Matrix
  
  Attaching package: 'panelr'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("panelr")
  -- 1. Error: (unknown) (@test_wbm.R#283)  --------------------------------------
  could not find function "arma"
  Backtrace:
   1. panelr::wbm_stan(...)
   2. brms::make_stancode(...)
   4. brms:::validate_formula.default(...)
   6. brms:::validate_formula.brmsformula(bf(formula), ...)
   7. brms:::validate_autocor(autocor)
   8. brms:::parse_ac(autocor)
   9. base::lapply(out, eval2)
  
  == testthat results  ===========================================================
  [ OK: 271 | SKIPPED: 0 | WARNINGS: 60 | FAILED: 1 ]
  1. Error: (unknown) (@test_wbm.R#283) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/pbdRPC.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11302 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11302 (sockconn)
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phateR.Rcheck/00install.out' for details.
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 203440 bytes (198 KB)
  ==================================================
  downloaded 198 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 203440 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 203440 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 269557 bytes (263 KB)
==================================================
downloaded 263 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      2.0Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  -- 1. Error: See if tagging five documents works, and if coarsening works (@test
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  -- 2. Error: See if extractor works (@test_extract_phrases.R#7)  ---------------
  unused argument (alist())
  Backtrace:
   1. documents[1:5, ]
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  == testthat results  ===========================================================
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#7) 
  2. Error: See if extractor works (@test_extract_phrases.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phyloseqGraphTest.Rcheck/00install.out' for details.
Warning in inla.print.version() :
  INLA_18.07.12: 32bit binaries are no longer supported!

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs   2.3Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PPRL.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(preText)
  preText: Diagnostics to Assess the Effects of Text Preprocessing Decisions
  Version 0.6.3 created on 2018-01-12.
  copyright (c) 2017, Matthew J. Denny, Penn State University
                      Arthur Spirling, NYU
  Type vignette('getting_started_with_preText') to get started.
  Development website: https://github.com/matthewjdenny/preText
  > 
  > test_check("preText")
  -- 1. Error: Small example works (@test_factorial_preprocessing.R#6)  ----------
  unused argument (alist())
  Backtrace:
   1. documents[1:10, ]
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Small example works (@test_factorial_preprocessing.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.1Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
    proj   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs   3.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.6Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.3Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rblpapi.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rcplex.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      3.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      13.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.5Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RcppXsimd)
  > 
  > test_check("RcppXsimd")
Running examples in 'RCrypto-Ex.R' failed
The error most likely occurred in:

> ### Name: CoinMarketCap_Ticker
> ### Title: 'Coinmarketcap' Select Ticker Symbol
> ### Aliases: CoinMarketCap_Ticker
> 
> ### ** Examples
> 
> MyData <- CoinMarketCap_Ticker(currency = "CAD",ticker = "ETH")
Error in symbol %in% c(ticker) : object 'symbol' not found
Calls: CoinMarketCap_Ticker ... as.data.frame -> filter -> filter.tbl_df -> filter_impl -> %in%
Execution halted
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: bad key
  -- 1. Error: Decryption with passphrase passthrough and armor works (@test-decry
  cannot open the connection
  Backtrace:
   1. base::readLines("file2-decrypt.txt")
   2. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: Decryption with passphrase passthrough and armor works (@test-decrypt.r#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: 'strncpy' output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rdsdp.Rcheck/00install.out' for details.
Found the following significant warnings:
  compile.cc:292:69: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class re2::Prog::Inst'; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/re2r.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.3Mb
Running 'testthat.R' [151s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(renv)
  
  Attaching package: 'renv'
  
  The following object is masked from 'package:stats':
  
      update
  
  The following objects are masked from 'package:utils':
  
      history, upgrade
  
  The following objects are masked from 'package:base':
  
      load, remove
  
  > 
  > renv:::renv_tests_init()
  > renv:::renv_tests_diagnostics()
  The following R libraries are set:
  
  	- D:/temp/Rtmp0oWVS7/renv-library-327c058f53d3c
  	- D:/temp/Rtmp0oWVS7/renv-system-library
  
  The following repositories are set:
  
  	CRAN: file:///D:\temp\Rtmp0oWVS7\renv-repos-327c073054375
  
  The following renv root directory is being used:
  
  	- D:\temp\Rtmp0oWVS7\renv-root-327c06744384c
  
  The following renv cache directory is being used:
  
  	- D:\temp\Rtmp0oWVS7\renv-root-327c06744384c/cache/v5/R-4.0-r77730/x86_64-w64-mingw32
  
  The following packages are available in the test repositories:
  
  	bread, breakfast, brunch, egg, halloween, oatmeal, packrat,
  	toast
  
  	R_LIBS      : <NA>
  	R_LIBS_SITE : "'no_such_dir'"
  	R_LIBS_USER : "'no_such_dir'"
  
  > 
  > test_check("renv")
  [4/4] -- 1. Error: we can retrieve files using file URIs (@test-retrieve.R#282)  -----
  (converted from warning) cannot open file 'D:/temp/Rtmp0oWVS7/renv-test-327c029833fa/target': No such file or directory
  Backtrace:
   1. testthat::expect_equal(readLines(target), "Hello, world!")
   4. base::readLines(target)
  
  == testthat results  ===========================================================
  [ OK: 304 | SKIPPED: 53 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: we can retrieve files using file URIs (@test-retrieve.R#282) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
Running examples in 'restfulr-Ex.R' failed
The error most likely occurred in:

> ### Name: RestContainer-class
> ### Title: RestContainer
> ### Aliases: class:RestContainer RestContainer-class RestContainer
> ###   [,RestContainer-method [<-,RestContainer-method
> ###   $,RestContainer-method [[,RestContainer-method
> ###   $<-,RestContainer-method [[<-,RestContainer-method
> ###   show,RestContainer-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> apache <- RestContainer("http://wiki.apache.org")
> apache$solr
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to wiki.apache.org port 80: Timed out
Calls: $ ... tryCatchOne -> doTryCatch -> <Anonymous> -> handleResponse
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs      2.4Mb
    swagger   1.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      69.2Mb
    pictures   1.3Mb
    proj       5.0Mb
Found the following significant warnings:
  IP2Location.c:339:35: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:893:39: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:900:41: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rgeolocate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    1.4Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RInside.Rcheck/00install.out' for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    lib    6.3Mb
    libs   8.0Mb
Found the following significant warnings:
  Rinit.c:251:21: warning: assignment to 'blah1' {aka 'int (*)(const char *, char *, int,  int)'} from incompatible pointer type 'int (*)(const char *, unsigned char *, int,  int)' [-Wincompatible-pointer-types]
  Rinit.c:257:21: warning: assignment to 'blah5' {aka 'int (*)(const char *)'} from incompatible pointer type 'int (*)(char *)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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. 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.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    exe  23.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rmagic.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.4Mb
    libs      2.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
Running examples in 'RNRCS-Ex.R' failed
The error most likely occurred in:

> ### Name: grabNRCS.elements
> ### Title: grabNRCS.elements
> ### Aliases: grabNRCS.elements
> ### Keywords: atmopsheric atmosphere, climate, data, environment,
> ###   environmental in-situ, weather
> 
> ### ** Examples
> 
> grabNRCS.elements(site_id='SCAN:2221')
Error in open.connection(x, "rb") : HTTP error 404.
Calls: grabNRCS.elements -> lapply -> FUN -> <Anonymous> -> read_html.default
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RobExtremes.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.0Mb
Found the following sources/headers with CR or CRLF line endings:
  src/qpoases/include/qpOASES.hpp
  src/qpoases/include/qpOASES/Constants.hpp
  src/qpoases/include/qpOASES/ConstraintProduct.hpp
  src/qpoases/include/qpOASES/Types.hpp
  src/qpoases/include/qpOASES/UnitTesting.hpp
  src/qpoases/include/qpOASES/Utils.hpp
Some Unix compilers require LF line endings.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.2Mb
    tests   1.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error(s) in re-building vignettes:
--- re-building 'rpredictit-vignette.Rmd' using rmarkdown
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'rpredictit-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Error(s) in re-building vignettes:
--- re-building 'rromeo.Rmd' using rmarkdown
Quitting from lines 16-35 (rromeo.Rmd) 
Error: processing vignette 'rromeo.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building 'rromeo.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/Rserve/libs/i386/Rserve.dll':
  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 'd:/Rcompile/CRANpkg/lib/4.0gcc8/Rserve/libs/x64/Rserve.dll':
  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/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', '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. 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.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSNNS.Rcheck/00install.out' for details.
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:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.78 0.14 3.92 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  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.4Mb
    libs  17.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstap.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2020-01-27 r77730)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.0.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Running examples in 'RYoudaoTranslate-Ex.R' failed
The error most likely occurred in:

> ### Name: RYoudaoTranslate-package
> ### Title: R package provide functions to translate English words into
> ###   Chinese.
> ### Aliases: RYoudaoTranslate-package RYoudaoTranslate
> ### Keywords: Youdao
> 
> ### ** Examples
> 
> 	library(RCurl)
> 	library(rjson)
> 	apikey = "498375134"
> 	keyfrom = "JustForTestYouDao"
> 	youdaoLookUp("youdao",api=apikey,keyfrom=keyfrom)
Error in fromJSON(url) : unexpected character 'T'
Calls: youdaoLookUp -> youdaoDisplay -> youdaoTranslate -> fromJSON
Execution halted
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installed size is  5.5Mb
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installed size is  5.2Mb
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installed size is  5.0Mb
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installed size is  6.5Mb
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installed size is 10.5Mb
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installed size is  7.9Mb
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Error(s) in re-building vignettes:
--- re-building 'Introduction_to_sidrar.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 72-85 (Introduction_to_sidrar.Rmd) 
Error: processing vignette 'Introduction_to_sidrar.Rmd' failed with diagnostics:
A solicitação de conexão sofreu timeout
--- failed re-building 'Introduction_to_sidrar.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SigTree.Rcheck/00install.out' for details.
installed size is  5.7Mb
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installed size is  5.1Mb
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installed size is  7.6Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/skeleSim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/smapr.Rcheck/00install.out' for details.
installed size is  6.7Mb
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Running 'testthat.R' [89s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.8 loaded.
  This is package "smooth", v2.5.5
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
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installed size is  6.6Mb
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Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, units

! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/SongEvo.Rch
eck/vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20populatio
n\%20size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'SciencesPo'
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installed size is  6.9Mb
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installed size is  6.7Mb
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installed size is 17.7Mb
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    help   5.3Mb
    libs   1.2Mb
installed size is  5.8Mb
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installed size is  9.4Mb
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installed size is  5.5Mb
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installed size is  5.4Mb
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installed size is  9.3Mb
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installed size is 10.6Mb
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installed size is  6.6Mb
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installed size is  5.2Mb
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installed size is  5.5Mb
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    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'Details.Rmd' using rmarkdown

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


Attaching package: 'gridExtra'

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

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 rows containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Details.Rmd'

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

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

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

Attaching package: 'tigris'

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

    plot

Loading required package: sp
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 
 Linking to sp version: 1.4-1 
 Polygon checking: TRUE 

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: viridisLite
Warning: Removed 1 rows containing missing values (geom_path).
--- finished re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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installed size is  5.1Mb
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installed size is 35.6Mb
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Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/superbiclust.Rcheck/00install.out' for details.
installed size is  8.8Mb
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    R      1.8Mb
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    libs   2.2Mb
installed size is 15.6Mb
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    libs  14.1Mb
installed size is  8.5Mb
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    R      1.0Mb
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installed size is  7.9Mb
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installed size is  5.9Mb
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installed size is 29.1Mb
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    doc        1.0Mb
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    tessdata  14.0Mb
installed size is  5.1Mb
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installed size is  8.6Mb
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installed size is  5.2Mb
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    libs      2.1Mb
installed size is  5.0Mb
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    libs         2.2Mb
    references   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/theseus.Rcheck/00install.out' for details.
installed size is 23.1Mb
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    examples  19.5Mb
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Running examples in 'tosca-Ex.R' failed
The error most likely occurred in:

> ### Name: as.textmeta.corpus
> ### Title: Transform corpus to textmeta
> ### Aliases: as.textmeta.corpus
> ### Keywords: manip
> 
> ### ** Examples
> 
> texts <- c("Give a Man a Fish, and You Feed Him for a Day.
+  Teach a Man To Fish, and You Feed Him for a Lifetime",
+  "So Long, and Thanks for All the Fish",
+  "A very able manipulative mathematician, Fisher enjoys a real mastery
+  in evaluating complicated multiple integrals.")
> 
> corp <- quanteda::corpus(x = texts)
> obj <- as.textmeta.corpus(corp, addMetadata = FALSE)
NOTE: No ID-column "id", set to ascending numbers
NOTE: No date-column "date", set to NA
NOTE: No title-column "title", set to NA
success
number of observations in text: 3 

NAs in text:
 NA.abs NA.rel
      0      0
---------------------------------------------------------------------- 

meta: 3 observations of 3 variables

NAs in meta:
      abs rel
id      0   0
date    3   1
title   3   1
---------------------------------------------------------------------- 

NAs in date: 3 (1)
> 
> quanteda::docvars(corp, "title") <- c("Fishing", "Don't panic!", "Sir Ronald")
> quanteda::docvars(corp, "date") <- c("1885-01-02", "1979-03-04", "1951-05-06")
> quanteda::docvars(corp, "id") <- c("A", "B", "C")
> quanteda::docvars(corp, "additionalVariable") <- 1:3
> 
> obj <- as.textmeta.corpus(corp)
Error in matrix(rep(tmp, each = length(tmpid)), nrow = length(tmpid)) : 
  'data' must be of a vector type, was 'NULL'
Calls: as.textmeta.corpus -> matrix
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/treeDA.Rcheck/00install.out' for details.
installed size is  7.6Mb
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    doc    4.3Mb
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installed size is 16.4Mb
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installed size is  8.1Mb
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installed size is 14.3Mb
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    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is  5.1Mb
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installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.9Mb
installed size is 25.0Mb
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    libs  23.2Mb
installed size is 79.7Mb
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    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.4Mb
    proj      5.0Mb
installed size is  9.9Mb
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    doc    1.0Mb
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installed size is 11.0Mb
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    doc           4.3Mb
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Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plo
t-1.pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20
rho-1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
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installed size is 14.3Mb
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    doc   11.9Mb
    libs   2.1Mb
installed size is  5.1Mb
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    R      1.2Mb
    libs   2.2Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/x13binary.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XML.Rcheck/00install.out' for details.
installed size is  5.6Mb
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    include   3.4Mb
    libs      2.1Mb
installed size is  5.4Mb
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    libs   5.1Mb
installed size is  5.2Mb
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    R      1.8Mb
    libs   2.4Mb
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘plot’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘plot’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
plot.abf2split: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
fillCSVData: no visible global function definition for ‘read.table’
fillData: no visible global function definition for ‘edit’
plotGraphs: no visible global function definition for ‘par’
plotGraphs: no visible global function definition for ‘plot’
plotGraphs: no visible global function definition for ‘lines’
plotGraphs: no visible global function definition for ‘legend’
plotGraphs: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Running examples in ‘admisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Interpret DNF/SOP expressions: compute, simplify, expand, translate
> ### Title: Functions to interpret and manupulate a SOP/DNF expression
> ### Aliases: compute sop simplify expand translate
> ### Keywords: functions
> 
> ### ** Examples
> 
> # -----
> # for compute()
> ## Not run: 
> ##D # make sure the package QCA is loaded
> ##D library(QCA)
> ##D data(LF)
> ##D compute("DEV*~IND + URB*STB", data = LF)
> ##D 
> ##D # calculating individual paths
> ##D compute("DEV*~IND + URB*STB", data = LF, separate = TRUE)
> ## End(Not run)
> 
> 
> # -----
> # for simplify(), also make sure the package QCA is loaded
> simplify("(A + B)(A + ~B)") # result is "A"

Error: Consider creating a truth table first, or formally specify the argument "outcome".

Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apyramid)
  > 
  > test_check("apyramid")
  ── 1. Failure: missing split data are removed before plotting (@test-age-pyramid
  `age_pyramid(dat, age_group = "AGE", na.rm = FALSE)` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 72 | SKIPPED: 11 | WARNINGS: 11 | FAILED: 1 ]
  1. Failure: missing split data are removed before plotting (@test-age-pyramid.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Dependence on R version ‘3.4.2’ not with patchlevel 0
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘plot’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘plot’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
plot.AUC: no visible global function definition for ‘plot’
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
Running examples in ‘auk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: auk_zerofill
> ### Title: Read and zero-fill an eBird data file
> ### Aliases: auk_zerofill auk_zerofill.data.frame auk_zerofill.character
> ###   auk_zerofill.auk_ebd collapse_zerofill
> 
> ### ** Examples
> 
> # read and zero-fill the ebd data
> f_ebd <- system.file("extdata/zerofill-ex_ebd.txt", package = "auk")
> f_smpl <- system.file("extdata/zerofill-ex_sampling.txt", package = "auk")
> auk_zerofill(x = f_ebd, sampling_events = f_smpl)
Zero-filled EBD: 619 unique checklists, for 3 species.
> 
> # use the species argument to only include a subset of species
> auk_zerofill(x = f_ebd, sampling_events = f_smpl,
+              species = "Collared Kingfisher")
Zero-filled EBD: 619 unique checklists, for 1 species.
> 
> # to return a data frame use collapse = TRUE
> ebd_df <- auk_zerofill(x = f_ebd, sampling_events = f_smpl, collapse = TRUE)

 *** caught segfault ***
address 0x1310, cause 'memory not mapped'

Traceback:
 1: regroup(attr(out, "groups"), environment())
 2: filter.tbl_df(x, dplyr::row_number(.data$taxon_order) == 1)
 3: dplyr::filter(x, dplyr::row_number(.data$taxon_order) == 1)
 4: auk_rollup(x, drop_higher = drop_higher)
 5: auk_zerofill.data.frame(x = ebd, sampling_events = sed, species = species,     collapse = collapse, unique = unique, complete = complete,     rollup = rollup)
 6: auk_zerofill(x = ebd, sampling_events = sed, species = species,     collapse = collapse, unique = unique, complete = complete,     rollup = rollup)
 7: auk_zerofill.character(x = f_ebd, sampling_events = f_smpl, collapse = TRUE)
 8: auk_zerofill(x = f_ebd, sampling_events = f_smpl, collapse = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  ── 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ─────────────────────
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘plot’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘plot’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
Dependence on R version ‘3.4.1’ not with patchlevel 0
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘plot’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘plot’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
plot.bbo: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable ‘sd’
plot.cvsvd: no visible global function definition for ‘plot’
plot.cvsvd: no visible global function definition for ‘lines’
plot.cvsvd: no visible global function definition for ‘segments’
plot.cvsvd: no visible global function definition for ‘points’
print.cvsvd: no visible binding for global variable ‘sd’
summary.cvsvd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘plot’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘plot’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘plot’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘plot’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘plot’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Running examples in ‘braQCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QCAdiff
> ### Title: QCA Case Difference
> ### Aliases: QCAdiff
> 
> ### ** Examples
> 
> data(rallies)
> P<-rallies$P
> R<-rallies$R
> C<-rallies$C
> B<-rallies$B
> 
> qca.data<-data.frame(P,R,C,B)
> rownames(qca.data)<-rownames(rallies)
> truth<-truthTable(qca.data,outcome="P",sort.by="incl",incl.cut1=0.2,show.cases=TRUE,n.cut=1)
> mod1<-minimize(truth,details=TRUE,show.cases=TRUE)

Error: Conditions 'b,c,r' do not match the set names from "snames" argument.

Execution halted
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘plot’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘plot’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘plot’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘plot’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘plot’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
plot.bursts: no visible global function definition for ‘plot’
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of ‘nc’ to ‘ncol’
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘plot’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘plot’
plot.ccd: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘plot’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
CM: no visible global function definition for ‘sd’
Erf: no visible global function definition for ‘pnorm’
Erfc: no visible global function definition for ‘pnorm’
boot.Cenarma: no visible global function definition for ‘coef’
boot.Cenarma: no visible global function definition for ‘arima.sim’
cenarma: no visible global function definition for ‘arima’
cenarma: no visible global function definition for ‘coef’
cenarma: no visible global function definition for ‘ARMAacf’
cenarma: no visible global function definition for ‘var’
plot.cents: no visible global function definition for ‘plot’
plot.cents: no visible global function definition for ‘segments’
plot.cents: no visible global function definition for ‘rgb’
plot.cents: no visible global function definition for ‘points’
rcarma: no visible global function definition for ‘arima.sim’
rcarma: no visible global function definition for ‘quantile’
scenNID: no visible global function definition for ‘sd’
se.Cenarma: no visible global function definition for ‘coef’
se.Cenarma: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
sw.plot : <anonymous>: no visible global function definition for
  ‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
  ‘lines’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
  ‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
  ‘median’
sw.threshold : <anonymous>: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘plot’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘plot’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘plot’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘plot’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘plot’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘plot’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘plot’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘plot’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
plotParabola: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘plot’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
CoxBoost: no visible global function definition for ‘Matrix’
CoxBoost: no visible binding for global variable ‘sd’
CoxBoost: no visible global function definition for ‘predict’
cv.CoxBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.CoxBoost: no visible global function definition for ‘mclapply’
cv.CoxBoost: no visible binding for global variable ‘sd’
estimPVal: no visible global function definition for ‘mclapply’
iCoxBoost: no visible global function definition for ‘terms’
iCoxBoost: no visible global function definition for ‘model.response’
iCoxBoost: no visible global function definition for ‘model.frame’
iCoxBoost: no visible global function definition for ‘model.matrix’
iCoxBoost: no visible global function definition for ‘Matrix’
plot.CoxBoost: no visible global function definition for ‘plot’
plot.CoxBoost: no visible global function definition for ‘lines’
plot.CoxBoost: no visible global function definition for ‘text’
predict.iCoxBoost: no visible global function definition for
  ‘model.response’
predict.iCoxBoost: no visible global function definition for
  ‘model.frame’
predict.iCoxBoost: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
comp.graph: no visible global function definition for ‘qnorm’
comp.graph: no visible global function definition for ‘plot’
comp.graph: no visible global function definition for ‘polygon’
comp.graph: no visible global function definition for ‘lines’
cox.ridge: no visible global function definition for ‘terms’
cox.ridge: no visible global function definition for ‘model.extract’
cox.ridge: no visible global function definition for ‘model.matrix’
cox.ridge: no visible binding for global variable ‘hat’
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘plot’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘plot’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘plot’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘plot’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘plot’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘plot’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
allCombs: no visible global function definition for ‘combn’
brute.search: no visible global function definition for ‘na.omit’
dag.draw: no visible global function definition for ‘plot’
dag.draw: no visible global function definition for ‘text’
dag.init: no visible global function definition for
  ‘installed.packages’
dag.legend: no visible global function definition for ‘text’
dag.letter: no visible global function definition for ‘text’
dag.move: no visible global function definition for ‘identify’
dag.move: no visible global function definition for ‘locator’
dag.sim: no visible global function definition for ‘rnorm’
dag.sim: no visible global function definition for ‘rbinom’
dag.sim : <anonymous>: no visible global function definition for
  ‘rbinom’
garrows: no visible global function definition for ‘arrows’
smoothArc: no visible global function definition for ‘points’
summary_dagRdag: no visible global function definition for ‘na.omit’
viv: no visible global function definition for ‘na.omit’
write.paths: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
drawBoard: no visible global function definition for ‘plot’
drawBoard: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘text’
drawHeatmap: no visible global function definition for ‘heat.colors’
drawHeatmap: no visible global function definition for ‘par’
drawHeatmap: no visible global function definition for ‘image’
drawHeatmap: no visible global function definition for ‘rect’
generalExpScores: no visible global function definition for ‘fft’
simpleExpScores: no visible global function definition for ‘mvfft’
simpleExpScores: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  ‘txtProgressBar’
datadict.profile: no visible global function definition for
  ‘setTxtProgressBar’
datadict_profile: no visible global function definition for
  ‘txtProgressBar’
datadict_profile: no visible global function definition for
  ‘setTxtProgressBar’
heatmap.quality: no visible global function definition for
  ‘colorRampPalette’
heatmap.quality: no visible global function definition for ‘heatmap’
heatmap_quality: no visible global function definition for
  ‘colorRampPalette’
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
scoreSum: no visible global function definition for ‘plot’
score_sum: no visible global function definition for ‘plot’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
plot.deamer: no visible global function definition for ‘plot’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘plot’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
bootbagg: no visible global function definition for ‘runif’
bootworpl: no visible global function definition for ‘runif’
des12: no visible global function definition for ‘rnorm’
des12: no visible global function definition for ‘runif’
eval.stage.gauss: no visible global function definition for ‘var’
plotparti: no visible global function definition for ‘plot’
plotparti: no visible global function definition for ‘lines’
plotpartilev: no visible global function definition for ‘plot’
plotpartilev: no visible global function definition for ‘polygon’
plotpartilev: no visible global function definition for ‘points’
simesi: no visible global function definition for ‘runif’
simesi3d: no visible global function definition for ‘runif’
simfssk: no visible global function definition for ‘rnorm’
simfssk: no visible global function definition for ‘runif’
simmix.delt: no visible global function definition for ‘rnorm’
simmix.delt: no visible global function definition for ‘runif’
simpp: no visible global function definition for ‘rnorm’
simpp: no visible global function definition for ‘runif’
simutree: no visible global function definition for ‘runif’
stage.gaussR: no visible global function definition for ‘var’
unidis: no visible global function definition for ‘runif’
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
MBD: no visible global function definition for ‘par’
MBD: no visible global function definition for ‘gray’
MBD: no visible global function definition for ‘matplot’
MBD: no visible global function definition for ‘polygon’
MBD: no visible global function definition for ‘lines’
MBD: no visible global function definition for ‘legend’
MBD: no visible global function definition for ‘matlines’
R.test: no visible global function definition for ‘runif’
R.test: no visible global function definition for ‘wilcox.test’
centralPlot: no visible global function definition for ‘par’
centralPlot: no visible global function definition for
  ‘colorRampPalette’
centralPlot: no visible global function definition for ‘matplot’
centralPlot: no visible global function definition for ‘matlines’
centralPlot: no visible global function definition for ‘legend’
scalecurve: no visible global function definition for ‘plot’
scalecurve: no visible global function definition for ‘lines’
scalecurve: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘matplot’
tmean: no visible global function definition for ‘matlines’
tmean: no visible global function definition for ‘lines’
tmean: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
VanWaerdenTest.default: no visible global function definition for
  ‘deparse1’
Undefined global functions or variables:
  deparse1
Running examples in ‘DescTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VanWaerdenTest
> ### Title: van der Waerden Test
> ### Aliases: VanWaerdenTest VanWaerdenTest.default VanWaerdenTest.formula
> ### Keywords: htest
> 
> ### ** Examples
> 
> ## Hollander & Wolfe (1973), 116.
> ## Mucociliary efficiency from the rate of removal of dust in normal
> ##  subjects, subjects with obstructive airway disease, and subjects
> ##  with asbestosis.
> x <- c(2.9, 3.0, 2.5, 2.6, 3.2) # normal subjects
> y <- c(3.8, 2.7, 4.0, 2.4)      # with obstructive airway disease
> z <- c(2.8, 3.4, 3.7, 2.2, 2.0) # with asbestosis
> 
> VanWaerdenTest(list(x, y, z))
Error in deparse1(substitute(x)) : could not find function "deparse1"
Calls: VanWaerdenTest -> VanWaerdenTest.default
Execution halted
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘plot’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘plot’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘plot’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
makeAdjMatrix: no visible global function definition for ‘combn’
plotPosteriorN: no visible global function definition for ‘plot’
plotPosteriorN: no visible global function definition for ‘title’
plotPosteriorN: no visible global function definition for ‘lines’
plotPosteriorN: no visible global function definition for ‘legend’
venn3: no visible global function definition for ‘plot’
venn3: no visible global function definition for ‘runif’
venn3: no visible global function definition for ‘points’
venn3: no visible global function definition for ‘lines’
venn3: no visible global function definition for ‘text’
venn4: no visible global function definition for ‘plot’
venn4: no visible global function definition for ‘lines’
venn4: no visible global function definition for ‘runif’
venn4: no visible global function definition for ‘points’
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  ‘coordinates<-’
fAssocplot: no visible global function definition for ‘plot’
fAssocplot: no visible global function definition for ‘coordinates’
fAssocplot: no visible global function definition for ‘text’
fAssocplot: no visible global function definition for ‘box’
fDrawfigure: no visible global function definition for ‘slot’
fDrawfigure : <anonymous>: no visible global function definition for
  ‘slot’
fDrawfigure: no visible global function definition for
  ‘SpatialPolygons’
fDrawfigure: no visible global function definition for ‘spsample’
fDrawfigure: no visible global function definition for ‘plot’
fDrawfigure: no visible global function definition for ‘image’
fDrawfigure: no visible global function definition for
  ‘colorRampPalette’
fDrawfigure: no visible global function definition for ‘points’
fRanXY : <anonymous>: no visible global function definition for ‘slot’
fRanXY : <anonymous>: no visible global function definition for
  ‘spsample’
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
aLine: no visible global function definition for ‘lines’
aLine: no visible global function definition for ‘ecdf’
dip.test: no visible global function definition for ‘complete.cases’
dip.test: no visible global function definition for ‘runif’
dip.test: no visible global function definition for ‘approx’
plot.dip: no visible global function definition for ‘par’
plot.dip: no visible global function definition for ‘ecdf’
plot.dip: no visible global function definition for ‘plot’
plot.dip: no visible global function definition for ‘title’
plot.dip: no visible global function definition for ‘abline’
plot.dip: no visible global function definition for ‘axis’
plot.dip: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for ‘as.dist’
gromov.hyperbolicity: no visible global function definition for
  ‘as.dist’
mcmc.target.seq: no visible global function definition for ‘runif’
phylo.diff: no visible global function definition for ‘par’
phylo.diff: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.