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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings compcodeR_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/compcodeR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'compcodeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compcodeR' version '1.24.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'rpanel'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'compcodeR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/compcodeR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'rpanel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DESeq.GLM.createRmd: no visible global function definition for
  'packageVersion'
DESeq.nbinom.createRmd: no visible global function definition for
  'packageVersion'
DESeq2.createRmd: no visible global function definition for
  'packageVersion'
DSS.createRmd: no visible global function definition for
  'packageVersion'
EBSeq.createRmd: no visible global function definition for
  'packageVersion'
NBPSeq.createRmd: no visible global function definition for
  'packageVersion'
NOISeq.prenorm.createRmd: no visible global function definition for
  'packageVersion'
TCC.createRmd: no visible global function definition for
  'packageVersion'
baySeq.createRmd: no visible global function definition for
  'packageVersion'
computeCorrelation: no visible global function definition for 'cor'
computeCorrelation: no visible global function definition for 'hclust'
computeCorrelation: no visible global function definition for 'as.dist'
computeCorrelation: no visible global function definition for
  'heat.colors'
computeOverlap: no visible global function definition for 'hclust'
computeOverlap: no visible global function definition for 'as.dist'
computeOverlap: no visible global function definition for 'heat.colors'
computeSignal: no visible binding for global variable 'sd'
createResultsRmdFile: no visible global function definition for
  'packageVersion'
edgeR.GLM.createRmd: no visible global function definition for
  'packageVersion'
edgeR.exact.createRmd: no visible global function definition for
  'packageVersion'
generateSyntheticData: no visible global function definition for
  'runif'
generateSyntheticData: no visible global function definition for 'rexp'
generateSyntheticData: no visible global function definition for
  'rnbinom'
generateSyntheticData: no visible global function definition for
  'rpois'
generateSyntheticData: no visible binding for global variable 'median'
logcpm.limma.createRmd: no visible global function definition for
  'packageVersion'
makeFalseDiscoveryCurves: no visible global function definition for
  'par'
makeFalseDiscoveryCurves: no visible global function definition for
  'lines'
makeFalseDiscoveryCurves: no visible global function definition for
  'legend'
makeROCcurves: no visible global function definition for 'par'
makeROCcurves: no visible global function definition for 'lines'
makeROCcurves: no visible global function definition for 'legend'
plotMASignificant: no visible global function definition for 'par'
plotResultTable: no visible global function definition for 'par'
plotScoreVsExpr: no visible global function definition for 'par'
plotScoreVsExpr: no visible global function definition for 'loess'
plotScoreVsExpr: no visible global function definition for 'lines'
plotScoreVsExpr: no visible global function definition for 'predict'
plotScoreVsOutlierEvidence: no visible global function definition for
  'par'
plotScoreVsOutlierEvidence: no visible global function definition for
  'loess'
plotScoreVsOutlierEvidence: no visible global function definition for
  'lines'
plotScoreVsOutlierEvidence: no visible global function definition for
  'predict'
plotScoreVsOutliers: no visible global function definition for 'par'
plotScoreVsOutliers: no visible binding for global variable 'na.omit'
plotScoreVsOutliers: no visible global function definition for 'title'
plotScoreVsOutliers: no visible global function definition for 'axis'
plotSignalForZeroCounts: no visible global function definition for
  'par'
sqrtcpm.limma.createRmd: no visible global function definition for
  'packageVersion'
ttest.createRmd: no visible global function definition for
  'packageVersion'
voom.limma.createRmd: no visible global function definition for
  'packageVersion'
voom.ttest.createRmd: no visible global function definition for
  'packageVersion'
vst.limma.createRmd: no visible global function definition for
  'packageVersion'
vst.ttest.createRmd: no visible global function definition for
  'packageVersion'
show,compData: no visible global function definition for 'head'
Undefined global functions or variables:
  as.dist axis cor hclust head heat.colors legend lines loess median
  na.omit packageVersion par predict rexp rnbinom rpois runif sd title
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "legend", "lines", "par", "title")
  importFrom("stats", "as.dist", "cor", "hclust", "loess", "median",
             "na.omit", "predict", "rexp", "rnbinom", "rpois", "runif",
             "sd")
  importFrom("utils", "head", "packageVersion")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
DESeq.nbinom.createRmd   91.61   2.25   93.88
NBPSeq.createRmd         76.23   1.97   78.38
EBSeq.createRmd          14.57   0.16   14.78
DESeq2.createRmd         12.15   0.84   13.00
DESeq.GLM.createRmd      11.76   0.50   12.33
DSS.createRmd             6.11   0.70    6.86
NOISeq.prenorm.createRmd  4.84   0.14    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
DESeq.nbinom.createRmd 87.22   2.54   89.77
NBPSeq.createRmd       53.62   1.63   55.25
DESeq.GLM.createRmd    17.82   0.44   18.26
DESeq2.createRmd       15.17   0.24   15.41
EBSeq.createRmd        14.94   0.01   14.97
DSS.createRmd           6.26   0.16    6.53
runComparison           3.36   0.14    6.40
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/compcodeR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/compcodeR_1.24.0.tar.gz && rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compcodeR.buildbin-libdir compcodeR_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL compcodeR_1.24.0.zip && rm compcodeR_1.24.0.tar.gz compcodeR_1.24.0.zip
###
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100 2346k  100 2346k    0     0  20.3M      0 --:--:-- --:--:-- --:--:-- 21.6M

install for i386

* installing *source* package 'compcodeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
** help
*** installing help indices
  converting help for package 'compcodeR'
    finding HTML links ... done
    DESeq.GLM.createRmd                     html  
    DESeq.nbinom.createRmd                  html  
    DESeq2.createRmd                        html  
    DSS.createRmd                           html  
    EBSeq.createRmd                         html  
    NBPSeq.createRmd                        html  
    NOISeq.prenorm.createRmd                html  
    TCC.createRmd                           html  
    baySeq.createRmd                        html  
    checkDataObject                         html  
    checkTableConsistency                   html  
    check_compData                          html  
    check_compData_results                  html  
    compData-class                          html  
    compData                                html  
    compcodeR-package                       html  
    convertListTocompData                   html  
    convertcompDataToList                   html  
    edgeR.GLM.createRmd                     html  
    edgeR.exact.createRmd                   html  
    generateCodeHTMLs                       html  
    generateSyntheticData                   html  
    listcreateRmd                           html  
    logcpm.limma.createRmd                  html  
    runComparison                           html  
    runComparisonGUI                        html  
    runDiffExp                              html  
    show-compData-method                    html  
    sqrtcpm.limma.createRmd                 html  
    summarizeSyntheticDataSet               html  
    ttest.createRmd                         html  
    voom.limma.createRmd                    html  
    voom.ttest.createRmd                    html  
    vst.limma.createRmd                     html  
    vst.ttest.createRmd                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'compcodeR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'gdata::reorder.factor' by 'gplots::reorder.factor' when loading 'compcodeR'
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.24.0.zip
* DONE (compcodeR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'compcodeR' successfully unpacked and MD5 sums checked