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CHECK report for compcodeR on tokay2

This page was generated on 2019-10-16 12:29:54 -0400 (Wed, 16 Oct 2019).

Package 328/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.20.1
Charlotte Soneson
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/compcodeR
Branch: RELEASE_3_9
Last Commit: 9f60a50
Last Changed Date: 2019-07-31 11:25:40 -0400 (Wed, 31 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.20.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings compcodeR_1.20.1.tar.gz
StartedAt: 2019-10-16 02:51:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:05:55 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 855.0 seconds
RetCode: 0
Status:  OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compcodeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings compcodeR_1.20.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/compcodeR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.20.1'
* 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 ... OK
* 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 or elapsed time > 5s
                        user system elapsed
DESeq.nbinom.createRmd 88.59   1.83   90.44
convertcompDataToList  54.75   3.67   58.42
NBPSeq.createRmd       56.92   0.46   57.56
show-compData-method   45.64   2.60   48.25
EBSeq.createRmd        17.00   0.11   17.27
DESeq.GLM.createRmd     8.28   0.23    8.62
DESeq2.createRmd        7.59   0.47    8.06
DSS.createRmd           5.42   0.59    6.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DESeq.nbinom.createRmd 73.45   1.64   75.09
NBPSeq.createRmd       55.42   1.03   56.56
show-compData-method   51.60   1.39   53.01
convertcompDataToList  50.47   0.00   50.47
EBSeq.createRmd        13.33   0.10   13.43
DESeq2.createRmd        8.98   0.16    9.16
DESeq.GLM.createRmd     8.15   0.09    8.25
DSS.createRmd           7.12   0.40    7.59
baySeq.createRmd        5.80   0.04    5.85
runComparison           4.83   0.17    7.46
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/compcodeR.Rcheck/00check.log'
for details.



Installation output

compcodeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/compcodeR_1.20.1.tar.gz && rm -rf compcodeR.buildbin-libdir && mkdir compcodeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compcodeR.buildbin-libdir compcodeR_1.20.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL compcodeR_1.20.1.zip && rm compcodeR_1.20.1.tar.gz compcodeR_1.20.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 88 2345k   88 2064k    0     0  3828k      0 --:--:-- --:--:-- --:--:-- 3872k
100 2345k  100 2345k    0     0  4314k      0 --:--:-- --:--:-- --:--:-- 4367k

install for i386

* installing *source* package 'compcodeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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
** testing if installed package can be loaded from final location
** 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
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.20.1.zip
* DONE (compcodeR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'compcodeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

compcodeR.Rcheck/examples_i386/compcodeR-Ex.timings

nameusersystemelapsed
DESeq.GLM.createRmd8.280.238.62
DESeq.nbinom.createRmd88.59 1.8390.44
DESeq2.createRmd7.590.478.06
DSS.createRmd5.420.596.08
EBSeq.createRmd17.00 0.1117.27
NBPSeq.createRmd56.92 0.4657.56
NOISeq.prenorm.createRmd4.020.284.30
TCC.createRmd3.560.153.79
baySeq.createRmd4.170.064.23
checkDataObject0.970.081.05
checkTableConsistency2.230.092.34
check_compData1.000.041.04
check_compData_results1.490.031.51
compData0.010.000.02
convertListTocompData000
convertcompDataToList54.75 3.6758.42
edgeR.GLM.createRmd1.270.061.33
edgeR.exact.createRmd1.480.031.51
generateCodeHTMLs1.770.031.80
generateSyntheticData1.010.001.02
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.500.020.51
runComparison3.610.144.19
runComparisonGUI000
runDiffExp1.890.031.92
show-compData-method45.64 2.6048.25
sqrtcpm.limma.createRmd1.260.031.30
summarizeSyntheticDataSet1.930.252.33
ttest.createRmd1.280.061.34
voom.limma.createRmd1.420.031.45
voom.ttest.createRmd0.580.060.64
vst.limma.createRmd0.560.070.63
vst.ttest.createRmd0.510.030.55

compcodeR.Rcheck/examples_x64/compcodeR-Ex.timings

nameusersystemelapsed
DESeq.GLM.createRmd8.150.098.25
DESeq.nbinom.createRmd73.45 1.6475.09
DESeq2.createRmd8.980.169.16
DSS.createRmd7.120.407.59
EBSeq.createRmd13.33 0.1013.43
NBPSeq.createRmd55.42 1.0356.56
NOISeq.prenorm.createRmd4.470.224.69
TCC.createRmd4.050.084.14
baySeq.createRmd5.800.045.85
checkDataObject0.360.070.42
checkTableConsistency1.220.071.30
check_compData1.690.001.68
check_compData_results0.780.050.83
compData0.010.000.02
convertListTocompData000
convertcompDataToList50.47 0.0050.47
edgeR.GLM.createRmd1.460.051.50
edgeR.exact.createRmd1.140.011.15
generateCodeHTMLs2.040.032.08
generateSyntheticData0.220.000.22
listcreateRmd0.020.000.01
logcpm.limma.createRmd0.700.052.00
runComparison4.830.177.46
runComparisonGUI000
runDiffExp0.800.070.86
show-compData-method51.60 1.3953.01
sqrtcpm.limma.createRmd0.750.030.78
summarizeSyntheticDataSet3.380.153.60
ttest.createRmd2.000.082.08
voom.limma.createRmd0.940.030.96
voom.ttest.createRmd0.760.030.80
vst.limma.createRmd2.410.072.47
vst.ttest.createRmd2.250.072.42