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CHECK report for compcodeR on merida1

This page was generated on 2019-04-16 11:57:36 -0400 (Tue, 16 Apr 2019).

Package 311/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.18.1
Charlotte Soneson
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/compcodeR
Branch: RELEASE_3_8
Last Commit: 9df43ba
Last Changed Date: 2019-01-04 13:26:05 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.18.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.18.1.tar.gz
StartedAt: 2019-04-15 23:09:52 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:16:51 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 419.1 seconds
RetCode: 0
Status:  OK 
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:compcodeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings compcodeR_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/compcodeR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compcodeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compcodeR’ version ‘1.18.1’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
DESeq.nbinom.createRmd   59.081  3.050  63.706
NBPSeq.createRmd         38.755  2.477  41.493
convertcompDataToList    10.950  8.190  19.374
show-compData-method     10.803  7.744  18.619
NOISeq.prenorm.createRmd 14.856  1.407  16.104
DESeq.GLM.createRmd      11.340  0.951  12.404
DESeq2.createRmd         11.016  0.864  11.846
EBSeq.createRmd           9.062  0.646   9.817
DSS.createRmd             7.247  0.765   8.002
baySeq.createRmd          6.556  0.469   7.077
* 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/compcodeR.Rcheck/00check.log’
for details.



Installation output

compcodeR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL compcodeR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘compcodeR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (compcodeR)

Tests output


Example timings

compcodeR.Rcheck/compcodeR-Ex.timings

nameusersystemelapsed
DESeq.GLM.createRmd11.340 0.95112.404
DESeq.nbinom.createRmd59.081 3.05063.706
DESeq2.createRmd11.016 0.86411.846
DSS.createRmd7.2470.7658.002
EBSeq.createRmd9.0620.6469.817
NBPSeq.createRmd38.755 2.47741.493
NOISeq.prenorm.createRmd14.856 1.40716.104
TCC.createRmd3.4310.2953.730
baySeq.createRmd6.5560.4697.077
checkDataObject0.2910.0650.355
checkTableConsistency1.5290.1651.700
check_compData0.2390.0440.282
check_compData_results0.7540.1000.886
compData0.0040.0010.005
convertListTocompData0.0060.0010.007
convertcompDataToList10.950 8.19019.374
edgeR.GLM.createRmd1.4690.1251.588
edgeR.exact.createRmd0.9640.0911.051
generateCodeHTMLs0.9010.1091.008
generateSyntheticData0.3800.0480.424
listcreateRmd0.0160.0000.016
logcpm.limma.createRmd0.6670.0910.753
runComparison3.8360.3324.174
runComparisonGUI0.0020.0010.002
runDiffExp0.8850.1161.004
show-compData-method10.803 7.74418.619
sqrtcpm.limma.createRmd0.6990.0960.790
summarizeSyntheticDataSet2.5690.2942.956
ttest.createRmd0.7020.0880.785
voom.limma.createRmd0.9180.1031.019
voom.ttest.createRmd0.7230.0860.808
vst.limma.createRmd0.9310.0971.024
vst.ttest.createRmd0.9210.0901.005