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BioC 3.5: CHECK report for compcodeR on tokay2

This page was generated on 2017-08-16 13:23:13 -0400 (Wed, 16 Aug 2017).

Package 265/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.12.0
Charlotte Soneson
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/compcodeR
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.12.0
Command: rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.12.0.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.12.0.tar.gz
StartedAt: 2017-08-15 22:54:04 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:02:40 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 516.1 seconds
RetCode: 0
Status:  OK  
CheckDir: compcodeR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.12.0.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/compcodeR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.12.0'
* 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 ... 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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.
* 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'
SAMseq.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 installed files from 'inst/doc' ... 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 79.75   1.97   81.71
NBPSeq.createRmd       51.98   1.12   53.24
EBSeq.createRmd        11.55   0.06   11.70
show-compData-method    7.14   2.78    9.92
DESeq.GLM.createRmd     9.19   0.17    9.38
convertcompDataToList   6.28   2.26    8.54
DESeq2.createRmd        6.23   0.20    6.44
baySeq.createRmd        5.39   0.04    5.43
runComparison           5.22   0.19    5.89
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
DESeq.nbinom.createRmd   79.26   1.89   81.15
NBPSeq.createRmd         52.03   0.92   53.09
DESeq.GLM.createRmd      12.87   0.35   13.22
EBSeq.createRmd          12.06   0.05   12.30
DESeq2.createRmd          8.98   0.15    9.16
show-compData-method      7.38   0.40    7.80
convertcompDataToList     6.86   0.34    7.21
runComparison             5.87   0.13    6.12
NOISeq.prenorm.createRmd  5.78   0.03    5.81
baySeq.createRmd          4.96   0.05    5.01
* 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-3.5-bioc/meat/compcodeR.Rcheck/00check.log'
for details.

compcodeR.Rcheck/00install.out:


install for i386

* installing *source* package 'compcodeR' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'compcodeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compcodeR' as compcodeR_1.12.0.zip
* DONE (compcodeR)

compcodeR.Rcheck/examples_i386/compcodeR-Ex.timings:

nameusersystemelapsed
DESeq.GLM.createRmd9.190.179.38
DESeq.nbinom.createRmd79.75 1.9781.71
DESeq2.createRmd6.230.206.44
DSS.createRmd1.420.071.48
EBSeq.createRmd11.55 0.0611.70
NBPSeq.createRmd51.98 1.1253.24
NOISeq.prenorm.createRmd4.360.104.45
SAMseq.createRmd1.830.041.97
TCC.createRmd4.200.154.41
baySeq.createRmd5.390.045.43
checkDataObject0.190.000.19
checkTableConsistency1.280.031.31
check_compData0.170.000.18
check_compData_results0.830.020.84
compData000
convertListTocompData0.020.000.02
convertcompDataToList6.282.268.54
edgeR.GLM.createRmd1.400.041.44
edgeR.exact.createRmd0.80.00.8
generateCodeHTMLs0.470.040.59
generateSyntheticData0.310.000.31
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.640.050.69
runComparison5.220.195.89
runComparisonGUI000
runDiffExp0.800.080.88
show-compData-method7.142.789.92
sqrtcpm.limma.createRmd0.50.00.5
summarizeSyntheticDataSet1.780.141.98
ttest.createRmd0.750.080.83
voom.limma.createRmd0.840.070.92
voom.ttest.createRmd0.600.070.66
vst.limma.createRmd0.790.030.82
vst.ttest.createRmd0.770.010.79

compcodeR.Rcheck/examples_x64/compcodeR-Ex.timings:

nameusersystemelapsed
DESeq.GLM.createRmd12.87 0.3513.22
DESeq.nbinom.createRmd79.26 1.8981.15
DESeq2.createRmd8.980.159.16
DSS.createRmd2.190.082.27
EBSeq.createRmd12.06 0.0512.30
NBPSeq.createRmd52.03 0.9253.09
NOISeq.prenorm.createRmd5.780.035.81
SAMseq.createRmd1.280.061.44
TCC.createRmd3.550.023.56
baySeq.createRmd4.960.055.01
checkDataObject0.220.000.22
checkTableConsistency1.750.041.80
check_compData0.330.000.33
check_compData_results1.550.021.56
compData0.010.000.01
convertListTocompData000
convertcompDataToList6.860.347.21
edgeR.GLM.createRmd1.410.001.40
edgeR.exact.createRmd0.870.020.89
generateCodeHTMLs0.570.010.68
generateSyntheticData0.290.000.29
listcreateRmd0.020.000.02
logcpm.limma.createRmd0.550.030.58
runComparison5.870.136.12
runComparisonGUI000
runDiffExp0.670.020.69
show-compData-method7.380.407.80
sqrtcpm.limma.createRmd0.450.020.47
summarizeSyntheticDataSet1.690.221.96
ttest.createRmd0.610.000.61
voom.limma.createRmd0.560.010.58
voom.ttest.createRmd0.480.020.50
vst.limma.createRmd0.600.010.61
vst.ttest.createRmd0.760.030.80