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BioC 3.4: CHECK report for compcodeR on moscato1

This page was generated on 2016-09-21 03:45:48 -0700 (Wed, 21 Sep 2016).

Package 242/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
compcodeR 1.9.2
Charlotte Soneson
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/compcodeR
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: compcodeR
Version: 1.9.2
Command: rm -rf compcodeR.buildbin-libdir compcodeR.Rcheck && mkdir compcodeR.buildbin-libdir compcodeR.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.9.2.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.9.2.tar.gz
StartedAt: 2016-09-20 06:17:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:27:33 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 584.1 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 && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=compcodeR.buildbin-libdir compcodeR_1.9.2.tar.gz >compcodeR.Rcheck\00install.out 2>&1 && cp compcodeR.Rcheck\00install.out compcodeR-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=compcodeR.buildbin-libdir --install="check:compcodeR-install.out" --force-multiarch --no-vignettes --timings compcodeR_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/compcodeR.Rcheck'
* using R version 3.3.1 (2016-06-21)
* 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 '1.9.2'
* 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 104.88   1.06  105.99
NBPSeq.createRmd        71.21   0.39   71.84
EBSeq.createRmd         13.97   0.04   14.34
DESeq.GLM.createRmd      9.74   0.17   10.44
show-compData-method     8.62   0.02    8.67
convertcompDataToList    7.99   0.08    8.07
baySeq.createRmd         5.76   0.03    5.80
DESeq2.createRmd         5.43   0.05    5.62
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
DESeq.nbinom.createRmd 96.69   1.22   97.92
NBPSeq.createRmd       63.59   0.40   64.29
DESeq.GLM.createRmd    12.23   0.08   12.87
EBSeq.createRmd        11.49   0.04   12.03
show-compData-method    8.99   0.00    8.98
convertcompDataToList   8.56   0.00    8.57
baySeq.createRmd        6.33   0.03    6.36
DESeq2.createRmd        5.54   0.04    5.59
* 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
  'D:/biocbld/bbs-3.4-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_1.9.2.zip
* DONE (compcodeR)

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

nameusersystemelapsed
DESeq.GLM.createRmd 9.74 0.1710.44
DESeq.nbinom.createRmd104.88 1.06105.99
DESeq2.createRmd5.430.055.62
DSS.createRmd1.450.001.75
EBSeq.createRmd13.97 0.0414.34
NBPSeq.createRmd71.21 0.3971.84
NOISeq.prenorm.createRmd3.810.033.84
SAMseq.createRmd1.590.001.78
TCC.createRmd2.960.083.26
baySeq.createRmd5.760.035.80
checkDataObject0.290.000.36
checkTableConsistency1.330.051.37
check_compData0.280.020.30
check_compData_results0.670.010.93
compData000
convertListTocompData000
convertcompDataToList7.990.088.07
edgeR.GLM.createRmd1.590.021.61
edgeR.exact.createRmd1.100.031.16
generateCodeHTMLs0.780.010.90
generateSyntheticData0.570.000.56
listcreateRmd0.010.000.02
logcpm.limma.createRmd0.520.030.54
runComparison3.100.083.62
runComparisonGUI000
runDiffExp0.690.030.74
show-compData-method8.620.028.67
sqrtcpm.limma.createRmd0.550.010.56
summarizeSyntheticDataSet1.470.161.65
ttest.createRmd0.600.030.64
voom.limma.createRmd0.720.020.73
voom.ttest.createRmd0.600.010.61
vst.limma.createRmd101
vst.ttest.createRmd0.670.030.70

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

nameusersystemelapsed
DESeq.GLM.createRmd12.23 0.0812.87
DESeq.nbinom.createRmd96.69 1.2297.92
DESeq2.createRmd5.540.045.59
DSS.createRmd1.590.031.95
EBSeq.createRmd11.49 0.0412.03
NBPSeq.createRmd63.59 0.4064.29
NOISeq.prenorm.createRmd4.300.034.34
SAMseq.createRmd1.370.071.54
TCC.createRmd2.710.012.73
baySeq.createRmd6.330.036.36
checkDataObject0.310.000.32
checkTableConsistency1.380.021.98
check_compData0.680.000.67
check_compData_results0.790.000.80
compData0.020.000.01
convertListTocompData000
convertcompDataToList8.560.008.57
edgeR.GLM.createRmd1.620.011.70
edgeR.exact.createRmd1.030.001.03
generateCodeHTMLs0.800.000.79
generateSyntheticData0.360.000.36
listcreateRmd000
logcpm.limma.createRmd0.560.030.59
runComparison3.330.133.64
runComparisonGUI000
runDiffExp0.810.010.83
show-compData-method8.990.008.98
sqrtcpm.limma.createRmd0.580.000.58
summarizeSyntheticDataSet1.540.181.73
ttest.createRmd0.560.030.60
voom.limma.createRmd0.750.010.76
voom.ttest.createRmd0.610.020.62
vst.limma.createRmd0.810.000.82
vst.ttest.createRmd0.720.030.87