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BioC 3.5: CHECK report for Repitools on veracruz2

This page was generated on 2017-10-18 14:29:33 -0400 (Wed, 18 Oct 2017).

Package 1099/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Repitools 1.22.0
Mark Robinson
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Repitools
Branch: RELEASE_3_5
Last Commit: 40074e5
Last Changed Date: 2017-04-24 15:45:44 -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: Repitools
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.22.0.tar.gz
StartedAt: 2017-10-18 08:08:34 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 08:17:40 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 545.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Repitools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘Repitools’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.cpgBoxplots: no visible global function definition for ‘pdf’
.cpgBoxplots: no visible global function definition for ‘par’
.cpgBoxplots: no visible global function definition for ‘dev.off’
.diracBetaDirac: no visible global function definition for ‘dbeta’
.doBiasPlot: no visible global function definition for ‘plot’
.doBiasPlot: no visible global function definition for ‘lines’
.doBiasPlot: no visible global function definition for ‘lowess’
.doChrPlot: no visible global function definition for ‘plot’
.doChrPlot: no visible global function definition for ‘points’
.doChrPlot: no visible global function definition for ‘abline’
.drawSegs : <anonymous>: no visible global function definition for
  ‘lines’
.makeClusters : clusterScores: no visible global function definition
  for ‘embed’
.makeClusters : clusterScores: no visible global function definition
  for ‘filter’
.methylEstbeta: no visible global function definition for ‘qnorm’
.mydmarginal: no visible global function definition for ‘dbeta’
.mydmarginalDBD: no visible global function definition for ‘dbeta’
.plotFreqs: no visible global function definition for ‘layout’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘matplot’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘abline’
.plotFreqs : <anonymous>: no visible global function definition for
  ‘legend’
determineOffset: no visible global function definition for ‘par’
determineOffset: no visible global function definition for ‘grid’
determineOffset: no visible global function definition for ‘abline’
determineOffset: no visible global function definition for ‘text’
getSampleOffsets: no visible global function definition for ‘grid’
getSampleOffsets: no visible global function definition for ‘abline’
loadPairFile: no visible global function definition for ‘read.table’
plotQdnaByCN: no visible global function definition for ‘layout’
plotQdnaByCN: no visible global function definition for ‘grid’
plotQdnaByCN: no visible global function definition for ‘abline’
plotQdnaByCN: no visible global function definition for ‘plot’
processNDF: no visible global function definition for ‘read.table’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
.blocksStats,GRangesList-GRanges: no visible global function definition
  for ‘p.adjust’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘t.test’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘pt’
.blocksStats,matrix-GRanges: no visible global function definition for
  ‘p.adjust’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for ‘lm’
GCadjustCopy,GRanges-matrix-GCAdjustParams : <anonymous>: no visible
  global function definition for ‘predict’
GCbiasPlots,AdjustedCopyEstimate: no visible global function definition
  for ‘par’
GCbiasPlots,AdjustedCopyEstimate : <anonymous>: no visible global
  function definition for ‘abline’
binPlots,ScoresList: no visible global function definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘layout’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘par’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘matplot’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot.new’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘legend’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘mtext’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘axis’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘plot.window’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘text’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘title’
binPlots,ScoresList : <anonymous>: no visible global function
  definition for ‘persp’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘par’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘matplot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘axis’
checkProbes,GRanges-GRanges : <anonymous> : <anonymous>: no visible
  global function definition for ‘matlines’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘plot’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘text’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘mtext’
checkProbes,GRanges-GRanges : <anonymous>: no visible global function
  definition for ‘abline’
chromosomeCNplots,AdjustedCopyEstimate: no visible global function
  definition for ‘par’
chromosomeCNplots,CopyEstimate : <anonymous>: no visible global
  function definition for ‘str’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘layout’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘par’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘plot.new’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘legend’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘matplot’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘axis’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘par’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘layout’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘matplot’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘axis’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘mtext’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘title’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot.new’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot.window’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘text’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘bxp’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘rect’
clusterPlots,ClusteredScoresList : <anonymous>: no visible global
  function definition for ‘abline’
clusterPlots,ClusteredScoresList: no visible global function definition
  for ‘plot’
clusterPlots,ScoresList: no visible global function definition for
  ‘kmeans’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘Arguments’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘pushState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘popState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getMainCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘indexOf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘enter’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘exit’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘countBases’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extract’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellCpgFile’
cpgBoxplots,matrix: no visible binding for global variable ‘Arguments’
cpgBoxplots,matrix: no visible global function definition for
  ‘pushState’
cpgBoxplots,matrix: no visible global function definition for
  ‘popState’
cpgBoxplots,matrix: no visible global function definition for ‘enter’
cpgBoxplots,matrix: no visible global function definition for ‘exit’
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
  for ‘DNAString’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘rainbow’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘plot’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘lines’
cpgDensityPlot,GRangesList: no visible global function definition for
  ‘legend’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘rainbow’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘plot’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘lines’
enrichmentPlot,GRangesList: no visible global function definition for
  ‘legend’
genQC,SequenceQCSet: no visible global function definition for
  ‘matplot’
genQC,SequenceQCSet: no visible global function definition for ‘legend’
genQC,SequenceQCSet: no visible global function definition for ‘par’
genQC,SequenceQCSet: no visible global function definition for ‘layout’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘par’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘matplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘abline’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘plot.new’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘legend’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘barplot’
genQC,SequenceQCSet : <anonymous>: no visible global function
  definition for ‘axis’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
  variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getChipType’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘par’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘plot’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘title’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘mtext’
plotClusters,GRanges : <anonymous>: no visible global function
  definition for ‘axis’
profilePlots,ScoresList: no visible global function definition for
  ‘rainbow’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘matplot’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘polygon’
profilePlots,ScoresList : <anonymous>: no visible global function
  definition for ‘legend’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
regionStats,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellPositionFile’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extract’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
  definition for ‘matchPattern’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extract’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
Undefined global functions or variables:
  Arguments AromaCellCpgFile AromaCellPositionFile
  AromaCellSequenceFile DNAString abline axis barplot bxp countBases
  dbeta dev.off embed enter exit extract extractMatrix filter getCdf
  getCellIndices getChipType getMainCdf getNames grid indexOf kmeans
  layout legend lines lm lowess matchPattern matlines matplot mtext
  nbrOfArrays nbrOfUnits p.adjust par pdf persp plot plot.new
  plot.window points polygon popState predict pt pushState qnorm
  rainbow read.table rect str t.test text title verbose
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "bxp", "grid",
             "layout", "legend", "lines", "matlines", "matplot", "mtext",
             "par", "persp", "plot", "plot.new", "plot.window", "points",
             "polygon", "rect", "text", "title")
  importFrom("stats", "dbeta", "embed", "filter", "kmeans", "lm",
             "lowess", "p.adjust", "predict", "pt", "qnorm", "t.test")
  importFrom("utils", "read.table", "str")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         52.213  7.078  43.070
empBayes          22.350  3.426  22.011
BayMethList-class  8.698  0.437   9.539
sequenceCalc       8.303  0.742   9.352
cpgDensityCalc     7.788  0.700   8.739
maskOut            5.175  0.480   5.901
determineOffset    4.751  0.510   5.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’
 OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck/00check.log’
for details.


Repitools.Rcheck/00install.out:

* installing *source* package ‘Repitools’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c const.c -o const.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c hyp2f1.c -o hyp2f1.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -D R_NO_REMAP -I. -fPIC  -Wall -g -O2  -c mtherr.c -o mtherr.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Repitools)

Repitools.Rcheck/Repitools-Ex.timings:

nameusersystemelapsed
BAM2GRanges1.2240.0121.335
BayMethList-class8.6980.4379.539
GCadjustCopy0.0010.0000.000
GCbiasPlots0.0010.0000.001
QdnaData0.1140.0050.124
abcdDNA0.0010.0000.001
absoluteCN0.0010.0000.001
annoDF2GR0.1050.0040.112
annoGR2DF0.1280.0030.132
annotationBlocksCounts0.3130.0040.330
annotationBlocksLookup0.0760.0020.081
annotationCounts0.1690.0070.188
annotationLookup0.1320.0030.137
binPlots1.8780.2342.185
blocksStats0.2220.0030.241
checkProbes0.1370.0020.144
chromosomeCNplots0.0020.0010.001
clusterPlots1.5170.1511.709
cpgDensityCalc7.7880.7008.739
cpgDensityPlot2.9770.4523.551
determineOffset4.7510.5105.433
empBayes22.350 3.42622.011
enrichmentCalc1.3710.2331.646
enrichmentPlot1.2760.2721.591
featureBlocks0.0190.0000.019
featureScores0.7510.1360.904
findClusters2.2290.0732.366
gcContentCalc3.8660.3814.463
genQC0.0010.0000.000
genomeBlocks0.0340.0000.035
getProbePositionsDf0.0010.0000.000
getSampleOffsets0.0010.0000.001
hyper0.0190.0000.028
loadPairFile0.0010.0000.000
loadSampleDirectory0.0010.0000.001
makeWindowLookupTable0.0500.0000.053
mappabilityCalc0.0000.0010.001
maskOut5.1750.4805.901
mergeReplicates0.7530.0470.838
methylEst52.213 7.07843.070
multiHeatmap0.0830.0030.094
plotClusters0.2540.0050.268
plotQdnaByCN000
processNDF0.0010.0000.000
profilePlots0.0000.0000.001
regionStats0.0010.0010.001
relativeCN0.1930.0020.204
sequenceCalc8.3030.7429.352
setCNVOffsets0.0000.0000.001
summarizeScores1.3370.2661.694
writeWig0.0010.0000.000