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BioC 3.5: CHECK report for Repitools on toluca2

This page was generated on 2017-04-23 14:35:49 -0400 (Sun, 23 Apr 2017).

Package 1096/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Repitools 1.21.1
Mark Robinson
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Repitools
Last Changed Rev: 128047 / Revision: 129046
Last Changed Date: 2017-04-04 17:10:28 -0400 (Tue, 04 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
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: 1.21.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.21.1.tar.gz
StartedAt: 2017-04-23 08:53:57 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 09:04:01 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 603.5 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_1.21.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Repitools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.21.1’
* 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         58.492  8.298  47.178
empBayes          27.385  4.419  25.450
BayMethList-class  9.983  0.439  10.459
cpgDensityCalc     8.748  0.740   9.529
sequenceCalc       8.524  0.705   9.285
determineOffset    5.825  0.503   6.341
maskOut            5.687  0.528   6.256
* 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 -I/usr/local/include/freetype2 -I/opt/X11/include  -D R_NO_REMAP -I. -fPIC  -Wall -mtune=core2 -g -O2  -c const.c -o const.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -D R_NO_REMAP -I. -fPIC  -Wall -mtune=core2 -g -O2  -c hyp2f1.c -o hyp2f1.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -D R_NO_REMAP -I. -fPIC  -Wall -mtune=core2 -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
BAM2GRanges1.1200.0101.141
BayMethList-class 9.983 0.43910.459
GCadjustCopy0.0010.0010.001
GCbiasPlots0.0010.0000.001
QdnaData0.1430.0050.148
abcdDNA0.0010.0000.001
absoluteCN0.0010.0000.001
annoDF2GR0.1030.0020.105
annoGR2DF0.2060.0080.216
annotationBlocksCounts0.3890.0040.396
annotationBlocksLookup0.0740.0010.074
annotationCounts0.1900.0050.197
annotationLookup0.1770.0040.185
binPlots2.5160.3142.841
blocksStats0.2760.0040.281
checkProbes0.1960.0040.201
chromosomeCNplots0.0010.0000.001
clusterPlots1.4070.1791.589
cpgDensityCalc8.7480.7409.529
cpgDensityPlot3.6570.5574.220
determineOffset5.8250.5036.341
empBayes27.385 4.41925.450
enrichmentCalc1.6750.2941.973
enrichmentPlot1.5460.2781.837
featureBlocks0.0200.0000.021
featureScores0.9680.1791.150
findClusters2.5540.0462.606
gcContentCalc4.0220.3774.434
genQC0.0010.0000.000
genomeBlocks0.0340.0000.034
getProbePositionsDf000
getSampleOffsets0.0000.0000.001
hyper0.0230.0000.024
loadPairFile0.0000.0000.001
loadSampleDirectory0.0010.0000.001
makeWindowLookupTable0.0550.0000.055
mappabilityCalc0.0000.0000.001
maskOut5.6870.5286.256
mergeReplicates0.8170.0550.883
methylEst58.492 8.29847.178
multiHeatmap0.0790.0020.082
plotClusters0.2220.0040.228
plotQdnaByCN0.0000.0000.001
processNDF000
profilePlots0.0000.0000.001
regionStats0.0010.0000.000
relativeCN0.1640.0020.166
sequenceCalc8.5240.7059.285
setCNVOffsets0.0010.0000.001
summarizeScores1.0230.2321.409
writeWig0.0010.0000.001