BioC 3.2: CHECK report for Repitools on oaxaca

Package: Repitools

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.16.0.tar.gz

StartedAt: 2016-04-23 03:41:21 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:51:02 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 580.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Repitools.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.16.0’
* 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 ... [31s/36s] 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
clusterPlots,ClusteredScoresList : .local : <anonymous>: warning in
  axis(2, at = c(y.min, (y.min + y.max)/2, y.max), label =
  score.labels): partial argument match of 'label' to 'labels'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible binding for
  global variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘extractMatrix’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible binding
  for global variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
  function definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable ‘Arguments’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘pushState’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘popState’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘getCdf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘getMainCdf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘indexOf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘enter’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘getCellIndices’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘exit’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable ‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘getChipType’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘countBases’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘extract’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘getNames’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
  definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
  variable ‘AromaCellCpgFile’
cpgBoxplots,matrix : .local: no visible binding for global variable
  ‘Arguments’
cpgBoxplots,matrix : .local: no visible global function definition for
  ‘pushState’
cpgBoxplots,matrix : .local: no visible global function definition for
  ‘popState’
cpgBoxplots,matrix : .local: no visible global function definition for
  ‘enter’
cpgBoxplots,matrix : .local: no visible global function definition for
  ‘exit’
cpgDensityCalc,GRanges-BSgenome : .local: no visible global function
  definition for ‘DNAString’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
  function definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible binding for
  global variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
  function definition for ‘getChipType’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘getCdf’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘getCellIndices’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘nbrOfArrays’
regionStats,AffymetrixCelSet : .local: no visible binding for global
  variable ‘AromaCellPositionFile’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘getChipType’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘extract’
regionStats,AffymetrixCelSet : .local: no visible global function
  definition for ‘extractMatrix’
sequenceCalc,GRanges-BSgenome : .local : <anonymous>: no visible global
  function definition for ‘matchPattern’
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for ‘getNames’
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for ‘extract’
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for ‘getCdf’
writeWig,AffymetrixCelSet : .local: no visible global function
  definition for ‘extractMatrix’
* 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 ... [191s/165s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         58.420  7.649  52.141
empBayes          24.606  3.735  23.436
cpgDensityCalc     9.070  0.749  12.836
BayMethList-class  9.302  0.425   9.979
sequenceCalc       6.557  0.479   7.037
determineOffset    6.344  0.611   6.960
maskOut            6.094  0.451   6.555
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [103s/105s]
 [103s/106s] 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-3.2-bioc/meat/Repitools.Rcheck/00check.log’
for details.

* 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-3.2-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)

name	user	system	elapsed
BAM2GRanges	0.232	0.017	0.402
BayMethList-class	9.302	0.425	9.979
GCadjustCopy	0.001	0.001	0.001
GCbiasPlots	0.001	0.000	0.001
QdnaData	0.176	0.004	0.180
abcdDNA	0.001	0.000	0.001
absoluteCN	0.001	0.001	0.001
annoDF2GR	0.021	0.000	0.022
annoGR2DF	0.166	0.005	0.176
annotationBlocksCounts	0.193	0.005	0.199
annotationBlocksLookup	0.064	0.001	0.066
annotationCounts	0.224	0.006	0.232
annotationLookup	0.108	0.010	0.119
binPlots	2.013	0.293	2.339
blocksStats	0.319	0.003	0.323
checkProbes	0.178	0.003	0.206
chromosomeCNplots	0.001	0.000	0.002
clusterPlots	1.735	0.165	1.903
cpgDensityCalc	9.070	0.749	12.836
cpgDensityPlot	4.003	0.554	4.607
determineOffset	6.344	0.611	6.960
empBayes	24.606	3.735	23.436
enrichmentCalc	1.812	0.296	2.112
enrichmentPlot	1.785	0.294	2.081
featureBlocks	0.029	0.000	0.030
featureScores	1.076	0.172	1.250
findClusters	2.634	0.072	2.712
gcContentCalc	3.927	0.364	4.296
genQC	0	0	0
genomeBlocks	0.040	0.001	0.041
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.001	0.000	0.000
hyper	0.002	0.001	0.002
loadPairFile	0.001	0.000	0.001
loadSampleDirectory	0.001	0.000	0.001
makeWindowLookupTable	0.086	0.000	0.086
mappabilityCalc	0.001	0.001	0.001
maskOut	6.094	0.451	6.555
mergeReplicates	0.806	0.078	0.885
methylEst	58.420	7.649	52.141
multiHeatmap	0.072	0.002	1.267
plotClusters	0.244	0.005	1.183
plotQdnaByCN	0.001	0.000	0.000
processNDF	0	0	0
profilePlots	0.000	0.001	0.001
regionStats	0.001	0.000	0.001
relativeCN	0.060	0.002	1.040
sequenceCalc	6.557	0.479	7.037
setCNVOffsets	0.001	0.000	0.002
summarizeScores	1.536	0.287	1.826
writeWig	0.001	0.000	0.000