BioC 3.2: CHECK report for Repitools on perceval

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: 2015-11-10 08:46:58 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:57:48 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 649.9 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 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [34s/34s] 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 ... [278s/175s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
methylEst         102.390 14.004  48.457
empBayes           40.633  6.870  24.955
cpgDensityCalc     12.110  1.108  13.304
sequenceCalc       12.005  1.006  13.013
BayMethList-class  11.601  0.617  12.282
determineOffset     6.866  0.742   7.608
maskOut             6.995  0.602   7.597
gcContentCalc       5.723  0.474   6.207
cpgDensityPlot      5.106  0.809   5.915
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [136s/137s]
 [137s/138s] 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c const.c -o const.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c hyp2f1.c -o hyp2f1.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=core2 -g -O2 -Wall  -c mtherr.c -o mtherr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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	0.214	0.018	0.252
BayMethList-class	11.601	0.617	12.282
GCadjustCopy	0.001	0.000	0.002
GCbiasPlots	0.001	0.000	0.001
QdnaData	0.282	0.005	0.287
abcdDNA	0.001	0.000	0.001
absoluteCN	0.001	0.000	0.001
annoDF2GR	0.022	0.000	0.023
annoGR2DF	0.275	0.004	0.280
annotationBlocksCounts	0.308	0.007	0.315
annotationBlocksLookup	0.074	0.002	0.078
annotationCounts	0.323	0.008	0.332
annotationLookup	0.106	0.015	0.121
binPlots	2.128	0.381	2.509
blocksStats	0.401	0.004	0.404
checkProbes	0.185	0.003	0.196
chromosomeCNplots	0.001	0.000	0.002
clusterPlots	1.949	0.237	2.185
cpgDensityCalc	12.110	1.108	13.304
cpgDensityPlot	5.106	0.809	5.915
determineOffset	6.866	0.742	7.608
empBayes	40.633	6.870	24.955
enrichmentCalc	2.091	0.397	2.487
enrichmentPlot	1.966	0.386	2.353
featureBlocks	0.026	0.000	0.026
featureScores	1.168	0.236	1.404
findClusters	2.805	0.055	2.860
gcContentCalc	5.723	0.474	6.207
genQC	0	0	0
genomeBlocks	0.044	0.001	0.044
getProbePositionsDf	0.001	0.000	0.001
getSampleOffsets	0.000	0.001	0.001
hyper	0.002	0.000	0.003
loadPairFile	0.001	0.000	0.001
loadSampleDirectory	0.001	0.000	0.001
makeWindowLookupTable	0.086	0.001	0.086
mappabilityCalc	0.000	0.000	0.001
maskOut	6.995	0.602	7.597
mergeReplicates	1.106	0.073	1.179
methylEst	102.390	14.004	48.457
multiHeatmap	0.091	0.004	0.096
plotClusters	0.358	0.008	0.368
plotQdnaByCN	0.001	0.001	0.001
processNDF	0.001	0.000	0.001
profilePlots	0	0	0
regionStats	0.001	0.000	0.001
relativeCN	0.070	0.003	0.096
sequenceCalc	12.005	1.006	13.013
setCNVOffsets	0	0	0
summarizeScores	1.206	0.371	1.576
writeWig	0.000	0.000	0.001