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: 2015-10-27 11:37:13 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:48:07 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 653.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

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


* 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/37s] 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 ... [279s/172s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
methylEst         100.778 14.206  43.673
empBayes           41.873  7.082  25.395
cpgDensityCalc     12.199  1.134  13.547
sequenceCalc       12.243  1.059  13.302
BayMethList-class  11.666  0.624  12.356
determineOffset     6.937  0.777   7.717
maskOut             7.066  0.603   7.671
gcContentCalc       5.719  0.464   6.185
cpgDensityPlot      5.203  0.834   6.039
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [137s/137s]
 [137s/137s] 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	0.210	0.018	0.241
BayMethList-class	11.666	0.624	12.356
GCadjustCopy	0.001	0.001	0.001
GCbiasPlots	0.001	0.000	0.001
QdnaData	0.280	0.006	0.285
abcdDNA	0.000	0.000	0.001
absoluteCN	0.001	0.000	0.001
annoDF2GR	0.023	0.000	0.024
annoGR2DF	0.273	0.004	0.279
annotationBlocksCounts	0.295	0.006	0.301
annotationBlocksLookup	0.064	0.002	0.068
annotationCounts	0.313	0.009	0.322
annotationLookup	0.101	0.015	0.116
binPlots	2.135	0.390	2.526
blocksStats	0.398	0.003	0.401
checkProbes	0.193	0.002	0.204
chromosomeCNplots	0.001	0.001	0.001
clusterPlots	1.983	0.252	2.236
cpgDensityCalc	12.199	1.134	13.547
cpgDensityPlot	5.203	0.834	6.039
determineOffset	6.937	0.777	7.717
empBayes	41.873	7.082	25.395
enrichmentCalc	2.087	0.403	2.490
enrichmentPlot	1.964	0.383	2.347
featureBlocks	0.025	0.000	0.026
featureScores	1.181	0.252	1.432
findClusters	2.765	0.054	2.820
gcContentCalc	5.719	0.464	6.185
genQC	0.001	0.000	0.000
genomeBlocks	0.041	0.000	0.042
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.001	0.000	0.001
hyper	0.002	0.000	0.002
loadPairFile	0.000	0.001	0.001
loadSampleDirectory	0.001	0.000	0.001
makeWindowLookupTable	0.080	0.000	0.081
mappabilityCalc	0.000	0.000	0.001
maskOut	7.066	0.603	7.671
mergeReplicates	1.133	0.072	1.206
methylEst	100.778	14.206	43.673
multiHeatmap	0.091	0.004	0.094
plotClusters	0.366	0.009	0.374
plotQdnaByCN	0.001	0.000	0.001
processNDF	0.001	0.000	0.001
profilePlots	0	0	0
regionStats	0.001	0.000	0.001
relativeCN	0.063	0.003	0.087
sequenceCalc	12.243	1.059	13.302
setCNVOffsets	0.001	0.000	0.000
summarizeScores	1.222	0.406	1.628
writeWig	0.000	0.000	0.001