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: 2015-10-27 07:11:39 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:21:17 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 578.0 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 (2015-08-14)
* 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 ... [27s/29s] 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 ... [195s/155s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         58.216  6.930  46.020
empBayes          25.331  3.698  24.395
sequenceCalc       9.251  0.807  10.073
cpgDensityCalc     9.276  0.739  10.177
BayMethList-class  9.118  0.413   9.610
determineOffset    6.117  0.573   6.710
maskOut            6.007  0.447   6.468
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [104s/104s]
 [104s/104s] 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	0.237	0.031	0.296
BayMethList-class	9.118	0.413	9.610
GCadjustCopy	0.001	0.000	0.000
GCbiasPlots	0.001	0.000	0.002
QdnaData	0.180	0.004	0.184
abcdDNA	0.000	0.000	0.001
absoluteCN	0.001	0.000	0.001
annoDF2GR	0.027	0.001	0.027
annoGR2DF	0.179	0.004	0.183
annotationBlocksCounts	0.206	0.006	0.213
annotationBlocksLookup	0.066	0.002	0.069
annotationCounts	0.216	0.007	0.222
annotationLookup	0.109	0.010	0.119
binPlots	2.020	0.293	2.334
blocksStats	0.318	0.003	0.321
checkProbes	0.166	0.002	0.187
chromosomeCNplots	0.001	0.000	0.001
clusterPlots	1.811	0.173	1.991
cpgDensityCalc	9.276	0.739	10.177
cpgDensityPlot	4.299	0.607	4.914
determineOffset	6.117	0.573	6.710
empBayes	25.331	3.698	24.395
enrichmentCalc	1.803	0.296	2.103
enrichmentPlot	2.167	0.315	2.485
featureBlocks	0.032	0.000	0.032
featureScores	1.116	0.178	1.295
findClusters	2.921	0.066	2.995
gcContentCalc	3.746	0.349	4.097
genQC	0.001	0.000	0.001
genomeBlocks	0.041	0.000	0.042
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.001	0.000	0.000
hyper	0.001	0.000	0.001
loadPairFile	0	0	0
loadSampleDirectory	0.001	0.000	0.001
makeWindowLookupTable	0.062	0.000	0.062
mappabilityCalc	0.001	0.000	0.001
maskOut	6.007	0.447	6.468
mergeReplicates	0.827	0.056	0.889
methylEst	58.216	6.930	46.020
multiHeatmap	0.070	0.002	0.072
plotClusters	0.261	0.005	0.267
plotQdnaByCN	0.000	0.000	0.001
processNDF	0.000	0.000	0.001
profilePlots	0	0	0
regionStats	0.001	0.000	0.001
relativeCN	0.065	0.001	0.096
sequenceCalc	9.251	0.807	10.073
setCNVOffsets	0.001	0.000	0.000
summarizeScores	1.099	0.156	1.256
writeWig	0.000	0.000	0.001