BioC 3.1: CHECK report for Repitools on zin2

Package: Repitools

Version: 1.14.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.14.0.tar.gz

StartedAt: 2015-10-09 04:51:17 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:59:40 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 502.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/Repitools.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.14.0’
* 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 ... [22s/22s] 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 ... [198s/178s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         87.986  1.160  73.709
empBayes          35.880  0.967  30.243
sequenceCalc      10.060  0.128  10.221
cpgDensityCalc     9.691  0.132   9.850
BayMethList-class  8.754  0.119   8.894
determineOffset    5.406  0.076   5.483
maskOut            5.225  0.012   6.687
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [103s/103s]
 [103s/103s] 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
  ‘/home/biocbuild/bbs-3.1-bioc/meat/Repitools.Rcheck/00check.log’
for details.

* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c const.c -o const.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c hyp2f1.c -o hyp2f1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -Wall -c mtherr.c -o mtherr.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	0.557	0.000	0.567
BayMethList-class	8.754	0.119	8.894
GCadjustCopy	0.001	0.000	0.001
GCbiasPlots	0.001	0.000	0.001
QdnaData	0.159	0.000	0.159
abcdDNA	0	0	0
absoluteCN	0	0	0
annoDF2GR	0.02	0.00	0.02
annoGR2DF	0.157	0.000	0.157
annotationBlocksCounts	0.162	0.004	0.166
annotationBlocksLookup	0.046	0.008	0.054
annotationCounts	0.185	0.008	0.194
annotationLookup	0.061	0.000	0.061
binPlots	1.803	0.012	1.817
blocksStats	0.239	0.000	0.239
checkProbes	0.156	0.000	0.156
chromosomeCNplots	0.001	0.000	0.001
clusterPlots	1.624	0.008	1.633
cpgDensityCalc	9.691	0.132	9.850
cpgDensityPlot	3.893	0.004	3.894
determineOffset	5.406	0.076	5.483
empBayes	35.880	0.967	30.243
enrichmentCalc	1.596	0.040	1.668
enrichmentPlot	1.645	0.004	1.649
featureBlocks	0.021	0.000	0.022
featureScores	1.035	0.000	1.034
findClusters	2.125	0.028	2.347
gcContentCalc	4.293	0.080	4.377
genQC	0.001	0.000	0.001
genomeBlocks	0.035	0.000	0.035
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.001	0.000	0.000
hyper	0.001	0.000	0.002
loadPairFile	0.001	0.000	0.001
loadSampleDirectory	0.001	0.000	0.000
makeWindowLookupTable	0.066	0.000	0.067
mappabilityCalc	0.001	0.000	0.001
maskOut	5.225	0.012	6.687
mergeReplicates	0.668	0.000	1.092
methylEst	87.986	1.160	73.709
multiHeatmap	0.056	0.000	0.056
plotClusters	0.198	0.004	0.202
plotQdnaByCN	0	0	0
processNDF	0.001	0.000	0.000
profilePlots	0	0	0
regionStats	0.001	0.000	0.001
relativeCN	0.050	0.004	0.054
sequenceCalc	10.060	0.128	10.221
setCNVOffsets	0	0	0
summarizeScores	1.092	0.004	1.107
writeWig	0	0	0