BioC 3.3: CHECK report for Repitools on linux2.bioconductor.org

Package: Repitools

Version: 1.17.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.17.0.tar.gz

StartedAt: 2015-10-27 07:21:40 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:30:14 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 514.5 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Repitools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.17.0’
* 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 ... [24s/24s] 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 : <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: no visible global function
  definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges: no visible binding for global
  variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges: no visible global function
  definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘Arguments’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘pushState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘popState’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getMainCdf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘indexOf’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘enter’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘exit’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘countBases’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extract’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
cpgBoxplots,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellCpgFile’
cpgBoxplots,matrix: no visible binding for global variable ‘Arguments’
cpgBoxplots,matrix: no visible global function definition for
  ‘pushState’
cpgBoxplots,matrix: no visible global function definition for
  ‘popState’
cpgBoxplots,matrix: no visible global function definition for ‘enter’
cpgBoxplots,matrix: no visible global function definition for ‘exit’
cpgDensityCalc,GRanges-BSgenome: no visible global function definition
  for ‘DNAString’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile: no visible binding for global
  variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile: no visible global function
  definition for ‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getCellIndices’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘nbrOfArrays’
regionStats,AffymetrixCelSet: no visible binding for global variable
  ‘AromaCellPositionFile’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘getChipType’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extract’
regionStats,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
sequenceCalc,GRanges-BSgenome : <anonymous>: no visible global function
  definition for ‘matchPattern’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getNames’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extract’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘getCdf’
writeWig,AffymetrixCelSet: no visible global function definition for
  ‘extractMatrix’
Undefined global functions or variables:
  Arguments AromaCellCpgFile AromaCellPositionFile
  AromaCellSequenceFile DNAString countBases enter exit extract
  extractMatrix getCdf getCellIndices getChipType getMainCdf getNames
  indexOf matchPattern nbrOfArrays nbrOfUnits popState pushState
  verbose
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [190s/162s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         79.149  1.735  55.446
empBayes          30.688  1.131  25.895
sequenceCalc      10.828  0.226  14.199
BayMethList-class 10.493  0.108  10.622
cpgDensityCalc     9.709  0.228   9.951
maskOut            6.073  0.048   6.129
determineOffset    5.370  0.068   5.449
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tests.R’ [106s/112s]
 [107s/112s] 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-3.3-bioc/meat/Repitools.Rcheck/00check.log’
for details.

* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -c const.c -o const.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -c hyp2f1.c -o hyp2f1.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fpic  -g -O2  -c mtherr.c -o mtherr.o
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.207	0.016	0.223
BayMethList-class	10.493	0.108	10.622
GCadjustCopy	0.001	0.000	0.000
GCbiasPlots	0.001	0.000	0.001
QdnaData	0.076	0.000	0.077
abcdDNA	0	0	0
absoluteCN	0.001	0.000	0.001
annoDF2GR	0.013	0.000	0.014
annoGR2DF	0.074	0.000	0.075
annotationBlocksCounts	0.089	0.004	0.093
annotationBlocksLookup	0.038	0.000	0.039
annotationCounts	0.102	0.000	0.101
annotationLookup	0.064	0.000	0.064
binPlots	1.734	0.032	1.769
blocksStats	0.137	0.008	0.145
checkProbes	0.106	0.000	0.107
chromosomeCNplots	0.001	0.000	0.001
clusterPlots	1.357	0.004	1.362
cpgDensityCalc	9.709	0.228	9.951
cpgDensityPlot	4.216	0.056	4.282
determineOffset	5.370	0.068	5.449
empBayes	30.688	1.131	25.895
enrichmentCalc	1.371	0.020	1.394
enrichmentPlot	1.797	0.017	1.813
featureBlocks	0.023	0.001	0.027
featureScores	0.954	0.000	0.955
findClusters	2.087	0.004	2.090
gcContentCalc	4.375	0.139	4.547
genQC	0.001	0.000	0.001
genomeBlocks	0.024	0.000	0.023
getProbePositionsDf	0.001	0.000	0.001
getSampleOffsets	0.001	0.000	0.001
hyper	0.002	0.000	0.002
loadPairFile	0	0	0
loadSampleDirectory	0	0	0
makeWindowLookupTable	0.049	0.000	0.049
mappabilityCalc	0.001	0.000	0.001
maskOut	6.073	0.048	6.129
mergeReplicates	0.772	0.000	0.782
methylEst	79.149	1.735	55.446
multiHeatmap	0.042	0.000	0.043
plotClusters	0.173	0.000	0.173
plotQdnaByCN	0.001	0.000	0.000
processNDF	0.001	0.000	0.001
profilePlots	0.001	0.000	0.001
regionStats	0.002	0.000	0.002
relativeCN	0.065	0.000	0.065
sequenceCalc	10.828	0.226	14.199
setCNVOffsets	0.001	0.000	0.000
summarizeScores	1.160	0.004	1.500
writeWig	0.000	0.000	0.001