BioC 2.13: CHECK report for Repitools on zin1

Package: Repitools

Version: 1.8.6

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.8.6.tar.gz

StartedAt: 2014-04-05 03:28:23 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:38:53 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 630.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Repitools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.8.6’
* 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 ... [28s/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 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 ... OK
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Repitools_vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [256s/227s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         90.902  1.428  65.145
empBayes          42.914  0.992  36.637
BayMethList-class 18.722  0.112  19.307
sequenceCalc      14.249  0.360  14.638
cpgDensityCalc    14.153  0.384  16.126
determineOffset   12.005  0.040  12.069
maskOut           10.437  0.108  11.011
cpgDensityPlot     8.820  0.064   8.913
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘tests.R’ [133s/134s]
 [134s/134s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Repitools.Rcheck/00check.log’
for details.

* installing *source* package ‘Repitools’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-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-2.13-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/usr/local/lib -o Repitools.so const.o hyp2f1.o mtherr.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘parallel::clusterApply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterApplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterCall’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterEvalQ’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterExport’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterMap’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterSplit’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parApply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parCapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parLapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parLapplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parRapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parSapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parSapplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘aroma.affymetrix::compare’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::detectCores’ when loading ‘Repitools’
in method for ‘.featureScores’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
in method for ‘regionStats’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
Creating a new generic function for ‘writeWig’ in package ‘Repitools’
in method for ‘writeWig’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘cpgBoxplots’ with signature ‘"AffymetrixCelSet"’: no definition for class “AffymetrixCelSet”
in method for ‘.blocksStats’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class “AffymetrixCelSet”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘parallel::clusterApply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterApplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterCall’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterEvalQ’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterExport’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterMap’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::clusterSplit’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parApply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parCapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parLapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parLapplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parRapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parSapply’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::parSapplyLB’ when loading ‘Repitools’
Warning: replacing previous import by ‘aroma.affymetrix::compare’ when loading ‘Repitools’
Warning: replacing previous import by ‘parallel::detectCores’ when loading ‘Repitools’
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	0.796	0.052	0.851
BayMethList-class	18.722	0.112	19.307
GCadjustCopy	0.000	0.004	0.004
GCbiasPlots	0.000	0.000	0.003
GDL2GRL	0.368	0.020	0.510
QdnaData	0.104	0.024	0.257
abcdDNA	0.000	0.000	0.001
absoluteCN	0.004	0.000	0.001
annoDF2GR	0.032	0.000	0.068
annoGR2DF	0.104	0.012	0.238
annotationBlocksCounts	0.168	0.012	0.261
annotationBlocksLookup	0.108	0.000	0.112
annotationCounts	0.192	0.008	0.211
annotationLookup	0.112	0.000	0.116
binPlots	2.968	0.008	4.044
blocksStats	0.324	0.004	0.645
checkProbes	0.272	0.000	0.371
chromosomeCNplots	0.000	0.000	0.001
clusterPlots	1.664	0.012	1.800
cpgDensityCalc	14.153	0.384	16.126
cpgDensityPlot	8.820	0.064	8.913
determineOffset	12.005	0.040	12.069
empBayes	42.914	0.992	36.637
enrichmentCalc	2.480	0.040	2.554
enrichmentPlot	2.156	0.008	2.167
featureBlocks	0.040	0.000	0.038
featureScores	1.888	0.000	1.889
findClusters	4.281	0.012	4.297
gcContentCalc	4.504	0.192	4.704
genQC	0.004	0.000	0.005
genomeBlocks	0.084	0.000	0.081
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.000	0.000	0.001
hyper	0.004	0.000	0.003
loadPairFile	0.000	0.000	0.001
loadSampleDirectory	0.004	0.000	0.001
makeWindowLookupTable	0.152	0.000	0.152
mappabilityCalc	0.004	0.000	0.001
maskOut	10.437	0.108	11.011
mergeReplicates	0.740	0.004	0.747
methylEst	90.902	1.428	65.145
multiHeatmap	0.072	0.004	0.075
plotClusters	0.204	0.024	0.230
plotQdnaByCN	0.000	0.000	0.001
processNDF	0.000	0.000	0.001
profilePlots	0.004	0.000	0.001
regionStats	0.004	0.000	0.003
relativeCN	0.100	0.004	0.105
sequenceCalc	14.249	0.360	14.638
setCNVOffsets	0.000	0.000	0.001
summarizeScores	2.012	0.028	2.054
writeWig	0.000	0.000	0.001