BioC 2.13: CHECK report for Repitools on perceval

Package: Repitools

Version: 1.8.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.8.6.tar.gz

StartedAt: 2014-04-05 03:48:36 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:07:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1132.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Repitools.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.6’
* 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 ... [53s/59s] 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 sizes of PDF files under ‘inst/doc’ ... 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 ... [420s/366s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         98.232 26.075  96.736
empBayes          53.020 12.421  63.644
BayMethList-class 32.358  1.501  34.498
sequenceCalc      21.208  2.664  24.306
cpgDensityCalc    19.285  2.518  21.964
determineOffset   16.064  1.906  18.392
maskOut           15.052  2.135  18.099
cpgDensityPlot    10.446  3.424  13.919
gcContentCalc      5.978  0.734   6.798
findClusters       5.704  0.133   5.856
binPlots           4.202  1.089   5.372
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘tests.R’ [213s/215s]
 [213s/216s] 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
  ‘/Users/biocbuild/bbs-2.13-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/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-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	1.664	0.063	1.832
BayMethList-class	32.358	1.501	34.498
GCadjustCopy	0.003	0.007	0.010
GCbiasPlots	0.004	0.009	0.013
GDL2GRL	0.759	0.061	0.833
QdnaData	0.262	0.017	0.320
abcdDNA	0.002	0.005	0.008
absoluteCN	0.003	0.008	0.010
annoDF2GR	0.044	0.008	0.052
annoGR2DF	0.270	0.019	0.291
annotationBlocksCounts	0.361	0.020	0.388
annotationBlocksLookup	0.182	0.016	0.199
annotationCounts	0.408	0.018	0.438
annotationLookup	0.180	0.008	0.193
binPlots	4.202	1.089	5.372
blocksStats	0.589	0.032	0.646
checkProbes	0.414	0.016	0.431
chromosomeCNplots	0.004	0.007	0.011
clusterPlots	3.252	0.684	3.954
cpgDensityCalc	19.285	2.518	21.964
cpgDensityPlot	10.446	3.424	13.919
determineOffset	16.064	1.906	18.392
empBayes	53.020	12.421	63.644
enrichmentCalc	3.685	1.053	4.799
enrichmentPlot	2.911	1.101	4.068
featureBlocks	0.060	0.031	0.090
featureScores	2.129	0.690	2.820
findClusters	5.704	0.133	5.856
gcContentCalc	5.978	0.734	6.798
genQC	0.012	0.006	0.020
genomeBlocks	0.104	0.006	0.112
getProbePositionsDf	0.721	0.124	0.889
getSampleOffsets	0.003	0.004	0.007
hyper	0.006	0.008	0.014
loadPairFile	0.003	0.006	0.009
loadSampleDirectory	0.003	0.006	0.009
makeWindowLookupTable	0.179	0.010	0.195
mappabilityCalc	0.002	0.005	0.010
maskOut	15.052	2.135	18.099
mergeReplicates	1.505	0.158	1.674
methylEst	98.232	26.075	96.736
multiHeatmap	0.132	0.025	0.157
plotClusters	0.421	0.065	0.488
plotQdnaByCN	0.003	0.004	0.007
processNDF	0.002	0.006	0.009
profilePlots	0.002	0.004	0.007
regionStats	0.006	0.013	0.019
relativeCN	0.153	0.012	0.183
sequenceCalc	21.208	2.664	24.306
setCNVOffsets	0.003	0.006	0.009
summarizeScores	2.187	0.868	3.158
writeWig	0.002	0.003	0.004