Package: Repitools

Version: 1.5.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.5.6.tar.gz

StartedAt: 2013-03-24 09:27:59 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:45:30 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 1050.4 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.5.6'
* 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 ... [25s/26s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 for portable 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 examples ... [245s/596s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         34.960  3.345 270.421
BayMethList-class 26.621  1.466  28.443
empBayes          20.558  2.134 137.999
cpgDensityCalc    18.520  2.388  21.067
maskOut           18.262  2.032  20.739
determineOffset   18.109  2.033  21.467
sequenceCalc      17.729  2.338  20.712
cpgDensityPlot    12.548  3.212  15.997
gcContentCalc      5.747  0.842   6.636
binPlots           5.397  1.109   6.532
enrichmentPlot     4.630  1.327   5.978
enrichmentCalc     4.512  1.421   5.939
findClusters       5.399  0.109   5.522
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'tests.R' [196s/200s]
 [197s/200s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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  -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  -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  -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 -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-2.12-bioc/meat/Repitools.Rcheck/Repitools/libs
** R
** data
** inst
** preparing package for lazy loading
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"
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
   'Repitools_vignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	1.170	0.041	1.244
BayMethList-class	26.621	1.466	28.443
GCadjustCopy	0.009	0.058	0.067
GCbiasPlots	0.005	0.013	0.017
GDL2GRL	0.441	0.063	0.511
QdnaData	0.119	0.014	0.134
abcdDNA	0.003	0.008	0.011
absoluteCN	0.005	0.009	0.015
annoDF2GR	0.053	0.009	0.062
annoGR2DF	0.046	0.013	0.059
annotationBlocksCounts	0.112	0.016	0.128
annotationBlocksLookup	0.099	0.008	0.109
annotationCounts	0.128	0.009	0.139
annotationLookup	0.136	0.019	0.156
binPlots	5.397	1.109	6.532
blocksStats	0.252	0.017	0.273
checkProbes	0.288	0.014	0.304
chromosomeCNplots	0.012	0.012	0.025
clusterPlots	3.414	0.657	4.141
cpgDensityCalc	18.520	2.388	21.067
cpgDensityPlot	12.548	3.212	15.997
determineOffset	18.109	2.033	21.467
empBayes	20.558	2.134	137.999
enrichmentCalc	4.512	1.421	5.939
enrichmentPlot	4.630	1.327	5.978
featureBlocks	0.062	0.016	0.079
featureScores	2.624	0.592	3.221
findClusters	5.399	0.109	5.522
gcContentCalc	5.747	0.842	6.636
genQC	0.003	0.003	0.005
genomeBlocks	0.106	0.005	0.111
getProbePositionsDf	0.002	0.004	0.007
getSampleOffsets	0.003	0.005	0.008
hyper	0.006	0.009	0.015
loadPairFile	0.003	0.007	0.012
loadSampleDirectory	0.004	0.006	0.010
makeWindowLookupTable	0.140	0.012	0.151
mappabilityCalc	0.004	0.007	0.010
maskOut	18.262	2.032	20.739
mergeReplicates	0.918	0.102	1.021
methylEst	34.960	3.345	270.421
multiHeatmap	0.958	0.255	1.267
plotClusters	0.164	0.011	0.178
plotQdnaByCN	0.003	0.007	0.010
processNDF	0.004	0.008	0.011
profilePlots	0.004	0.007	0.010
regionStats	0.006	0.012	0.018
relativeCN	0.193	0.017	0.240
sequenceCalc	17.729	2.338	20.712
setCNVOffsets	0.003	0.005	0.008
summarizeScores	2.308	0.789	3.265
writeWig	0.002	0.004	0.007