Package: Repitools

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.6.0.tar.gz

StartedAt: 2013-05-01 10:04:15 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:23:27 -0700 (Wed, 01 May 2013)

EllapsedTime: 1151.6 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 Patched (2013-04-08 r62531)
* 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 '1.6.0'
* 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/28s] 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 ... [4m/11m] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
methylEst         36.601  3.357 288.699
BayMethList-class 27.097  1.513  29.130
cpgDensityCalc    24.949  2.625  27.897
sequenceCalc      24.554  2.458  27.892
empBayes          23.032  2.183 140.821
determineOffset   19.027  1.847  21.103
maskOut           18.492  2.010  21.064
cpgDensityPlot    16.457  3.205  19.998
enrichmentPlot     5.279  1.358   6.703
gcContentCalc      5.794  0.802   6.730
enrichmentCalc     5.057  1.394   6.510
binPlots           4.801  1.175   6.041
findClusters       5.660  0.139   5.836
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'tests.R' [253s/260s]
 [254s/260s] 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c const.c -o const.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c hyp2f1.c -o hyp2f1.o
hyp2f1.c:242:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        aid = 2 - id;
            ˜ ˜˜^˜˜˜
hyp2f1.c:352:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                aid = id;
                    ˜ ^˜
hyp2f1.c:359:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                aid = -id;
                    ˜ ^˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -D R_NO_REMAP -I. -fPIC  -mtune=native -ggdb -O0 -Wall -pedantic -Wconversion -c mtherr.c -o mtherr.o
clang -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-2.12-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
** testing if installed package can be loaded
* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	1.227	0.061	1.379
BayMethList-class	27.097	1.513	29.130
GCadjustCopy	0.004	0.009	0.013
GCbiasPlots	0.009	0.038	0.048
GDL2GRL	0.401	0.027	0.441
QdnaData	0.128	0.015	0.144
abcdDNA	0.004	0.006	0.008
absoluteCN	0.005	0.008	0.012
annoDF2GR	0.043	0.006	0.049
annoGR2DF	0.036	0.011	0.047
annotationBlocksCounts	0.109	0.013	0.123
annotationBlocksLookup	0.094	0.008	0.107
annotationCounts	0.124	0.012	0.136
annotationLookup	0.145	0.010	0.157
binPlots	4.801	1.175	6.041
blocksStats	0.295	0.016	0.313
checkProbes	0.276	0.014	0.298
chromosomeCNplots	0.012	0.010	0.022
clusterPlots	3.598	0.706	4.347
cpgDensityCalc	24.949	2.625	27.897
cpgDensityPlot	16.457	3.205	19.998
determineOffset	19.027	1.847	21.103
empBayes	23.032	2.183	140.821
enrichmentCalc	5.057	1.394	6.510
enrichmentPlot	5.279	1.358	6.703
featureBlocks	0.054	0.006	0.061
featureScores	3.204	0.603	3.861
findClusters	5.660	0.139	5.836
gcContentCalc	5.794	0.802	6.730
genQC	0.009	0.006	0.016
genomeBlocks	0.100	0.005	0.105
getProbePositionsDf	0.002	0.004	0.006
getSampleOffsets	0.003	0.005	0.008
hyper	0.007	0.009	0.017
loadPairFile	0.004	0.008	0.012
loadSampleDirectory	0.005	0.009	0.015
makeWindowLookupTable	0.138	0.012	0.150
mappabilityCalc	0.003	0.007	0.010
maskOut	18.492	2.010	21.064
mergeReplicates	0.892	0.075	0.977
methylEst	36.601	3.357	288.699
multiHeatmap	1.014	0.271	1.650
plotClusters	0.162	0.012	0.188
plotQdnaByCN	0.003	0.005	0.008
processNDF	0.003	0.005	0.036
profilePlots	0.002	0.004	0.006
regionStats	0.006	0.012	0.019
relativeCN	0.197	0.019	0.243
sequenceCalc	24.554	2.458	27.892
setCNVOffsets	0.014	0.113	0.128
summarizeScores	2.563	0.720	3.312
writeWig	0.003	0.004	0.006