Package: Repitools

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.4.2.tar.gz

StartedAt: 2013-03-25 01:01:54 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:10:34 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 519.3 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Repitools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.4.2'
* 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 whether package 'Repitools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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.
The following files should probably not be installed:
  'analyses1.tex', 'analyses2.tex', 'datasets.tex', 'qc.tex',
  'sInfo.tex', 'utilities.tex', 'visualisations.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
cpgDensityCalc 17.423  4.893  24.142
sequenceCalc   14.905  4.004  20.089
cpgDensityPlot 10.104  3.660  15.100
binPlots        7.859  1.741  10.283
gcContentCalc   4.825  1.037   6.925
clusterPlots    3.695  1.228   5.488
findClusters    4.405  0.137   7.486
enrichmentPlot  2.382  1.200   7.236
enrichmentCalc  2.374  1.143   6.498
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'tests.R'
 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-2.11-bioc/meat/Repitools.Rcheck/00check.log'
for details.

* installing *source* package 'Repitools' ...
** 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	1.191	0.072	1.469
GCadjustCopy	0.000	0.000	0.001
GCbiasPlots	0	0	0
GDL2GRL	0.370	0.029	0.455
QdnaData	0.118	0.009	0.137
abcdDNA	0.000	0.001	0.001
absoluteCN	0.000	0.000	0.001
annoDF2GR	0.037	0.001	0.041
annoGR2DF	0.037	0.001	0.041
annotationBlocksCounts	0.128	0.001	0.143
annotationBlocksLookup	0.093	0.001	0.102
annotationCounts	0.107	0.001	0.115
annotationLookup	0.115	0.001	0.134
binPlots	7.859	1.741	10.283
blocksStats	0.257	0.033	0.303
checkProbes	0.244	0.008	0.259
chromosomeCNplots	0.000	0.000	0.001
clusterPlots	3.695	1.228	5.488
cpgDensityCalc	17.423	4.893	24.142
cpgDensityPlot	10.104	3.660	15.100
enrichmentCalc	2.374	1.143	6.498
enrichmentPlot	2.382	1.200	7.236
featureBlocks	0.039	0.001	0.039
featureScores	1.696	0.668	4.560
findClusters	4.405	0.137	7.486
gcContentCalc	4.825	1.037	6.925
genQC	0	0	0
genomeBlocks	0.084	0.002	0.086
getProbePositionsDf	0.000	0.000	0.001
getSampleOffsets	0.000	0.000	0.001
loadPairFile	0	0	0
loadSampleDirectory	0.000	0.001	0.000
makeWindowLookupTable	0.127	0.001	0.128
mappabilityCalc	0	0	0
mergeReplicates	0.381	0.056	0.448
multiHeatmap	0.346	0.123	0.492
plotClusters	0.141	0.024	0.168
plotQdnaByCN	0	0	0
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0.001	0.000	0.001
relativeCN	0.150	0.021	0.204
sequenceCalc	14.905	4.004	20.089
setCNVOffsets	0	0	0
summarizeScores	1.788	0.901	2.794
writeWig	0.000	0.000	0.001