Package: Repitools

Version: 1.5.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_1.5.0.tar.gz

StartedAt: 2013-01-16 05:48:13 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:54:46 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 393.5 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Repitools.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.5.0’
* 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 ... 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 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 13.337  0.896  14.397
sequenceCalc    9.717  0.892  10.614
cpgDensityPlot  9.000  0.128   9.175
binPlots        8.817  0.180   9.013
* 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
  ‘/loc/home/biocbuild/bbs-2.12-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	0.504	0.020	0.561
GCadjustCopy	0.008	0.004	0.012
GCbiasPlots	0.016	0.000	0.017
GDL2GRL	0.380	0.008	0.388
QdnaData	0.108	0.004	0.112
abcdDNA	0.020	0.000	0.018
absoluteCN	0.020	0.000	0.021
annoDF2GR	0.044	0.000	0.045
annoGR2DF	0.044	0.000	0.045
annotationBlocksCounts	0.152	0.000	0.149
annotationBlocksLookup	0.128	0.000	0.128
annotationCounts	0.128	0.000	0.125
annotationLookup	0.12	0.00	0.12
binPlots	8.817	0.180	9.013
blocksStats	0.228	0.008	0.237
checkProbes	0.260	0.004	0.265
chromosomeCNplots	0.012	0.000	0.012
clusterPlots	3.260	0.180	3.444
cpgDensityCalc	13.337	0.896	14.397
cpgDensityPlot	9.000	0.128	9.175
enrichmentCalc	3.321	0.016	3.336
enrichmentPlot	2.916	0.000	2.917
featureBlocks	0.048	0.000	0.048
featureScores	1.704	0.000	1.703
findClusters	4.596	0.000	4.598
gcContentCalc	3.776	0.452	4.229
genQC	0.004	0.000	0.003
genomeBlocks	0.072	0.000	0.074
getProbePositionsDf	0.004	0.000	0.003
getSampleOffsets	0.000	0.000	0.003
loadPairFile	0.004	0.000	0.004
loadSampleDirectory	0.004	0.000	0.005
makeWindowLookupTable	0.120	0.000	0.117
mappabilityCalc	0.004	0.000	0.003
mergeReplicates	0.460	0.024	0.482
multiHeatmap	0.296	0.128	0.437
plotClusters	0.128	0.004	0.130
plotQdnaByCN	0.004	0.000	0.004
processNDF	0.004	0.000	0.005
profilePlots	0.004	0.000	0.003
regionStats	0.004	0.004	0.009
relativeCN	0.156	0.008	0.189
sequenceCalc	9.717	0.892	10.614
setCNVOffsets	0.000	0.004	0.005
summarizeScores	1.672	0.008	1.684
writeWig	0.004	0.000	0.003