Package: Repitools

Version: 0.99.17

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings Repitools_0.99.17.tar.gz

StartedAt: 2011-07-07 02:02:25 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 02:07:37 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 311.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Repitools.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Repitools.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* 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 ‘0.99.17’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... WARNING
Undocumented S4 classes:
  ‘AffymetrixCdfFile’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 examples ... OK
* 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

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/Repitools.Rcheck/00check.log’
for details

* installing *source* package ‘Repitools’ ...
** R
** data
** inst
** preparing package for lazy loading
in method for ‘GCadjustCopy’ with signature ‘"GRanges","matrix","GCAdjustParams"’: no definition for class "GCAdjustParams"
in method for ‘GCadjustCopy’ with signature ‘"data.frame","matrix","GCAdjustParams"’: no definition for class "GCAdjustParams"
in method for ‘GCbiasPlots’ with signature ‘"CopyEstimate"’: no definition for class "CopyEstimate"
in method for ‘absoluteCN’ with signature ‘"GRanges","matrix","GCAdjustParams"’: no definition for class "GCAdjustParams"
in method for ‘absoluteCN’ with signature ‘"data.frame","matrix","GCAdjustParams"’: no definition for class "GCAdjustParams"
in method for ‘binPlots’ with signature ‘"ScoresList"’: no definition for class "ScoresList"
in method for ‘.blocksStats’ with signature ‘"AffymetrixCelSet","GRanges"’: no definition for class "AffymetrixCelSet"
in method for ‘chromosomeCNplots’ with signature ‘"CopyEstimate"’: no definition for class "CopyEstimate"
in method for ‘cpgBoxplots’ with signature ‘"AffymetrixCelSet"’: no definition for class "AffymetrixCelSet"
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"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Repitools_vignette.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded

* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	0.772	0.032	0.814
GCadjustCopy	0	0	0
GCbiasPlots	0	0	0
GDL2GRL	0.804	0.016	0.846
absoluteCN	0.000	0.000	0.001
annoDF2GR	0.108	0.008	0.121
annoGR2DF	0.108	0.000	0.108
annotationBlocksCounts	0.204	0.004	0.211
annotationBlocksLookup	0.184	0.008	0.198
annotationCounts	0.184	0.004	0.190
annotationLookup	0.168	0.012	0.179
binPlots	7.148	0.216	7.386
blocksStats	0.261	0.008	0.270
checkProbes	0.320	0.000	0.319
chromosomeCNplots	0	0	0
clusterPlots	2.736	0.176	2.930
cpgDensityCalc	11.060	1.004	12.117
cpgDensityPlot	7.381	0.164	7.683
doSeqStats	0	0	0
enrichmentCalc	2.640	0.000	2.641
enrichmentPlot	2.576	0.008	2.586
featureBlocks	0.100	0.000	0.099
featureScores	1.816	0.020	1.847
findClusters	3.345	0.012	3.353
gcContentCalc	3.584	0.336	3.924
genQC	0.004	0.000	0.000
genomeBlocks	0.132	0.004	0.139
getProbePositionsDf	0	0	0
loadPairFile	0	0	0
loadSampleDirectory	0.000	0.004	0.001
makeWindowLookupTable	0.168	0.004	0.172
mappabilityCalc	0	0	0
mergeReplicates	0.688	0.072	0.762
multiHeatmap	0.296	0.136	0.445
plotClusters	0.180	0.016	0.196
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0	0	0
relativeCN	0.144	0.008	0.151
sequenceCalc	8.792	0.812	9.703
summarizeScores	1.580	0.020	1.684
writeWig	0	0	0