Package: Repitools

Version: 1.0.11

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Repitools_1.0.11.tar.gz

StartedAt: 2012-03-24 03:41:06 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:50:27 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 560.9 seconds

RetCode: 0

Status:  OK

CheckDir: Repitools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/Repitools.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.0.11'
* 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 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 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

* 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 ...
*** tangling vignette sources ...
   'Repitools_vignette.Rnw' using 'UTF-8' 
** testing if installed package can be loaded

* DONE (Repitools)

name	user	system	elapsed
BAM2GRanges	3.001	0.101	3.183
GCadjustCopy	0.001	0.000	0.001
GCbiasPlots	0.001	0.001	0.000
GDL2GRL	0.753	0.019	0.774
absoluteCN	0.001	0.000	0.000
annoDF2GR	0.160	0.007	0.167
annoGR2DF	0.154	0.006	0.160
annotationBlocksCounts	0.241	0.005	0.246
annotationBlocksLookup	0.205	0.005	0.212
annotationCounts	0.236	0.005	0.242
annotationLookup	0.238	0.005	0.244
binPlots	8.387	1.207	9.618
blocksStats	0.390	0.022	0.417
checkProbes	0.403	0.009	0.413
chromosomeCNplots	0	0	0
clusterPlots	4.829	0.779	5.664
cpgDensityCalc	21.919	3.952	26.055
cpgDensityPlot	14.882	3.420	18.371
enrichmentCalc	4.761	1.455	6.232
enrichmentPlot	4.540	1.470	6.093
featureBlocks	0.179	0.006	0.186
featureScores	3.026	0.695	3.742
findClusters	4.918	0.130	5.107
gcContentCalc	6.318	0.890	7.259
genQC	0	0	0
genomeBlocks	0.232	0.007	0.238
getProbePositionsDf	0.000	0.001	0.000
loadPairFile	0.000	0.000	0.001
loadSampleDirectory	0.001	0.001	0.001
makeWindowLookupTable	0.262	0.009	0.272
mappabilityCalc	0	0	0
mergeReplicates	0.757	0.095	0.855
multiHeatmap	0.460	0.103	0.562
plotClusters	0.301	0.038	0.340
processNDF	0	0	0
profilePlots	0	0	0
regionStats	0.000	0.000	0.001
relativeCN	0.304	0.019	0.362
sequenceCalc	19.861	3.886	23.807
summarizeScores	3.101	0.825	3.940
writeWig	0	0	0