Package: htSeqTools

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch htSeqTools_1.3.0.tar.gz

StartedAt: 2012-06-21 00:57:38 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:01:05 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 206.6 seconds

RetCode: 0

Status:  OK

CheckDir: htSeqTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/htSeqTools.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'htSeqTools/DESCRIPTION' ... OK
* this is package 'htSeqTools' version '1.3.0'
* 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 whether package 'htSeqTools' 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 installed files from 'inst/doc' ... OK
* checking examples ... 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 'htSeqTools' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'htSeqTools'
Creating a generic function for 'lines' from package 'graphics' in package 'htSeqTools'
** help
*** installing help indices
** building package indices
** installing vignettes
   'htSeqTools.Rnw' 
** testing if installed package can be loaded

* DONE (htSeqTools)

name	user	system	elapsed
alignPeaks	0.246	0.009	0.257
cmds	5.285	0.743	6.176
cmdsFit-class	0.001	0.000	0.002
cmdsFit	0.000	0.001	0.000
countHitsWindow	0.080	0.001	0.089
coverageDiff	0.174	0.022	0.201
enrichedChrRegions	2.270	0.007	2.323
enrichedPeaks	0.936	0.009	0.979
enrichedRegions	0.314	0.004	0.333
extendRanges	0.223	0.001	0.225
fdrEnrichedCounts	0.203	0.011	0.241
filterDuplReads	0.506	0.013	0.560
giniCoverage	0.601	0.019	0.636
gridCover-class	0	0	0
htSample	0.410	0.023	0.454
islandCounts	0.361	0.004	0.368
listOverlap	0.010	0.001	0.010
mergeRegions	0.085	0.001	0.091
plot-methods	0.000	0.001	0.001
plotChrRegions	0.024	0.001	0.026
regionsCoverage	0	0	0
rowLogRegLRT	0.003	0.000	0.003
ssdCoverage	0.475	0.003	0.480
stdPeakLocation	0.105	0.002	0.107