Package: Genominator

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.13.0.tar.gz

StartedAt: 2013-03-25 02:41:44 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:44:47 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 183.5 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Genominator.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Genominator/DESCRIPTION' ... OK
* this is package 'Genominator' version '1.13.0'
* 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 'Genominator' can be installed ... [12s/12s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [37s/37s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
addPrimingWeights 7.738  0.259   8.031
* 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 'Genominator' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Genominator.Rnw' 
   'plotting.Rnw' 
   'withShortRead.Rnw' 
** testing if installed package can be loaded
* DONE (Genominator)

name	user	system	elapsed
ExpData	0.007	0.005	0.012
addPrimingWeights	7.738	0.259	8.031
aggregateExpData	1.606	0.031	1.640
applyMapped	1.367	0.093	1.486
collapseExpData	2.816	0.119	2.943
computeCoverage	1.024	0.050	1.081
computePrimingWeights	0.409	0.057	0.471
getRegion	0.222	0.011	0.233
importFromAlignedReads	0.005	0.007	0.011
importToExpData	0.498	0.018	0.523
joinExpData	3.987	0.073	4.076
makeGeneRepresentation	0.315	0.017	0.333
mergeWithAnnotation	0.449	0.016	0.466
plot.genominator.coverage	3.088	0.138	3.231
plot.genominator.goodness.of.fit	1.071	0.086	1.160
regionGoodnessOfFit-methods	1.033	0.086	1.123
splitByAnnotation	1.111	0.023	1.134
summarizeByAnnotation	0.473	0.017	0.491
summarizeExpData	0.603	0.019	0.624
validAnnotation	0.028	0.007	0.035
yeastAnno	0.254	0.028	0.282