Package: Genominator

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Genominator_1.12.0.tar.gz

StartedAt: 2013-03-24 23:42:34 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:45:08 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 154.0 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/Genominator.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.12.0'
* 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 'Genominator' 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 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
addPrimingWeights 5.548  0.220   5.812
joinExpData       4.972  0.077   5.099
* 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	0.001	0.000	0.001
addPrimingWeights	5.548	0.220	5.812
aggregateExpData	1.989	0.029	2.022
applyMapped	1.643	0.121	1.778
collapseExpData	2.917	0.148	3.074
computeCoverage	1.197	0.059	1.272
computePrimingWeights	0.374	0.061	0.442
getRegion	0.266	0.004	0.276
importFromAlignedReads	0.000	0.000	0.001
importToExpData	0.541	0.013	0.557
joinExpData	4.972	0.077	5.099
makeGeneRepresentation	0.313	0.012	0.325
mergeWithAnnotation	0.559	0.009	0.568
plot.genominator.coverage	3.614	0.141	3.777
plot.genominator.goodness.of.fit	0.841	0.062	0.929
regionGoodnessOfFit-methods	0.888	0.059	0.967
splitByAnnotation	1.096	0.017	1.135
summarizeByAnnotation	0.563	0.010	0.581
summarizeExpData	0.736	0.014	0.771
validAnnotation	0.024	0.003	0.028
yeastAnno	0.227	0.024	0.257