Package: GeneExpressionSignature

Version: 1.5.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneExpressionSignature_1.5.1.tar.gz

StartedAt: 2013-03-25 02:34:19 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:37:28 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 189.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneExpressionSignature.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 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.5.1'
* 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 'GeneExpressionSignature' can be installed ... [15s/15s] 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 ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
SignatureDistance 17.414  2.972  20.493
ScoreGSEA         15.732  2.696  18.482
ScorePGSEA        10.830  2.323  13.230
RankMerging        7.373  0.847   8.248
* 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 'GeneExpressionSignature' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GeneExpressionSignature.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	7.373	0.847	8.248
ScoreGSEA	15.732	2.696	18.482
ScorePGSEA	10.830	2.323	13.230
SignatureDistance	17.414	2.972	20.493
exampleSet	0.438	0.022	0.460
getRLs	0.997	0.100	1.099