Package: GeneExpressionSignature

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GeneExpressionSignature_1.6.0.tar.gz

StartedAt: 2013-05-01 05:41:22 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:44:51 -0700 (Wed, 01 May 2013)

EllapsedTime: 208.4 seconds

RetCode: 0

Status:  OK

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GeneExpressionSignature.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.6.0'
* 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 'GeneExpressionSignature' can be installed ... [14s/14s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [75s/79s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ScoreGSEA         17.972  2.788  21.728
SignatureDistance 17.655  2.657  21.551
ScorePGSEA        13.879  2.218  16.648
RankMerging        9.158  0.687  10.098
* 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
** testing if installed package can be loaded
* DONE (GeneExpressionSignature)

name	user	system	elapsed
RankMerging	9.158	0.687	10.098
ScoreGSEA	17.972	2.788	21.728
ScorePGSEA	13.879	2.218	16.648
SignatureDistance	17.655	2.657	21.551
exampleSet	0.397	0.037	0.448
getRLs	1.323	0.082	1.440