Package: PGSEA

Version: 1.33.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PGSEA_1.33.0.tar.gz

StartedAt: 2013-03-25 04:01:02 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:04:54 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 231.6 seconds

RetCode: 0

Status:  OK

CheckDir: PGSEA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PGSEA.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 'PGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PGSEA' version '1.33.0'
* 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 'PGSEA' can be installed ... [14s/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 ... NOTE
aggregateExprs: warning in mget(ids, env = Env, ifnotfound = NA):
  partial argument match of 'env' to 'envir'
* 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 ... [88s/88s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
go2smc 71.708  3.074  74.939
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/PGSEA.Rcheck/00check.log'
for details.

* installing *source* package 'PGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'PGSEA.Rnw' 
   'PGSEA2.Rnw' 
** testing if installed package can be loaded
* DONE (PGSEA)

name	user	system	elapsed
GOLUBmcs	0.128	0.014	0.144
PGSEA	1.169	0.131	1.306
VAIgsc	1.576	0.092	1.673
VAImcs	0.294	0.020	0.314
aggregateExprs	0.546	0.065	0.623
convertSmc	0.012	0.008	0.020
editSmc	0.070	0.015	0.085
go2smc	71.708	3.074	74.939
kegg2smc	1.103	0.048	1.151
nbEset	0.195	0.015	0.210
readGmt	0.084	0.014	0.101
readSmc	0.082	0.016	0.099
scanSmc	0.036	0.015	0.051
smcPlot	0.625	0.125	0.754
writeGmt	0.054	0.012	0.068
writeSmc	0.078	0.016	0.095