BioC 2.12: CHECK report for GOstats on petty

Package: GOstats

Version: 2.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GOstats_2.26.0.tar.gz

StartedAt: 2013-10-08 22:36:58 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:43:27 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 388.8 seconds

RetCode: 0

Status:  OK

CheckDir: GOstats.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GOstats.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GOstats/DESCRIPTION' ... OK
* this is package 'GOstats' version '2.26.0'
* 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 'GOstats' can be installed ... [24s/24s] 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 ... [33s/33s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
probeSetSummary 7.435  0.193   7.639
shortestPath    6.487  0.143   6.643
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [125s/126s]
 [125s/126s] OK
* 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 'GOstats' ...
** 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 (GOstats)

name	user	system	elapsed
Ndists	0.337	0.020	0.360
compCorrGraph	0.472	0.011	0.482
compGdist	0.259	0.018	0.279
idx2dimnames	0.050	0.015	0.065
makeGOGraph	2.653	0.112	2.800
notConn	0.053	0.008	0.061
oneGOGraph	1.664	0.034	1.705
probeSetSummary	7.435	0.193	7.639
shortestPath	6.487	0.143	6.643
simLL	1.624	0.074	1.706
triadCensus	0.016	0.004	0.020