Package: goProfiles

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.21.0.tar.gz

StartedAt: 2013-03-24 06:01:29 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 06:06:03 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 273.2 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'goProfiles/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'goProfiles' version '1.21.0'
* 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 'goProfiles' 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 ... NOTE
BioCprobes2Entrez: warning in mget(probeslist, env = myenvir,
  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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'fancyhdr.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [144s/146s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     42.247  0.602  43.740
fisherGOProfiles     13.108  0.328  13.552
printProfiles        11.169  0.253  11.454
plotProfiles         11.044  0.225  11.296
basicProfile         10.458  0.401  11.752
mergeProfilesLists   10.395  0.191  10.616
compSummary           8.133  0.225   8.575
compareGOProfiles     8.068  0.126   8.201
equivalentGOProfiles  7.664  0.095   7.862
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
CD4ids	0.040	0.006	0.046
GOTermsList	0.005	0.003	0.007
basicProfile	10.458	0.401	11.752
compSummary	8.133	0.225	8.575
compareGOProfiles	8.068	0.126	8.201
compareGeneLists	42.247	0.602	43.740
compareProfilesLists	0.016	0.009	0.030
contractedProfile	3.663	0.046	3.787
conversionFunctions	0.079	0.011	0.091
drosophila	0.006	0.005	0.011
equivSummary	0.016	0.007	0.023
equivalentGOProfiles	7.664	0.095	7.862
expandedLevel	2.790	0.089	2.912
expandedProfile	1.582	0.034	1.622
fisherGOProfiles	13.108	0.328	13.552
fitGOProfile	0.029	0.004	0.034
hugoIds	0.023	0.003	0.026
mergeProfilesLists	10.395	0.191	10.616
ngenes	3.423	0.062	3.496
omimIds	0.010	0.004	0.014
plotProfiles	11.044	0.225	11.296
printProfiles	11.169	0.253	11.454
prostateIds	0.025	0.011	0.037