Package: goProfiles

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.19.0.tar.gz

StartedAt: 2012-06-21 00:34:41 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:38:01 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 199.5 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/goProfiles.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'goProfiles/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'goProfiles' version '1.19.0'
* 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 whether package 'goProfiles' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 sizes of PDF files under 'inst/doc' ... 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 ... 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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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	0.031	0.005	0.036
GOTermsList	0.001	0.000	0.001
basicProfile	5.738	0.344	6.601
compSummary	4.271	0.103	4.551
compareGOProfiles	4.081	0.049	4.145
compareGeneLists	18.670	0.243	19.136
compareProfilesLists	0.000	0.000	0.001
contractedProfile	1.732	0.021	1.764
conversionFunctions	0.072	0.005	0.077
drosophila	0.003	0.001	0.005
equivSummary	0.000	0.001	0.000
equivalentGOProfiles	3.723	0.042	3.788
expandedLevel	2.025	0.068	2.109
expandedProfile	0.838	0.015	0.857
fisherGOProfiles	6.805	0.212	7.052
fitGOProfile	0.000	0.000	0.001
hugoIds	0.030	0.001	0.032
mergeProfilesLists	5.474	0.154	5.663
ngenes	1.778	0.023	1.810
omimIds	0.010	0.001	0.012
plotProfiles	5.284	0.156	5.466
printProfiles	5.099	0.161	5.294
prostateIds	0.008	0.001	0.009