Package: goProfiles

Version: 1.20.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.20.0.tar.gz

StartedAt: 2013-03-25 01:49:55 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:53:45 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 230.2 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/goProfiles.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goProfiles/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goProfiles’ version ‘1.20.0’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     30.718  0.192  33.629
fisherGOProfiles     10.752  0.096  11.225
plotProfiles          8.345  0.116   9.257
printProfiles         8.248  0.084   8.915
basicProfile          7.808  0.112   9.190
mergeProfilesLists    7.693  0.040   8.623
compareGOProfiles     6.608  0.016   6.794
compSummary           6.377  0.052   7.438
equivalentGOProfiles  6.081  0.100   7.136
* 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
  ‘/loc/home/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	0.020	0.000	0.018
GOTermsList	0	0	0
basicProfile	7.808	0.112	9.190
compSummary	6.377	0.052	7.438
compareGOProfiles	6.608	0.016	6.794
compareGeneLists	30.718	0.192	33.629
compareProfilesLists	0	0	0
contractedProfile	3.068	0.076	4.184
conversionFunctions	0.056	0.004	0.150
drosophila	0.004	0.000	0.003
equivSummary	0	0	0
equivalentGOProfiles	6.081	0.100	7.136
expandedLevel	2.128	0.024	2.219
expandedProfile	1.144	0.004	1.163
fisherGOProfiles	10.752	0.096	11.225
fitGOProfile	0	0	0
hugoIds	0.016	0.000	0.034
mergeProfilesLists	7.693	0.040	8.623
ngenes	2.848	0.004	3.101
omimIds	0.000	0.004	0.057
plotProfiles	8.345	0.116	9.257
printProfiles	8.248	0.084	8.915
prostateIds	0.004	0.000	0.006