Package: goProfiles

Version: 1.21.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.21.0.tar.gz

StartedAt: 2013-01-16 03:10:41 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:13:18 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 157.0 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.21.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
compareGeneLists 12.080  0.068  12.162
fisherGOProfiles  7.288  0.016   7.311
basicProfile      6.840  0.124   7.089
printProfiles     5.184  0.032   5.224
* 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-2.12-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	0.028	0.008	0.034
GOTermsList	0.016	0.000	0.016
basicProfile	6.840	0.124	7.089
compSummary	2.548	0.052	2.603
compareGOProfiles	2.641	0.020	2.662
compareGeneLists	12.080	0.068	12.162
compareProfilesLists	0.012	0.004	0.018
contractedProfile	1.092	0.024	1.116
conversionFunctions	0.060	0.012	0.072
drosophila	0.000	0.004	0.005
equivSummary	0.016	0.000	0.018
equivalentGOProfiles	2.413	0.020	2.437
expandedLevel	2.388	0.028	2.430
expandedProfile	0.488	0.004	0.491
fisherGOProfiles	7.288	0.016	7.311
fitGOProfile	0.004	0.004	0.005
hugoIds	0.016	0.000	0.017
mergeProfilesLists	4.480	0.024	4.508
ngenes	1.221	0.008	1.230
omimIds	0.036	0.004	0.043
plotProfiles	4.184	0.028	4.214
printProfiles	5.184	0.032	5.224
prostateIds	0.032	0.000	0.033