Package: goProfiles

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.22.0.tar.gz

StartedAt: 2013-05-01 06:19:05 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:24:34 -0700 (Wed, 01 May 2013)

EllapsedTime: 328.4 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 Patched (2013-04-08 r62531)
* 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 '1.22.0'
* 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 ... [13s/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 ... [196s/201s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     60.644  0.765  63.670
fisherGOProfiles     16.825  0.342  17.408
mergeProfilesLists   16.279  0.245  16.721
printProfiles        15.126  0.241  15.512
plotProfiles         14.768  0.263  15.196
basicProfile         12.508  0.405  14.066
compSummary          11.755  0.262  12.539
compareGOProfiles    11.227  0.115  11.529
equivalentGOProfiles 11.008  0.085  11.190
ngenes                5.489  0.076   5.626
contractedProfile     5.387  0.070   5.511
* 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
** testing if installed package can be loaded
* DONE (goProfiles)

name	user	system	elapsed
CD4ids	0.034	0.006	0.040
GOTermsList	0.007	0.003	0.010
basicProfile	12.508	0.405	14.066
compSummary	11.755	0.262	12.539
compareGOProfiles	11.227	0.115	11.529
compareGeneLists	60.644	0.765	63.670
compareProfilesLists	0.015	0.007	0.023
contractedProfile	5.387	0.070	5.511
conversionFunctions	0.085	0.013	0.100
drosophila	0.006	0.005	0.011
equivSummary	0.021	0.009	0.030
equivalentGOProfiles	11.008	0.085	11.190
expandedLevel	3.039	0.086	3.225
expandedProfile	2.228	0.024	2.275
fisherGOProfiles	16.825	0.342	17.408
fitGOProfile	0.003	0.003	0.007
hugoIds	0.023	0.005	0.029
mergeProfilesLists	16.279	0.245	16.721
ngenes	5.489	0.076	5.626
omimIds	0.033	0.009	0.044
plotProfiles	14.768	0.263	15.196
printProfiles	15.126	0.241	15.512
prostateIds	0.008	0.004	0.014