Package: goProfiles

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.20.0.tar.gz

StartedAt: 2013-03-24 23:49:21 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:53:05 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 224.3 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 2.15.3 (2013-03-01)
* 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 '1.20.0'
* 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 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
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     36.076  1.829  38.330
fisherGOProfiles     10.362  0.553  11.130
mergeProfilesLists    8.768  0.425   9.271
plotProfiles          8.742  0.432   9.337
printProfiles         8.429  0.417   9.005
basicProfile          7.952  0.501   8.656
compSummary           7.328  0.390   7.868
equivalentGOProfiles  6.835  0.376   7.297
compareGOProfiles     6.673  0.328   7.166
* 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	0.024	0.006	0.029
GOTermsList	0	0	0
basicProfile	7.952	0.501	8.656
compSummary	7.328	0.390	7.868
compareGOProfiles	6.673	0.328	7.166
compareGeneLists	36.076	1.829	38.330
compareProfilesLists	0	0	0
contractedProfile	3.316	0.159	3.505
conversionFunctions	0.058	0.008	0.066
drosophila	0.002	0.001	0.004
equivSummary	0	0	0
equivalentGOProfiles	6.835	0.376	7.297
expandedLevel	2.367	0.081	2.477
expandedProfile	1.437	0.079	1.530
fisherGOProfiles	10.362	0.553	11.130
fitGOProfile	0	0	0
hugoIds	0.019	0.001	0.020
mergeProfilesLists	8.768	0.425	9.271
ngenes	3.526	0.165	3.718
omimIds	0.008	0.001	0.009
plotProfiles	8.742	0.432	9.337
printProfiles	8.429	0.417	9.005
prostateIds	0.006	0.001	0.007