BioC 2.13: CHECK report for goProfiles on perceval

Package: goProfiles

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.24.0.tar.gz

StartedAt: 2014-04-05 01:43:16 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:47:34 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 257.9 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/goProfiles.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.24.0’
* 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 ... [12s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘Biobase’ ‘GO.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘goProfiles.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [139s/141s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     39.777  0.478  40.907
fisherGOProfiles     13.858  0.251  14.236
basicProfile         10.693  0.306  11.082
plotProfiles         10.778  0.197  11.154
printProfiles        10.558  0.181  10.854
mergeProfilesLists   10.065  0.200  10.378
compSummary           7.927  0.164   8.180
compareGOProfiles     7.751  0.088   7.924
equivalentGOProfiles  7.092  0.084   7.381
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.032	0.006	0.037
GOTermsList	0.009	0.000	0.010
basicProfile	10.693	0.306	11.082
compSummary	7.927	0.164	8.180
compareGOProfiles	7.751	0.088	7.924
compareGeneLists	39.777	0.478	40.907
compareProfilesLists	0.019	0.006	0.025
contractedProfile	3.466	0.045	3.605
conversionFunctions	0.068	0.010	0.078
drosophila	0.005	0.004	0.010
equivSummary	0.003	0.006	0.009
equivalentGOProfiles	7.092	0.084	7.381
expandedLevel	3.006	0.073	3.108
expandedProfile	1.391	0.026	1.433
fisherGOProfiles	13.858	0.251	14.236
fitGOProfile	0.002	0.004	0.007
hugoIds	0.021	0.004	0.026
mergeProfilesLists	10.065	0.200	10.378
ngenes	3.543	0.054	3.630
omimIds	0.054	0.006	0.061
plotProfiles	10.778	0.197	11.154
printProfiles	10.558	0.181	10.854
prostateIds	0.046	0.003	0.050