BioC 2.13: CHECK report for goProfiles on zin1

Package: goProfiles

Version: 1.24.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.24.0.tar.gz

StartedAt: 2014-04-05 01:36:03 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:38:30 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 147.1 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/goProfiles.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.24.0’
* 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 ... [7s/7s] 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 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 ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
compareGeneLists   24.153  0.064  24.258
fisherGOProfiles    7.500  0.032   7.556
mergeProfilesLists  6.709  0.036   6.770
plotProfiles        6.576  0.008   6.611
printProfiles       5.797  0.008   5.814
basicProfile        5.484  0.052   5.553
* 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
  ‘/home/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	0.020	0.000	0.019
GOTermsList	0.004	0.000	0.004
basicProfile	5.484	0.052	5.553
compSummary	4.596	0.036	4.645
compareGOProfiles	4.557	0.052	4.614
compareGeneLists	24.153	0.064	24.258
compareProfilesLists	0.008	0.000	0.009
contractedProfile	2.304	0.008	2.347
conversionFunctions	0.056	0.000	0.057
drosophila	0.008	0.000	0.009
equivSummary	0.004	0.000	0.007
equivalentGOProfiles	4.845	0.016	4.922
expandedLevel	1.440	0.000	1.441
expandedProfile	0.916	0.008	0.925
fisherGOProfiles	7.500	0.032	7.556
fitGOProfile	0.012	0.000	0.012
hugoIds	0.016	0.000	0.015
mergeProfilesLists	6.709	0.036	6.770
ngenes	2.412	0.012	2.491
omimIds	0.004	0.000	0.010
plotProfiles	6.576	0.008	6.611
printProfiles	5.797	0.008	5.814
prostateIds	0.004	0.000	0.006