BioC 2.14: CHECK report for goProfiles on petty

Package: goProfiles

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.26.0.tar.gz

StartedAt: 2014-10-07 22:16:07 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:21:52 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 345.0 seconds

RetCode: 0

Status:  OK

CheckDir: goProfiles.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch goProfiles_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/goProfiles.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.26.0’
* 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 ... [16s/16s] 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 loading without being on the library search path ... 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [177s/178s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     56.282  0.269  56.827
fisherGOProfiles     14.822  0.160  15.029
plotProfiles         13.397  0.118  13.623
mergeProfilesLists   12.832  0.106  12.969
printProfiles        12.631  0.130  12.799
basicProfile         11.691  0.284  12.046
compSummary          10.753  0.133  10.940
compareGOProfiles    10.792  0.053  10.884
equivalentGOProfiles 10.295  0.053  10.396
ngenes                5.126  0.034   5.184
contractedProfile     5.045  0.029   5.087
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.048	0.004	0.052
GOTermsList	0.001	0.000	0.001
basicProfile	11.691	0.284	12.046
compSummary	10.753	0.133	10.940
compareGOProfiles	10.792	0.053	10.884
compareGeneLists	56.282	0.269	56.827
compareProfilesLists	0.002	0.000	0.002
contractedProfile	5.045	0.029	5.087
conversionFunctions	0.108	0.005	0.114
drosophila	0.005	0.001	0.005
equivSummary	0.002	0.000	0.002
equivalentGOProfiles	10.295	0.053	10.396
expandedLevel	1.850	0.045	1.898
expandedProfile	2.222	0.023	2.249
fisherGOProfiles	14.822	0.160	15.029
fitGOProfile	0.001	0.000	0.001
hugoIds	0.032	0.001	0.032
mergeProfilesLists	12.832	0.106	12.969
ngenes	5.126	0.034	5.184
omimIds	0.012	0.001	0.012
plotProfiles	13.397	0.118	13.623
printProfiles	12.631	0.130	12.799
prostateIds	0.008	0.001	0.009