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Package 282/658HostnameOS / ArchBUILDCHECKBUILD BIN
goProfiles 1.21.0
Alex Sanchez
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/goProfiles
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: goProfiles
Version: 1.21.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings goProfiles_1.21.0.tar.gz
StartedAt: 2013-03-25 02:04:33 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:09:51 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 318.3 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.21.0’
* 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 ... [15s/15s] 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 ... [167s/172s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
compareGeneLists     47.267  0.228  49.402
fisherGOProfiles     15.517  0.040  15.781
printProfiles        13.933  0.096  14.314
basicProfile         13.757  0.204  14.033
mergeProfilesLists   13.749  0.040  14.093
plotProfiles         12.477  0.076  12.564
equivalentGOProfiles  9.349  0.056   9.733
compareGOProfiles     9.189  0.064   9.941
compSummary           8.804  0.056   9.024
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck/00check.log’
for details.

goProfiles.Rcheck/00install.out:

* 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)

goProfiles.Rcheck/goProfiles-Ex.timings:

nameusersystemelapsed
CD4ids0.0280.0080.035
GOTermsList0.0080.0000.009
basicProfile13.757 0.20414.033
compSummary8.8040.0569.024
compareGOProfiles9.1890.0649.941
compareGeneLists47.267 0.22849.402
compareProfilesLists0.0200.0120.031
contractedProfile4.2200.0364.262
conversionFunctions0.1120.0080.120
drosophila0.0080.0040.013
equivSummary0.0360.0000.034
equivalentGOProfiles9.3490.0569.733
expandedLevel4.2360.0164.281
expandedProfile1.7400.0001.743
fisherGOProfiles15.517 0.04015.781
fitGOProfile0.0080.0000.007
hugoIds0.0680.0000.068
mergeProfilesLists13.749 0.04014.093
ngenes4.2000.0404.515
omimIds0.0440.0040.049
plotProfiles12.477 0.07612.564
printProfiles13.933 0.09614.314
prostateIds0.0640.0000.063