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Package 270/631HostnameOS / ArchBUILDCHECKBUILD BIN
goProfiles 1.21.0
Alex Sanchez
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/goProfiles
Last Changed Rev: 70052 / Revision: 72575
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 
lamb2 Linux (openSUSE 11.4) / 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: 2013-01-16 03:10:41 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 03:13:18 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 157.0 seconds
RetCode: 0
Status:  OK 
CheckDir: goProfiles.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/goProfiles.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
compareGeneLists 12.080  0.068  12.162
fisherGOProfiles  7.288  0.016   7.311
basicProfile      6.840  0.124   7.089
printProfiles     5.184  0.032   5.224
* 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
  ‘/loc/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
CD4ids0.0280.0080.034
GOTermsList0.0160.0000.016
basicProfile6.8400.1247.089
compSummary2.5480.0522.603
compareGOProfiles2.6410.0202.662
compareGeneLists12.080 0.06812.162
compareProfilesLists0.0120.0040.018
contractedProfile1.0920.0241.116
conversionFunctions0.0600.0120.072
drosophila0.0000.0040.005
equivSummary0.0160.0000.018
equivalentGOProfiles2.4130.0202.437
expandedLevel2.3880.0282.430
expandedProfile0.4880.0040.491
fisherGOProfiles7.2880.0167.311
fitGOProfile0.0040.0040.005
hugoIds0.0160.0000.017
mergeProfilesLists4.4800.0244.508
ngenes1.2210.0081.230
omimIds0.0360.0040.043
plotProfiles4.1840.0284.214
printProfiles5.1840.0325.224
prostateIds0.0320.0000.033