Package: annotationTools

Version: 1.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotationTools_1.34.0.tar.gz

StartedAt: 2013-05-01 02:19:48 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:20:36 -0700 (Wed, 01 May 2013)

EllapsedTime: 48.9 seconds

RetCode: 0

Status:  OK

CheckDir: annotationTools.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/annotationTools.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotationTools/DESCRIPTION' ... OK
* this is package 'annotationTools' version '1.34.0'
* 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 'annotationTools' can be installed ... [4s/4s] 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... NOTE
prepare_Rd: compactList.Rd:22: Dropping empty section \references
prepare_Rd: getANNOTATION.Rd:31: Dropping empty section \references
prepare_Rd: getGENEID.Rd:32: Dropping empty section \references
prepare_Rd: getGENEONTOLOGY.Rd:35: Dropping empty section \references
prepare_Rd: getGENESYMBOL.Rd:32: Dropping empty section \references
prepare_Rd: getGENETITLE.Rd:32: Dropping empty section \references
prepare_Rd: getHOMOLOG.Rd:40: Dropping empty section \references
prepare_Rd: getMULTIANNOTATION.Rd:29: Dropping empty section \references
prepare_Rd: getOrthologousProbesets.Rd:28: Dropping empty section \references
prepare_Rd: getPROBESET.Rd:32: Dropping empty section \references
prepare_Rd: listToCharacterVector.Rd:20: Dropping empty section \references
prepare_Rd: ps2ps.Rd:27: Dropping empty section \references
* 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' ... OK
* checking examples ... [2s/3s] OK
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/annotationTools.Rcheck/00check.log'
for details.

* installing *source* package 'annotationTools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package 'annotationTools'
* DONE (annotationTools)

name	user	system	elapsed
compactList	0.017	0.002	0.020
getANNOTATION	0.019	0.001	0.020
getGENEID	0.042	0.005	0.067
getGENEONTOLOGY	0.044	0.005	0.051
getGENESYMBOL	0.103	0.005	0.109
getGENETITLE	0.040	0.003	0.044
getHOMOLOG	0.039	0.005	0.045
getMULTIANNOTATION	0.015	0.003	0.018
getOrthologousProbesets	0.086	0.006	0.093
getPROBESET	0.044	0.003	0.048
listToCharacterVector	0.012	0.001	0.014
ps2ps	0.019	0.001	0.021