Package: annotationTools

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch annotationTools_1.23.0.tar.gz

StartedAt: 2011-03-17 15:31:39 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:32:04 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 24.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: annotationTools.Rcheck

Warnings: NA

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/annotationTools.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'annotationTools/DESCRIPTION' ... OK
* this is package 'annotationTools' version '1.23.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'annotationTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
  homologene_part.data
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'annotationTools-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGENEID
> ### Title: Find gene IDs
> ### Aliases: getGENEID
> ### Keywords: manip
> 
> ### ** Examples
> 
> ##example Affymetrix annotation file and its location
> annotationFile<-'HG-U133_Plus_2_annot_part.csv'
> dataDirectory<-system.file('data',package='annotationTools')
> 
> ##load annotation file
> annotation<-read.csv(paste(dataDirectory,annotationFile,sep='/'),colClasses='character',comment.char='#')
Warning in file(file, "rt") :
  cannot open file '/Users/biocbuild/bbs-2.8-bioc/meat/annotationTools.Rcheck/annotationTools/data/HG-U133_Plus_2_annot_part.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted

* installing *source* package 'annotationTools' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (annotationTools)

name	user	system	elapsed
compactList	0.001	0.000	0.001
getANNOTATION	0.003	0.001	0.003