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Package 27/444HostnameOS / ArchBUILDCHECKBUILD BIN
annotationTools 1.23.0
Alexandre Kuhn
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotationTools
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ ERROR ] OK 

Summary

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

Command output

* 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

annotationTools.Rcheck/00install.out:

* 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)

annotationTools.Rcheck/annotationTools-Ex.timings:

nameusersystemelapsed
compactList0.0010.0000.001
getANNOTATION0.0030.0010.003