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Package 175/479HostnameOS / ArchBUILDCHECKBUILD BIN
gene2pathway 2.3.0
Holger Froehlich
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gene2pathway
Last Changed Rev: 54802 / Revision: 56603
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  ERROR 
pitt Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: gene2pathway
Version: 2.3.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch gene2pathway_2.3.0.tar.gz
StartedAt: 2011-07-07 01:50:34 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 01:53:39 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 185.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: gene2pathway.Rcheck
Warnings: NA

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/gene2pathway.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gene2pathway/DESCRIPTION' ... OK
* this is package 'gene2pathway' version '2.3.0'
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: doMC
* checking if this is a source package ... OK
* checking whether package 'gene2pathway' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
* checking package directory ... OK
* checking for portable file names ... 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 ... NOTE
gene2pathway: no visible global function definition for 'registerDoMC'
gene2pathway: no visible global function definition for '%dopar%'
gene2pathway: no visible global function definition for 'foreach'
gene2pathway: no visible binding for global variable 'g'
gene2pathway: no visible binding for global variable 'p'
gene2pathway.signaltrans: no visible global function definition for
  'registerDoMC'
gene2pathway.signaltrans: no visible global function definition for
  '%dopar%'
gene2pathway.signaltrans: no visible global function definition for
  'foreach'
gene2pathway.signaltrans: no visible binding for global variable 'p'
getKEGGHierarchy: no visible binding for global variable 'keggOrthDF'
predict.gene2pathway : testallBag: no visible global function
  definition for '%dopar%'
predict.gene2pathway : testallBag: no visible global function
  definition for 'foreach'
predict.gene2pathway : testallBag: no visible binding for global
  variable 'm'
predict.gene2pathway: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  '%dopar%'
test.overrepresentation: no visible global function definition for
  'foreach'
test.overrepresentation: no visible binding for global variable 'p'
trainallBag: no visible global function definition for 'registerDoMC'
trainallBag: no visible global function definition for '%dopar%'
trainallBag: no visible global function definition for 'foreach'
* 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 ...Warning: running command '"E:/biocbld/bbs-2.9-bioc/R/bin/i386/Rterm.exe"  --vanilla --slave -f E:\biocbld\bbs-2.9-bioc\tmpdir\RtmpOyGvC8\Rin3d9d528c' had status 128
 OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'gene2pathway-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ORF2Entrez
> ### Title: Conversion locus tag -> Entrez ID and Entrez ID -> locus tag
> ###   according to KEGG
> ### Aliases: ORF2Entrez Entrez2ORF
> ### Keywords: file
> 
> ### ** Examples
> 
> 	entrez=ORF2Entrez("Dmel_CG4942", organism="dme")
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : 
  Server denied you to change to the given directory
Calls: ORF2Entrez -> <Anonymous> -> <Anonymous> -> curlPerform -> .Call
Execution halted

gene2pathway.Rcheck/00install.out:

* installing *source* package 'gene2pathway' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: DBI

Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'gene2pathway.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (gene2pathway)

gene2pathway.Rcheck/gene2pathway-Ex.timings:

nameusersystemelapsed