Package: gene2pathway

Version: 2.2.0

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch gene2pathway_2.2.0.tar.gz

StartedAt: 2011-09-07 13:40:26 -0700 (Wed, 07 Sep 2011)

EndedAt: 2011-09-07 13:43:26 -0700 (Wed, 07 Sep 2011)

EllapsedTime: 180.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: gene2pathway.Rcheck

Warnings: NA

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck'
* using R version 2.13.1 (2011-07-08)
* 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 '2.2.0'
* 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 ... 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

* 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 ...
** testing if installed package can be loaded

* DONE (gene2pathway)

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