Package: BSgenome

Version: 1.3.7

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check BSgenome_1.3.7.tar.gz

RetCode: 1

Time: 46.5 seconds

Status: ERROR

CheckDir: BSgenome.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/BSgenome.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.3.7'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BSgenome' can be installed ... 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... 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 ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating BSgenome-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'BSgenome-Ex.R' failed.
The error most likely occurred in:

> ### * BSgenome-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: BSgenome-class
> ### Title: The BSgenome class
> ### Aliases: class:BSgenome BSgenome-class BSgenome seqnames
> ###   seqnames,BSgenome-method mseqnames mseqnames,BSgenome-method
> ###   names,BSgenome-method initialize,BSgenome-method show,BSgenome-method
> ###   length,BSgenome-method [[,BSgenome-method [[<-,BSgenome-method
> ###   $,BSgenome-method unload unload,BSgenome-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>   library(BSgenome.Celegans.UCSC.ce2)
>   length(Celegans)
[1] 11
>   Celegans
Caenorhabditis elegans genome:

  Single sequences (DNAString objects, see '?seqnames'):
    chrI          chrII         chrIII        chrIV         chrV        
    chrM          chrX          upstream1000  upstream2000  upstream5000

  Multiple sequences (BStringViews objects, see '?mseqnames'):
    BSgenome.Celegans.UCSC.ce2  

  (use the '$' or '[[' operator to access a given sequence)
> 
>   ## Access chromosome V (BStringViews object) with
>   Celegans[["chrV"]]
Warning: cannot open compressed file ''
Error in readChar(con, 5) : cannot open the connection
Execution halted

* Installing *source* package 'BSgenome' ...
** R
** save image
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: Biostrings
Creating a new generic function for "names" in "BSgenome"
** help
 >>> Building/Updating help pages for package 'BSgenome'
     Formats: text html latex example 
  BSgenome-class                    text    html    latex   example
  available.genomes                 text    html    latex   example
  buildDataFiles                    text    html    latex   example
  getSeq                            text    html    latex   example
** building package indices ...
* DONE (BSgenome)