Package: REDseq

Version: 0.99.3

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --force-multiarch --no-vignettes --timings REDseq_0.99.3.tar.gz

StartedAt: 2011-07-01 02:13:22 -0700 (Fri, 01 Jul 2011)

EndedAt: 2011-07-01 02:17:12 -0700 (Fri, 01 Jul 2011)

EllapsedTime: 230.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: REDseq.Rcheck

Warnings: NA

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/REDseq.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'REDseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'REDseq' version '0.99.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'REDseq' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'REDseq-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildREmap
> ### Title: Build a genome wide cut site map for a Restriction Enzyme (RE)
> ### Aliases: buildREmap
> ### Keywords: misc
> 
> ### ** Examples
> 
> 	library(ChIPpeakAnno)
> 	REpatternFilePath = system.file("extdata", "examplePattern.fa", package="REDseq")
> 	library(BSgenome.Celegans.UCSC.ce2)
> 	buildREmap( REpatternFilePath, BSgenomeName=Celegans, outfile="example.REmap")
Error in buildREmap(REpatternFilePath, BSgenomeName = Celegans, outfile = "example.REmap") : 
  outfile specified as example.REmap already exists! Please rename the outfile!
Execution halted

* installing *source* package 'REDseq' ...
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'REDseq.Rnw' 
** testing if installed package can be loaded
Warning messages:
1: replacing previous import 'space' when loading 'IRanges' 
2: replacing previous import 'getSeq' when loading 'BSgenome' 

* DONE (REDseq)

name	user	system	elapsed
REDseq-package	0	0	0
assignSeq2REsite	0.92	0.02	0.93
binom.test.REDseq	0.02	0.00	0.02