* using log directory 'D:/biocbld/auto-build-work-area/bioc-1.7/buildSandbox/checkOutput/GeneR.Rcheck'
* using R version 2.2.0, 2005-10-10 
* checking for file 'GeneR/DESCRIPTION' ... OK
* this is package 'GeneR' version '1.4.0'
* checking if this is a source package ... OK
* checking whether package 'GeneR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* creating GeneR-Ex.R ... OK
* checking examples ... ERROR
Running examples in GeneR-Ex.R failed.
The error most likely occurred in:

> ### * readseq
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ReadSeq
> ### Title: Read a sequence from a Fasta, Embl or GeneBank file.
> ### Aliases: readSeq readFasta readGbk readEmbl strReadFasta strReadGbk
> ###   strReadEmbl
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Get a sequence from Ncbi
> seqNcbi("BY608190",file="BY608190.gbk",type="G")
trying URL 'http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&qty=1&c_start=1&send=Send&sendto=t&from=begin&to=end&extrafeatpresent=1&ef_MGC=16&dopt=gbwithparts&list_uids=BY608190'
Content type 'text/plain' length unknown
opened URL
downloaded 6013 bytes

[1] 1
> 
> ## Read Gbk file to buffer 0
> readGbk("BY608190.gbk")
[1] 0
> 
> ## Or to a character string
> strReadGbk("BY608190.gbk")
[1] "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
> 
> ## Write to Fasta file
> writeFasta(file='toto.fa')
[1] 0
> 
> ## Make an index to this file
> indexFasta('toto.fa')
[1] 1
> readFasta (file="toto.fa",path=".",seqno=0,from=1,to=159)
[1] "endseq plus grand que sizeSeq"
[1] -1
> 
> ## Show seqence on buffer 0
> getSeq()
[1] "Empty buffer"
[1] "Nothing in buffer"
Le buffer 0 est vide
Warning in getSeq() : error in the transformation of the limits
NULL
> 
> ## Make a Fake file
> writeEmblLine(file='toto.embl',code='AC',header='tmp',append=FALSE)
[1] 1
> writeEmblSeq(file='toto.embl')
[1] "Empty buffer"
[1] "Nothing in buffer"
Le buffer 0 est vide
Warning in getSeq(seqno) : error in the transformation of the limits
Error in comp[1, "A"] : incorrect number of dimensions
Execution halted