[BioC] Biostrings and A. thaliana genome sequence

[Herve Pages]

Hi René,

Rene Dreos (JIC) wrote:
> Herve, thanks a lot for your reply, but unfortunately R is installed on a machine for which I am not the root and the only user... so I can not easily upload R version without the approval of administrator and other users.
> 
> Is it possible for me to build the Arabidopsis genome package by myself and use it with the older R and Biostrings versions?

Unfortunately this is not simple because of the numerous things that have changed
in Biostrings/BSgenome since BioC 2.1 and the latest BSgenome packages in BioC 2.2
rely on these changes in order to work properly.

Hopefully you manage to download and compile your own instance of R-2.7.0
as Joern suggested. This is very easy to do on Linux and, in case you are stuck,
there is a lot of useful information and resources available around on this topic
(like the R-help mailing list and the "R Installation and Administration" manual
on CRAN).

Cheers,
H.

> 
> Cheers
> René
> 
> 
> -----Original Message-----
> From: Herve Pages [mailto:hpages at fhcrc.org] 
> Sent: 14 April 2008 20:27
> To: Rene Dreos (JIC)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Biostrings and A. thaliana genome sequence
> 
> Hi René,
> 
> Rene Dreos (JIC) wrote:
>> Hello list,
>>
>>  
>>
>> I would like to use Biostrings to work with A. thaliana genome sequence. But, when I tried to extract the sequence from BSgenome.Athaliana.TAIR.01222004 library I've got the following errors. Does anyone know why this happen and how I can solve it?
>>
>>  
>>
>>> library("Biostrings", lib.loc="/common/users/dreosr/unix/software/lib")
>>> library("BSgenome", lib.loc="/common/users/dreosr/unix/software/lib")
>>> library("BSgenome.Athaliana.TAIR.01222004", lib.loc="/common/users/dreosr/unix/software/lib")
>>> Athaliana$chr1
>> Error in readChar(con, 5) : cannot open the connection
>>
>> In addition: Warning message:
>>
>> In readChar(con, 5) :
>>
>>   cannot open compressed file '', probable reason 'No such file or directory'
>>
>>> Athaliana[[chr1]]
>> Error in readChar(con, 5) : cannot open the connection
>>
>> In addition: Warning message:
>>
>> In readChar(con, 5) :
>>
>>   cannot open compressed file '', probable reason 'No such file or directory'
>>
>>  
>>
>>> sessionInfo()
>> R version 2.6.2 (2008-02-08) 
>>
>> x86_64-redhat-linux-gnu 
>>
>>  
>>
>> locale:
>>
>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>>
>>  
>>
>> attached base packages:
>>
>>  [1] grid      splines   tools     stats     graphics  grDevices utils    
>>
>>  [8] datasets  methods   base     
>>
>>  
>>
>> other attached packages:
>>
>>  [1] BSgenome.Athaliana.TAIR.01222004_1.3.1
>>
>>  [2] BSgenome_1.6.2                        
>>
>>  [3] Biostrings_2.6.6                      
>>
>>  [4] WiggeNorm_1.0                         
>>
>>  [5] quantsmooth_1.4.0                     
>>
>>  [6] quantreg_4.17                         
>>
>>  [7] SparseM_0.75                          
>>
>>  [8] lodplot_1.1                           
>>
>>  [9] gcrma_2.10.0                          
>>
>> [10] matchprobes_1.10.0                    
>>
>> [11] affxparser_1.10.2                     
>>
>> [12] affy_1.16.0                           
>>
>> [13] preprocessCore_1.0.0                  
>>
>> [14] affyio_1.6.1                          
>>
>> [15] Biobase_1.16.3
>>
>>  
> 
> You are using R 2.6.2 + BioC 2.1 (current release) but BSgenome.Athaliana.TAIR.01222004 1.3.1
> belongs to BioC 2.2 so unless you know exactly what you are doing, this is not a recommended
> situation.
> Anyway, because of some recent changes in Biostrings/BSgenome, BSgenome.Athaliana.TAIR.01222004
> 1.3.1 was broken even for R-2.7.0 + BioC 2.2 users. I've fixed it and the new version of the
> package (1.3.3) will be available thru biocLite() in about 30 minutes. Note that you need
> R-2.7.0 + the latest versions of Biostrings/BSgenome in order to use any of the latest versions
> of the BSgenome.* packages (1.3.3, the 1.3.1 versions are broken and will be fixed ASAP).
> 
> Cheers,
> H.