[BioC] BSgenome package - add the bos taurus genome

[Herve Pages]

Hi Joao,

Please don't email me privately for those matters. Use the mailing list
where other people might be able to help you. Also other people that
have the same problem (today or in 2 years -- the mailing list is
archived) could benefit from your experience.

João Fadista wrote:
> Hi Herve,
> 
> I downloaded the package as you told me but it gave an error:
> 
> 
> 'tar' is not recognized as an internal or external command,
> operable program or batch file.
> Error: cannot untar the package
> 
> The downloaded packages are in
>         C:\Documents and Settings\jofa\Local Settings\Temp\RtmpNdyPKI\downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>   installation of package 'BSgenome.Btaurus.UCSC.bosTau3' had non-zero exit status


You need to provide your sessionInfo() + the exact commands that produced
this error. Without this information, there is no way anybody can help you.

It looks like you tried to install a source packages on a Windows machine
that doesn't have the required tools for doing this but it's hard to know
with so little information provided.

The important part of the instructions I gave you in my previous email
was: "... if your Windows box is configured to install from source ..."
Getting your Windows box properly configured to install from source is an
_absolute requirement_ if you want to use BioC devel.
This requires that you first install R devel from source (+ all the R tools).
See section 3 of the "R Installation and Administration" for how to do this.
Otherwise, just wait the next BioC release (end of April). Also it could be
that a Windows version of BSgenome.Btaurus.UCSC.bosTau3 is made available
in BioC devel before the release but there is no precise plan for this.

Cheers,
H.


> 
> 
> Is there something I did wrong?
> 
> Best regards,
> João Fadista
> 
> 
> 
>  
> 
> -----Original Message-----
> From: Herve Pages [mailto:hpages at fhcrc.org] 
> Sent: Saturday, March 15, 2008 2:12 AM
> To: João Fadista
> Cc: bioc
> Subject: Re: [BioC] BSgenome package - add the bos taurus genome
> 
> Hi João,
> 
> Sorry I forgot to mention that the package is only available as a source package. The Windows and Mac OS X binaries will come later.
> In the mean time, if your Windows box is configured to install from source, you can do:
> 
>   > options(pkgType="source")
>   > library(BSgenome)
>   > available.genomes()   # now you should see it!
>   > source("http://bioconductor.org/biocLite.R")
>   > biocLite("BSgenome.Btaurus.UCSC.bosTau3")
> 
> Cheers,
> H.
> 
> 
> João Fadista wrote:
>> Dear Herve,
>>
>> I Installed the R devel and the BioC devel (I suppose) but I was not able to get the package:
>>
>>> library(BSgenome)
>>> available.genomes()
>>  [1] "BSgenome.Amellifera.UCSC.apiMel2"    
>>  [2] "BSgenome.Athaliana.TAIR.01222004"    
>>  [3] "BSgenome.Celegans.UCSC.ce2"          
>>  [4] "BSgenome.Dmelanogaster.BDGP.Release5"
>>  [5] "BSgenome.Dmelanogaster.FlyBase.r51"  
>>  [6] "BSgenome.Dmelanogaster.UCSC.dm2"     
>>  [7] "BSgenome.Ggallus.UCSC.galGal3"       
>>  [8] "BSgenome.Hsapiens.UCSC.hg16"         
>>  [9] "BSgenome.Hsapiens.UCSC.hg17"         
>> [10] "BSgenome.Hsapiens.UCSC.hg18"         
>> [11] "BSgenome.Mmusculus.UCSC.mm6"         
>> [12] "BSgenome.Mmusculus.UCSC.mm7"         
>> [13] "BSgenome.Mmusculus.UCSC.mm8"         
>> [14] "BSgenome.Mmusculus.UCSC.mm9"         
>> [15] "BSgenome.Scerevisiae.UCSC.sacCer1"   
>>
>>> source("http://bioconductor.org/biocLite.R")
>> Warning messages:
>> 1: In safeSource() : Redefining 'biocinstall'
>> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
>> 3: In safeSource() : Redefining 'biocinstallRepos'
>>
>>> biocLite("BSgenome.Btaurus.UCSC.bosTau3")
>> Running biocinstall version 2.2.2 with R version 2.7.0 (under 
>> development) Your version of R requires version 2.2 of Bioconductor.
>> Warning message:
>> package 'BSgenome.Btaurus.UCSC.bosTau3' is not available
>>
>>> sessionInfo()
>> R version 2.7.0 Under development (unstable) (2008-03-11 r44737)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
>> States.1252;LC_MONETARY=English_United 
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods   base     
>>
>> other attached packages:
>> [1] BSgenome_1.7.4    Biostrings_2.7.32 Biobase_1.99.2
>>
>>
>>
>> Did I make something wrong?
>>
>>
>> Best regards,
>> João
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Herve Pages [mailto:hpages at fhcrc.org]
>> Sent: Wednesday, March 12, 2008 4:21 AM
>> To: João Fadista
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] BSgenome package - add the bos taurus genome
>>
>> Hi João,
>>
>> João Fadista wrote:
>>> Yes, it´s that version. Thanks a lot. When you add the package please let me know.
>> I've just added BSgenome.Btaurus.UCSC.bosTau3 to our public repository (for BioC devel only). From R 2.7.0:
>>
>>   > library(BSgenome)
>>   > available.genomes()
>>    [1] "BSgenome.Amellifera.UCSC.apiMel2"
>>    [2] "BSgenome.Athaliana.TAIR.01222004"
>>    [3] "BSgenome.Btaurus.UCSC.bosTau3"
>>    [4] "BSgenome.Celegans.UCSC.ce2"
>>    [5] "BSgenome.Dmelanogaster.BDGP.Release5"
>>    [6] "BSgenome.Dmelanogaster.FlyBase.r51"
>>    [7] "BSgenome.Dmelanogaster.UCSC.dm2"
>>    [8] "BSgenome.Ggallus.UCSC.galGal3"
>>    [9] "BSgenome.Hsapiens.UCSC.hg16"
>>   [10] "BSgenome.Hsapiens.UCSC.hg17"
>>   [11] "BSgenome.Hsapiens.UCSC.hg18"
>>   [12] "BSgenome.Mmusculus.UCSC.mm6"
>>   [13] "BSgenome.Mmusculus.UCSC.mm7"
>>   [14] "BSgenome.Mmusculus.UCSC.mm8"
>>   [15] "BSgenome.Mmusculus.UCSC.mm9"
>>   [16] "BSgenome.Scerevisiae.UCSC.sacCer1"
>>
>> Install as usual with biocLite():
>>
>>   > source("http://bioconductor.org/biocLite.R")
>>   > biocLite("BSgenome.Btaurus.UCSC.bosTau3")
>>
>> It's big (736.7 Mb) so depending on your connection it might take a while.
>> Let me know in case of problems.
>>
>> Cheers,
>> H.
>