[BioC] BSgenome installation error

[Hervé Pagès]

Hi Mohamed,

Any reason why you are using a 4 year old version of R / Bioconductor?
I can't tell what's causing the tar extraction problem you are facing,
and maybe you'll still have this problem with the latest version of
R / Bioconductor (R 2.14, BioC 2.9), but, at least, by updating your
installation, you'll be running the same version as everybody else on
this list, which is also the only version we support.

Cheers,
H.


On 02/13/2012 12:00 PM, Mohamed Radhouane Aniba wrote:
> Hello everyone
>
> I am trying to install the human genome but I am facing an unusual problem
> here is the error message
>
>> biocLite("BSgenome.Hsapiens.UCSC.hg18")
> Running biocinstall version 2.2.11 with R version 2.7.2
> Your version of R requires version 2.2 of BioConductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>    argument 'lib' is missing: using '/fs/sh-code/Software/RLIBS/'
> trying URL 'http://bioconductor.org/packages/2.2/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz'
> Content type 'application/x-gzip' length 874579720 bytes (834.1 Mb)
> opened URL
> ========================================
> downloaded 834.1 Mb
>
> tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes
> tar: Skipping to next header
> tar: Archive contains obsolescent base-64 headers
> tar: Error exit delayed from previous errors
> ERROR: cannot extract package from '/tmp/RtmprYAQfG/downloaded_packages/BSgenome.Hsapiens.UCSC.hg18_1.3.7.tar.gz'
>
> The downloaded packages are in
> 	/tmp/RtmprYAQfG/downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>    installation of package 'BSgenome.Hsapiens.UCSC.hg18' had non-zero exit status
>
>
> Is this "tar: BSgenome.Hsapiens.UCSC.hg18/inst/extdata/chr19.rda: Wrote only 6656 of 10240 bytes" related to a quota or an available space ?
> this is the only reason I can imagine.
>
> Thanks for your help
>
> Rad
>
>
>
>
>
>
> Radhouane Aniba
> Bioinformatics Postdoctoral Research Scientist
> Institute for Advanced Computer Studies
> Center for Bioinformatics and Computational Biology (CBCB)
> University of Maryland, College Park
> MD 20742
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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