did you check how much space is left in /tmp and /fs on your computer?

it is trying to extract the per-chromosome data files and running out of
space, or so it seems.


On Mon, Feb 13, 2012 at 12:00 PM, Mohamed Radhouane Aniba <aradwen@gmail.com
> 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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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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