Looks like some sort of cache or something is stale. It's trying to install
the old devel versions of the Bioc 2.13 packages.

Michael


On Mon, Nov 11, 2013 at 9:32 AM, heyi xiao <xiaoheyiyh@yahoo.com> wrote:

> I tried to install VariantTools under R version 3.0.1 on my Linux machine.
> It failed due to dependencies not available (error message below). Any
> suggestion or help would be appreciated.
>
>
> > biocLite("VariantTools", type="source")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.11.4), R version 3.0.1.
> Installing package(s) 'VariantTools'
> also installing the dependencies XVector, IRanges, GenomicRanges, gmapR,
> BiocParallel
>
> trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4.tar.gz
> '
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4.tar.gz
> '
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open: HTTP status was '404 Not Found'
> Warning in download.packages(pkgs, destdir = tmpd, available = available,
>  :
>   download of package XVector failed
> trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19.38.tar.gz
> '
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19.38.tar.gz
> '
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>   cannot open: HTTP status was '404 Not Found'
> Warning in download.packages(pkgs, destdir = tmpd, available = available,
>  :
>   download of package IRanges failed
> …
>
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