[BioC] VariantTools installation problem: dependencies not available

Martin Morgan mtmorgan at fhcrc.org
Mon Nov 11 19:32:23 CET 2013


On 11/11/2013 10:10 AM, heyi xiao wrote:
> Hi Michael,
> You mean that URL “http://bioconductor.org/packages/2.13/bioc/src/contrib/” points to the old devel versions? But it looks like the 2.13 branch, or is it the same thing? I didn’t specify anything in the installation as you see in my code, with or without type="source" gives the same problem.
> What shall I do now? Thanks!

I can't really understand what's going wrong, but I'd start by

   R --vanilla

and then

   source("http://bioconductor.org/biocLite.R")
   biocLite("BiocInstaller")

which should end up with BiocInstaller v. 1.12.0

   Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help

If there are still problems, it might be helpful to try installing XVector itself

   biocLite("XVector")

and visiting via a browser

   http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES

which should have lines like

   Package: XVector
   Version: 0.2.0

to indicate that XVector_0.2.0.tar.gz should be returned. If this file reports 
something different in the web browser, e.g., Version: 0.1.4, then my guess is 
that your institution has some kind of proxy mechanism in place, and this is 
stale -- you'd need to speak with your system administrator.

The output of

   biocinstallRepos()

might be helpful.

Martin

> Heyi
>
> --------------------------------------------
> On Mon, 11/11/13, Michael Lawrence <lawrence.michael at gene.com> wrote:
>
>   Subject: Re: [BioC] VariantTools installation problem: dependencies not available
>
>   Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
>   Date: Monday, November 11, 2013, 12:46 PM
>
>   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
>
>
>
>
>   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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