[BioC] VariantTools installation problem: dependencies not available

Steve Lianoglou lianoglou.steve at gene.com
Mon Nov 11 19:30:57 CET 2013


Hi,

Can you please provide the output of sessionInfo()?

Also, you are running R-3.0.1 when bioc2.13 is "tied' to R-3.0.2.

Instead of diagnosing your current setup, I suspect if you "simply"
upgrade to R-3.0.2, then:

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

Will probably work. Could you try to upgrade R first then reinstall
your bioconductor universe via biocLite?

HTH,
-steve


On Mon, Nov 11, 2013 at 10:10 AM, heyi xiao <xiaoheyiyh at yahoo.com> 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!
> 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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-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech



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