[BioC] VariantTools installation problem: dependencies not available

heyi xiao xiaoheyiyh at yahoo.com
Mon Nov 11 19:10:11 CET 2013


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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