[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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