[BioC] VariantTools installation problem: dependencies not available

heyi xiao xiaoheyiyh at yahoo.com
Mon Nov 11 21:24:47 CET 2013


Hi Steve and Martin,
Thanks for all the suggestions. Following Martin’s suggestion, I started a new session using:
R –vanilla
Then,
source("http://bioconductor.org/biocLite.R")
biocLite("VariantTools")
Now VariantTools and dependencies are installed fine.

BTW, one question here: Is there any special advantage of using GSNAP (besides calling within R through gmapR) over BWA in reads mapping? GSNAP should be slower.
Heyi

--------------------------------------------
On Mon, 11/11/13, Martin Morgan <mtmorgan at fhcrc.org> wrote:

 Subject: Re: [BioC] VariantTools installation problem: dependencies not available

el at gene.com>
 Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
 Date: Monday, November 11, 2013, 1:32 PM

 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.
[[elided Yahoo spam]]

 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
 >
 >   …
 >
 >
 >
 >   _______________________________________________
 >
 >   Bioconductor mailing list
 >
 >   Bioconductor at r-project.org
 >
 >   https://stat.ethz.ch/mailman/listinfo/bioconductor
 >
 >   Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
 >
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 > Bioconductor mailing list
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 >


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