[BioC] VariantTools installation problem: dependencies not available
heyi xiao
xiaoheyiyh at yahoo.com
Tue Nov 12 18:36:47 CET 2013
Thanks Michael, for all the info!
--------------------------------------------
On Tue, 11/12/13, Michael Lawrence <lawrence.michael at gene.com> wrote:
Subject: Re: [BioC] VariantTools installation problem: dependencies not available
Cc: "Michael Lawrence" <lawrence.michael at gene.com>, "Martin Morgan" <mtmorgan at fhcrc.org>, "bioconductor at r-project.org" <bioconductor at r-project.org>
Date: Tuesday, November 12, 2013, 12:24 AM
I would recommend to use
GSNAP for RNA-seq data. For Exome/WGS, it makes little
difference. GSNAP has recently undergone an optimization
spree that improves performance by an order of magnitude,
but those changes are not yet reflected in the version
embedded within gmapR. If you do use GSNAP with paired end
data, we recommend setting clip_overlaps to TRUE, so that
overlapping ends are hard clipped and variants in the
overlap are not double counted by bam_tally.
On Mon, Nov 11, 2013
wrote:
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
"Michael Lawrence" <lawrence.michael 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
>
> …
>
>
>
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