[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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