[BioC] VariantTools installation problem: dependencies not available

heyi xiao xiaoheyiyh at yahoo.com
Mon Nov 11 18:32:02 CET 2013


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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