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  • installing goseq

    I am trying to install goseq in R, but receiving installation errors. It looks like other packages are missing when I try to install those other packages I get install errors too, which also suggest that packages are missing. How can I install R along with its necessary packages?

    Thanks!

  • #2
    This is the message that I receive when trying to run goseq:


    Warning messages:
    1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘XML’ had non-zero exit status
    2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘RCurl’ had non-zero exit status
    3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘biomaRt’ had non-zero exit status
    4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘rtracklayer’ had non-zero exit status
    5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘GenomicFeatures’ had non-zero exit status
    6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘geneLenDataBase’ had non-zero exit status
    7: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
    installation of package ‘goseq’ had non-zero exit status
    8: installed directory not writable, cannot update packages 'foreign', 'MASS',
    'mgcv', 'nlme', 'survival'
    > library(goseq)
    Error in library(goseq) : there is no package called ‘goseq’
    >

    Comment


    • #3
      It looks like I have everything installed except XML which is preventing other packages from installing. But when I look at linux system, XML is installed. How can I get it to work in R so that I can install other goseq packages.

      Thanks!

      Comment

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