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Old 05-29-2012, 01:10 PM   #1
chknbio
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Location: Baltimore

Join Date: May 2012
Posts: 14
Default 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!
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Old 05-29-2012, 01:15 PM   #2
chknbio
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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’
>
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Old 05-29-2012, 02:00 PM   #3
chknbio
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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!
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