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Old 12-10-2010, 08:27 AM   #1
PFS
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Location: USA

Join Date: Mar 2010
Posts: 55
Default problems installing package goseq

I have been having trouble installing the package goseq. I followed the instructions, but got the following message:

> source("http://bioconductor.org/biocLite.R")
> biocLite("goseq",dependencies=TRUE)
Using R version 2.10.1, biocinstall version 2.5.11.
Installing Bioconductor version 2.5 packages:
[1] "goseq"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘goseq’ is not available

Any suggestions? I am not particularly familiar with the language R, so I don't know how to dig deeper to solve the issue.

Thanks!
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Old 12-13-2010, 02:25 PM   #2
MDY
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Location: Melbourne

Join Date: Jun 2010
Posts: 7
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Hi PFS,

goseq requires a newer version of R than the one you are using. If you update to the latest version and try again everything should work.

Cheers,

Matt
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Old 05-29-2012, 01:18 PM   #3
chknbio
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Location: Baltimore

Join Date: May 2012
Posts: 14
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I am also having a problem installing 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’
>

Could you please help me to find a resolution.

Thanks.
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