problems installing package goseq

PFS · 12-10-2010, 08:27 AM

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!

MDY · 12-13-2010, 02:25 PM

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

chknbio · 05-29-2012, 01:18 PM

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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12-10-2010, 08:27 AM	#1
PFS Member Location: USA Join Date: Mar 2010 Posts: 55	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!

12-13-2010, 02:25 PM	#2
MDY Junior Member Location: Melbourne Join Date: Jun 2010 Posts: 7	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

05-29-2012, 01:18 PM	#3
chknbio Member Location: Baltimore Join Date: May 2012 Posts: 14	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.