Loraine, Ann | 3 Aug 2012 22:39
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easyRNASeq install problem

Hello,

I'm trying to set up easyRNASeq on a cluster system (where I don't have root) and am getting this error:

> biocLite("easyRNASeq")
Using R version 2.11.1, biocinstall version 2.6.10.
Installing Bioconductor version 2.6 packages:
[1] "easyRNASeq"
Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  argument 'lib' is missing: using '/lustre/home/aloraine/R/x86_64-pc-linux-gnu-library/2.11'
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘easyRNASeq’ is not available

I found documentation that explains that this error message "package 'something' is not available' means
that some dependencies are missing, which can happen if a package is not available for a given system.

This system is Linux, and I would think that would not be a problem here.

> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
(Continue reading)

Wolfgang Huber | 4 Aug 2012 12:33
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Re: easyRNASeq install problem

Ann,

please use current version of R, 2.15.1.
Yours is two years out of date.

	Best wishes
	Wolfgang

Aug/3/12 10:39 PM, Loraine, Ann scripsit::
> Hello,
>
> I'm trying to set up easyRNASeq on a cluster system (where I don't have root) and am getting this error:
>
>> biocLite("easyRNASeq")
> Using R version 2.11.1, biocinstall version 2.6.10.
> Installing Bioconductor version 2.6 packages:
> [1] "easyRNASeq"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>    argument 'lib' is missing: using '/lustre/home/aloraine/R/x86_64-pc-linux-gnu-library/2.11'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>    package ‘easyRNASeq’ is not available
>
> I found documentation that explains that this error message "package 'something' is not available'
means that some dependencies are missing, which can happen if a package is not available for a given system.
>
> This system is Linux, and I would think that would not be a problem here.
>
(Continue reading)

Sean Davis | 4 Aug 2012 12:34
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Re: easyRNASeq install problem

On Fri, Aug 3, 2012 at 4:39 PM, Loraine, Ann <Ann.Loraine@...> wrote:

> Hello,
>
> I'm trying to set up easyRNASeq on a cluster system (where I don't have
> root) and am getting this error:
>
> > biocLite("easyRNASeq")
> Using R version 2.11.1, biocinstall version 2.6.10.
> Installing Bioconductor version 2.6 packages:
> [1] "easyRNASeq"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>   argument 'lib' is missing: using
> '/lustre/home/aloraine/R/x86_64-pc-linux-gnu-library/2.11'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ‘easyRNASeq’ is not available
>
>
Hi, Ann.

easyRNASeq is not available for R version 2.11.  You will need to upgrade
your R version to the latest version to get the easyRNASeq package.

Sean

> I found documentation that explains that this error message "package
> 'something' is not available' means that some dependencies are missing,
(Continue reading)


Gmane