[R] select repositories under linux

[Prof Brian Ripley]

On Tue, 22 Jan 2008, James W. MacDonald wrote:

> This is questionable advice for many CRAN packages, and horrible advice
> for a Bioconductor package. If there are any dependencies (and BioC
> packages often have many, and their dependencies may have
> dependencies...) you can end up in download hell, all because you have
> ignored the functionality that exists in R to handle such things.

But unfortunately the advice below is equally 'questionable'.

> As other posters have noted, you can use setRepositories(). You can also
> set this in your .Rprofile file with something like
>
> options(repos=(CRAN="http://ACloseRepository"))
>
> so you don't have to do anything interactively.

That is not what setRepositories() does: it is what chooseCRANmirror() 
does and does not help here.

> Then use install.packages(), with dependencies=TRUE if you think there
> may be dependencies (although I don't think it hurts if there are none).

The default (dependencies=NA) was chosen for good reasons ... it selects 
the dependencies you need to run the package, and not others needed to 
e.g. check it.

> For Bioconductor packages, use biocLite()
>
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("GEOquery")

which advice should be clarified by noting that is just a wrapper to the R 
facilities to handle multiple repositories, and if you are going to learn 
to use those anyway for other repositories it is not necessary to do it 
via the wrapper.

setRepositories(ind=c(1,3:6))  # Windows ind = c(1,2, 4:7)
... use install.packages for any CRAN or BioC package
*BUT* beware that some packages have incompatible versions on the two
repositories and that this will pick the largest version number for such.


> Best,
>
> Jim
>
>
> Gabor Csardi wrote:
>> Eleni, download the package (I assume you know where it is),
>> on Linux you will need the source package. Then from R type
>>
>> install.packages("<the file you downloaded>", repos=NULL)
>>
>> Gabor
>>
>> On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
>>> Hi all,
>>>
>>> I am trying to install the package "GEOquery" in unix. I have downloaded the
>>> standard version of R and this package is not contained in the default. I
>>> know that I can select repositories under windows but I don't know how to do
>>> it in unix. Does anyone have any idea on this?
>>>
>>> Thank you in advance,
>>> Eleni
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> ______________________________________________
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595