[Bioc-devel] Problem installing packages using biocLite

[Martin Morgan]

On 05/12/2010 02:32 AM, Muino, Jose wrote:
> Hi Joern,
> 
> Thanks for your answer.
> Indeed, I was using an older version (2.8.1).
> 
> I am the author of the CSAR package, and the most common email that I
> get is from users that can not install it using BiocLite (I guess
> because they are also using an old R version). 
> 
> Perhaps, will it be possible to include the information that you need
> the last R version to run the last BiocLite version on each package
> website? Exactly, where it is said:
> 
> "To install this package, start R and enter:
>     source("http://bioconductor.org/biocLite.R")
>     biocLite("CSAR")
> "
> 
> Say something like:
> "To install this package, start R and enter:
>     source("http://bioconductor.org/biocLite.R")
>     biocLite("CSAR")
> If you have any problem with the installation, check if you have the
> last R version

Thanks Jose for the suggestion; adding additional information to the
package 'landing page' is a good idea; probably there will be changes
during this release cycle, but not immediately (packages can fail to
install for a variety of reasons).

Martin

> "
> 
> Thanks,
> Jose
> 
> Dr. Jose M Muino
> Plant Research International B.V.
> Droevendaalsesteeg 1
> P.O. Box 16, 6700 AA Wageningen, The Netherlands
> Phone: +0317-481122.
> E-mail: jose.muino at wur.nl
> http://www.pri.wur.nl 
>  
> 
>> -----Original Message-----
>> From: Joern Toedling [mailto:Joern.Toedling at curie.fr] 
>> Sent: woensdag 12 mei 2010 10:35
>> To: Muino, Jose; bioc-devel at stat.math.ethz.ch
>> Subject: Re: [Bioc-devel] Problem installing packages using biocLite
>>
>> Hi Jose,
>>
>> perhaps you are not using the newest version of R (2.11)? 
>> biocLite only gets the Bioconductor package versions that 
>> match the version of R that you are calling biocLite from. So 
>> if you use an older version of R, you will only get older 
>> versions of Bioconductor, which may not include certain packages.
>> This is also why we always ask for the output of 
>> sessionInfo() to be appended to questions asked on this list, 
>> so please do so next time.
>>
>> And btw, I think this was rather a question for the normal 
>> Bioc list than for Bioc-devel.
>>
>> Regards,
>> Joern
>>
>>
>> On Wed, 12 May 2010 09:36:42 +0200, Muino, Jose wrote
>>> Hi,
>>>
>>> I was trying to install the package CSAR from biocLite using
>>>
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("CSAR")
>>>
>>> But it doesn't work, I have a message saying that "Warning message:
>>> package 'CSAR' is not available "
>>>
>>> I also was trying to install PICS with biocLite, and I have 
>> the same 
>>> problem.
>>>
>>> Perhaps, is this a common problem for packages submitted to the new 
>>> bioconductor version?
>>>
>>> Thanks,
>>> Jose
>>>
>>
>>
> 
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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