[BioC] Anything wrong with http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13

[Steve Lianoglou]

Hi Peng,

On Wed, Jan 18, 2012 at 11:54 AM, Peng Yu <pengyu.ut at gmail.com> wrote:
> On Wed, Jan 18, 2012 at 10:41 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> Hi Peng,
>>
>> Not the optimal solution, but maybe you can download the (source)
>> packages for the chip you want?
>>
>> It looks like "Version 14" are the packages appropriate for R 2.13:
>>
>> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v14
>
>
> Thanks Steve.
>
> I just notice that it says "Bioconductor 2.9 (R-2.14)" on
> http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/nucleR.html.
> I upgrade my R installation to R-2.14.1. Now the problem is gone. I'm
> not sure it is requires that R has to be higher than some version,
> which seems to be unnecessary.

On the contrary, it is necessary ;-)

As (I think) you know, each release of bioconductor corresponds to a
particular version of R. It's possible that some API's (or whatever)
change as R matures, and bioconductor packages will track against
these.

Also, the functionality in bioconductor packages change over time ...
for example, in Bioc 2.9, Rsamtools can now read tabix files (where
that functionality wasn't available before). Perhaps nucleR depends on
some functionality in IRanges, GenomicRanges, ShortRead, or whatever
that was not available in previous versions of the package.

And lastly, it seems nucleR wasn't in the bioconductor repo before v.
2.9, so ... anyway, I guess you get the idea ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact