[BioC] error in locateVariants for a GRanges object

Steve Lianoglou mailinglist.honeypot at gmail.com
Sun Mar 11 19:02:25 CET 2012

Hi Franceso,

I haven't been following this thread too closely, but:

On Sun, Mar 11, 2012 at 1:39 PM, Lescai, Francesco <f.lescai at ucl.ac.uk> wrote:
> and I checked on the website for the 2.10 release and the Mac version of the packages seems to be still 2.6.2.
> Is there any other package I can try to install manually?
> It seems now I cannot access to the developer wiki of BioC.

If you set `type="source"`, you should grab the latest version of the
package (for some reason the builds are trailing), ie:

R> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene", type="source")

That should get you the latest version ... it's downloading and
installing for me.

I'm not sure if this will fix your problems (not sure what they are).
If it doesn't, perhaps you may want to try another round of upgrading
your packages via `biocLite` using the `type="source"` trick.

If that doesn't work, I'm at a loss, if I were in your shoes, I'd
likely take "the nuclear option" and blow out all bioconductor
packages I have installed and reinstalling them to make sure
everything is feng shui, but there's no guarantee that will work for
you either, so ... do at your own risk.


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

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