[Bioc-sig-seq] Rsamtools problem

[Kasper Daniel Hansen]

Could this be related to the issues regarding pulling from svn vs.
using biocLite that I asked about in a different context some weeks
ago.  The tarball pulled from biocLite is only updated if the version
number is bumped.

Kasper

On Wed, Feb 17, 2010 at 2:47 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Wed, Feb 17, 2010 at 2:07 PM, Droit Arnaud <Arnaud.Droit at ircm.qc.ca> wrote:
>> Hi Patrick,
>>
>> Thanks for your reply.
>> I have install the latest Biostrings (2.15.21), rtracklayer (1.7.4), ShortRead (1.5.15), IRanges (1.5.46), BSgenome (1.15.4) and Biostrings (2.15.21) packages and I sill received the same error message when I tried to install Rsamtools.
>> I have also tried it with the packages directly from the SVN account (rtracklayer 1.7.9,....) but there is still too many error that appeared.
>>
>> If you have any other ideas (platform, version, 64 bit ...), please let me know?
>
> That's weird ... just this morning I pulled recent versions of
> IRanges, Biostrings, BSgenome, ShortRead, Rsamtools, and rtracklayer
> from SVN. They are at revision 44736.
>
> I did an `R CMD INSTALL --clean` of all of those packages and they
> seem to install fine (I haven't really used them today, though).
>
> For what it's worth, I do get that ''.__C__file', '.__C__connection''
> errors from the GenomicFeatures package. I don't actually use that
> package, though, and I didn't see it mentioned in your email, but I
> thought I'd include that so you don't feel like you're going crazy, or
> something :-)
>
> Also, I'm on OS X.6.2 and using R version 2.11.0 Under development
> (unstable) (2010-02-15 r51142).
>
> -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
>
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