[Bioc-sig-seq] Rsamtools problem

[Hervé Pagès]

Hi Arnaud, Kasper,

Yes it's probably a version bump related issue, sorry. After the latest
changes I did in Biostrings/Rsamtools (in order to put them in sync), I
did bump Rsamtools' version but I forgot to bump Biostrings' version.
It's done now and Biostrings 2.15.22 will be available thru biocLite()
at midnight tonight (Seattle time). Also you might want to make sure
you have the latest version of BSgenome (thru biocLite()) before you
pull out and reinstall the latest version of Rsamtools from svn.

We are planning to add Rsamtools to the devel builds in the next few
weeks (maybe 2-3 weeks) so, in theory, there won't be any need to pull
out stuff from svn anymore.

Cheers,
H.


Kasper Daniel Hansen wrote:
> 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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>>
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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