[BioC] Rsamtools from biocLite using R-devel

[Kasper Daniel Hansen]

Right now, I still get Rsamtools 1.1.17 when I use biocLite, which
indicates that either the problem has not been fixed or the solution
has not propagated to the tarballs.

BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
Using R version 2.13.0 (R-devel), biocinstall version 2.8.1.
Installing Bioconductor version 2.8 packages:
[1] "Rsamtools"
Please wait...

trying URL 'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/Rsamtools_1.1.17.tar.gz'
Content type 'application/x-gzip' length 1862549 bytes (1.8 Mb)
opened URL
=======


Kasper

On Thu, Oct 28, 2010 at 10:41 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
>
> On Thu, Oct 28, 2010 at 7:06 AM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>>
>> Just a note about this: so far I have not seen any resolution.  And
>> according to the devel build logs the R-devel on lamb2 (which I assume
>> is being used for generating the source tarballs, but I could be
>> completely wrong) is from 9-30 which is almost a month old (which kind
>> of surprised me) (pelham is 1.5 months old).
>>
>
>
> Kasper,
> R and Rsamtools should play well together now on lamb2. R 2.13 has been
> updated on all build nodes in the last couple of days. The build report is
> out of date due to other issues which will be resolved today.
> Thanks
> Dan
>
>
>
>>
>> Kasper
>>
>> On Tue, Oct 26, 2010 at 4:11 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> > On 10/26/2010 12:47 PM, Kasper Daniel Hansen wrote:
>> >> When I try to use biocLite to upgrade my Rsamtools under R-devel,
>> >> biocLite reports that it tries to use the 2.8 repository (correct),
>> >> but it tries to download Rsamtools 1.1.17 whereas the version of
>> >> Rsamtools installed using R-2.12 is version 1.2.0 (later than 1.1.17)
>> >> and the version accessible from subversion is version 1.3.2.
>> >>
>> >> I suspect this has something to do with the recent problem with
>> >> R-devel and biocLite and also by the fact that Rsamtools currently
>> >> does not seem to build under any platform.
>> >>
>> >> Besides the obvious problem, I am running into problems with my
>> >> existing Rsamtools because normalizePath has been moved from utils to
>> >> base (which is commented on in NAMESPACE).  Coincidently, it seems
>> >> that the issue that makes Rsamtools 1.3.2 fail to build is also
>> >> related to the use of normalizePath that may have its arguments
>> >> changed,
>> >
>> > yes you and I are ahead of the build system -- Rsamtools wants
>> > normalizePath to be in base, but R-devel on the build system was not (it
>> > has been updated very recently) current enough for that. So you were
>> > getting the last Rsamtools that the 'devel' portion of the build system
>> > correctly built, v. 1.1.17.
>> >
>> > This is being straightened out, and should be back to normal over the
>> > next day or so. The short-term solution is to install Rsamtools from
>> > source, from an svn checkout
>> >
>> >  http://bioconductor.org/developers/source-control/
>> >
>> > Martin
>> >
>> >>
>> >> Kasper
>> >>
>> >> _______________________________________________
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>> >
>> >
>> > --
>> > Computational Biology
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>> >
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>> >
>>
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>
>