On Thu, Oct 28, 2010 at 7:06 AM, Kasper Daniel Hansen <
kasperdanielhansen@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out of date due to other issues which will be resolved today.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@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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> >
> > Location: M1-B861
> > Telephone: 206 667-2793
> >
>
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