[BioC] Rsamtools from biocLite using R-devel

Martin Morgan mtmorgan at fhcrc.org
Tue Oct 26 22:11:02 CEST 2010

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



> Kasper
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