[BioC] Rsamtools from biocLite using R-devel

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Oct 28 16:06:45 CEST 2010

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).


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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