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 out of date due to other issues which will be resolved today.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 >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at stat.math.ethz.ch >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > -- >> > Computational Biology >> > Fred Hutchinson Cancer Research Center >> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> > >> > Location: M1-B861 >> > Telephone: 206 667-2793 >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >