Hi Paul

The issue was (on my end at least) fixed this afternoon (EST time).  I now
get the new version of Rsamtools (and a lot of other core packages) when I
use biocLite under R-devel.  But earlier today the source tarball was
broken.

I have no idea why a svn checkout would not work.  As far as I know, that
has been working for some days.  Did you remember to rebuild the source
tarball before installing, like
  R-devel CMD build Rsamtools
  R-devel CMD INSTALL Rsamtools_1.3.3.tar.gz
Note that your svn checkout version should certainly be 1.3.3.

I would recommend
R> source("http://www.bioconductor.org/biocLite.R")
R> update.packages(repos = biocinstallrepos())
in a fresh R-devel session.

Double-check that the version of Rsamtools it is downloading is something
like 1.3.3 (and not 1.1.17).

Given the problems there has been the last couple of days it might be nice
if you report back whether or not you got this fixed.

Kasper


On Mon, Nov 1, 2010 at 9:43 PM, Paul Leo <p.leo@uq.edu.au> wrote:

>  It appears this is a known issue, was the fix time just optimistic?
>
>
> I did a svn checkout today abs R and Rsamtools do not play nice.
> ShortRead will not load without Rsamtools either....
>
>
>
>
>
>
>
>
> ** preparing package for lazy loading
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>     Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
>     pmin.int, rbind, rep.int
> , table
>
> Error : object ‘normalizePath’ is not exported by 'namespace:utils'
> ERROR: lazy loading failed for package ‘Rsamtools’
> * removing ‘/home/pleo/R_latest/library/Rsamtools’
>
> The downloaded packages are in
> 	‘/tmp/RtmpuHAod7/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages() :
>   installation of package 'Rsamtools' had non-zero exit status
>
> > sessionInfo()
> R version 2.13.0 Under development (unstable) (2010-11-01 r53513)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.13.0 tools_2.13.0
>
>
>
>   -----Original Message-----
> *From*: Dan Tenenbaum <dtenenba@fhcrc.org<Dan%20Tenenbaum%20%3cdtenenba@fhcrc.org%3e>
> >
> *To*: Kasper Daniel Hansen <kasperdanielhansen@gmail.com<Kasper%20Daniel%20Hansen%20%3ckasperdanielhansen@gmail.com%3e>
> >
> *Cc*: BioC <bioconductor@stat.math.ethz.ch<BioC%20%3cbioconductor@stat.math.ethz.ch%3e>
> >
> *Subject*: Re: [BioC] Rsamtools from biocLite using R-devel
> *Date*: Thu, 28 Oct 2010 07:41:22 -0700
>
>
> 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
> > >>
> > >> _______________________________________________
> > >> Bioconductor mailing list
> > >> Bioconductor@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
> > >
> >
> > _______________________________________________
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>
> >
> >
>
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