[Bioc-devel] BioC 2.2 builds

[Herve Pages]

Hi all,

2 days ago, we've created the BioC 2.1 release branch in our Subversion
repository, but... the release is not yet finalized! If everything is
working out as expected, we will announce it tomorrow Oct, Friday 5th.

However, basic support for a new BioC devel cycle is ready. This new
devel cycle will rely on R-2.7 and will be called BioC 2.2.

We are already building BioC 2.2 daily:

  http://bioconductor.org/checkResults/2.2/bioc-LATEST/

Note that:

  - This line

      URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks

    at the top of the report indicates that we are building the devel
    versions of the packages (they all have an odd y in their version
    number x.y.z). Compare with the BioC 2.1 builds:

      http://bioconductor.org/checkResults/2.1/bioc-LATEST/

    where the URL line indicates that we are building the release
    versions of the packages (they all have an even y in their version
    number x.y.z). Just a reminder that we've bumped all these version
    numbers in release and devel 2 days ago.

  - Of course, the build system uses R-2.7.0 for the BioC 2.2 builds.

  - We only build software packages on 64-bit SUSE Linux 10.1 and Windows
    Server 2003 for now (FYI, we are planning to upgrade our build machine
    OSes very soon).

  - As usual, source packages that pass 'R CMD check' on lamb1 with no
    error (they can have warnings though) are made publicly available
    by being pushed to the public software repo for BioC 2.2:

      http://bioconductor.org/packages/2.2/bioc/

    Note that, as usual, you might find it more convenient to browse the
    BioC 2.2 packages by navigating thru the bioc views:

      http://bioconductor.org/packages/2.2/BiocViews.html

  - As always, the easiest way to install BioC 2.2 packages is to use
    biocLite() from R-2.7.0:

      > source("http://bioconductor.org/biocLite.R")
      > biocLite("mypackage") # install
      > update.packages(rep=biocinstallRepos()) # update all packages

Finally, if you are mirroring the Bioconductor package repositories, we've
updated this page:

  http://bioconductor.org/download/mirrors/mirror-howto.html

Please, let us know if you have any questions. Thanks!

Cheers,
H.