Differences between revisions 9 and 10
Revision 9 as of 2005-06-05 19:30:54
Size: 2867
Editor: anonymous
Comment:
Revision 10 as of 2005-06-06 13:27:08
Size: 2680
Editor: anonymous
Comment:
Deletions are marked like this. Additions are marked like this.
Line 36: Line 36:
Dirk still has the .deb he built almost a year ago. CRAN has spdep_0.3-12. Maybe Steffen can tell us if/why it didn't build? No, he cannot at the moment but will investigate.
   * r-cran-grdevices
This needs an update in cran2deb to flag it as a) doesn't need builds
and b) doesn't need to generate 'Depends: r-cran-grdevices' as it is part of
r-base-core.
   * r-cran-process (depended on by r-cran-camassclass)
Strange build error: Error in .DESC[["Package"]] : subscript out of bounds
   * r-cran-grdevices [fixed - as now in r-base-core]
   * r-cran-process (depended on by r-cran-camassclass)j
Line 43: Line 40:
This one had some build or license issues. Or maybe both. Steffen has not seen this one in his R mirror.
Line 51: Line 48:
All conflict with r-cran-gregmisc that was split upstream a while ago. All conflict with r-cran-gregmisc that was split upstream a while ago. The next round of builds will address these issues.
Line 53: Line 50:
Conflicts with r-other-gking-matchit ... its maintainer Chris was contacted, being asked for a rename and invited to join the force. Conflicts with r-other-gking-matchit ... its maintainer Chris was contacted, being asked for a rename and invited to join the fojke.

Debian CRAN/BIOC package archive

The {alioth:pkg-bioc} is working on Debian packages repository for the GNU R ( http://www.r-project.org ) libraries at CRAN ( http://cran.r-project.org/ ) and ?BioConductor ( http://www.bioconductor.org ).

These pages (will) contain information on how the packages are build, where apt repository mirrors are located, etc. These subprojects are available at this moment:

  • ["DebianCRAN"]
  • ["DebianBIOC"]

Remaining issues

  • Permanent sponsor of disk space is seeked
  • Conflicts between R's package update facility and the update of Debian packages are not resolved.

Mirrors

There is no permanent apt-get repository available at this moment. And, thus, no mirrors either :) For i386 an initial automated repository is available for CRAN at

deb http://public.pzr.uni-rostock.de/~moeller/mirror ./

For a repository for ?BioConductor, only thought as a first start, you might consider to address a manual effort that is now already outdated at

deb http://bioinformatics.pzr.uni-rostock.de/~moeller/debian ./

However, it this is the exact problem of that stimulated this community effort for automated builds in the first place.

Remaining problems with some of the packages

Many thanks to Elija and Dirk for their first investigations.

  • Unresolved dependencies
    • r-cran-spdep

Strange build error: Error in .DESC?"Package" : subscript out of bounds

  • r-cran-grdevices [fixed - as now in r-base-core]
  • r-cran-process (depended on by r-cran-camassclass)j
  • r-cran-akima

Steffen has not seen this one in his R mirror.

  • Missing titles -- bogus data from cran?
    • r-cran-dse
    • r-cran-tframe

r-cran-tframe is part of r-cran-dse

  • r-cran-gap
  • Conflicts with existing packages in R
    • r-cran-gtools, r-cran-gdata, ...

All conflict with r-cran-gregmisc that was split upstream a while ago. The next round of builds will address these issues.

  • r-cran-matchit

Conflicts with r-other-gking-matchit ... its maintainer Chris was contacted, being asked for a rename and invited to join the fojke.

Advocacy

  • Importance of this effort for Debian
    • Peace of mind for scientific researchers using Debian
      • It is all in
      • It ia all up to date
      • Easily updateable
    • Improved link of Debian with upstream developers
  • Importance of this effort for initiatives within and associated with Debian
    • Debian-Med custom debian distribution is strengthened by ?BioConductor

    • Commercial efforts distributing Debian-derived Bioinformatics solutions are likely to improve over an inclusion of ?BioConductor and CRAN.