[Debichem-devel] Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

[Dirk Eddelbuettel]

First off, let me apologize. I clearly did this the wrong way and should have
contacted -release and -devel beforehand. My bad -- I'm sorry for extra work
this created for the release managers and maintainer, particularly at this
time.

R 3.0.0 was released on April 3 as scheduled. As usual, I built a package the
morning of, and all build daemons are current. (There was also an unrelated
bug which is why were at 3.0.0-2.)  The release team kindly put a block on
it, so it will make it into testing.  Good.

Preceding the release and following it, we have rebuilt the vast number of
"r-cran-*" packages used my R, and which do need a rebuild, plus a few
building against R such as python-rpy.  Currently, in my unstable pbuilder
chroot (and thanks to Chris for the showpkg trick)

  root at max:/# apt-cache showpkg r-base-core | grep "r-base-core 3" | wc -l      
  127

So 127 packages are already taken care of.  On the other hand, we still have
~50 packages needing work:

  root at max:/# apt-cache showpkg r-base-core | grep "r-base-core 2" | wc -l                                                                                     52

A few of these are false positives though. Looking more closely via

   root at max:/# for p in `apt-cache showpkg r-base-core | grep "r-base-core 2" | sort | awk -F, '{print $1}'`; \
	do echo -n "$p,"; apt-cache show $p | grep Maintainer | sed -e 's/.*<//' -e 's/>$//'; done

gets us a nice little csv data set we can print in R:

R> print(todo[ order(todo[,2]), ], row.names=FALSE)
                       pkg                                              maint
            r-bioc-biobase       debian-med-packaging at lists.alioth.debian.org
       r-bioc-biocgenerics       debian-med-packaging at lists.alioth.debian.org
         r-bioc-cummerbund       debian-med-packaging at lists.alioth.debian.org
              r-bioc-edger       debian-med-packaging at lists.alioth.debian.org
         r-bioc-hilbertvis       debian-med-packaging at lists.alioth.debian.org
              r-bioc-limma       debian-med-packaging at lists.alioth.debian.org
             r-bioc-qvalue       debian-med-packaging at lists.alioth.debian.org
           r-cran-combinat       debian-med-packaging at lists.alioth.debian.org
               r-cran-deal       debian-med-packaging at lists.alioth.debian.org
       r-cran-diagnosismed       debian-med-packaging at lists.alioth.debian.org
                r-cran-epi       debian-med-packaging at lists.alioth.debian.org
           r-cran-epibasix       debian-med-packaging at lists.alioth.debian.org
            r-cran-epicalc       debian-med-packaging at lists.alioth.debian.org
               r-cran-epir       debian-med-packaging at lists.alioth.debian.org
           r-cran-epitools       debian-med-packaging at lists.alioth.debian.org
                r-cran-evd       debian-med-packaging at lists.alioth.debian.org
            r-cran-genabel       debian-med-packaging at lists.alioth.debian.org
           r-cran-genetics       debian-med-packaging at lists.alioth.debian.org
            r-cran-ggplot2       debian-med-packaging at lists.alioth.debian.org
        r-cran-haplo.stats       debian-med-packaging at lists.alioth.debian.org
                r-cran-psy       debian-med-packaging at lists.alioth.debian.org
            r-cran-pvclust       debian-med-packaging at lists.alioth.debian.org
       r-cran-randomforest       debian-med-packaging at lists.alioth.debian.org
            r-cran-reshape       debian-med-packaging at lists.alioth.debian.org
           r-cran-reshape2       debian-med-packaging at lists.alioth.debian.org
               r-cran-rocr       debian-med-packaging at lists.alioth.debian.org
            r-cran-rsqlite       debian-med-packaging at lists.alioth.debian.org
            r-cran-stringr       debian-med-packaging at lists.alioth.debian.org
              r-cran-vegan       debian-med-packaging at lists.alioth.debian.org
             r-other-bio3d       debian-med-packaging at lists.alioth.debian.org
        r-other-mott-happy       debian-med-packaging at lists.alioth.debian.org
              r-cran-amore debian-science-maintainers at lists.alioth.debian.org
                r-cran-msm debian-science-maintainers at lists.alioth.debian.org
            r-cran-plotrix debian-science-maintainers at lists.alioth.debian.org
                 r-cran-sp debian-science-maintainers at lists.alioth.debian.org
                r-cran-spc debian-science-maintainers at lists.alioth.debian.org
      r-cran-teachingdemos debian-science-maintainers at lists.alioth.debian.org
                r-cran-vcd debian-science-maintainers at lists.alioth.debian.org
             r-cran-xtable debian-science-maintainers at lists.alioth.debian.org
         r-cran-maldiquant             debichem-devel at lists.alioth.debian.org
 r-cran-readbrukerflexdata             debichem-devel at lists.alioth.debian.org
                   littler                                     edd at debian.org
          python-nwsserver                                     edd at debian.org
           r-cran-gregmisc                                     edd at debian.org
             r-cran-misc3d                                     edd at debian.org
                r-cran-erm                                     jdg at debian.org
       r-cran-raschsampler                                     jdg at debian.org
               r-cran-pscl                                lawrencc at debian.org
         r-noncran-lindsey                                lawrencc at debian.org
        postgresql-9.1-plr                                    myon at debian.org
      r-cran-scatterplot3d                                      rinni at gmx.net
                    rkward                         tfry at users.sourceforge.net
R> 

I have taken care of my two r-cran-* package, and I know littler is a false
positive.  postgresql-r may also work, same for rkward -- the _external_ R
API did not change, but the package use did.

I have CC'ed all relevant maintainer who were not already on the list and
will follow-up.  I can help and pitch in, please contact me off-list.  

Special thanks to Charles and Chris who already uploaded a number of packages
too. 

Thanks,  Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com