Re: Further Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

2013-04-15 Thread Andreas Tille 
On Sat, Apr 13, 2013 at 09:48:05PM +0200, Anton Gladky wrote:
 On 04/13/2013 04:18 PM, Dirk Eddelbuettel wrote:
  
  So here is where we stand, with little improvement from last week: [1]
  
root@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 | \
awk -F, '/^r-/ {print $2,$1}' | sort  
 
debian-med-packag...@lists.alioth.debian.org r-bioc-cummerbund
...
debichem-de...@lists.alioth.debian.org r-cran-readbrukerflexdata
i...@maintz.de r-cran-gtable
lawre...@debian.org r-cran-pscl
root@max:/# 
 
 Cool, considering the deep freeze...

+1

As previous discussion has shown the R change is at least questionable.
I personally will not upgrade any R related package in Debian Med or
Debian Science before Wheezy is released - I'm fine if anybody else
wants to spend time into this, provided the relevant team VCS will be
updated.

Kind regards

   Andreas.

-- 
http://fam-tille.de


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Re: Further Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

2013-04-15 Thread Jonathan Dowland 
On Sat, Apr 13, 2013 at 09:18:05AM -0500, Dirk Eddelbuettel wrote:
 Charles, failing that, shall we coordinate off-list?  Re-building in chroot
 takes about a minute or two each but sadly some of these package appear
 effectively orphaned (eg gpplot2, single upload 15 months ago -- is that
 really work done to Debian standards?)

Perhaps I misread this, but it seemed you are criticising folks for not working
on things which don't impact wheezy?


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Re: Further Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

2013-04-14 Thread Charles Plessy 
Le Sat, Apr 13, 2013 at 09:18:05AM -0500, Dirk Eddelbuettel a écrit :
 
 I would be really terrific if the the debian-med, debian-science, debichem
 teams could update some of these packages.  
 
 Charles, failing that, shall we coordinate off-list?  Re-building in chroot
 takes about a minute or two each but sadly some of these package appear
 effectively orphaned (eg gpplot2, single upload 15 months ago -- is that
 really work done to Debian standards?)

Hi Dirk and everybody,

my pace is aproximately one package per day, partly because instead of
rebuilding I take the opportunity to upgrade when new upstream releases are
available (and as you noted, a lot accumulated during the Freeze).

Everybody's help is welcome, especially for the trivial rebuilds.  We have our
packages managed in Subversion and Git repository, but if this is bothering, I
think that we can cut corners with a simple NMU with no changes, that will be a
branch in the version tree.

Also, for the architecture-dependant packages, we can request binary NMUs,
although I have been reluctant to do so in order to not disturb the Release
team.

For ggplot2, we are working on the update (#700862), but it needs the
introduction of new packages (r-cran-gtable, accepted this week, and
r-cran-scales, to be uploaded).  For the short term, I just uploaded a NMU to
rebuild the package.

Have a nice Sunday,

-- 
Charles


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Further Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

2013-04-13 Thread Dirk Eddelbuettel 

So here is where we stand, with little improvement from last week: [1]

  root@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 | \
  awk -F, '/^r-/ {print $2,$1}' | sort  
   
  debian-med-packag...@lists.alioth.debian.org r-bioc-cummerbund
  debian-med-packag...@lists.alioth.debian.org r-bioc-edger
  debian-med-packag...@lists.alioth.debian.org r-bioc-hilbertvis
  debian-med-packag...@lists.alioth.debian.org r-bioc-limma
  debian-med-packag...@lists.alioth.debian.org r-bioc-qvalue
  debian-med-packag...@lists.alioth.debian.org r-cran-combinat
  debian-med-packag...@lists.alioth.debian.org r-cran-deal
  debian-med-packag...@lists.alioth.debian.org r-cran-diagnosismed
  debian-med-packag...@lists.alioth.debian.org r-cran-dichromat
  debian-med-packag...@lists.alioth.debian.org r-cran-epi
  debian-med-packag...@lists.alioth.debian.org r-cran-epibasix
  debian-med-packag...@lists.alioth.debian.org r-cran-epicalc
  debian-med-packag...@lists.alioth.debian.org r-cran-epir
  debian-med-packag...@lists.alioth.debian.org r-cran-epitools
  debian-med-packag...@lists.alioth.debian.org r-cran-evd
  debian-med-packag...@lists.alioth.debian.org r-cran-genabel
  debian-med-packag...@lists.alioth.debian.org r-cran-genetics
  debian-med-packag...@lists.alioth.debian.org r-cran-ggplot2
  debian-med-packag...@lists.alioth.debian.org r-cran-haplo.stats
  debian-med-packag...@lists.alioth.debian.org r-cran-labeling
  debian-med-packag...@lists.alioth.debian.org r-cran-psy
  debian-med-packag...@lists.alioth.debian.org r-cran-pvclust
  debian-med-packag...@lists.alioth.debian.org r-cran-randomforest
  debian-med-packag...@lists.alioth.debian.org r-cran-reshape2
  debian-med-packag...@lists.alioth.debian.org r-cran-rocr
  debian-med-packag...@lists.alioth.debian.org r-cran-stringr
  debian-med-packag...@lists.alioth.debian.org r-other-mott-happy
  debian-science-maintain...@lists.alioth.debian.org r-cran-amore
  debian-science-maintain...@lists.alioth.debian.org r-cran-msm
  debian-science-maintain...@lists.alioth.debian.org r-cran-plotrix
  debian-science-maintain...@lists.alioth.debian.org r-cran-sp
  debian-science-maintain...@lists.alioth.debian.org r-cran-spc
  debian-science-maintain...@lists.alioth.debian.org r-cran-teachingdemos
  debian-science-maintain...@lists.alioth.debian.org r-cran-vcd
  debian-science-maintain...@lists.alioth.debian.org r-cran-xtable
  debichem-de...@lists.alioth.debian.org r-cran-maldiquant
  debichem-de...@lists.alioth.debian.org r-cran-readbrukerflexdata
  i...@maintz.de r-cran-gtable
  lawre...@debian.org r-cran-pscl
  root@max:/# 

I would be really terrific if the the debian-med, debian-science, debichem
teams could update some of these packages.  

Charles, failing that, shall we coordinate off-list?  Re-building in chroot
takes about a minute or two each but sadly some of these package appear
effectively orphaned (eg gpplot2, single upload 15 months ago -- is that
really work done to Debian standards?)

Dirk  

[1] I filtered out things like littler (works fine with R 3.0.0),
python-nwsserver (uses pipes, is fine too) and postgresql-9.1-plr which I
suspect is fine just like littler is.
  
-- 
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com


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Re: Further Update on R 3.0.0 migration (Was: R 3.0.0 and required rebuilds of all reverse Depends: of R)

2013-04-13 Thread Anton Gladky 
On 04/13/2013 04:18 PM, Dirk Eddelbuettel wrote:
 
 So here is where we stand, with little improvement from last week: [1]
 
   root@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 | \
 awk -F, '/^r-/ {print $2,$1}' | sort  

   debian-med-packag...@lists.alioth.debian.org r-bioc-cummerbund
   debian-med-packag...@lists.alioth.debian.org r-bioc-edger
   debian-med-packag...@lists.alioth.debian.org r-bioc-hilbertvis
   debian-med-packag...@lists.alioth.debian.org r-bioc-limma
   debian-med-packag...@lists.alioth.debian.org r-bioc-qvalue
   debian-med-packag...@lists.alioth.debian.org r-cran-combinat
   debian-med-packag...@lists.alioth.debian.org r-cran-deal
   debian-med-packag...@lists.alioth.debian.org r-cran-diagnosismed
   debian-med-packag...@lists.alioth.debian.org r-cran-dichromat
   debian-med-packag...@lists.alioth.debian.org r-cran-epi
   debian-med-packag...@lists.alioth.debian.org r-cran-epibasix
   debian-med-packag...@lists.alioth.debian.org r-cran-epicalc
   debian-med-packag...@lists.alioth.debian.org r-cran-epir
   debian-med-packag...@lists.alioth.debian.org r-cran-epitools
   debian-med-packag...@lists.alioth.debian.org r-cran-evd
   debian-med-packag...@lists.alioth.debian.org r-cran-genabel
   debian-med-packag...@lists.alioth.debian.org r-cran-genetics
   debian-med-packag...@lists.alioth.debian.org r-cran-ggplot2
   debian-med-packag...@lists.alioth.debian.org r-cran-haplo.stats
   debian-med-packag...@lists.alioth.debian.org r-cran-labeling
   debian-med-packag...@lists.alioth.debian.org r-cran-psy
   debian-med-packag...@lists.alioth.debian.org r-cran-pvclust
   debian-med-packag...@lists.alioth.debian.org r-cran-randomforest
   debian-med-packag...@lists.alioth.debian.org r-cran-reshape2
   debian-med-packag...@lists.alioth.debian.org r-cran-rocr
   debian-med-packag...@lists.alioth.debian.org r-cran-stringr
   debian-med-packag...@lists.alioth.debian.org r-other-mott-happy
   debian-science-maintain...@lists.alioth.debian.org r-cran-amore
   debian-science-maintain...@lists.alioth.debian.org r-cran-msm
   debian-science-maintain...@lists.alioth.debian.org r-cran-plotrix
   debian-science-maintain...@lists.alioth.debian.org r-cran-sp
   debian-science-maintain...@lists.alioth.debian.org r-cran-spc
   debian-science-maintain...@lists.alioth.debian.org r-cran-teachingdemos
   debian-science-maintain...@lists.alioth.debian.org r-cran-vcd
   debian-science-maintain...@lists.alioth.debian.org r-cran-xtable
   debichem-de...@lists.alioth.debian.org r-cran-maldiquant
   debichem-de...@lists.alioth.debian.org r-cran-readbrukerflexdata
   i...@maintz.de r-cran-gtable
   lawre...@debian.org r-cran-pscl
   root@max:/# 

Cool, considering the deep freeze...

Anton



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