[pkg-bioc] CVS %p

[CVS User smoe-guest]

Update of /cvsroot/pkg-bioc/tools
In directory alioth:/tmp/cvs-serv9368

Modified Files:
	cran2deb.pl r_pkg_prepare.sh r_pkg_update.pl 
Log Message:
Hello,

it seems like I have in this instant built my first package with pbuilder.
David did a fantastic job preparing the r_pkg_ scripts - many thanks.

What's new:

* cran2deb.pl:
  - pbuilder is chosen by cran2deb.pl if the directory and the /usr/sbin/pbuilder
    are existing and no other method is specified. The cran2deb script hence
    does not need the argument to use pbuilder and is in sync with the description
    on the Wiki page.

* r_pkg_*
  - moved from etch to lenny (hey, we got a release in the meantime :-) )
    cdebootstrap fails when specifying 'sid', to spot that took me an hour,
    someone with more insights please elucidate this one and send a bug
    report/fix.
  - added stable, testing and unstable to /etc/apt/sources.list, the r-base-dev
    otherwise could not find the r-base-core 2.5
  - some also allowing for --create-bioc in the argument check ... David, how could
    you forget about it :o)

What we now need I think is just a slight bit of an instruction. The
Wiki page is about right there. Something noteworthy to add, learning
from my erroneous expectations, is that r_pkg_prepare only prepares the
chroot and that it is only the r_pkg_update and only when called as specified
in the wiki that creates it .... however trivial it is.

The error below so I presume results of our undecent build order, right?
I am afraid that it was me who was once promising some improvements on
this front.  Sigh. Maybe after this salad waiting downstairs for me.

Best regards

Steffen


This far I have gotten, the r-cran-reshape is not in the build folder, reshape was not yet attempted to be built:

************************************************
Packaging 'DescribeDisplay', ( using pbuilder)
************************************************
Description file is available at describedisplay-0.1.3/DESCRIPTION
*** No patches found for package DescribeDisplay
*** No extra targets found for package DescribeDisplay
building package builds/r-cran-describedisplay_0.1.3-0.r2d.1_all.deb ...
W: /nfshome/moeller/.pbuilderrc does not exist
  -> Logging to ../describedisplay_0.1.3.log
Errors during the creation|upgrade of pbuilder !
=== start tail -30 describedisplay_0.1.3.log ===
Get:9 http://ftp.de.debian.org sid/non-free Packages/DiffIndex [2023B]
Fetched 10.7kB in 1s (6719B/s)
Reading package lists...
 -> user script /local/debian/home/moeller/debian/alioth/bioc/pbuilder/14332/tmp/hooks/D70apt finished
dpkg-architecture: warning: no utmp entry available and LOGNAME not defined; using uid of process (0)
 -> Attempting to parse the build-deps
 -> Considering build-dep r-base-dev (>> 2.3.0)
   -> Trying r-base-dev
 -> Considering build-dep debhelper (>> 4.0.0)
   -> Trying debhelper
 -> Considering build-dep cdbs
   -> Trying cdbs
 -> Considering build-dep r-cran-reshape
   -> Trying r-cran-reshape
       -> Cannot install r-cran-reshape; apt errors follow:
Reading package lists...
Building dependency tree...
E: Couldn't find package r-cran-reshape
W: Unable to locate package r-cran-reshape
E: Could not satisfy build-dependency.
E: pbuilder-satisfydepends failed.
Copying back the cached apt archive contents
 -> unmounting /nfshome/moeller/debian_moeller/debian/alioth/bioc/omegahat/builds/ filesystem
 -> unmounting /nfshome/moeller/debian_moeller/debian/alioth/bioc/cran/builds/ filesystem
 -> unmounting /nfshome/moeller/debian_moeller/debian/alioth/bioc/bioc-1.9/builds/ filesystem
 -> unmounting dev/pts filesystem
 -> unmounting proc filesystem
 -> cleaning the build env
    -> removing directory /local/debian/home/moeller/debian/alioth/bioc/pbuilder/14332 and its subdirectories
cd describedisplay-0.1.3 ; pdebuild --buildsourceroot fakeroot --pbuilderroot sudo --logfile ../describedisplay_0.1.3.log --buildresult ../.././builds -- --basetgz ../../../i386_base.tgz --buildplace ../../../pbuilder --aptconfdir /nfshome/moeller/debian_moeller/debian/alioth/bioc/apt/apt --aptcache /nfshome/moeller/debian_moeller/debian/alioth/bioc/apt/aptcache --hookdir /nfshome/moeller/debian_moeller/debian/alioth/bioc/pbuilder-hook --bindmounts /nfshome/moeller/debian_moeller/debian/alioth/bioc/bioc-1.9/builds/ --bindmounts /nfshome/moeller/debian_moeller/debian/alioth/bioc/cran/builds/ --bindmounts /nfshome/moeller/debian_moeller/debian/alioth/bioc/omegahat/builds/
=== end   tail -30 describedisplay_0.1.3.log ===
build failed for builds/r-cran-describedisplay_0.1.3-0.r2d.1_all.deb
        built in builds/describedisplay-0.1.3
       logged as builds/describedisplay_0.1.3.log