[pkg-bioc] pbuilder does not find newly built packages

[Steffen Moeller]

Hi, it is time for me to say good night. I found the last issue with my 
pbuilder-hook that works on bioc while I am compiling cran :-/  We do not 
lose too much if we make the hook run on all our build directories regardless
what repository we are working with, do we? Well, maybe we do for 1700 
packages ...

Here my changed hook (also added the ()s)

#!/bin/sh
for m in cran bioc-1.9 omegahat; do
  (cd /nfshome/moeller/debian_moeller/debian/alioth/bioc/${m}/ &&
  /usr/bin/dpkg-scanpackages builds /dev/null | gzip > builds/Packages.gz )
done
/usr/bin/apt-get update

It went on for 24 packages (record!) and then failed for sensominer since the 
hopach package indeed was not yet built. It was assigned to the bioc 
repository but presented both in cran and in bioc, the latter repository's 
version was newer, but sensominer in cran depends on it. For now it is 
reassigned to cran.

No more tries for tonight

Steffen

************************************************
Packaging #4: 'msm', (using pbuilder)
************************************************
Description file is available at msm-0.7/DESCRIPTION
*** No patches found for package msm
*** No extra targets found for package msm
building package builds/r-cran-msm_0.7-0.r2d.1_i386.deb ...
W: /nfshome/moeller/.pbuilderrc does not exist
  -> Logging to ../msm_0.7.log
Now removing directory 'msm-0.7' ... ok.


************************************************
Packaging #6: 'eiPack', (using pbuilder)
************************************************
Description file is available at eipack-0.1.2/DESCRIPTION
*** No patches found for package eiPack
*** No extra targets found for package eiPack
building package builds/r-cran-eipack_0.1.2-0.r2d.1_i386.deb ...
W: /nfshome/moeller/.pbuilderrc does not exist
  -> Logging to ../eipack_0.1.2.log
Errors during the creation|upgrade of pbuilder !
=== start tail -30 eipack_0.1.2.log ===
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-vr
   -> Trying r-cran-vr
 -> Considering build-dep r-cran-coda
   -> Trying r-cran-coda
 -> Considering build-dep r-cran-msm
   -> Trying r-cran-msm
       -> Cannot install r-cran-msm; apt errors follow:
Reading package lists...
Building dependency tree...
E: Couldn't find package r-cran-msm
W: Unable to locate package r-cran-msm
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/7241 and its 
subdirectories
cd eipack-0.1.2 ; pdebuild --buildsourceroot fakeroot --pbuilderroot 
sudo --logfile ../eipack_0.1.2.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/

-- 

Dr. Steffen Möller
University of Lübeck
Institute for Neuro- and Bioinformatics
Ratzeburger Allee 160
23538 Lübeck
Germany
T: +49 451 500 5504
F: +49 451 500 5502
moeller at inb.uni-luebeck.de
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