[Debian-med-packaging] Bug#726801: biomaj: fails to install with Recommends enabled

[Andreas Beckmann]

I can reproduce this problem in pbuilder using the sid tarball as created by piuparts and the following commands:

sudo pbuilder login --basetgz /srv/piuparts/slave/basetgz/sid_amd64.tar.gz

export DEBIAN_FRONTEND=noninteractive
sed -i /mysql/d /usr/sbin/policy-rc.d
sed -i 's/main/main contrib non-free/' /etc/apt/sources.list
apt-get update
apt-get install --install-recommends biomaj-watcher

The problem obvioulsy depends on the actual set of packages the are being installed and starting from a different base may yield a different result.

On 2013-11-07 00:12, Andreas Beckmann wrote:
>> On 11/05/2013 06:08 PM, gregor herrmann wrote:
>>> Oh, and I don't find the lines you quoted above in the log in
>>> #726801.
> 
> A new log was on the way to the bug, but got stuck somewhere.

trying again ... here is my analysis of the java dependency cycle

default-jre is configured before biomaj, so dependency fulfilled

openjdk-7-jre-headless is configured after default-jre, but

Package: default-jre
Source: java-common (0.49)
Version: 1:1.7-49
Depends: default-jre-headless (= 1:1.7-49), openjdk-7-jre (>= 7~u3-2.1.1)

Package: default-jre-headless
Source: java-common (0.49)
Version: 1:1.7-49
Depends: openjdk-7-jre-headless (>= 7~u3-2.1.1), java-common

Package: openjdk-7-jre-headless
Source: openjdk-7
Version: 7u25-2.3.12-4
Provides: java-runtime-headless, java2-runtime-headless, java5-runtime-headless, java6-runtime-headless, java7-runtime-headless
Depends: openjdk-7-jre-lib (= 7u25-2.3.12-4), ca-certificates-java, tzdata-java, java-common (>= 0.28), libcups2 (>= 1.4.0), liblcms2-2, libjpeg8 (>= 8c), libnss3 (>= 2:3.13.4), libpcsclite1, libc6 (>= 2.14), libfontconfig1 (>= 2.10.0), libfreetype6 (>= 2.2.1), libgcc1 (>= 1:4.1.1), libglib2.0-0 (>= 2.26.0), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4)

Package: java-common
Version: 0.49
Depends: *nothing*

Package: openjdk-7-jre-lib
Source: openjdk-7
Version: 7u25-2.3.12-4
Depends: openjdk-7-jre-headless (>= 7~b130~pre0)
* first cycle *

Package: ca-certificates-java
Version: 20130815
Depends: ca-certificates (>= 20121114), openjdk-6-jre-headless (>= 6b16-1.6.1-2) | java6-runtime-headless, libnss3 (>= 3.12.10-2~)
* second cycle *

Package: openjdk-7-jre
Source: openjdk-7
Version: 7u25-2.3.12-4
Provides: java-runtime, java2-runtime, java5-runtime, java6-runtime, java7-runtime
Depends: openjdk-7-jre-headless (= 7u25-2.3.12-4), libasound2 (>= 1.0.16), libatk1.0-0 (>= 1.12.4), libc6 (>= 2.14), libcairo2 (>= 1.2.4), libcups2 (>= 1.4.0), libfontconfig1 (>= 2.10.0), libfreetype6 (>= 2.2.1), libgdk-pixbuf2.0-0 (>= 2.22.0), libgif4 (>= 4.1.4), libglib2.0-0 (>= 2.16.0), libgtk2.0-0 (>= 2.8.0), libjpeg8 (>= 8c), libpango-1.0-0 (>= 1.14.0), libpangocairo-1.0-0 (>= 1.14.0), libpangoft2-1.0-0 (>= 1.14.0), libpng12-0 (>= 1.2.13-4), libpulse0 (>= 0.99.1), libx11-6, libxext6, libxi6, libxrender1, libxtst6, zlib1g (>= 1:1.1.4), libxrandr2, libxinerama1, libgl1-mesa-glx | libgl1, libatk-wrapper-java-jni (>= 0.30.4-0ubuntu2)


There are bugs in
* java stuff for having circular dependencies
* apt or dpkg for bad handling of this cycle:
  if a dependency cycle has to be broken, all packages that depend on a package in the cycle
  but are not part of the cycle itself, have to be configured after *all* packages in the
  cycle have been configured

Andreas
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