[Debian-med-packaging] Bug#826903: biomaj: installation with skipping mysql database configuration breaks package manager

[Matthias Ernst]

Package: biomaj
Version: 1.2.3-7
Severity: critical
Tags: d-i
Justification: breaks the whole system

Dear Maintainer,

I installed a fresh debian testing using net installer.
I have used advanced graphical setup.
I selected DebianScience. When asked to configure MySQL database connection
for BioMAJ, I chose to don't configure it.
The installer preceeds some hours configuring other packages.
When configuring BioMAJ, it broke up. At this moment, GRUB has not been installed.
>From this point, apt-get did not do anything. It just told me it could not connect to the server.
I had to reboot without grub and install grub manually in recovery mode.
sudo has not been installed at this moment. I had to apt-get purge biomaj
in recovery mode to get sudo working (I had disabled the root user).


-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 4.5.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages biomaj depends on:
ii  ant                            1.9.7-3
ii  ant-contrib                    1.0~b3+svn177-7
ii  ant-optional                   1.9.7-3
ii  debconf [debconf-2.0]          1.5.59
ii  default-jre [java6-runtime]    2:1.8-57
ii  junit4                         4.12-4
ii  libcommons-cli-java            1.3.1-3
ii  libcommons-codec-java          1.10-1
ii  libcommons-dbcp-java           1.4-5
ii  libcommons-httpclient-java     3.1-12
ii  libcommons-logging-java        1.2-1
ii  libcommons-net-java            3.4-2
ii  libcommons-pool-java           1.6-2
ii  libhsqldb-java                 2.3.4-1
ii  libjcommon-java                1.0.16-5
ii  libjdom1-java                  1.1.3-1
ii  libjets3t-java                 0.8.1+dfsg-2
ii  libjgoodies-forms-java         1.6.0-4
ii  libjsch-java                   0.1.53-1
ii  liblog4j1.2-java               1.2.17-7
ii  libmail-java                   1.5.5-1
ii  libmysql-java                  5.1.38-1
ii  liboro-java                    2.0.8a-11
ii  libregexp-java                 1.5-3
ii  libsaxonhe-java                9.5.1.1+dfsg-1
ii  mysql-client                   5.6.30-1
ii  openjdk-8-jre [java6-runtime]  8u91-b14-2
ii  perl                           5.22.2-1

biomaj recommends no packages.

Versions of packages biomaj suggests:
ii  blast2          1:2.2.26.20120620-10+b1
pn  mysql-server    <none>
ii  ncbi-tools-bin  6.1.20120620-10+b1

-- debconf information:
  biomaj/mysql_host:
* biomaj/mysql: false
  biomaj/mysql_login: