[Debian-med-packaging] Bug#939832: chado-utils: installation error

[Olivier Sallou]

On 12/4/19 12:37 PM, Andreas Tille wrote:
> Control: tags -1 moreinfo
> Control: tags -1 unreproducible
>
> Hi Olivier,
>
> chado-utils installs nicely on my testing system.  Does the
> issue persist on your side or can we close this bug?

I could reproduce in a docker container on buster (and sid) after an apt
update and upgrade


apt/sources.list:

/# more /etc/apt/sources.list
# deb http://snapshot.debian.org/archive/debian/20190910T000000Z buster main
deb http://deb.debian.org/debian buster main
# deb
http://snapshot.debian.org/archive/debian-security/20190910T000000Z
buster/updates main
deb http://security.debian.org/debian-security buster/updates main
# deb http://snapshot.debian.org/archive/debian/20190910T000000Z
buster-updates main
deb http://deb.debian.org/debian buster-updates main

An apt-get install chado-utils ends with:


dpkg: error processing package libchado-perl (--configure):
 installed libchado-perl package post-installation script subprocess
returned error exit status 2
Setting up libxmlrpc-lite-perl (0.717-2) ...
dpkg: dependency problems prevent configuration of chado-utils:
 chado-utils depends on libchado-perl; however:
  Package libchado-perl is not configured yet.
.....

.....

Errors were encountered while processing:
 libchado-perl
 chado-utils
E: Sub-process /usr/bin/dpkg returned an error code (1)


The error occurs in fact at libchado-perl:

Setting up libchado-perl (1.31-5) ...^M
dpkg: error processing package libchado-perl (--configure):^M
 installed libchado-perl package post-installation script subprocess
returned error exit status 2^M
Setting up libxmlrpc-lite-perl (0.717-2) ...^M
dpkg: dependency problems prevent configuration of chado-utils:^M
 chado-utils depends on libchado-perl; however:^M
  Package libchado-perl is not configured yet.^M
^M
dpkg: error processing package chado-utils (--configure):^M
 dependency problems - leaving unconfigured^M


If I run manually the postinstall script, it "works", an exit code of
102 is executed (which is fine and trapped by script).

If I rerun it I get an exitcode = 2 on line 47 (perl Makefile.PL update
....)

This is my issue during apt install .


It seems that it expects in env vars either: CHADO_DB_USERNAME or USER

In container "world" , $USER is not set, so neither is available.

So in postinst, I think we should add

    export CHADO_DB_USERNAME=chado

next to export CHADO_DB_NAME






>
> Kind regards
>
>     Andreas.
>
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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