[Debian-med-packaging] Bug#921495: libbio-perl-perl: Package not upgradable, file conflicts.

[Andreas Tille]

Control: tags -1 help

Hi David,

as far as I know you are involved into bioperl and might be the most
competent person for this problem.  I've found the following competing
filed in bioperl and bioperl-run:


bioperl-run(master) $ find . -name "Analysis.pm" -o -name "AnalysisFactory.pm"
./lib/Bio/Tools/Run/AnalysisFactory.pm
./lib/Bio/Tools/Run/Analysis.pm

bioperl(master) $ find . -name "Analysis.pm" -o -name "AnalysisFactory.pm"
./lib/Bio/Tools/Run/AnalysisFactory.pm
./lib/Bio/Tools/Run/Analysis.pm


Any suggestion how to deal with this sensibly?  I would expect some
soonish release of bioperl-run which does not contain these files any
more, but you might know better.

Kind regards

      Andreas.

On Wed, Feb 06, 2019 at 07:40:25AM +0100, Nicolas Patrois wrote:
> Package: libbio-perl-perl
> Version: 1.7.2-3
> Severity: normal
> 
> Dear Maintainer,
> 
> The package can’t be upgraded because one of its files
> (/usr/share/man/man3/Bio::Tools::Run::Analysis.3pm.gz) conflicts with libbio-
> perl-run-perl.
> 
> 
> 
> -- System Information:
> Debian Release: buster/sid
>   APT prefers unstable
>   APT policy: (500, 'unstable')
> Architecture: i386 (i686)
> 
> Kernel: Linux 4.17.0-3-686-pae (SMP w/3 CPU cores)
> Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
> Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR:fr:en_GB:en (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
> 
> Versions of packages libbio-perl-perl depends on:
> ii  libdata-stag-perl  0.14-2
> ii  libio-string-perl  1.08-3
> ii  perl               5.28.1-4
> 
> Versions of packages libbio-perl-perl recommends:
> ii  libace-perl                     1.92-8+b1
> ii  libalgorithm-munkres-perl       0.08-3
> pn  libarray-compare-perl           <none>
> ii  libbio-asn1-entrezgene-perl     1.720-2
> ii  libbio-perl-run-perl            1.7.2-4
> ii  libclone-perl                   0.41-1+b1
> ii  libconvert-binary-c-perl        0.78-1+b4
> pn  libdbd-mysql-perl               <none>
> pn  libdbd-pg-perl                  <none>
> pn  libdbd-sqlite3-perl             <none>
> pn  libgd-perl                      <none>
> ii  libgraph-perl                   1:0.9704-1
> ii  libgraphviz-perl                2.22-1
> ii  libhtml-parser-perl             3.72-3+b3
> ii  libhtml-tableextract-perl       2.15-1
> ii  liblist-moreutils-perl          0.416-1+b4
> ii  libpostscript-perl              0.06-3
> ii  libset-scalar-perl              1.29-2
> ii  libsoap-lite-perl               1.27-1
> ii  libsort-naturally-perl          1.03-2
> ii  libspreadsheet-parseexcel-perl  0.6500-1
> ii  libspreadsheet-writeexcel-perl  2.40-1
> pn  libstorable-perl                <none>
> pn  libsvg-graph-perl               <none>
> ii  libsvg-perl                     2.84-1
> ii  liburi-perl                     1.76-1
> ii  libwww-perl                     6.36-1
> ii  libxml-dom-xpath-perl           0.14-3
> ii  libxml-libxml-perl              2.0133+dfsg-1
> ii  libxml-parser-perl              2.44-2+b4
> ii  libxml-sax-perl                 1.00+dfsg-1
> ii  libxml-sax-writer-perl          0.57-1
> ii  libxml-simple-perl              2.25-1
> ii  libxml-twig-perl                1:3.50-1
> ii  libxml-writer-perl              0.625-1
> 
> Versions of packages libbio-perl-perl suggests:
> pn  bioperl                  <none>
> pn  libxml-sax-expatxs-perl  <none>
> 
> -- no debconf information
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