[Debian-med-packaging] Bug#650412: Bug#650412: bioperl: missing Recommends:/Suggests:

[Charles Plessy]

Le Tue, Nov 29, 2011 at 05:22:53PM +0100, Luca Capello a écrit :
> Package: bioperl
> Version: 1.6.901-1
> Severity: important
> Usertags: unige.ch-jmlab
> 
> Hi there!
> 
> IMHO bioperl should have a more detailed Recommends: or Suggests:, given
> that most of its binaries does not work out of the box.  Here a list of
> what should be added after a simple `$BINARY -help` run on a up-to-date
> sid chroot.  Please note that I did the test above twice, the first time
> without the bioperl-run package installed.
> 
> NB1, some of this dependencies are already Recommends: for
>      libbio-perl-perl, but given that the binaries are provided by
>      bioperl, either we move the Recommends: or we provide a
>      README.Debian to this package.  However, I think that at least
>      perl-doc and groff-base should be added unconditionally to bioperl
>      Recommends: (not to Depends: simply because they require 16.6 MB
>      more, for nothing).
> 
> NB2, this should be double-checked, I was not expecting so many problems
>      when I started and at some point I thought of getting lost.  So
>      please be patient if there are some errors...
> 
> |---------------------------+------------------------------+------------------------------------------------------------|
> | binary                    | `binary -help` output        | missing dependencies                                       |
> |---------------------------+------------------------------+------------------------------------------------------------|
> | bp_aacomp                 |                              |                                                            |
> | bp_biblio                 | need perl-doc, nroff         | perl-doc, groff-base                                       |
> | bp_biofetch_genbank_proxy | missing Perl module          | libhttp-message-perl (HTTP/Request/Common.pm)              |
> |                           | missing Perl module          | libwww-perl (LWP/UserAgent.pm)                             |
> |                           | missing Perl module          | libcache-cache-perl (Cache/FileCache.pm)                   |
> |                           | Unknown database [no help]   |                                                            |
> | bp_bioflat_index          | unknown option [no help]     |                                                            |
> |                           | Bio::Root::Exception         | please provide a base directory with the --location option |
> | bp_biogetseq              | need perl-doc, nroff         | perl-doc, groff-base                                       |
> | bp_blast2tree             | missing Perl module          | libbio-perl-run-perl (Bio/Tools/Run/Alignment/Clustalw.pm) |
> |                           | need perl-doc, nroff         | perl-doc, groff-base                                       |
> |                           |                              | [help contains "tree_from_seqsearch"                       |
(et cætera).

Thank you Lucas for this very detailed analysis.

The packages recommended by libbio-perl-perl are so because of they are listed
in the DEPENDENCIES and Build.PL files in its sources, or because of
dh-make-perl at the time the package was prepared or refreshed.  I am not
completely sure if the scripts distributed in the bioperl package were taken
into account, and we can indeed add explicit Recommends statements to the
bioperl package, even in the case that would be satisfied transitively through
the libbio-perl-perl package.

Some programs need perldoc for their --help option, and recommending perl-doc
looks necessary as well.  However, I looked at what happens after removing
groff, and the --help option displays the POD version, which is well readable,
so it is not needed to depend on groff-base.

Would you like to send a patch or commit directly to the subversion repository ?

Have a nice day,

-- 
Charles