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

[Luca Capello]

tags 650412 + patch
thanks

Hi there!

Please use proper quoting, there is no need for so much lines of my
useless words ;-)

On Wed, 30 Nov 2011 00:18:24 +0100, Charles Plessy wrote:
> Le Tue, Nov 29, 2011 at 05:22:53PM +0100, Luca Capello a écrit :
>> IMHO bioperl should have a more detailed Recommends: or Suggests:,
[...]
> Thank you Lucas for this very detailed analysis.
            ^^^^^ 
'Luca', but I am used to French speakers mispelling my name....

> 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.

Still, IMHO recommending another package which is roughly 1/4 of
perl-doc when installed is not useless, especially given that without it
there is an error, albeit minor:
=====
(base-sid)root at gismo:/# apt-get --download-only install perl-doc
[...]
The following NEW packages will be installed:
  perl-doc
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 8161 kB of archives.
After this operation, 13.2 MB of additional disk space will be used.
[...]

(base-sid)root at gismo:/# apt-get --download-only install groff-base
[...]
The following NEW packages will be installed:
  groff-base
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 1150 kB of archives.
After this operation, 3363 kB of additional disk space will be used.
[...]

(base-sid)root at gismo:/#
=====

Or, if you put my words in another way, why does perl-doc want nroff
when the POD version is enough?

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

Why all the Debian Med people is trying to get me helping them?  ;-)

Here is the patch:

--8<---------------cut here---------------start------------->8---
Index: debian/control
===================================================================
--- debian/control	(revision 8928)
+++ debian/control	(working copy)
@@ -54,13 +54,81 @@
 Package: bioperl
 Architecture: all
 Depends: libbio-perl-perl ( = ${source:Version} ), ${misc:Depends}, ${perl:Depends}
-Recommends: bioperl-run ( >= 1.6.0 )
+Recommends: bioperl-run ( >= 1.6.0 ),
+# for the following see #650412
+# most of `binary -help` outputs
+ perl-doc,
+# some libraries already in libbio-perl-perl's Recommends:
+# bp_biofetch_genbank_proxy
+ libhttp-message-perl,
+ libwww-perl,
+ libcache-cache-perl,
+# bp_blast2tree
+ libbio-perl-run-perl,
+# bp_bulk_load_gff
+ libdbi-perl,
+# bp_chaos_plot
+ libgd-gd2-perl,
+# bp_das_server
+ libapache-dbi-perl,
+# bp_download_query_genbank
+ liburi-perl,
+## libwww-perl
+# bp_einfo
+## liburi-perl
+## libhttp-message-perl
+ libxml-simple-perl,
+## libwww-perl
+# bp_fast_load_gff
+## libdbi-perl
+# bp_fetch [not for local indexing]
+## libwww-perl
+# bp_flanks
+## libhttp-message-perl
+## libwww-perl
+# bp_genbank2gff
+## libhttp-message-perl
+## libwww-perl
+## libdbi-perl
+# bp_genbank2gff3
+ libyaml-perl,
+## libwww-perl
+# bp_hivq
+## libhttp-message-perl
+## libwww-perl
+## libxml-simple-perl
+# bp_meta_gff
+## libdbi-perl
+# bp_netinstall
+## libwww-perl
+# bp_pairwise_kaks
+## libbio-perl-run-perl
+# bp_process_wormbase
+ libace-perl,
+# bp_query_entrez_taxa
+## libwww-perl
+# bp_remote_blast
+## libwww-perl
+# bp_revtrans-motif
+ liblist-moreutils-perl,
+# bp_taxid4species
+## libwww-perl
+ libxml-twig-perl,
+# bp_taxonomy2tree
+ libset-scalar-perl
+Suggests: groff-base
 Description: Perl tools for computational molecular biology
  The Bioperl project is a coordinated effort to collect computational methods
  routinely used in bioinformatics into a set of standard CPAN-style,
  well-documented, and freely available Perl modules. It is well-accepted
  throughout the community and used in many high-profile projects, e.g.,
  Ensembl.
+ .
+ The recommended packages are needed to run some of the included
+ binaries, for a detailed explanation including the specific Perl
+ modules please see README.Debian.
+ .
+ The suggested package enhances the manual pages.
 
 Package: libbio-perl-perl
 Section: perl
Index: debian/changelog
===================================================================
--- debian/changelog	(revision 8928)
+++ debian/changelog	(working copy)
@@ -1,3 +1,14 @@
+bioperl (1.6.901-2) UNRELEASED; urgency=low
+
+  [ Luca Capello ]
+  * debian/control:
+    + add Recommends: to some libraries already in libbio-perl-perl's
+      for binaries showing help output (Closes: #650412).
+  * debian/README.Debian:
+    + new file with a more detailed explanation about the above.
+
+ --
+
 bioperl (1.6.901-1) unstable; urgency=low
 
   * New upstream release.
--8<---------------cut here---------------end--------------->8---

Thx, bye,
Gismo / Luca
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