Your message dated Wed, 14 Dec 2011 09:02:24 +0000
with message-id <[email protected]>
and subject line Bug#650412: fixed in bioperl 1.6.901-2
has caused the Debian Bug report #650412,
regarding bioperl: missing Recommends:/Suggests:
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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--
650412: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650412
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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" |
| bp_bulk_load_gff | missing Perl module | libdbi-perl
(DBI.pm) |
| | unknown option [help] |
|
| | | [help contains
"bulk_load_gff.pl" |
| | | [help contains
"(bp_)fast_load_gff.pl" |
| | | [help contains
"(bp_)load_gff.pl" |
| bp_chaos_plot | missing Perl module | libgd-gd2-perl
(GD.pm) |
| | unknown option [help] |
|
| | | [help contains
"chaos_plot" |
| bp_classify_hits_kingdom | need perl-doc, nroff | perl-doc
|
| bp_composite_LD | need perl-doc, nroff | perl-doc
|
| bp_das_server | missing Perl module | libapache-dbi-perl
(Apache/DBI.pm) |
| | invalid request [no help] |
|
| bp_dbsplit | unknown option [no help] |
|
| bp_download_query_genbank | missing Perl module | liburi-perl
(URI/Escape.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | need perl-doc, nroff | perl-doc
|
| bp_einfo | missing Perl module | liburi-perl
(URI.pm) |
| | missing Perl module |
libhttp-message-perl (HTTP/Request.pm) |
| | missing Perl module | libxml-simple-perl
(XML/Simple.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | need perl-doc, nroff | perl-doc
|
| bp_extract_feature_seq | unknown option [no help] |
|
| | Bio::Root::Exception | file argument
provided, but with an undefined value |
| bp_fast_load_gff | missing Perl module | libdbi-perl
(DBI.pm) |
| | unknown option [help] |
|
| | | [help contains
"(bp_)fast_load_gff.pl" |
| | | [help contains
"(bp_)bulk_load_gff.pl" |
| | | [help contains
"(bp_)load_gff.pl" |
| bp_fastam9_to_table | need perl-doc, nroff | perl-doc,
groff-base |
| bp_fetch | unknown option |
|
| | missing Perl module | libwww-perl
(LWP.pm) [not for local indexing] |
| | need perl-doc, nroff | perl-doc,
groff-base |
| | | [help contains
"bp_fetch.pl"] |
| bp_filter_search | unknown option [no help] |
|
| bp_flanks | missing Perl module |
libhttp-message-perl (HTTP/Request/Common.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | need perl-doc, nroff | perl-doc,
groff-base |
| | | [help contains
"flanks" |
| bp_gccalc | | [help contains
"gccalc.pl"] |
| bp_genbank2gff | missing Perl module |
libhttp-message-perl (HTTP/Request/Common.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | missing Perl module | libdbi-perl
(DBI.pm) |
| | unknown option [help] |
|
| bp_genbank2gff3 | missing Perl module | libyaml-perl
(YAML.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | | [help contains
"genbank2gff3.pl" |
| | | [help contains
"gmod_bulk_load_gff3.pl" |
| bp_generate_histogram | unknown option [help] |
|
| bp_heterogeneity_test | need perl-doc, nroff | perl-doc,
groff-base |
| bp_hivq | missing Perl module |
libhttp-message-perl (HTTP/Request/Common.pm) |
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | missing Perl module | libxml-simple-perl
(XML/Simple.pm) |
| | unknown option [no help] |
|
| | need perl-doc, nroff | perl-doc,
groff-base |
| | | [help via `perldoc
-F /usr/bin/bp_hivq`] |
| bp_hmmer_to_table | need perl-doc, nroff | perl-doc,
groff-base |
| bp_index | unknown option |
|
| | need perl-doc, nroff | perl-doc,
groff-base |
| bp_load_gff | unknown option [help] |
|
| | | [help contains
"(bp_)load_gff.pl" |
| | | [help contains
"bp_fast_load_gff.pl" |
| | | [help contains
"(bp_)bulk_load_gff.pl" |
| bp_local_taxonomydb_query | need perl-doc, nroff | perl-doc,
groff-base |
| bp_make_mrna_protein | | [help contains
"make_mrna_protein.pl"] |
| bp_mask_by_search | need perl-doc, nroff | perl-doc,
groff-base |
| bp_meta_gff | missing Perl module | libdbi-perl
(DBI.pm) |
| | unknown option [help] |
|
| bp_mrtrans | need perl-doc, nroff | perl-doc,
groff-base |
| bp_mutate | need perl-doc, nroff | perl-doc,
groff-base |
| bp_netinstall | missing Perl module | LWP/Simple.pm
|
| | | [help contains
"bp_netinstall.pl" |
| bp_nexus2nh | unknown option [hangs up] |
|
| bp_nrdb | unknown option |
|
| | need perl-doc, nroff | perl-doc,
groff-base |
| bp_oligo_count | |
|
| bp_pairwise_kaks | need bioperl-run |
libbio-perl-run-perl |
| | need perl-doc, nroff | perl-doc,
groff-basec |
| | | [help contains
"pairwise_kaks.PLS" |
| bp_parse_hmmsearch | need perl-doc, nroff | perl-doc,
groff-basec |
| bp_process_gadfly | | [help contains
"process_gadfly.pl"] |
| | | [help contains
"bulk_load_gff.pl"] |
| bp_process_sgd | | [help contains
"process_sgd.pl"] |
| | | [help contains
"bulk_load_gff.pl"] |
| bp_process_wormbase | missing Perl module | libace-perl
(Ace.pm) |
| | | [help contains
"process_wormbase.pl" |
| | | [help contains
"bulk_load_gff.pl" |
| bp_query_entrez_taxa | unknown option [no help] |
|
| | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| bp_remote_blast | missing Perl module | libwww-perl
(LWP.pm) |
| | need perl-doc, nroff | perl-doc,
groff-base |
| | | [help contains
"remote_blast.pl" |
| bp_revtrans-motif | missing Perl module |
liblist-moreutils-perl (List/MoreUtils.pm) |
| | need perl-doc, nroff | perl-doc,
groff-base |
| bp_search2BSML | need perl-doc, nroff | perl-doc,
groff-base |
| bp_search2alnblocks | need perl-doc, nroff | perl-doc,
groff-base |
| bp_search2gff | need perl-doc, nroff | perl-doc,
groff-base |
| bp_search2table | unknown option [no help] |
|
| bp_search2tribe | need perl-doc, nroff | perl-doc,
groff-base |
| bp_seq_length | unknown option |
|
| | need perl-doc, nroff | perl-doc,
groff-base |
| bp_seqconvert | |
|
| bp_seqfeature_delete | unknown option [help] |
|
| bp_seqfeature_gff3 | unknown option [help] |
|
| bp_seqfeature_load | |
|
| bp_seqret | unknown option [no help] |
|
| bp_seqretsplit | can not open -help [no help] |
|
| bp_split_seq | unknown option [no help] |
|
| bp_sreformat | |
|
| bp_taxid4species | missing Perl module | libwww-perl
(LWP/UserAgent.pm) |
| | missing Perl module | libxml-twig-perl
(XML/Twig.pm) |
| bp_taxonomy2tree | missing Perl module | libset-scalar-perl
(Set/Scalar.pm) |
| | unknown option [no help] |
|
| | Bio::Root::Exception | Cannot open node
file 'nodes.dmp' for reading |
| bp_translate_seq | unknown option [no help] |
|
| bp_tree2pag | need perl-doc, nroff | perl-doc,
groff-base |
| bp_unflatten_seq | need perl-doc, nroff | perl-doc,
groff-base |
|---------------------------+------------------------------+------------------------------------------------------------|
And here the ones added when installing bioperl-run (all of these
scripts are provided with the .pl extension, see #190753):
|-------------------------------------+--------------------------+---------------------------------|
| binary | `binary -help` output | missing
dependencies |
|-------------------------------------+--------------------------+---------------------------------|
| bp_bioperl_application_installer.pl | installation [no help] |
|
| | .pl extension |
|
| bp_multi_hmmsearch.pl | unknown option [no help] |
|
| | .pl extension |
|
| bp_panalysis.pl | | [help
contains "panalysis.PLS"] |
| | .pl extension |
|
| bp_run_neighbor.pl | need perl-doc, nroff | perl-doc,
groff-base |
| | .pl extension |
|
| bp_run_protdist.pl | need perl-doc, nroff | perl-doc,
groff-base |
| | .pl extension |
|
|-------------------------------------+--------------------------+---------------------------------|
Thx, bye,
Gismo / Luca
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.0.0-2-amd64 (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C)
Shell: /bin/sh linked to /bin/dash
Versions of packages bioperl depends on:
ii libbio-perl-perl 1.6.901-1
ii perl 5.12.4-6
Versions of packages bioperl recommends:
ii bioperl-run 1.6.9-1
bioperl suggests no packages.
-- no debconf information
pgpsUEvWVkrgT.pgp
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: bioperl
Source-Version: 1.6.901-2
We believe that the bug you reported is fixed in the latest version of
bioperl, which is due to be installed in the Debian FTP archive:
bioperl_1.6.901-2.debian.tar.gz
to main/b/bioperl/bioperl_1.6.901-2.debian.tar.gz
bioperl_1.6.901-2.dsc
to main/b/bioperl/bioperl_1.6.901-2.dsc
bioperl_1.6.901-2_all.deb
to main/b/bioperl/bioperl_1.6.901-2_all.deb
libbio-perl-perl_1.6.901-2_all.deb
to main/b/bioperl/libbio-perl-perl_1.6.901-2_all.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated bioperl package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Wed, 14 Dec 2011 09:11:41 +0100
Source: bioperl
Binary: bioperl libbio-perl-perl
Architecture: source all
Version: 1.6.901-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
bioperl - Perl tools for computational molecular biology
libbio-perl-perl - BioPerl core perl modules
Closes: 650412
Changes:
bioperl (1.6.901-2) unstable; 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.
.
[ Andreas Tille ]
* debian/source/format: 3.0 (quilt)
* Added myself to Uploaders
Checksums-Sha1:
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529ffae3fe3b1f246ac99b9c86cc2c116c0a4ab3 10852 bioperl_1.6.901-2.debian.tar.gz
13b2a319c932c1b4e31205856c8bb7309b2ac2e0 464486 bioperl_1.6.901-2_all.deb
a3c9ed9f961e5ad20222e27b1827476931200cf0 6150916
libbio-perl-perl_1.6.901-2_all.deb
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Files:
f2e586bf9e867375fea986407caade5a 2243 science optional bioperl_1.6.901-2.dsc
366d1ea67749c87d89d74ccf4c7fb786 10852 science optional
bioperl_1.6.901-2.debian.tar.gz
07f21ace6bfaf6d05ddb2f1a9e031d3b 464486 science optional
bioperl_1.6.901-2_all.deb
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