[Debian-med-packaging] Bug#650412: bioperl: missing Recommends:/Suggests:
Luca Capello
luca at pca.it
Tue Nov 29 16:22:53 UTC 2011
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
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