Re: Bulk RFS Re: Packages needed for the bioperl restructuring
Continuing my last mail ...
On Sun, Sep 15, 2019 at 07:48:39AM +0200, Andreas Tille wrote:
> On Sun, Sep 15, 2019 at 01:31:35AM +0900, Michael Crusoe wrote:
> > gbp clone git@salsa.debian.org:med-team/libbio-db-biofetch-perl.git
>
> Please use lintian-brush 0.28 (from unstable/testing). It does a better
> job with debian/upstream/metadata. I just "polished" with this version.
> I also fixed the interpreter path inside the example.
>
> > and 5 more below:
>
> I'll do this later - real life things for today.
>
> Thanks a lot for your preparation
>
> Andreas.
>
> > On Sat, Sep 14, 2019 at 7:25 PM Michael Crusoe <michael.crusoe@gmail.com>
> > wrote:
> > >
> > > BTW, we should care for bioperl more seriosly to reflect the restructuring
> > >> of the upstream code.
> > >>
> > >
> > > as of bioperl version 1.7.3 2019-01-30:
> > >
> > > Bio::DB::Ace
> > >
> >
> > gbp clone git@salsa.debian.org:med-team/libbio-db-ace-perl.git
Done.
> >
> > > Bio::DB::EMBL
> > >
> >
> > gbp clone git@salsa.debian.org:med-team/libbio-db-embl-perl.git
Here I get a failure:
...
dh_auto_test
make -j4 test TEST_VERBOSE=1
make[1]: Entering directory '/build/libbio-db-embl-perl-1.7.4'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ...........
1..1
ok 1 - Bio/DB/EMBL.pm loaded ok
ok
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
# No tests run!
t/EMBL.t .................
1..16
1..0 # Skipped: no host: www.google.com
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 16/16 subtests
Test Summary Report
-------------------
t/EMBL.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: More than one plan found in TAP output
Bad plan. You planned 16 tests but ran 0.
Files=5, Tests=1, 1 wallclock secs ( 0.02 usr 0.02 sys + 0.28 cusr 0.02 csys = 0.34 CPU)
Result: FAIL
Failed 1/5 test programs. 0/1 subtests failed.
(Please git pull for minor changes)
> > > Optional dependency for bioperl_1.7.5-1/bin/bp_fetch
> > >
> > > Bio::DB::GFF::Adaptor::*
> > > Bio::DB::GFF::Aggregator::*
> > > Bio::DB::GFF::Feature
> > > Bio::DB::GFF::RelSegment
> > >
> >
> > gbp clone git@salsa.debian.org:med-team/libbio-db-gff-perl.git
Done.
> >
> > > Bio::DB::SeqFeature::*
> > > Used in gbrowse, see
> > > https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929506
> > >
> >
> > gbp clone git@salsa.debian.org:med-team/libbio-db-seqfeature-perl.git
Done.
> > > Bio::DB::GenBank
> > > needed for an example script in libtfbs-perl:
> > > https://codesearch.debian.net/show?file=libtfbs-perl_0.7.1-2%2Fexamples%2Fscript1.pl&line=2
> > > Its tests are still passing
> > > https://ci.debian.net/packages/libt/libtfbs-perl/
> > > Also optional dependency for bioperl_1.7.5-1/bin/bp_fetch
> > >
> >
> > Package is at https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl
> > but it is blocked by
> > https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl
Which at least needs also libbio-seqio-entrezgene-perl which is not on
Salsa yet. Please git pull for some automatic changes.
> > > Bio::DB::SwissProt
> > > Optional dependency for bioperl itself:
> > > https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Ft%2FRemoteDB%2FSeqRead_fail.t&line=26
> > >
> >
> > Waiting on https://github.com/bioperl/Bio-DB-SwissProt/issues/2
> >
> >
> > > Bio::LiveSeq::*
> > > Optional dependency of bioperl itself
> > > https://codesearch.debian.net/search?q=Bio%3A%3ALiveSeq&literal=1
> > >
> >
> > Waiting on https://github.com/bioperl/Bio-LiveSeq/issues/2
> >
> >
> > > Bio::SeqIO::entrezgene
> > > Optional dependency of libbio-asn1-entrezgene-perl
> > >
> >
> > Also waiting on https://github.com/bioperl/Bio-Variation/issues/2
Added another vote (no idea whether that might be helpful.
> > > Bio::Taxonomy::*
> > > Possible optional dependency of
> > > https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Flib%2FBio%2FTaxon.pm&line=139
> > >
> >
> > Waiting on https://github.com/bioperl/Bio-Variation/issues/2
> >
> >
> > >
> > > Bio::Cluster::*
> > >
> >
> > Packaging at https://salsa.debian.org/med-team/libbio-cluster-perl but also
> > waiting on Bio::Variation to be published to CPAN
Waiting ... (but also please git pull as for every other package here)
> >
> > > Bio::Tools::Run::RemoteBlast
> > >
> >
> > gbp clone git@salsa.debian.org:
> > med-team/libbio-tools-run-remoteblast-perl.git
Done.
> > > Dependency of bioperl-run:
> > > https://codesearch.debian.net/show?file=bioperl-run_1.7.3-1%2Ft%2FTools%2FRun%2FRemoteBlast.t&line=16
> > > bioperl-run is failing tests:
> > > https://ci.debian.net/data/autopkgtest/unstable/amd64/b/bioperl-run/2952351/log.gz
> > > Can't locate File/Sort.pm
> > > Can't locate Bio/DB/EUtilities.pm
> > > Can't locate Bio/FeatureIO.pm
> > > Can't locate Bio/Cluster/SequenceFamily.pm
> > >
> > > Bio::Tools::pSW
> > > Optional dependency of bioperl
> > > https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Fexamples%2Falign%2Faligntutorial.pl&line=1
> > >
> >
> > No longer maintained as per
> > https://github.com/bioperl/bioperl-ext#overall-notes
OK, I hope I just did all you wanted me to do - if not please ping
back.
Thanks for your work on this
Andreas.
--
http://fam-tille.de
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