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 [email protected]: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 <[email protected]> > > 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 [email protected]:med-team/libbio-db-ace-perl.git
Done. > > > > > Bio::DB::EMBL > > > > > > > gbp clone [email protected]: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 [email protected]: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 [email protected]: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 [email protected]: > > 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
