On Sat, Sep 14, 2019 at 12:58 AM Andreas Tille <[email protected]> wrote:
BTW, we should care for bioperl more seriosly to reflect the restructuring > of the upstream code. > Checking their changelog, here are some other modules that have their own packages since the Buster bioperl release 1.7.2: as of bioperl version 1.7.5 2019-02-11: Bio::Symbol::* (no results in https://codesearch.debian.net/) as of bioperl version 1.7.3 2019-01-30: Bio::DB::Ace Bio::DB::EMBL 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 Bio::DB::SeqFeature::* Used in gbrowse, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929506 Bio::DB::GFF::Typename appears to be optional requirement for libbio-graphics-perl whose tests have been failing since 2019-02-07 due to missing dependencies: https://ci.debian.net/packages/libb/libbio-graphics-perl/unstable/amd64/ libbio-graphics-perl also needs Bio::DB::SeqFeature::* 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 Bio::DB::GenPept one example script in bioperl itself: https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Fexamples%2Ftk%2Fgsequence.pl&line=15 also optional dependency for bioperl_1.7.5-1/bin/bp_fetch 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 Bio::LiveSeq::* Optional dependency of bioperl itself https://codesearch.debian.net/search?q=Bio%3A%3ALiveSeq&literal=1 Bio::SeqIO::entrezgene Optional dependency of libbio-asn1-entrezgene-perl Bio::Taxonomy::* Possible optional dependency of https://codesearch.debian.net/show?file=bioperl_1.7.5-1%2Flib%2FBio%2FTaxon.pm&line=139 Bio::Cluster::* Bio::Tools::Run::RemoteBlast 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 Bio::Align::Graphics Bio::AlignIO::nexml Bio::AlignIO::stockholm Bio::Assembly::* Bio::ClusterI::* Bio::ClusterIO::* Bio::DB::BioFetch Bio::DB::CUTG Bio::DB::EntrezGene Bio::DB::Expression::* Bio::DB::GFF Bio::DB::GFF::Featname Bio::DB::GFF::Homol Bio::DB::GFF::Segment Bio::DB::HIV::* Bio::DB::MeSH Bio::DB::NCBIHelper Bio::DB::Query::GenBank Bio::DB::Query::HIVQuery Bio::DB::RefSeq Bio::DB::SeqVersion::* Bio::DB::TFBS::* Bio::DB::Taxonomy::entrez Bio::DB::Taxonomy::sqlite Bio::DB::Universal Bio::Draw::Pictogram Bio::Factory::MapFactoryI Bio::Index::Hmmer Bio::Index::Stockholm Bio::Map::* Bio::MapIO::* Bio::MolEvol::CodonModel Bio::Nexml::Factory Bio::NexmlIO Bio::Phenotype::* Bio::PhyloNetwork::* Bio::PopGen::* Bio::Restriction::* Bio::Root::Build Bio::Search::HSP::HMMERHSP Bio::Search::HSP::HmmpfamHSP Bio::Search::Hit::HMMERHit Bio::Search::Hit::HmmpfamHit Bio::Search::Hit::hmmer3Hit Bio::Search::Result::HMMERResult Bio::Search::Result::HmmpfamResult Bio::Search::Result::hmmer3Result Bio::SearchDist Bio::SearchIO::hmmer2 Bio::SearchIO::hmmer3 Bio::SearchIO::hmmer_pull Bio::SeqEvolution::* Bio::SeqFeature::SiRNA::* Bio::SeqIO::abi Bio::SeqIO::agave Bio::SeqIO::alf Bio::SeqIO::chadoxml Bio::SeqIO::chaos Bio::SeqIO::chaosxml Bio::SeqIO::ctf Bio::SeqIO::excel Bio::SeqIO::exp Bio::SeqIO::flybase_chadoxml Bio::SeqIO::lasergene Bio::SeqIO::nexml Bio::SeqIO::pln Bio::SeqIO::strider Bio::SeqIO::ztr Bio::Structure::* Bio::Tools::AlignFactory Bio::Tools::Analysis::* (except SimpleAnalysisBase) Bio::Tools::Gel Bio::Tools::HMMER::* Bio::Tools::Hmmpfam Bio::Tools::Phylo::Gumby Bio::Tools::Protparam Bio::Tools::SiRNA::* Bio::Tools::dpAlign Bio::Tree::AlleleNode Bio::Tree::Draw::Cladogram Bio::TreeIO::nexml Bio::TreeIO::svggraph Bio::Variation::* None of the above have any results in https://codesearch.debian.net/ > > Thanks for your work on this > > Andreas. > > -- > http://fam-tille.de > > -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/> https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670> [email protected] +1 480 627 9108
