Bug 234573 (perl-bioperl)

picking up for review.

This is really great! I'm looking forward to see bioperl in Fedora.

This review blocked by now package perl-Bio-ASN1-EntrezGene.

As mock build gave me
Error: Missing Dependency: perl(Bio::Index::AbstractSeq) is needed by package
perl-Bio-ASN1-EntrezGene

But I really confused when i checked cpan, I found that missing depencecy is
actually part of this(perl-bioperl) package then why its reported as its needed
by perl-Bio-ASN1-EntrezGene?

I am referring to
http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/EntrezGene.pm#PREREQUISITE

Need some help But for time being not blocking CVS request already made for
perl-Bio-ASN1-EntrezGene package.

The problem is a circular BuildRequires on perl-Bio-ASN1-EntrezGene package.  I
have removed this in this update:

* Mon Apr 02 2007 Alex Lancaster <alexl.net> 1.5.2_102-3
- Remove BuildRequires: perl(Bio::ASN1::EntrezGene), creates a
  circular dependency, the dependency is still found at install-time.

Spec URL: http://allele5.biol.berkeley.edu/~alex/fedora/perl-bioperl.spec
SRPM URL:
http://allele5.biol.berkeley.edu/~alex/fedora/perl-bioperl-1.5.2_102-3.src.rpm

As an aside, there is currently a discussion on the bioperl-l list about where
bioperl should live, on Fedora or in a third-party repository like
http://biopackages.net/.  See the thread at:

http://lists.open-bio.org/pipermail/bioperl-l/2007-March/thread.html#25279

One of the issue is in addition to this base bioperl package residing here,
there is bioperl-run which has interfaces to a number of non-free packages such
as Clustal which couldn't be packaged in Fedora.  Possibilities are:

1. Host the bioperl - the interfaces to non-free packages on Fedora and package
the non-free interfaces on biopackages.net
2. Host all bioperl-* packages on biopackages.net

I lean towards 1), but splitting up a single tarball across distributions can be
rather messy.  Ideas welcome.

(In reply to comment #6)
> 
> 1. Host the bioperl - the interfaces to non-free packages on Fedora 

Should read:

Host all of bioperl minus the interfaces to non-free packages on Fedora 

Created attachment 151548 [details]
Failed mock build's build.log

Attaching Mock build.log for your reference for further changes for make test
and is removing perl-Bio-ASN1-EntrezGene as BR is OK? Its giving warning in
build.log now.

It looks like many, if not, most, tests require network access, so we may have
to disable all of them.  It's OK to remove perl-Bio-ASN-EntrezGene, as it's the
only workaround  that will allow it to be installed (this is what upstream does
anyway).  It is added back as an auto-generated Requires for install-time, so
it's OK.

* Tue Apr 03 2007 Alex Lancaster <alexl.net> 1.5.2_102-4
- Disable tests because many of them require network access, add
  _with_check macro so they can be enabled during testing.

Spec URL: http://allele5.biol.berkeley.edu/~alex/fedora/perl-bioperl.spec
SRPM URL:
http://allele5.biol.berkeley.edu/~alex/fedora/perl-bioperl-1.5.2_102-4.src.rpm

Starting Review
Like to Note here first that build.log gave
Checking prerequisites...
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]
 * Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene)

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

    * Could not connect to test database
Checking features:
  BioDBSeqFeature_mysql....disabled
  BioDBGFF.................enabled
  BioDBSeqFeature_BDB......enabled

which seems not problematic.

(In reply to comment #11)
 
> ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
> of the modules indicated above before proceeding with this installation
> 
>     * Could not connect to test database
> Checking features:
>   BioDBSeqFeature_mysql....disabled
>   BioDBGFF.................enabled
>   BioDBSeqFeature_BDB......enabled
> 
> which seems not problematic.

Yep, it's just a warning, it must be ignored because of the circular build
dependency.

New SRPM URL:
http://allele5.biol.berkeley.edu/~alex/fedora/perl-bioperl-1.5.2_102-5.src.rpm

Review:
+ package builds in mock (development i386).
+ rpmlint is silent for SRPM and for RPM.
+ source files match upstream url
71f22246979ee5d6e19d547319962eea  bioperl-1.5.2_102.tar.bz2
+ package meets naming and packaging guidelines.
+ specfile is properly named, is cleanly written
+ Spec file is written in American English.
+ Spec file is legible.
+ dist tag is present.
+ build root is correct.
+ license is open source-compatible.
+ License text is included in package.
+ %doc is present.
+ BuildRequires are proper.
+ %clean is present.
+ package installed properly.
+ Macro use appears rather consistent.
+ Package contains code, not content.
+ no headers or static libraries.
+ no .pc file present.
+ no -devel subpackage
+ no .la files.
+ no translations are available
+ Does owns the directories it creates.
+ no scriptlets present.
+ no duplicates in %files.
+ file permissions are appropriate.
+ make test disabled.
+ Provides: perl(Bio::Align::AlignI) perl(Bio::Align::DNAStatistics)
perl(Bio::Align::PairwiseStatistics) perl(Bio::Align::ProteinStatistics)
perl(Bio::Align::StatisticsI) perl(Bio::Align::Utilities) perl(Bio::AlignIO)
perl(Bio::AlignIO::bl2seq) perl(Bio::AlignIO::clustalw)
perl(Bio::AlignIO::emboss) perl(Bio::AlignIO::fasta)
perl(Bio::AlignIO::largemultifasta) perl(Bio::AlignIO::maf)
perl(Bio::AlignIO::mase) perl(Bio::AlignIO::mega) perl(Bio::AlignIO::meme)
perl(Bio::AlignIO::metafasta) perl(Bio::AlignIO::msf) perl(Bio::AlignIO::nexus)
perl(Bio::AlignIO::pfam) perl(Bio::AlignIO::phylip) perl(Bio::AlignIO::po)
perl(Bio::AlignIO::prodom) perl(Bio::AlignIO::psi) perl(Bio::AlignIO::selex)
perl(Bio::AlignIO::stockholm) perl(Bio::AnalysisI) perl(Bio::AnalysisI::JobI)
perl(Bio::AnalysisParserI) perl(Bio::AnalysisResultI) perl(Bio::AnnotatableI)
perl(Bio::Annotation::AnnotationFactory) perl(Bio::Annotation::Collection)
perl(Bio::Annotation::Comment) perl(Bio::Annotation::DBLink)
perl(Bio::Annotation::OntologyTerm) perl(Bio::Annotation::Reference)
perl(Bio::Annotation::SimpleValue) perl(Bio::Annotation::StructuredValue)
perl(Bio::Annotation::Target) perl(Bio::Annotation::TypeManager)
perl(Bio::AnnotationCollectionI) perl(Bio::AnnotationI)
perl(Bio::Assembly::Contig) perl(Bio::Assembly::ContigAnalysis)
perl(Bio::Assembly::IO) perl(Bio::Assembly::IO::ace)
perl(Bio::Assembly::IO::phrap) perl(Bio::Assembly::Scaffold)
perl(Bio::Assembly::ScaffoldI) perl(Bio::Assembly::Singlet) perl(Bio::Biblio)
perl(Bio::Biblio::Article) perl(Bio::Biblio::BiblioBase) perl(Bio::Biblio::Book)
perl(Bio::Biblio::BookArticle) perl(Bio::Biblio::IO)
perl(Bio::Biblio::IO::medline2ref) perl(Bio::Biblio::IO::medlinexml)
perl(Bio::Biblio::IO::pubmed2ref) perl(Bio::Biblio::IO::pubmedxml)
perl(Bio::Biblio::Journal) perl(Bio::Biblio::JournalArticle)
perl(Bio::Biblio::MedlineArticle) perl(Bio::Biblio::MedlineBook)
perl(Bio::Biblio::MedlineBookArticle) perl(Bio::Biblio::MedlineJournal)
perl(Bio::Biblio::MedlineJournalArticle) perl(Bio::Biblio::Organisation)
perl(Bio::Biblio::Patent) perl(Bio::Biblio::Person)
perl(Bio::Biblio::Proceeding) perl(Bio::Biblio::Provider)
perl(Bio::Biblio::PubmedArticle) perl(Bio::Biblio::PubmedBookArticle)
perl(Bio::Biblio::PubmedJournalArticle) perl(Bio::Biblio::Ref)
perl(Bio::Biblio::Service) perl(Bio::Biblio::TechReport)
perl(Bio::Biblio::Thesis) perl(Bio::Biblio::WebResource)
perl(Bio::Cluster::ClusterFactory) perl(Bio::Cluster::FamilyI)
perl(Bio::Cluster::SequenceFamily) perl(Bio::Cluster::UniGene)
perl(Bio::Cluster::UniGeneI) perl(Bio::ClusterI) perl(Bio::ClusterIO)
perl(Bio::ClusterIO::dbsnp) perl(Bio::ClusterIO::unigene)
perl(Bio::CodonUsage::IO) perl(Bio::CodonUsage::Table) perl(Bio::ConfigData)
perl(Bio::Coordinate::Chain) perl(Bio::Coordinate::Collection)
perl(Bio::Coordinate::ExtrapolatingPair) perl(Bio::Coordinate::GeneMapper)
perl(Bio::Coordinate::Graph) perl(Bio::Coordinate::MapperI)
perl(Bio::Coordinate::Pair) perl(Bio::Coordinate::Result)
perl(Bio::Coordinate::Result::Gap) perl(Bio::Coordinate::Result::Match)
perl(Bio::Coordinate::ResultI) perl(Bio::Coordinate::Utils) perl(Bio::DB::Ace)
perl(Bio::DB::Biblio::biofetch) perl(Bio::DB::Biblio::eutils)
perl(Bio::DB::Biblio::pdf) perl(Bio::DB::Biblio::soap) perl(Bio::DB::BiblioI)
perl(Bio::DB::BioFetch) perl(Bio::DB::CUTG) perl(Bio::DB::DBFetch)
perl(Bio::DB::EMBL) perl(Bio::DB::EUtilities) perl(Bio::DB::EUtilities::Cookie)
perl(Bio::DB::EUtilities::ElinkData) perl(Bio::DB::EUtilities::efetch)
perl(Bio::DB::EUtilities::egquery) perl(Bio::DB::EUtilities::einfo)
perl(Bio::DB::EUtilities::elink) perl(Bio::DB::EUtilities::epost)
perl(Bio::DB::EUtilities::esearch) perl(Bio::DB::EUtilities::esummary)
perl(Bio::DB::EntrezGene) perl(Bio::DB::Expression)
perl(Bio::DB::Expression::geo) perl(Bio::DB::Failover) perl(Bio::DB::Fasta)
perl(Bio::DB::Fasta::Stream) perl(Bio::DB::FileCache) perl(Bio::DB::Flat)
perl(Bio::DB::Flat::BDB) perl(Bio::DB::Flat::BDB::embl)
perl(Bio::DB::Flat::BDB::fasta) perl(Bio::DB::Flat::BDB::genbank)
perl(Bio::DB::Flat::BDB::swiss) perl(Bio::DB::Flat::BDB::swissprot)
perl(Bio::DB::Flat::BinarySearch) perl(Bio::DB::GDB) perl(Bio::DB::GFF)
perl(Bio::DB::GFF::Adaptor::ace) perl(Bio::DB::GFF::Adaptor::berkeleydb)
perl(Bio::DB::GFF::Adaptor::berkeleydb::iterator)
perl(Bio::DB::GFF::Adaptor::biofetch)
perl(Bio::DB::GFF::Adaptor::biofetch_oracle) perl(Bio::DB::GFF::Adaptor::dbi)
perl(Bio::DB::GFF::Adaptor::dbi::caching_handle)
perl(Bio::DB::GFF::Adaptor::dbi::faux_dbh)

APPROVED.

In reply to comment 4:

> As mock build gave me
> Error: Missing Dependency: perl(Bio::Index::AbstractSeq)
> is needed by package perl-Bio-ASN1-EntrezGene

It is broken in the needsign queue, too, as extras-repoclosure
also detects this. I've blacklisted the builds for now (FC-5,
FC-6, development).

(In reply to comment #14)
> In reply to comment 4:
> 
> > As mock build gave me
> > Error: Missing Dependency: perl(Bio::Index::AbstractSeq)
> > is needed by package perl-Bio-ASN1-EntrezGene
> 
> It is broken in the needsign queue, too, as extras-repoclosure
> also detects this. I've blacklisted the builds for now (FC-5,
> FC-6, development).

These packages depend on each other, so once this package is built,
perl-Bio-ASN1-EntrezGene will have it's dependency satisfied.  It no longer
needs perl-Bio-ASN1-EntrezGene at build-time.

New Package CVS Request
=======================
Package Name: perl-bioperl
Short Description: A package of Perl tools for computational molecular biology
Owners: alexl.net
Branches: FC-5 FC-6
InitialCC: 

This directory exists in CVS as an orphaned package.

What provides 'perl(Bio::Index::AbstractSeq)'?
Comment 13 doesn't list it.
But the module is part of bioperl.
So what's wrong in the dependencies?

The dependencies are like this ===>

rpm -q --requires perl-Bio-ASN1-EntrezGene | grep Bio
perl(Bio::ASN1::EntrezGene)  
perl(Bio::ASN1::Sequence)  
perl(Bio::Index::AbstractSeq) 

rpm -q --provides perl-Bio-ASN1-EntrezGene
perl(Bio::ASN1::EntrezGene) = 1.09
perl(Bio::ASN1::EntrezGene::Indexer) = 1.09
perl(Bio::ASN1::Sequence) = 1.09
perl(Bio::ASN1::Sequence::Indexer) = 1.09
perl-Bio-ASN1-EntrezGene = 1.091-2

rpm -q --requires perl-bioperl | grep Bio::ASN1
perl(Bio::ASN1::EntrezGene)  

rpm -q --provides perl-bioperl | grep Abstract
perl(Bio::Index::Abstract)  
perl(Bio::Index::AbstractSeq)  

Okay, then your list in comment 13 is truncated.

Created attachment 151551 [details]
Complete provides list

Yes, I've attached the full list the result of:

rpm -q --provides perl-bioperl > /tmp/bioperl-provides

I think the Summary can be shortened to
"Perl tools for computational molecular biology".

CVS ownership added.

Alex, you may need to be careful with the old FC-5 and FC-6 branches
since they still contain the previous packaging.

Builds and installs in devel.  Closing bug.