Running make test of bioperl-live reveals some modules are not installed on my system. I would prefer bioperl to require those modules to be installed automatically before bioperl is emerged on my ststem: The following is the out of make test: t/chaosxml...................Data::Stag::Writer not installed, cannot perform chaosxml tests t/Compatible.................No Set::Scalar. Unable to test Bio::Tree::Compatible t/DB.........................Bio::ASN1::EntrezGene not found, Bio::DB::EntrezGene module is not usable. Skipping tests. t/entrezgene.................Bio::ASN1::EntrezGene not installed, skipping tests t/interpro...................XML::DOM::XPath not found - skipping interpro tests t/protgraph..................Class::AutoClass or Clone not installed. This means that the module is not usable. Skipping tests
Few more: External Module Ace, Aceperl, is not installed on this computer. The Bio::DB::Ace in Bioperl needs it for access of ACeDB database External Module SVG::Graph, Generate optional SVG output, is not installed on this computer. The Bio::TreeIO::svggraph in Bioperl needs it for creating SVG images External Module Bio::ASN1::EntrezGene, Entrez Gene Bioperl Parser, is not installed on this computer. The Bio::SeqIO::entrezgene in Bioperl needs it for Parsers External Module XML::DOM::XPath, XML parser, is not installed on this computer. The in Bioperl needs it for Bio::SeqIO::interpro External Module Convert::Binary::C, Binary Data Conversion using C Types, is not installed on this computer. The Bio::SeqIO::strider in Bioperl needs it for Parsers External Module Data::Stag::Writer, XML writer, is not installed on this computer. The in Bioperl needs it for Bio::SeqIO::chaosxml External Module Set::Scalar, Bio::Tree::Compatible, is not installed on this computer. The Bio::Tree::Compatible in Bioperl needs it for proper operation External Module Class::AutoClass, Protocol for object creation, is not installed on this computer. The Bio::Graph::SimpleGraph in Bioperl needs it for creating objects Information: Some perl modules are missing, listed above. The only functionality that will be affected is also described above, the rest of bioperl will work fine. The installation of these external packages is very simple. You can read more about bioperl external dependencies in the INSTALL file or at: http://bioperl.org/Core/Latest/INSTALL
This will change a lot in bioperl-1.6. Compared to bioperl1.5 it was split into more packages, so some extra ebuild will have to be created.
It looks like this one isn't valid anymore. Please reopen if I am wrong.
# USE=test emerge -pv bioperl [ebuild R ] sci-biology/bioperl-1.6.1 USE="db graphviz network run sqlite -minimal" 0 kB # USE=test emerge bioperl [cut] >>> Emerging (1 of 1) sci-biology/bioperl-1.6.1 * BioPerl-1.6.1.tar.bz2 RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] * CPV: sci-biology/bioperl-1.6.1 * REPO: gentoo * USE: db elibc_glibc graphviz kernel_linux network run sqlite test userland_GNU x86 >>> Unpacking source... >>> Unpacking BioPerl-1.6.1.tar.bz2 to /var/tmp/portage/sci-biology/bioperl-1.6.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/bioperl-1.6.1/work >>> Preparing source in /var/tmp/portage/sci-biology/bioperl-1.6.1/work/BioPerl-1.6.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/bioperl-1.6.1/work/BioPerl-1.6.1 ... * Using Module::Build * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/sci-biology/bioperl-1.6.1/image/ --create_packlist=0 Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] Checking prerequisites... recommends: * Optional prerequisite Ace is not installed (wanted for access of ACeDB database, used by Bio::DB::Ace and Bio::DB::GFF::Adaptor::ace) * Optional prerequisite Array::Compare is not installed (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork) * Optional prerequisite Bio::ASN1::EntrezGene is not installed (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular dependency!]) * Optional prerequisite GraphViz is not installed (wanted for Phylogenetic Network Visulization, used by Bio::PhyloNetwork::GraphViz) * Optional prerequisite SVG::Graph is not installed (wanted for creating SVG images, used by Bio::TreeIO::svggraph) * Optional prerequisite Spreadsheet::WriteExcel is not installed (wanted for writing Excel files, used by Bio::Microarray::Tools::ReseqChip) * Optional prerequisite XML::DOM::XPath is not installed (wanted for parsing interpro features, used by Bio::FeatureIO::interpro) Checking features: Network...................enabled BioDBSeqFeature_mysql.....enabled BioDBGFF..................enabled BioDBSeqFeature_BDB.......enabled BioDBSeqFeature_SQLite....disabled - DBD::SQLite is not installed BioDBSeqFeature_Pg........disabled - DBD::Pg is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store live database tests? y/n [n] - will not run the BioDBGFF or BioDBSeqFeature live database tests Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively? [a] - will install all scripts Do you want to run tests that require connection to servers across the internet (likely to cause some failures)? y/n [n] - will not run internet-requiring tests Creating new 'MYMETA.yml' with configuration results Creating new 'Build' script for 'BioPerl' version '1.006001' >>> Source configured.
(In reply to comment #4) Unable to reproduce, check your setup. All the packages you listed in your build output exist in Portage and are listed as optional dependencies of Bioperl.
