Sources are in bioperl-1.5.2_102.tar.bz2 and not in bioperl-1.5.2.tar.bz2 so I ahd to touch the ebuild of 1.5.1-r1.
Created attachment 119710 [details] bioperl-1.5.2.ebuild
Created attachment 119712 [details] bioperl-1.5.2.ebuild Updated ebuild, but still not working correctly, as the build step requires user interaction.
Created attachment 179059 [details] bioperl-1.5.2.ebuild Fixed ebuild. Should be error-free. Tested lightly.
Created attachment 179060 [details] bioperl-1.5.2.ebuild Improved the /etc/env.d/22bioperl file (actually not much useful anyway as long as user has sci-biology/ncbi-tools) -- which are not REQUIREd by this package.
ribosome - any ETA on this? need help?
Created attachment 181908 [details] files/bioperl Forgot to attach the files/bioperl file.
Actually, the DEPENDs on sci-libs/io_lib could be dropped completely. A not yet existing sci-biology/bioperl-ext should REQUIRE <sci-libs/io_lib-1.9. See http://www.bioperl.org/wiki/Ext_package for details.
Bioperl 1.6.0 compiles fine but requires perl 5.10, which is in perl-experimental. This is due to a dependency on a newer version of CPAN.pm than perl 5.8 provides. We need to either remove/handle that dependency manually or wait for perl 5.10 to hit the main tree.
The BioPerl distribution has been split into several sub-packages. From http://www.bioperl.org/wiki/Getting_BioPerl : * Core package provides the main parsers, this is the basic package and it's required by all the other packages (bioperl-live Subversion directory) * Run package provides wrappers for executing some 60 common bioinformatics applications (bioperl-run in Subversion) * BioPerl db is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in Subversion). * Network package parses and analyzes protein-protein interaction data (bioperl-network in Subversion). * GUI package includes some basic widgets in Perl-Tk (bioperl-gui in Subversion). * Ext package is for C-language extensions including some alignment algorithms and an interface to the Staden IO library (bioperl-ext in Subversion). * Pedigree package is for manipulating genotype, marker, and individual data for linkage studies (bioperl-pedigree in Subversion) * Microarray package has preliminary objects for manipulating some microarray data formats (bioperl-microarray in Subversion) * Pipeline package is a project for creating analysis pipelines out of bioperl-run modules (bioperl-pipeline in Subversion).
I have committed the ebuild bioperl-1.6.0 into the main tree in testing. Be advised: - The ebuild is incomplete, as it does not pull the following recommended dependencies advertised by the package: # >=dev-lang/perl-5.10.0 (includes cpan >= 1.81) # dev-perl/SVG-Graph # dev-perl/Ace # dev-perl/Bio-ASN1-EntrezGene # dev-perl/XML-DOM-XPath # dev-perl/Convert-Binary-C - The ebuild is not informed of the new BioPerl subproject structure, but that's OK for testing purposes, as nothing but the core has been released in 1.6.0 at this time (from http://www.bioperl.org/wiki/Getting_BioPerl : "Only core modules have been released for 1.6 at this time, but the accompanying packages (run,network,db) will be released soon after.") Eventually sci-biology/bioperl will become a metapackage and we'll create bioperl-core, bioperl-db, etc. (bioperl-run is already there) - Non-x86 keywords are dropped, I'll need other archs to test this. - I haven't tested this much. Please test.
Finally, the following dependencies in the 1.5.1 ebuild are no longer advertised by the package, and I need verification from the testers that they are no longer needed by the core package (some or all of these will be required by the split sub-packages): # Deprecated/unrecognized deps from 1.5 series (to be verified): #virtual/perl-File-Temp #dev-perl/IO-String #dev-perl/IO-stringy #virtual/perl-Storable #dev-perl/libxml-perl #dev-perl/Text-Shellwords #~sci-libs/io_lib-1.8.12b #!>=sci-libs/io_lib-1.9 # gd? ( # >=dev-perl/GD-1.32-r1 # dev-perl/SVG # dev-perl/GD-SVG # ) # mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
New ebuilds in tree: bioperl-1.6.0-r1 bioperl-9999 bioperl-run-1.6.1 bioperl-run-9999 bioperl-network-1.6.0 bioperl-network-9999 bioperl-db-1.6.0 bioperl-db-9999 biosql-1.0.1 ... and various Perl dependencies for bioperl (all in core). Please test/comment.
Installed fine on ~x86. Did only very light testing of bioperl itself. Thanks.
Stable on x86 and amd64. Please reopen if you need other archs.
