Viewing all changes in revision 3.
- Committer: Bazaar Package Importer
- Date: 2009-09-03 11:00:03 UTC
- mfrom: (1.1.1 upstream)
- Revision ID: james.westby@ubuntu.com-20090903110003-11of27rxner5vnl9
* New upstream release.
*Â debian/patches/10-wrong-path-for-interpreter.patch:Â removed
  (fixed upstream).
* debian/watch updated (bioperl -> BioPerl).
* debian/rules refreshed with dh-make-perl 0.53.
  - Disabled installation of examples (removed upstream).
  - Removed the correction of file permission of Pise documentation
    (removed upstream).
  - Removed patching facilities (no patches anymore).
  - Disabled tests as I experience failures with t/Eponine.t despite
    this program is not installed.
*Â debian/copyright:
  - Removed vanity lines about debianization and debian copyright.
  - Incremented years to 2009.
  - Updated to latest experimentation of the machine-readable license summary.
*Â debian/control:
  - Incremented Standards-Version to reflect conformance on new Policy
    (dropped versionned build-dependancy on Perl).
  - Removed build-dependancy on quilt (no patches anymore).
  - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
  - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
    libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
  - Build-depends on libarray-compare-perl and libtree-dagnode-perl
    (otherwise tests fail).Â
  - Depend on amap-align instead of amap (Closes: #541274).
*Â debian/patches/10-wrong-path-for-interpreter.patch:Â removed
  (fixed upstream).
* debian/watch updated (bioperl -> BioPerl).
* debian/rules refreshed with dh-make-perl 0.53.
  - Disabled installation of examples (removed upstream).
  - Removed the correction of file permission of Pise documentation
    (removed upstream).
  - Removed patching facilities (no patches anymore).
  - Disabled tests as I experience failures with t/Eponine.t despite
    this program is not installed.
*Â debian/copyright:
  - Removed vanity lines about debianization and debian copyright.
  - Incremented years to 2009.
  - Updated to latest experimentation of the machine-readable license summary.
*Â debian/control:
  - Incremented Standards-Version to reflect conformance on new Policy
    (dropped versionned build-dependancy on Perl).
  - Removed build-dependancy on quilt (no patches anymore).
  - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
  - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
    libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
  - Build-depends on libarray-compare-perl and libtree-dagnode-perl
    (otherwise tests fail).Â
  - Depend on amap-align instead of amap (Closes: #541274).
- files added:
- Bio/Installer/Hyphy.pm
- Bio/Tools/Run/Phylo/Hyphy
- Bio/Tools/Run/Phylo/Njtree
- Bio/Tools/Run/Phylo/Phast
- t/data/gerp
- t/data/gumby
- t/data/taxdump
- t/lib/Sub
- t/lib/Test/Harness
- files removed:
- Bio/Tools/Run/AbstractRunner.pm
- Bio/Tools/Run/Phylo/Forester
- Bio/Tools/Run/PiseApplication
- debian/patches
- examples
- examples/pise
- files modified:
- Bio/Factory/EMBOSS.pm *
- Build.PL *
- scripts/run_neighbor.PLS *
- scripts/run_protdist.PLS *
- t/Amap.t *
- t/Blat.t *
- t/Coil.t *
- t/DBA.t *
- t/LVB.t *
- t/PAML.t *
- t/Seg.t *
- t/Sim4.t *
- t/data/FootPrinter.seq.fa *
- t/data/Genscan.FastA *
- t/data/NM_002254.gb *
- t/data/Phrap.fa *
- t/data/Primer3.fa *
- t/data/Prints_prot.FastA *
- t/data/TribeMCL.bls *
- t/data/TribeMCL.desc *
- t/data/amino.fa *
- t/data/blat_dna.fa *
- t/data/cel-cbr-fam.aln *
- t/data/codeml.mlc *
- t/data/coil_protein_input *
- t/data/consense.treefile *
- t/data/cysprot.msf *
- t/data/cysprot1a.fa *
- t/data/cysprot1a.msf *
- t/data/cysprot1b.fa *
- t/data/cysprot1b.msf *
- t/data/dba1a.fa *
- t/data/dba1b.fa *
- t/data/dba2.fa *
- t/data/dna1.fa *
- t/data/dna2.fa *
- t/data/ecolitst.fa *
- t/data/eponine.fa *
- t/data/exonerate_cdna.fa *
- t/data/exonerate_cdna_rev.fa *
- t/data/exonerate_genomic.fa *
- t/data/exonerate_genomic_rev.fa *
- t/data/fasta.fa *
- t/data/fastalib.fa *
- t/data/fastaprot.fa *
- t/data/fontfile *
- t/data/gf-s85.phylip *
- t/data/hmmpfam_protein_input *
- t/data/human.genomic *
- t/data/lagan_dna.fa *
- t/data/lvb.fa *
- t/data/lvb_sequential.phy *
- t/data/neighbor.dist *
- t/data/new_dna.fa *
- t/data/new_pep.fa *
- t/data/pfam_sample_R11 *
- t/data/primate_query.fa *
- t/data/primate_target.fa *
- t/data/prints.dat *
- t/data/profile_prot.FastA *
- t/data/prosite.dat *
- t/data/protpars.phy *
- t/data/ps1.fa *
- t/data/repeatmasker.fa *
- t/data/road.pep *
- t/data/signalp_input_protein *
- t/data/sim4_cdna.fa *
- t/data/sim4_database.fa *
- t/data/sim4_genomic.fa *
- t/data/test.txt *
- t/data/test_prot.FastA *
- t/data/tree_of_life *
- t/data/treefile.example *
- t/data/vista.cls *
- t/data/vista.gff *
- t/lib/Test/Builder.pm *
- t/lib/Test/Builder/Module.pm *
- t/lib/Test/Builder/Tester.pm *
- t/lib/Test/More.pm *
- t/lib/Test/Simple.pm *
- t/lib/Test/Tutorial.pod *
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