Update to 1.007001 Upstream changes: 1.7.1 - "Election" [Bugs] * Minor release to incorporate fix for CPAN indexing, which prevented proper updates [cjfields] * Fix problem in managing Target attribute for gff3 [Jukes34] * Minor bug fixes related to NCBI HTTPS support [cjfields] 1.7.0 - "Disney" [New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!! * Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!) [Code changes] * Previously deprecated modules removed * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif * Bio::DB::SeqHound has been removed due to the service no longer being available * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN * Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be added on CPAN [New features] * Docker instances of tagged releases are available! [hlapp] * NCBI HTTPS support [mjohnson and others] * Bio::SearchIO::infernal - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo] * Bio::Search::HSP::ModelHSP - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH reports [pcantalupo] * Bio::Search::Result::INFERNALResult - Added new module to represent features of Infernal reports [pcantalupo] * Bio::DB::Taxonomy SQLite option [cjfields] * WrapperBase quoted option values [majensen] * Various documentation fixes and updates [bosborne] [Bug Fixes] * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields] * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne] * NeXML parser fixes [fjossandon] * Bug fix for Bio::DB::SeqFeature memory adapter [lstein] * RT 103272 : SeqFeature database deletion skipped features with a decimal - Joshua Fortriede (Xenbase) * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon] * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon] * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon] * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields] * Issue #84: EMBL format wrapping problem [nyamned] * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon] * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex or compiled C code (when Inline::C is installed) [rocky] * Fix various Bio::Tools::Analysis remote server config problems [cjfields] * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon] * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon] * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef to be consistent with "$hit->bits" behaviour [fjossandon] * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF aminoacids made "next_seq" confused and broke the parser [fjossandon] * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table Definition, so now "join(complement(C..D),complement(A..B))" is equivalent to "complement(join(A..B,C..D))" [fjossandon] * For the many many many fixes that weren't mentioned - blame the release guy!diff -r1.32 -r1.33 pkgsrc/biology/bioperl/Makefile
(wen)
@@ -1,18 +1,17 @@ | @@ -1,18 +1,17 @@ | |||
1 | # $NetBSD: Makefile,v 1.32 2016/07/09 06:37:50 wiz Exp $ | 1 | # $NetBSD: Makefile,v 1.33 2016/11/06 08:05:24 wen Exp $ | |
2 | 2 | |||
3 | DISTNAME= BioPerl-1.6.924 | 3 | DISTNAME= BioPerl-1.007001 | |
4 | PKGNAME= ${DISTNAME:tl} | 4 | PKGNAME= ${DISTNAME:tl} | |
5 | PKGREVISION= 2 | |||
6 | CATEGORIES= biology perl5 | 5 | CATEGORIES= biology perl5 | |
7 | MASTER_SITES= ${MASTER_SITE_PERL_CPAN:=Bio/} | 6 | MASTER_SITES= ${MASTER_SITE_PERL_CPAN:=Bio/} | |
8 | 7 | |||
9 | MAINTAINER= filip@joyent.com | 8 | MAINTAINER= filip@joyent.com | |
10 | HOMEPAGE= http://www.bioperl.org/ | 9 | HOMEPAGE= http://www.bioperl.org/ | |
11 | COMMENT= Perl tools for computational molecular biology | 10 | COMMENT= Perl tools for computational molecular biology | |
12 | LICENSE= ${PERL5_LICENSE} | 11 | LICENSE= ${PERL5_LICENSE} | |
13 | 12 | |||
14 | #BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build | 13 | #BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build | |
15 | BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most | 14 | BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most | |
16 | 15 | |||
17 | DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres | 16 | DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres | |
18 | DEPENDS+= p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare | 17 | DEPENDS+= p5-Array-Compare-[0-9]*:../../devel/p5-Array-Compare |
@@ -1,14 +1,14 @@ | @@ -1,14 +1,14 @@ | |||
1 | @comment $NetBSD: PLIST,v 1.3 2014/02/20 14:44:16 fhajny Exp $ | 1 | @comment $NetBSD: PLIST,v 1.4 2016/11/06 08:05:24 wen Exp $ | |
2 | share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl | 2 | share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl | |
3 | share/examples/bioperl/align/FastAlign.pl | 3 | share/examples/bioperl/align/FastAlign.pl | |
4 | share/examples/bioperl/align/align_on_codons.pl | 4 | share/examples/bioperl/align/align_on_codons.pl | |
5 | share/examples/bioperl/align/aligntutorial.pl | 5 | share/examples/bioperl/align/aligntutorial.pl | |
6 | share/examples/bioperl/align/clustalw.pl | 6 | share/examples/bioperl/align/clustalw.pl | |
7 | share/examples/bioperl/align/simplealign.pl | 7 | share/examples/bioperl/align/simplealign.pl | |
8 | share/examples/bioperl/bioperl.pl | 8 | share/examples/bioperl/bioperl.pl | |
9 | share/examples/bioperl/cluster/dbsnp.pl | 9 | share/examples/bioperl/cluster/dbsnp.pl | |
10 | share/examples/bioperl/contributed/nmrpdb_parse.pl | 10 | share/examples/bioperl/contributed/nmrpdb_parse.pl | |
11 | share/examples/bioperl/contributed/prosite2perl.pl | 11 | share/examples/bioperl/contributed/prosite2perl.pl | |
12 | share/examples/bioperl/contributed/rebase2list.pl | 12 | share/examples/bioperl/contributed/rebase2list.pl | |
13 | share/examples/bioperl/db/dbfetch | 13 | share/examples/bioperl/db/dbfetch | |
14 | share/examples/bioperl/db/est_tissue_query.pl | 14 | share/examples/bioperl/db/est_tissue_query.pl | |
@@ -20,28 +20,26 @@ share/examples/bioperl/db/use_registry.p | @@ -20,28 +20,26 @@ share/examples/bioperl/db/use_registry.p | |||
20 | share/examples/bioperl/generate_random_seq.pl | 20 | share/examples/bioperl/generate_random_seq.pl | |
21 | share/examples/bioperl/liveseq/change_gene.pl | 21 | share/examples/bioperl/liveseq/change_gene.pl | |
22 | share/examples/bioperl/longorf.pl | 22 | share/examples/bioperl/longorf.pl | |
23 | share/examples/bioperl/make_primers.pl | 23 | share/examples/bioperl/make_primers.pl | |
24 | share/examples/bioperl/popgen/parse_calc_stats.pl | 24 | share/examples/bioperl/popgen/parse_calc_stats.pl | |
25 | share/examples/bioperl/quality/svgtrace.pl | 25 | share/examples/bioperl/quality/svgtrace.pl | |
26 | share/examples/bioperl/rev_and_trans.pl | 26 | share/examples/bioperl/rev_and_trans.pl | |
27 | share/examples/bioperl/revcom_dir.pl | 27 | share/examples/bioperl/revcom_dir.pl | |
28 | share/examples/bioperl/root/README | 28 | share/examples/bioperl/root/README | |
29 | share/examples/bioperl/root/exceptions1.pl | 29 | share/examples/bioperl/root/exceptions1.pl | |
30 | share/examples/bioperl/root/exceptions2.pl | 30 | share/examples/bioperl/root/exceptions2.pl | |
31 | share/examples/bioperl/root/exceptions3.pl | 31 | share/examples/bioperl/root/exceptions3.pl | |
32 | share/examples/bioperl/root/exceptions4.pl | 32 | share/examples/bioperl/root/exceptions4.pl | |
33 | share/examples/bioperl/root/lib/TestInterface.pm | |||
34 | share/examples/bioperl/root/lib/TestObject.pm | |||
35 | share/examples/bioperl/searchio/blast_example.pl | 33 | share/examples/bioperl/searchio/blast_example.pl | |
36 | share/examples/bioperl/searchio/custom_writer.pl | 34 | share/examples/bioperl/searchio/custom_writer.pl | |
37 | share/examples/bioperl/searchio/hitwriter.pl | 35 | share/examples/bioperl/searchio/hitwriter.pl | |
38 | share/examples/bioperl/searchio/hspwriter.pl | 36 | share/examples/bioperl/searchio/hspwriter.pl | |
39 | share/examples/bioperl/searchio/htmlwriter.pl | 37 | share/examples/bioperl/searchio/htmlwriter.pl | |
40 | share/examples/bioperl/searchio/psiblast_features.pl | 38 | share/examples/bioperl/searchio/psiblast_features.pl | |
41 | share/examples/bioperl/searchio/psiblast_iterations.pl | 39 | share/examples/bioperl/searchio/psiblast_iterations.pl | |
42 | share/examples/bioperl/searchio/rawwriter.pl | 40 | share/examples/bioperl/searchio/rawwriter.pl | |
43 | share/examples/bioperl/searchio/resultwriter.pl | 41 | share/examples/bioperl/searchio/resultwriter.pl | |
44 | share/examples/bioperl/searchio/waba2gff.pl | 42 | share/examples/bioperl/searchio/waba2gff.pl | |
45 | share/examples/bioperl/searchio/waba2gff3.pl | 43 | share/examples/bioperl/searchio/waba2gff3.pl | |
46 | share/examples/bioperl/sirna/TAG | 44 | share/examples/bioperl/sirna/TAG | |
47 | share/examples/bioperl/sirna/rnai_finder.cgi | 45 | share/examples/bioperl/sirna/rnai_finder.cgi |
@@ -1,6 +1,6 @@ | @@ -1,6 +1,6 @@ | |||
1 | $NetBSD: distinfo,v 1.7 2015/11/02 18:42:20 agc Exp $ | 1 | $NetBSD: distinfo,v 1.8 2016/11/06 08:05:24 wen Exp $ | |
2 | 2 | |||
3 | SHA1 (BioPerl-1.6.924.tar.gz) = 74986dad54192a1e53b1da6b632877a782763140 | 3 | SHA1 (BioPerl-1.007001.tar.gz) = 13a3e7a30d68ee32d735921668839eda668771f4 | |
4 | RMD160 (BioPerl-1.6.924.tar.gz) = 0723177a285607b95bf32114f6723f74873fe553 | 4 | RMD160 (BioPerl-1.007001.tar.gz) = c433044f47f5827f480836329487bf5780c9f480 | |
5 | SHA512 (BioPerl-1.6.924.tar.gz) = 49f732ece2c1d9ed39f951e51dd1c201f1ed528d3e5b765cd770b8992ecf5c4ef6bce2d38a261581c25d8d49dbbb17f1e15c897be1beed800ff5b8079b68503a | 5 | SHA512 (BioPerl-1.007001.tar.gz) = 6ab6af9d8fa74a299870273f2843872af099764997aa1b03f88248502f9ed1b74f4f577b67befa1ae8c18ee2640c029a08a403e2dec5b1cdea41f2b86c82c11b | |
6 | Size (BioPerl-1.6.924.tar.gz) = 12623118 bytes | 6 | Size (BioPerl-1.007001.tar.gz) = 12486953 bytes |