head 1.4; access; symbols pkgsrc-2013Q4:1.3.0.62 pkgsrc-2013Q4-base:1.3 pkgsrc-2013Q3:1.3.0.60 pkgsrc-2013Q3-base:1.3 pkgsrc-2013Q2:1.3.0.58 pkgsrc-2013Q2-base:1.3 pkgsrc-2013Q1:1.3.0.56 pkgsrc-2013Q1-base:1.3 pkgsrc-2012Q4:1.3.0.54 pkgsrc-2012Q4-base:1.3 pkgsrc-2012Q3:1.3.0.52 pkgsrc-2012Q3-base:1.3 pkgsrc-2012Q2:1.3.0.50 pkgsrc-2012Q2-base:1.3 pkgsrc-2012Q1:1.3.0.48 pkgsrc-2012Q1-base:1.3 pkgsrc-2011Q4:1.3.0.46 pkgsrc-2011Q4-base:1.3 pkgsrc-2011Q3:1.3.0.44 pkgsrc-2011Q3-base:1.3 pkgsrc-2011Q2:1.3.0.42 pkgsrc-2011Q2-base:1.3 pkgsrc-2011Q1:1.3.0.40 pkgsrc-2011Q1-base:1.3 pkgsrc-2010Q4:1.3.0.38 pkgsrc-2010Q4-base:1.3 pkgsrc-2010Q3:1.3.0.36 pkgsrc-2010Q3-base:1.3 pkgsrc-2010Q2:1.3.0.34 pkgsrc-2010Q2-base:1.3 pkgsrc-2010Q1:1.3.0.32 pkgsrc-2010Q1-base:1.3 pkgsrc-2009Q4:1.3.0.30 pkgsrc-2009Q4-base:1.3 pkgsrc-2009Q3:1.3.0.28 pkgsrc-2009Q3-base:1.3 pkgsrc-2009Q2:1.3.0.26 pkgsrc-2009Q2-base:1.3 pkgsrc-2009Q1:1.3.0.24 pkgsrc-2009Q1-base:1.3 pkgsrc-2008Q4:1.3.0.22 pkgsrc-2008Q4-base:1.3 pkgsrc-2008Q3:1.3.0.20 pkgsrc-2008Q3-base:1.3 cube-native-xorg:1.3.0.18 cube-native-xorg-base:1.3 pkgsrc-2008Q2:1.3.0.16 pkgsrc-2008Q2-base:1.3 cwrapper:1.3.0.14 pkgsrc-2008Q1:1.3.0.12 pkgsrc-2008Q1-base:1.3 pkgsrc-2007Q4:1.3.0.10 pkgsrc-2007Q4-base:1.3 pkgsrc-2007Q3:1.3.0.8 pkgsrc-2007Q3-base:1.3 pkgsrc-2007Q2:1.3.0.6 pkgsrc-2007Q2-base:1.3 pkgsrc-2007Q1:1.3.0.4 pkgsrc-2007Q1-base:1.3 pkgsrc-2006Q4:1.3.0.2 pkgsrc-2006Q4-base:1.3 pkgsrc-2006Q3:1.2.0.24 pkgsrc-2006Q3-base:1.2 pkgsrc-2006Q2:1.2.0.22 pkgsrc-2006Q2-base:1.2 pkgsrc-2006Q1:1.2.0.20 pkgsrc-2006Q1-base:1.2 pkgsrc-2005Q4:1.2.0.18 pkgsrc-2005Q4-base:1.2 pkgsrc-2005Q3:1.2.0.16 pkgsrc-2005Q3-base:1.2 pkgsrc-2005Q2:1.2.0.14 pkgsrc-2005Q2-base:1.2 pkgsrc-2005Q1:1.2.0.12 pkgsrc-2005Q1-base:1.2 pkgsrc-2004Q4:1.2.0.10 pkgsrc-2004Q4-base:1.2 pkgsrc-2004Q3:1.2.0.8 pkgsrc-2004Q3-base:1.2 pkgsrc-2004Q2:1.2.0.6 pkgsrc-2004Q2-base:1.2 pkgsrc-2004Q1:1.2.0.4 pkgsrc-2004Q1-base:1.2 pkgsrc-2003Q4:1.2.0.2 pkgsrc-2003Q4-base:1.2 buildlink2-base:1.2 netbsd-1-5-RELEASE:1.1.1.1 netbsd-1-4-PATCH003:1.1.1.1 netbsd-1-4-PATCH002:1.1.1.1 comdex-fall-1999:1.1.1.1 netbsd-1-4-PATCH001:1.1.1.1 netbsd-1-4-RELEASE:1.1.1.1 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.4 date 2014.02.20.14.44.16; author fhajny; state dead; branches; next 1.3; commitid Ght08sVqZUkEGQpx; 1.3 date 2006.10.02.21.34.28; author rillig; state Exp; branches; next 1.2; 1.2 date 2001.04.05.21.48.41; author jtb; state dead; branches; next 1.1; 1.1 date 99.04.16.14.43.36; author rh; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 99.04.16.14.43.36; author rh; state Exp; branches; next ; desc @@ 1.4 log @Update biology/bioperl to 1.6.923. Way too many changes (0.7.0 was released in 2001!). See changelog at: https://github.com/bioperl/bioperl-live/blob/master/Changes @ text @$NetBSD: patch-aa,v 1.3 2006/10/02 21:34:28 rillig Exp $ If LWP::UserAgent is not available, exit before the module is required implicitly by Bio::DB::GDB. --- t/GDB.t.orig 2001-03-01 10:11:15.000000000 +0100 +++ t/GDB.t 2006-10-02 23:30:15.000000000 +0200 @@@@ -33,10 +33,9 @@@@ BEGIN { foreach ( 1..$NUMTESTS) { skip(1,1); } $error = 1; } -} - -if( $error == 1 ) { - exit(0); + if( $error == 1 ) { + exit(0); + } } use Bio::DB::GDB; @ 1.3 log @Fixed one unit test. @ text @d1 1 a1 1 $NetBSD$ @ 1.2 log @Updated to bioperl-0.7.0. Revision history for Bioperl core modules 0.7 Large number of changes, including refactoring of the Object system, new parsers, new functionality and all round better system. Highlights are: o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI; Bio::Root::IO for I/O and file/handle capabilities. o Imported BPlite modules from Ian Korf for BLAST parsing. This is considered the supported BLAST parser; Bio::Tools::Blast.pm will eventually phase out due to lack of support. o Improved Sequence Feature model. Added complete location modelling (with fuzzy and compound locations). See Bio::LocationI and the modules under Bio/Location. Added support in Genbank/EMBL format parsing to completely parse feature tables for complex locations. o Moved special support for databanks etc to specialized modules under Bio/Seq/. One of these supports very large sequences through a temporary file as a backend. o Explicit Gene, Transcript and Exon SeqFeature objects, supporting CDS retrieval and exon shuffling. o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and DB/GDB (the latter has platform-specific limitations). o New analysis parser framework for HT sequence annotation (see Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory) o New Alignment IO framework o New Index modules (Swissprot) o New modules for running Blast within perl (Bio::Tools::Run::StandAloneBlast). Added modules for running Multiple Sequence Alignment tools ClustalW and TCoffee (Bio::Tools::Run::Alignment). o New Cookbook-style tutorial (see bptutorial.pl). Improved documentation across the package. o Much improved cross platform support. Many known incompatibilities have been fixed; however, NT and Mac do not work across the entire setup (see PLATFORMS). o Many bug fixes, code restructuring, etc. Overall stability and maintainability benefit a lot. o A total of 957 automatic tests 0.6.2 There are very few functionality changes but a large number of software improvements/bug fixes across the package. o The EMBL/GenBank parsing are improved. o The Swissprot reading is improved. Swissprot writing is disabled as it doesn't work at all. This needs to wait for 0.7 release o BLAST reports with no hits are correctly parsed. o Several other bugs of the BLAST parser (regular expressions, ...) fixed. o Old syntax calls have been replaced with more modern syntax o Modules that did not work at all, in particular the Sim4 set have been removed o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair have improved compliance with interface specs and documentation o Mailing list documentation updated throughout the distribution o Most minor bug fixes have happened. o The scripts in /examples now work and have the modern syntax rather than the deprecated syntax 0.6.1 Sun April 2 2000 o Sequences can have Sequence Features attached to them - The sequence features can be read from or written to EMBL and GenBank style flat files o Objects for Annotation, including References (but not full medline abstracts), Database links and Comments are provided o A Species object to represent nodes on a taxonomy tree is provided o The ability to parse HMMER and Sim4 output has been added o The Blast parsing has been improved, with better PSI-BLAST support and better overall behaviour. o Flat file indexed databases provide both random access and sequential access to their component sequences. o A CodonTable object has been written with all known CodonTables accessible. o A number of new lightweight analysis tools have been added, such as molecular weight determination. The 0.6 release also has improved software engineering o The sequence objects have been rewritten, providing more maintainable and easier to implement objects. These objects are backwardly compatible with the 0.05.1 objects o Many objects are defined in terms of interfaces and then a Perl implementation has been provided. The interfaces are found in the 'I' files (module names ending in 'I'). This means that it is possible to wrap C/CORBA/SQL access as true "bioperl" objects, compatible with the rest of bioperl. o The SeqIO system has been overhauled to provide better processing and perl-like automatic interpretation of <> over arguments. o Many more tests have been added (a total of 172 automatic tests are now run before release). 0.05.1 Tue Jun 29 05:30:44 1999 - Central distribution now requires Perl 5.004. This was done to get around 5.003-based problems in Bio/Index/* and SimpleAlign. - Various bug fixes in the Bio::Tools::Blast modules including better exception handling and PSI-Blast support. See Bio/Tools/Blast/CHANGES for more. - Fixed the Parse mechanism in Seq.pm to use readseq. Follow the instructions in README for how to install it (basically, you have to edit Parse.pm). - Improved documentation of Seq.pm, indicating where objects are returned and where strings are returned. - Fixed uninitialized warnings in Bio::Root::Object.pm and Bio::Tools::SeqPattern.pm. - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52. 0.05 Sun Apr 25 01:14:11 1999 - Bio::Tools::Blast modules have less memory problems and faster parsing. Webblast uses LWP and supports more functionality. See Bio/Tools/Blast/CHANGES for more. - The Bio::SeqIO system has been started, moving the sequence reformatting code out of the sequence object - The Bio::Index:: system has been started, providing generic index capabilities and specifically works for Fasta formatted databases and EMBL .dat formatted databases - The Bio::DB:: system started, providing access to databases, both via flat file + index (see above) and via http to NCBI - The scripts/ directory, where industrial strength scripts are put has been started. - Many changes - a better distribution all round. @ text @d1 1 a1 1 $NetBSD: patch-aa,v 1.1 1999/04/16 14:43:36 rh Exp $ d3 17 a19 3 --- Compile/SW/Makefile.PL.orig Fri Dec 11 08:24:25 1998 +++ Compile/SW/Makefile.PL Mon Mar 1 11:37:15 1999 @@@@ -13,9 +13,9 @@@@ d21 1 a21 10 sub MY::postamble{ ' -$(MYEXTLIB): libs/libsw$(LIB_EXT) +$(MYEXTLIB): DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; export DEFINE INC CC; \ - cd libs && $(MAKE) libsw.a -e + cd libs && $(MAKE) libsw$(LIB_EXT) -e '; } @ 1.1 log @Initial revision @ text @d1 1 a1 1 $NetBSD$ @ 1.1.1.1 log @Initial import of bioperl-0.04.4, based on the collection of packages submitted in PR pkg/7075 by Brook Milligan, with several modifications. @ text @@