Update to 1.002004

Upstream changes:
1.002004 - 2014-07-09
  - fix prerequisite declarations for older toolchain

1.002003 - 2014-07-09
  - module loading is now done while importing, making it unnecessary to load
    them beforehand (RT#96995, Christian Walde)

1.002002 - 2014-05-06
  - minor metadata updates

1.002001 - 2014-03-04
  - fix tests and Makefile.PL to support perl 5.6
Updated devel/p5-Import-Into to 1.002004
Update to 0.62

Upstream changes:
0.62 Sun Jul 13 21:49:16 PDT 2014
 - Actually make the 5.8.1 change I said I did in 0.61

0.61 Sun Jul 13 21:47:14 PDT 2014
 - Make Inline dep on perl 5.8.1 per The Lancaster Consensus
 - https://github.com/Perl-Toolchain-Gang/toolchain-site/blob/master/lancas
   ter-consensus.md#minimum-supported-perl
 - Fix Metadata errors

0.60 Sun Jul 13 21:19:48 PDT 2014
 - Use the new ZD Contributing file

0.59 Sat Jul 12 12:11:10 PDT 2014
 - Finish migrating and updating docs

0.58 Fri Jul 11 07:02:12 BST 2014
 - Fix tabs, add $VERSIONs, fix prereqs

0.57 Fri Jul 11 02:05:00 BST 2014
 - Inline::C separated from Inline

0.56_03 Thu Jul 10 13:36:04 BST 2014
 - The "with" interface changed slightly - to get right $language use
   $_[-1].
 - Add Contrib file

0.56_02 Thu Jul 10 03:36:04 BST 2014
 - Remove AutoLoader stuff.

0.56_01 Wed Jul  9 17:10:04 PDT 2014
 - Move to Zilla-Dist
 - Remove Inline::C from Inline dist

0.56 9 Jul 2014
 - Clean up formatting and whitespace
 - Removed a "sleep" from Inline::Foo::build

0.55_05 8 Jul 2014
 - Make "with" hook return undef croak, test that.

0.55_04 8 Jul 2014
 - Suppress warnings in older perls from C/t/14void_arg_PRD.t.
 - setruid throws exception not just on Win32 - trap in t/08taint.t.
 - C/t/14void_arg_PRD.t - Fix typo.

0.55_03 1 Jul 2014
 - Update ToDo to post 0.44(!)
 - repository cpan metadata added, typo fixes (thanks dsteinbrunner)
 - Update "with" hook to be class method, not function (and test).
 - Make "make dist" update C/C.pm and Inline::MakeMaker's $VERSION.
 - Undo change disabling BUILD_NOISY for Win32 when shell eq 'cmd'

0.55_02 date Sun 22 Jun 2014
 - Version updated to 0.55_02 and released to CPAN
 - Inline.pm - additional changes to -T handling. (Thanks Ed J).

0.55_01 date Mon 5 May 2014
 - Update version number to 0.55_01

0.55 date Mon 28 Apr 2014
 - Version 0.55 released to CPAN

0.54_05 date Sun 13 Apr 2014
 - Update version number to 0.54_05.
 - Inline.pod - Add documentation regarding "with" and modules. (Thanks to
   Ed J.)

0.54_04 date Wed 10 Apr 2014
 - Add META.yml & META.json to distro
 - Released to CPAN.

0.54_03 date Wed 9 Apr 2014
 - Released to CPAN. (No changes from 0.54_01.)

0.54_01 Mon 31 Mar 2014
 - Update version nmuyber to 0.54_01
 - Makefile.PL - add META_MERGE info (thanks David Steinbrunner).
 - Inline.pod - Correct typos (thanks David Steinbrunner).

0.54 Sat 29 Mar 2014
 - Update version number to 0.54
 - Release version 0.54 to CPAN

0.53_02 Fri 7 Mar 2014
 - Update version to 0.53_02

0.53_01 Thurs 12 Sep 2013
 - Inline.pm - Update version number to 0.53_01

0.53 Wed 1 May 2013
 - Version 0.53 released to CPAN

0.52_02 Wed 24 Apr 2013
 - Version 0.52_02 released to CPAN

0.52_01 Thurs 11 Apr 2013
 - Version 0.52_01 released to CPAN
 - Inline.pm - in sub read_DATA() replace:
     @{$DATA{$pkg}} = split /(?m)(__\S+?__\n)/, $data
     with:
     @{$DATA{$pkg}} = split /(?m)^[ \t]{0,}(__\S+?__\n)/, $data;
     Otherwise some non-markers can be treated as markers.
     Thanks to Chris Nighswonger and Stefan Seifert.
     Added C/t/21read_DATA.t and C/t/22read_DATA_2.t as the test cases.
     NOTE: This is not a complete fix - it's still possible to
	   write code (albeit in an unorthodox fashion) such
	   that a non-marker can be treated as a marker.


0.52 Thurs 07 Mar 2013
 - Version 0.52 released to CPAN

0.51_03 Wed 28 Nov 2012
 - Version 0.51_03 released to CPAN

0.51_02 Tues 20 Nov 2012
 - Version 0.51_02 released to CPAN

0.51_01 Tues 20 Nov 2012
 - Version 0.51_01 released to CPAN

0.51 Sat 13 Oct 2012
 - Version 0.51 released to CPAN.

0.50_03 Mon 8 Oct 2012
 - Version 0.50_03 released to CPAN.

0.50_02 Tues 14 Feb 2012
 - Inline.pm - Bump version number to 0.50_02

0.50_01 Wed 8 Feb 2012
 - Inline.pm - Add a warning prior to croaking with
   M62_invalid_config_file(). That way, we'll at least see what $config
   contains. This is in response to FAIL report
   http://www.cpantesters.org/cpan/report/3287249c-5151-11e1-9dba-4238887bd
   19e
 - Bump version number to 0.50_01

0.50 Tues 7 Feb 2012
 - Version 0.50 released to CPAN
 - Inline.pm - Bump version number to 0.50

0.49_02 Fri 3 Feb 2012
 - Version 0.49_02 released to CPAN
 - Inline.pm - Bring version numbering into line with recommendations made
   in http://perldoc.perl.org/perlmodstyle.html#Version-numbering

0.49_01 Sun 25 Dec 2011
 - As the result of input from David Oswald
 - Inline.pod - Changes relating to "CONFIGURE_REQUIRES" and fix typo
   reported in ticket 73108.
 - Inline-FAQ.pod - Changes relating to "CONFIGURE_REQUIRES"
 - Inline.pm - Bump version to 0.49_01
 - lib/Inline/MakeMaker.pm - Bump version to 0.49_01

0.49 Thurs 8 Dec 2011
 - Version 0.49 released to CPAN
 - Inline.pm - small alteration to M19_usage_language error message

0.48_02 Fri 9 Sept 2011
 - Bump Inline version to 0.48_02

0.48_01 Mon 11 Apr 2011
 - Version 0.48_01 released to CPAN
 - t/05files.t - Have t/05files.t provide a reason for skipping the tests.
 - Inline.pm - Create REWRITE_CONFIG_FILE config option.
 - Makefile.PL - Test::Warn 0.23 or later needed for perl-5.13 and later.
   (Older perls need 0.21 or later).
Updated devel/p5-Inline to 0.62
Add hack for using gcc builtin atomic function, missing for i386.
PR pkg/48990.

Bump PKGREVISION.
Sync GCC_REQD with meta-pkgs/boost/Makefile.common.

PR pkg/49000, PR pkg/48981, PR pkg/48980.
Update to 2.6.9.

While here,
* Add 2.6 to COMMENT.
* Use pkgsrc framework way for dynamic plist generation.
Updated lang/py26-html-docs to 2.6.9
Update to 2.7.8.

While here,
* Add 2.7 to COMMENT.
* Use pkgsrc framework way for dynamic plist generation.
Updated lang/py27-html-docs to 2.7.8
Some packaging improvements.
* prevent to use deprecated doc/html hier.
* install whole contents, especially css and js are useful parts.
* use static PLIST.

Bump PKGREVISION.
Updated lang/py26-html-docs to 2.6.9nb1
Some packaging improvements.
* prevent to use derecated doc/html hier.
* install whole contents, especially css and js are useful parts.
* use static PLIST.

Bump PKGREVISION.
Updated lang/py27-html-docs to 2.7.8nb1
Import py33-html-docs-3.3.5 as lang/py33-html-docs.
PR pkg/48929.

HTML Documentation for Python 3.3
Added lang/py33-html-docs version 3.3.5
Import py34-html-docs-3.4.1 as lang/py34-html-docs.
PR pkg/48967

HTML Documentation for Python 3.4
Added lang/py34-html-docs version 3.4.1
+ py{33,34}-html-docs
Update to 1.6.924

Upstream changes:
1.6.924

    [Significant changes]

    * Bug/feature issue tracking has moved to GitHub Issues:
          https://github.com/bioperl/bioperl-live/issues
    * DB_File has been demoted from "required" to "recommended",
      which should make easier for Windows users to install BioPerl
      if they don't need that module.

    [New features]

    * Bio::Search::HSP::GenericHSP
        - Bug #3370, added a "posterior_string" method to retrieve the
          posterior probability lines (PP) from HMMER3 reports [fjossandon]
        - Added a "consensus_string" method to retrieve the consensus
          structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
    * Bio::SearchIO::hmmer2
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Query Length and Hit Length are reported when the alignment
          runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
    * Bio::SearchIO::hmmer3
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Hit Length is reported when the alignment runs until the end
          of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
        - Implemented the capture of the posterior probability lines [fjossandon]
        - Completed the development of NHMMER parsing, including alignments [fjossandon]
    * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
        - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
          "min_score", "min_bits, and "hit_filter" methods from
          'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
          This means that the Bio::SearchIO->new() parameters '-signif', '-score',
          '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
          besides Blast, instead of being ignored. Added tests for all moved methods
          using HMMER outputs and run the full test suite and everything pass [fjossandon]
    * Bio::SeqIO::MultiFile
        - Autodetection of file format [fangly]
    * Bio::Tools::GuessSeqFormat:
        - Format detection from non-seekable filehandles such as STDIN [fangly]

    [Bug fixes]

    * Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
    * Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
    * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
    * Abstract: Fixed ActivePerl incapability of removing temporary files
      because of problems closing tied filehandles [fjossandon]
    * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
      because ActivePerl were producing a ".index.pag" and ".index.dir"
      files instead of a single ".index" file (like Strawberry Perl).
      Now those temporary files are correctly considered and deleted. [fjossandon]
    * Test files: Added missing module requirements (DB_File and Data::Stag)
      to several tests files that were failing because those modules were
      not present. Now those test files are correctly skipped instead. [fjossandon]
    * Blast: Added support to changes in bl2seq from BLAST+ output, which
      now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
    * Phylip: Return undef in "next_aln" at file end to avoid
      an infinite loop [yschensandiego]
    * HMMER3: When a hit description is too long, it is truncated in
      the Scores table. In those cases, the more complete description from
      the Annotation line (>>) will be used [fjossandon]
    * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
      since it is now used by HMMER3 format in alignments [fjossandon]
    * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
      to return undef if the query/hit length is unknown (like in some
      HMMER outputs), to avoid division by 0 crashes. Also "query_length"
      now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
    * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
      added support to multi-query reports, reduced code redundancy,
      and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
    * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
    * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
    * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
    * Fixed some Bio::Root::Utilities subroutines [fjossandon]
    * Double-quotes on paths are needed in some places [fjossandon]
    * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
    * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
    * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
      with the latest changes made in their own repositories [fjossandon]
    * General synching of files with the master branch [fjossandon]
    * Fixed tests failing in Windows because of using Linux commands [fjossandon]
    * Closed many open filehandles that prevented temporary files deletion [fjossandon]
    * Fixed broken MeSH parser [fjossandon]
    * Fixed missing detection of format in SeqIO when given a -string [fangly]