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No upstream changelog.
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Upstream changes:
5.92 Sun Jun 1 00:15:44 MST 2014
- fixed reserved-word clash when compiling with C++
-- use 'classname' instead of 'class'
-- ref. SHA.xs (rt.cpan.org #96090)
- silenced MSC compiler warning about signed/unsigned comparison
-- ref. SHA.xs (rt.cpan.org #95830)
5.91 Fri May 16 10:21:44 MST 2014
- restored original 'addfile' for use on opened file handles
-- allows callbacks in place of actual files
-- ref. IO::Callback (rt.cpan.org #95643)
- re-established inheritance from Digest::base
-- to pick up future Digest enhancements automatically
- cleaned up documentation
5.90 Wed May 7 07:57:08 MST 2014
- consolidated all dynamic memory allocation into XSUBs
-- streamlines referencing of SHA objects
-- simplifies DESTROYing of objects
- enhanced Makefile.PL to allow 'use warnings'
-- automatically reverts to $^W for early Perls
- scrubbed C and Perl code to remove all compiler warnings
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Upstream changes:
0.22 Sun Jun 1 00:15:46 MST 2014
- fixed reserved-word clash when compiling with C++
-- use 'classname' instead of 'class'
-- ref. SHA3.xs (rt.cpan.org #96090)
0.21 Fri May 16 10:21:46 MST 2014
- restored original 'addfile' for use on opened file handles
-- allows callbacks in place of actual files
-- ref. IO::Callback (rt.cpan.org #95643)
- re-established inheritance from Digest::base
-- to pick up future Digest enhancements automatically
- cleaned up documentation
0.20 Wed May 7 07:57:10 MST 2014
- consolidated all dynamic memory allocation into XSUBs
-- streamlines referencing of SHA3 objects
-- simplifies DESTROYing of objects
- enhanced Makefile.PL to allow 'use warnings'
-- automatically reverts to $^W for early Perls
- scrubbed C and Perl code to remove all compiler warnings
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libsocket is needed.
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Upstream changes:
1.005004 - 2014-03-06
- make sure meta files list extra modules as recommendations, not requirements
1.005003 - 2014-02-12
- added support for PUREPERL_ONLY (rt#91407)
- fixed using strictures->VERSION to query the version (rt#92965)
1.005002 - 2013-12-10
- extra prereqs will be listed as hard prerequisites if a compiler is
available
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It has no S_ISSOCK.
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Upstream changes:
2014 07 11
- Fixed RT #94902: abbreviation parsing in .perltidyrc files was not
working for multi-line abbreviations. Thanks to Eric Fung for
supplying a patch.
- Fixed RT #95708, misparsing of a hash when the first key was a perl
keyword, causing a semicolon to be incorrectly added.
- Fixed RT #94338 for-loop in a parenthesized block-map. A code block within
parentheses of a map, sort, or grep function was being mistokenized. In
rare cases this could produce in an incorrect error message. The fix will
produce some minor formatting changes. Thanks to Daniel Trizen
discovering and documenting this.
- Fixed RT #94354, excess indentation for stacked tokens. Thanks to
Colin Williams for supplying a patch.
- Added support for experimental postfix dereferencing notation introduced in
perl 5.20. RT #96021.
- Updated documentation to clarify the behavior of the -io flag
in response to RT #95709. You can add -noll or -l=0 to prevent
long comments from being outdented when -io is used.
- Added a check to prevent a problem reported in RT #81866, where large
scripts which had been compressed to a single line could not be formatted
because of a check for VERSION for MakeMaker. The workaround was to
use -nvpl, but this shouldn't be necessary now.
- Fixed RT #96101; Closing brace of anonymous sub in a list was being
indented. For example, the closing brace of the anonymous sub below
will now be lined up with the word 'callback'. This problem
occured if there was no comma after the closing brace of the anonymous sub.
This update may cause minor changes to formatting of code with lists
of anonymous subs, especially TK code.
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Add LICENSE
Upstream changes:
Version 1.000 (2013-08-13)
Switched to standard X.YYYZZZ versioning.
Replaced ChangeLog with changes.pod.
Updated 'clean' arguments in Makefile.PL.
Updated Agent.pm and replaced old README.
Version 0.308 (2013-08-10)
Changed license to the Artistic License 2.0.
Replaced META.yml with META.json.
Fixed tests for Carp behavior and file permissions.
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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]
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PR pkg/48967
HTML Documentation for Python 3.4
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PR pkg/48929.
HTML Documentation for Python 3.3
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* prevent to use derecated doc/html hier.
* install whole contents, especially css and js are useful parts.
* use static PLIST.
Bump PKGREVISION.
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* prevent to use deprecated doc/html hier.
* install whole contents, especially css and js are useful parts.
* use static PLIST.
Bump PKGREVISION.
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While here,
* Add 2.7 to COMMENT.
* Use pkgsrc framework way for dynamic plist generation.
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While here,
* Add 2.6 to COMMENT.
* Use pkgsrc framework way for dynamic plist generation.
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PR pkg/49000, PR pkg/48981, PR pkg/48980.
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PR pkg/48990.
Bump PKGREVISION.
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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).
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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
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www/drupal7 7.29
www/drupal6 6.32
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Drupal 6.32, 2014-07-16
----------------------
- Fixed security issues (multiple vulnerabilities). See SA-CORE-2014-003.
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Drupal 7.29, 2014-07-16
----------------------
- Fixed security issues (multiple vulnerabilities). See SA-CORE-2014-003.
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===========
* Speed optimizations.
* Change the output when using the ``qr`` script to use ASCII rather than
just colors, better using the terminal real estate.
* Fix a bug in passing bytecode data directly when in Python 3.
* Substation speed optimizations to best-fit algorithm (thanks Jacob Welsh!).
Version 5.0.1
-------------
* Update version numbers correctly.
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* Mark code as safe HTML (to avoid escaping by Jinja, et alia).
* Update to work back to 0.6.1
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