doc: Updated devel/p5-Alien-Base-ModuleBuild to 1.15

(wiz)

p5-Alien-Base-ModuleBuild: update to 1.15.

1.15      2020-08-28 09:50:28 -0600
  - Move inline tests from this distro to Acme::Alien::DontPanic
    and Acme::Alien::DontPanic2 (gh#22)

(wiz)

doc: Updated devel/p5-Algorithm-CheckDigits to 1.3.3

(wiz)

p5-Algorithm-CheckDigits: update to 1.3.3.

v1.3.3 Di 14. Jul 19:20:56 CEST 2020
- reworked lib/Algorithm/CheckDigits.pm, allow 10-digit numbers,
  allow prepending of 'BE' before the digits
- fix Bug #132950

(wiz)

doc: Updated databases/p5-perl-ldap to 0.66

(wiz)

p5-perl-ldap: update to 0.66.

0.66 -- Tue Apr 16 11:23:55 CEST 2019

Enhancements
* Entry.pm: accept more options in ldif()
* inc/: refresh install tools
* contrib/ldifsort: new option -h
* documentation extensions
* typo fixes

Bug Fixes
* contrib/schema2ad: fix syntax calculation
* Refresh.pm: fix get_ttl() method
* DSML: fix detection of auxiliary object classes

(wiz)

doc: Updated databases/p5-Tie-DBI to 1.08

(wiz)

p5-Tie-DBI: update to 1.08.

1.08 Sat Jan 18 2020 Todd Rinaldo
    Switch testing to github actions
update MANIFEST and .gitignorew
Switch to github issues

1.07 Tue Apr 12 2016 Todd Rinaldo
    Stop using vars in favor of ours
    Add Travis support
    Debian QA tool tidy fix
    Apply Perl::Tidy 20150815 and track .perltidyrc
    Fixes RT 104338 - prepare fails when a question mark appears in a text field
    Add an explicit minimum version of perl supported
    Add warnings.

(wiz)

doc: Updated databases/p5-SQL-Translator to 1.61

(wiz)

p5-SQL-Translator: update to 1.61.

1.61 - 2020-04-19
* Fixes for Sybase producer
* Support CHECK (expr) for SQLite and MySQLoids
* Avoid accidentally whole objects in YAML output
* Prettify comment generation
* Tyop fixes

(wiz)

doc: Updated databases/p5-SQL-Abstract to 1.87

(wiz)

p5-SQL-Abstract: update to 1.87.

1.87 - 2020-06-02
    - Add runtime dependency on Test::Deep and Test::Builder::Module for
      SQL::Abstract::Test (RT#131623)

(wiz)

doc: Updated devel/p5-Coro to 6.57nb1

(wiz)

p5-Coro: disable JIT on NetBSD, reduces problems.

Bump PKGREVISION.

(wiz)

doc: Updated databases/p5-Rose-DB-Object to 0.819

(wiz)

p5-Rose-DB-Object: update to 0.819.

0.819 (06.16.2020) - John Siracusa <siracusa@gmail.com>

    * Attempt to fix a failing test by adding a workaround for an undef
      return value from crypt().

0.818 (06.08.2020) - John Siracusa <siracusa@gmail.com>

    * Fixed tests that were failing due to "future" dates that are
      now in the past (RT 132782)

0.817 (04.05.2020) - John Siracusa <siracusa@gmail.com>

    * Added missing module load in Rose::DB::Object::Metadata::Util
      (RT 132300)

0.816 (04.03.2020) - John Siracusa <siracusa@gmail.com>

    * Updated to support DBD::Pg 3.8.0 and later.

(wiz)

doc: Updated databases/p5-Rose-DB to 0.783

(wiz)

p5-Rose-DB: update to 0.783.

0.783 (04.06.2020) - John Siracusa <siracusa@gmail.com>

    * Fixed a bug in DBD::Pg version detection.

0.782 (04.03.2020) - John Siracusa <siracusa@gmail.com>

    * Added workarounds for changes to the behavior of the TABLE_CAT catalog
      name key in DBD::Pg 3.8.0 and later.

0.781 (01.06.2020) - John Siracusa <siracusa@gmail.com>

    * Corrected the MANIFEST file. Fixed MariaDB test counts.

0.780 (01.06.2020) - John Siracusa <siracusa@gmail.com>

    * Added basic support for MariaDB. (Patch by Peter Karman.)

0.779 (08.09.2019) - John Siracusa <siracusa@gmail.com>

    * Added skip_locked support for PostgreSQL. (Patch by fhendrikx.)

(wiz)

doc: Updated databases/p5-Redis to 1.998

(wiz)

p5-Redis: update to 1.998.

1.998    2020-08-18 11:04:12+02:00 Europe/Paris

  * remove test expression that is problematic on OpenBSD and NetBSD

1.997    2020-80-17 10:03:00+01:00 Europe/Paris

  * various travis fixes
  * #112 applied
  * enable unix socket tests by enabling them in the local test server
  * #144: change exists into defined
  * #146: Fix sentinel option typo

1.996    2020-03-05 16:17:21+01:00 Europe/Paris

1.996    2020-03-05 11:56:11+01:00 Europe/Paris
  * #139: Fix for "Unexpected error condition 104/linux"

1.995    2019-07-22 11:20:07+02:00 Europe/Paris
  * revert #136, remove deps that are in core, as it breaks builds in some setup

1.994    2019-07-22 07:51:57+02:00 Europe/Paris
  * Don't send SELECT if current database equals the one being selected (@dallaylaen, #132)

1.993    2019-07-22 07:01:30+02:00 Europe/Paris
  * fix missing deps (@manwar, #136 )

1.992    2019-07-21 18:27:23+02:00 Europe/Paris
  * relax the check in 04-pipeline.t about unknown command output (#130)

(wiz)

doc: Updated databases/p5-Parse-Dia-SQL to 0.31

(wiz)

p5-Parse-Dia-SQL: update to 0.31.

0.31 Wed Jun 17 22:29:02 CEST 2020
  Merged PR "Support `drop table if exists`"
  Thanks to biaocy
  https://github.com/aff/Parse-Dia-SQL/pull/9

(wiz)

doc: Updated databases/p5-Fsdb to 2.69

(wiz)

p5-Fsdb: update to 2.69.

Changes not found.

(wiz)

doc: Updated databases/p5-DBIx-SearchBuilder to 1.68

(wiz)

p5-DBIx-SearchBuilder: update to 1.68.

1.68 2020-07-06
- Avoid segmentation faults on disconnect on MariaDB 10.2+

(wiz)

doc: Updated databases/p5-DBIx-Class-Helpers to 2.036000

(wiz)

p5-DBIx-Class-Helpers: update to 2.036000.

2.036000  2020-03-28 14:16:39-07:00 America/Los_Angeles
- fix remove_columns shortcut to add the 'remove_columns' attribute
  in case it is missing (Karen Etheridge, #101)
- Add support for query condition to results_exist() and
  results_exist_as_query() in Helper::ResultSet::Shortcut::ResultsExist
  (Daniel B旦hmer, GH#102)

2.035000  2020-02-21 08:38:42-08:00 America/Los_Angeles
- add remove_columns shortcut (Karen Etheridge, GH#100)

(wiz)

doc: Updated databases/p5-DBIx-Class to 0.082842

(wiz)

p5-DBIx-Class: update to 0.082842.

0.082842 2020-06-16 20:10 (UTC)
    * New Features
        - An on_connect rebase_sqlmaker call allowing experimentation with
          non-core SQL generators on a per-$schema-instance basis
          https://is.gd/DBIC_rebase_sqlmaker
        - Automatically detect and use multi-column IN on recent versions of
          libsqlite: ... WHERE ( foo, bar ) IN ( SELECT foo, bar FROM ... )

    * Fixes
        - Fix silent failure to retrieve a primary key (RT#80283) or worse:
          returning an incorrect value (RT#115381) in case a rdbms-side autoinc
          column is declared as PK with the is_auto_increment attribute unset
        - Fix overly-aggressive condition unrolling, corrupting custom ops with
          array arguments (RT#132390)
        - Fix docs on how to properly use Moo(se) in ResultSet's, and fix a
          corner case of ->count not functioning properly when the old recipe
          was being used (GH#105)
        - Fix incorrect ::Storage->_ping() behavior under Sybase (RT#114214)
        - Work around breakage in Hash::Merge by soft-requiring Clone as part
          of the replicated subsystem (RT#124321)

    * Misc
        - DBIC_TRACE_PROFILE=... now uses a ::Storage::Statistics subclass
          DBIx::Class::Storage::Debug::PrettyTrace which properly ships as a
          part of this distrinbution
        - Switch out SQL::Abstract dependency with a slower moving dist
        - Remove Data::Page dependency by inlining its entirety into the core
          DBIx::Class::ResultSet::Pager (RT#130686)

(wiz)

doc: Added databases/p5-SQL-Abstract-Classic version 1.91

(wiz)

databases/Makefile: + p5-SQL-Abstract-Classic

(wiz)

databases/p5-SQL-Abstract-Classic: import p5-SQL-Abstract-Classic-1.91

This module was inspired by the excellent DBIx::Abstract. However,
in using that module I found that what I really wanted to do was
generate SQL, but still retain complete control over my statement
handles and use the DBI interface. So, I set out to create an
abstract SQL generation module.

(wiz)

doc: Updated databases/p5-DBI-Shell to 11.97

(wiz)

p5-DBI-Shell: update to 11.97.

11.97
  - Add missing dependencies.
  - Document some awkward behaviour. RT#21200

11.96_03
  - Add options for handling of booleans. RT#53311 (Mike Pomraning)

11.96_02
  - Add missing versions to this file. RT#39187
  - Be more helpful if DBI::Shell::Spool is missing. RT#24538
  - Give every .pm a version identifier.

11.96_01
  - Suppress warning in DBI::Format::SQLMinus. RT#123216 (Kent Fredric)

11.96
  - Automatically save command history.
  - Remove warning message.
  - Correct links in POD to work in metacpan.
  - Tidy up metadata.

11.95_03
  - Correct sense of interactivity check.

11.95_02
  - Use IO::Interactive.

11.95_01
  - Resolved RT#123215, warning from File::Find.
  - Added RT#65253, permit empty passwords.
  - Resolved RT#121136, testing without "." in @INC.
  - Resolved RT#73873, warning fix.
  - Possibly resolved RT#12167, missing dependency on DBI.
  - Switch build to Dist::Zilla.

(wiz)

doc: Updated databases/p5-DBD-postgresql to 3.14.2

(wiz)

p5-DBD-postgresql: update to 3.14.2.

Version 3.14.2  (released August 13, 2020)

- Fix ENV typo in the test suite
  [Gregor Herrmann]

- Renamed and enhanced test helper script: dbdpg_test_postgres_versions.pl
  [Greg Sabino Mullane]

Version 3.14.1  (released August 12, 2020)

- Force the version string so undefined errors in the "driver" sub go away.
  [Greg Sabino Mullane]
  (RT ticket #83057)

Version 3.14.0  (released July 19, 2020)

- The $dbh->primary_key_info and $dbh->foreign_key_info methods will now always return
    a statement handle, even with no matches. Previously, they returned undef directly.
  Callers can check if the returned handle contains any rows.
  [Greg Sabino Mullane]

- The $dbh->tables method will always return a list, even if it is empty.
  [Greg Sabino Mullane]

- Add pg_lo_tell64, pg_lo_seek64, and pg_lo_truncate64, for anyone dealing
    with really, really, really large 'large objects'. Requires Postgres 9.3 or better.
  [Greg Sabino Mullane]
  (RT ticket #123561)

- Allow test to run again when using a non-superuser to connect
  [Greg Sabino Mullane]
  (RT ticket #132865)

- Adjust tests to force loading proper version of DBD::Pg every time.
  [Greg Sabino Mullane]

- Removed the long-deprecated _pg_use_catalog method.
  [Greg Sabino Mullane]

- Many improvements and changes to the test suite.
  [Greg Sabino Mullane]

Version 3.13.0  (released June 17, 2020)

- Redo the "last_result" internals in dbdimp.c, which
    fixes a memory leak.
  [Greg Sabino Mullane]
  (RT ticket #132812)

- Fix regression in Perl length() for returned query results
  [Jon Jensen]
  (Github issue #72)

- Make $sth->finish() do a little less. Notably, even
    after calling finish(), pg_error_field will still work
    on the last action performed.
  [Greg Sabino Mullane]

- Tweak tests so Windows boxes pass
  [Greg Sabino Mullane]

Version 3.12.3  (released June 5, 2020)

- Prevent DBI from flipping AutoCommit to 'on' after a failed commit
  [Greg Sabino Mullane]
  (Github issue #71)

Version 3.12.2  (released June 4, 2020)

- Revert overly aggressive testing shortcut as it can cause installs to fail
  [Greg Sabino Mullane, with apologies]

Version 3.12.1  (released June 3, 2020)

- Remove test that assumed '(12,34)' is an invalid entry for type "circle",
    as the Postgres source code changed this behavior on April 7, 2020
  [Greg Sabino Mullane]
  (RT ticket #132740)

Version 3.12.0  (released May 7, 2020)

- Add CONTRIBUTING.md file

- Return the table info row last in statistics_info.
  This fixes statistics_info on pre-8.3 servers.
  [Dagfinn Ilmari Mannsåker]

- Fix ASC_OR_DESC field in statistics_info
  [Dagfinn Ilmari Mannsåker]

- Indicate NULL ordering in statistics_info
  [Dagfinn Ilmari Mannsåker]

Version 3.11.1  (released April 28, 2020)

- Adjust Makefile to fix failing 'fulltest' target on BSD systems
  [Slaven Rezić]
  (RT ticket #132412)

Version 3.11.0  (released April 23, 2020)

- Indicate non-key index columns (INCLUDE) in statistics_info
  [Dagfinn Ilmari Mannsåker]

- Return an empty result set instead of undef from statistics_info
    when the requested table doesn't exist and $unique_only is false.
  [Dagfinn Ilmari Mannsåker]

- Fix segfault during st destroy
  [Gregory Oschwald]
  (Github pull request #66)
  (Github issue #57)

- Improve testing for table_info()
  [Greg Sabino Mullane]
  (Github issue #67)

- Improve UTF-8 wording in docs
  [Felipe Gasper]
  (Github pull request #65)

Version 3.10.5  (released March 23, 2020)

- Minor adjustment for Windows build
  (RT ticket #131752)

- Allow test suite to work on an EnterpriseDB server
  [H.Merijn Brand]
  (RT ticket #132203)

- Add small warning regarding ShowErrorStatement
  (RT ticket #120268)

Version 3.10.4  (released February 3, 2020)

- Allow localtime from Time::Piece to be used directly as a bind value again.
  This applies to all "magical" arrays.
  [Greg Sabino Mullane]
  (Github issue #63)

- Force tests to NOT run in parallel.
  [Greg Sabino Mullane]
  (RT ticket #130834)

Version 3.10.3  (released January 20, 2020)

- Set things cleared via PQclear to NULL as soon as possible, to remove race conditions
  [Greg Sabino Mullane]
  (RT ticket #131522)

Version 3.10.2  (released January 17, 2020)

- Adjust tests to pass on 32-bit machines
  [Greg Sabino Mullane]
  (RT ticket #131482)

Version 3.10.1  (released January 13, 2020)

- Prevent double-free memory errors
  [Greg Sabino Mullane]
  (RT ticket #130681)

- Fix crash when pg_error_field is called
  [Greg Sabino Mullane]
  (RT ticket #130721)

- Update the list of Postgres reserved words in quote.c

Version 3.10.0  (released September 3, 2019)

- Prevent memory leak related to pg_error_field
  [Greg Sabino Mullane]
  (RT ticket #130430)

- Fix for bug by making sure pg_error_field works properly when switching between
    do-with-params and do-without-params.
  [Greg Sabino Mullane]
  (Github issue #57)

- If a commit or rollback fails, do not set BegunWork
  [Greg Sabino Mullane]
  (Github issue #40)

- Treat partitioned tables same as regular tables for column_info, table_info,
    and foreign_key_info (i.e. support pg_class.relkind = 'p')
  [Octavian R. Corlade]
  (Github pull request #55)

- Allow last_insert_id() to work against inherited tables
  [Greg Sabino Mullane]
  (RT ticket #52441)

- Add DBI SQL_BLOB, SQL_BINARY and SQL_LONGVARBINARY types as alias for PG_BYTEA
  [Pali]
  (Github pull request #58)

(wiz)

doc: Updated databases/p5-DBD-SQLite to 1.66

(wiz)

p5-DBD-SQLite: update to 1.66.

1.66 2020-08-30
    - Switched to a production version

1.65_03 2020-07-27
    - Upgraded SQLite to 3.32.3

1.65_02 2020-02-08
    - Upgraded SQLite to 3.31.1

1.65_01 2020-01-18
    - Upgraded SQLite to 3.30.1
    - Added several SQL_ types as alias (pali++)
    - Fixed two initialization issues (ppisar++)
    - Allowed create_function to return an array reference
      to specify the type of the value

(wiz)

doc: Updated print/zathura-pdf-mupdf to 0.3.6

(leot)

zathura-pdf-mupdf: Update to 0.3.6

Changes:
0.3.6
-----
- Compatible with mupdf 1.17

(leot)

doc: Updated print/zathura to 0.4.7

(leot)

zathura: Update to 0.4.7

Changes:
0.4.7
-----
- Fix invalid zoom when opening document with 'adjust-open width' option
- Various fixes and improvements
- Updated translations

(leot)

doc: Updated databases/p5-DBD-ODBC to 1.61

(wiz)

p5-DBD-ODBC: update to 1.61.

1.61 2020-01-30

  [BUG FIXES]

  Fix 12blob.t test by pali
  Fix searching for ODBC libraries in system by pali (#15)

  [ENHANCEMENTS]

  use PERL_NO_GET_CONTEXT for more performance by markusbeth (#13)

  [MISCELLANEOUS]

  Fix travis builds for older Perls by pali

(wiz)

doc: Updated databases/p5-DBD-Mock to 1.55

(wiz)

p5-DBD-Mock: update to 1.55.

1.55 2019-12-30T14:20:00Z
    - Fixed bug rt131264 t/033_table_info.t fails (with older DBI)

1.54 2019-12-23T12:44:22Z
    - Added Bernhard Graf's 'Feature: one shot failure' merge request.
    - Fixed description of the failure attribute of mock_add_resultset. It
      no longer claims to support a hash ref (as it doesn't). Thanks to
      Bernhard Graf for both the bug report and a merge request that fixes it.
    - Fixed bug where it wasn't possible to replace a regular expression
      mock resultset. Thanks to Bernhard Graf for both the bug report and
      a merge request that fixes it.
    - Fixed bug where the failure attribute wasn't working with regular
      expression mock resultsets. Thanks to Bernhard Graf for both the bug
      report and a merge request that fixes it.

1.53 2019-12-03T10:50:57Z
    - Error handling in mock_add_resultset is no longer experimental
    - Attribute Aliasing is no longer experimental

1.52 2019-10-28T11:35:41Z
    - Added in callback feature for result sets so that their contents
      can be more dynamic.

1.51 2019-10-23T11:43:51Z
    - Fixed issue with using attribute aliases alongside a driver DSN
      in the DBI->connect call

1.50 2019-10-22T19:37:26Z
    - Added attribute aliases support for MariaDB

(wiz)

doc: Updated databases/p5-DBD-CSV to 0.55

(wiz)

p5-DBD-CSV: update to 0.55.

0.55 - 2020-07-27, H.Merijn Brand
    * Free unref scalar test fixed in Text::CSV_XS 1.35
    * It's 2019
    * Provide cpanfile
    * Doc enhancements
    * It's 2020
    * Make csv_ & f_ aliasses more consistently available (issue #7)

(wiz)

doc: Updated biology/bioperl to 1.7.7

(wiz)

bioperl: update to 1.7.7.

1.7.7    2019-12-07 13:41:36-06:00 America/Chicago

    * The program bp_chaos_plot has been removed.

    * GD is now no longer a dependency, suggestion or requirement.

    * #321 - GenBank format fix for un-quoted features, text wrapping

    * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
      and a 'private' _sleep() function that mirror those from
      Bio::DB::WebDBSeqI, primarily for compliance with potential website
      restrictions for the number and frequency of queries (e.g. NCBI eUtils).

    * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
      in last release.

1.7.6    2019-08-28 12:37:01+01:00 Europe/London

    * The program bp_classify_hits_kingdom has been removed and is
      now part of the examples documentation instead.

    * GD is now listed as a suggestion instead of a requirement.  The
      bp_chaos_plot program will now work with the GD module.

    * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
      to compute Transfer Bootstrap Expectation (TBE) for internal
      nodes based on the methods outlined in Lemoine et al, Nature,
      2018.

    * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
      sequence in the stream faster but not perfect.

1.7.5    2019-02-11 14:57:45+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution with
      independent development:

          Bio::Symbol::*

    * The Bio::Seq::SeqWithQuality module, which was deprecated since
      2001, was finally removed.

    * The deprecated() method has been deprecated.  It is recommended
      to use Carp::carp to warn.

    * The following methods have been deprecated for a long while and
      have now been removed:

          Bio::Align::AlignI->no_residues
          Bio::Align::AlignI->no_sequences
          Bio::LocatableSeq->no_gap
          Bio::LocatableSeq->no_sequences
          Bio::SeqFeature::Generic->slurp_gff_file
          Bio::SimpleAlign->no_residues
          Bio::SimpleAlign->no_sequences

1.7.4    2019-02-05 16:23:53+00:00 Europe/London

    * Fix Bio::Root::Test, and the testuite, to properly check for
      internet connection and the NO_NETWORK_TESTING environment
      variable.  Previously, tests that required internet connection
      were not being skipped, causing tests to fail.

1.7.3    2019-01-30 13:30:34+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution.  They have
      been integrated into other module distributions for independent
      development:

          Bio::Align::Graphics
          Bio::AlignIO::nexml
          Bio::AlignIO::stockholm
          Bio::Assembly::*
          Bio::Cluster::*
          Bio::ClusterI::*
          Bio::ClusterIO::*
          Bio::DB::Ace
          Bio::DB::BioFetch
          Bio::DB::CUTG
          Bio::DB::EMBL
          Bio::DB::EntrezGene
          Bio::DB::Expression::*
          Bio::DB::GFF
          Bio::DB::GFF::Adaptor::*
          Bio::DB::GFF::Aggregator::*
          Bio::DB::GFF::Featname
          Bio::DB::GFF::Feature
          Bio::DB::GFF::Homol
          Bio::DB::GFF::RelSegment
          Bio::DB::GFF::Segment
          Bio::DB::GFF::Typename
          Bio::DB::GenBank
          Bio::DB::GenPept
          Bio::DB::HIV::*
          Bio::DB::MeSH
          Bio::DB::NCBIHelper
          Bio::DB::Query::GenBank
          Bio::DB::Query::HIVQuery
          Bio::DB::RefSeq
          Bio::DB::SeqFeature::*
          Bio::DB::SeqVersion::*
          Bio::DB::SwissProt
          Bio::DB::TFBS::*
          Bio::DB::Taxonomy::entrez
          Bio::DB::Taxonomy::sqlite
          Bio::DB::Universal
          Bio::Draw::Pictogram
          Bio::Factory::MapFactoryI
          Bio::Index::Hmmer
          Bio::Index::Stockholm
          Bio::LiveSeq::*
          Bio::Map::*
          Bio::MapIO::*
          Bio::MolEvol::CodonModel
          Bio::Nexml::Factory
          Bio::NexmlIO
          Bio::Perl
          Bio::Phenotype::*
          Bio::PhyloNetwork::*
          Bio::PopGen::*
          Bio::Restriction::*
          Bio::Root::Build
          Bio::Search::HSP::HMMERHSP
          Bio::Search::HSP::HmmpfamHSP
          Bio::Search::Hit::HMMERHit
          Bio::Search::Hit::HmmpfamHit
          Bio::Search::Hit::hmmer3Hit
          Bio::Search::Result::HMMERResult
          Bio::Search::Result::HmmpfamResult
          Bio::Search::Result::hmmer3Result
          Bio::SearchDist
          Bio::SearchIO::hmmer
          Bio::SearchIO::hmmer2
          Bio::SearchIO::hmmer3
          Bio::SearchIO::hmmer_pull
          Bio::SeqEvolution::*
          Bio::SeqFeature::SiRNA::*
          Bio::SeqIO::abi
          Bio::SeqIO::agave
          Bio::SeqIO::alf
          Bio::SeqIO::chadoxml
          Bio::SeqIO::chaos
          Bio::SeqIO::chaosxml
          Bio::SeqIO::ctf
          Bio::SeqIO::entrezgene
          Bio::SeqIO::excel
          Bio::SeqIO::exp
          Bio::SeqIO::flybase_chadoxml
          Bio::SeqIO::lasergene
          Bio::SeqIO::nexml
          Bio::SeqIO::pln
          Bio::SeqIO::strider
          Bio::SeqIO::ztr
          Bio::Structure::*
          Bio::Taxonomy::*
          Bio::Tools::AlignFactory
          Bio::Tools::Analysis::* (except SimpleAnalysisBase)
          Bio::Tools::Gel
          Bio::Tools::HMMER::*
          Bio::Tools::Hmmpfam
          Bio::Tools::Phylo::Gumby
          Bio::Tools::Protparam
          Bio::Tools::Run::RemoteBlast
          Bio::Tools::SiRNA::*
          Bio::Tools::dpAlign
          Bio::Tools::pSW
          Bio::Tree::AlleleNode
          Bio::Tree::Draw::Cladogram
          Bio::TreeIO::nexml
          Bio::TreeIO::svggraph
          Bio::Variation::*

    * The following modules are new in the BioPerl distribution.  They
      have been previously released in the BioPerl-Run distribution.
      This will enable smaller distributions that provide a
      Bio::Tool::Run interface, to be only dependent on the BioPerl
      distribution instead of the whole (very large) BioPerl-Run:

          Bio::Tools::Run::Analysis
          Bio::Tools::Run::AnalysisFactory
          Bio::Tools::Run::Phylo::PhyloBase
          Bio::Tools::Run::WrapperBase
          Bio::Tools::Run::WrapperBase::CommandExts

    * The following programs have been removed:

          bp_biofetch_genbank_proxy
          bp_blast2tree
          bp_bulk_load_gff
          bp_composite_LD
          bp_das_server
          bp_download_query_genbank
          bp_fast_load_gff
          bp_flanks
          bp_genbank2gff
          bp_generate_histogram
          bp_heterogeneity_test
          bp_hivq
          bp_hmmer_to_table
          bp_load_gff
          bp_meta_gff
          bp_netinstall
          bp_parse_hmmsearch
          bp_process_wormbase
          bp_query_entrez_taxa
          bp_remote_blast
          bp_seqfeature_delete
          bp_seqfeature_gff3
          bp_seqfeature_load

    * Because of the move of so many modules and programs into
      separate distributions, the following modules are no longer
      prerequisites:

          Ace
          Ace::Sequence::Homol
          Algorithm::Munkres
          Apache::DBI
          Archive::Tar
          Array::Compare
          Bio::ASN1::EntrezGene
          Bio::Expression::Contact
          Bio::Expression::DataSet
          Bio::Expression::Platform
          Bio::Expression::Sample
          Bio::Ext::Align
          Bio::GMOD::CMap::Utils
          Bio::Phylo::Factory
          Bio::Phylo::Forest::Tree
          Bio::Phylo::IO
          Bio::Phylo::Matrices
          Bio::Phylo::Matrices::Datum
          Bio::Phylo::Matrices::Matrix
          Bio::SeqFeature::Annotated
          Bio::SeqIO::staden::read
          Bio::Tools::Run::Alignment::Clustalw
          Bio::Tools::Run::Ensembl
          Bio::Tools::Run::Phylo::Molphy::ProtML
          Bio::Tools::Run::Phylo::Phylip::Neighbor
          Bio::Tools::Run::Phylo::Phylip::ProtDist
          Bio::Tools::Run::Phylo::Phylip::ProtPars
          Bio::Tools::Run::Samtools
          CGI
          CPAN
          Cache::FileCache
          Config
          Convert::Binary::C
          DBD::Pg
          DBD::SQLite
          Data::Stag::XMLWriter
          Encode
          English
          ExtUtils::Install
          ExtUtils::Manifest
          File::Glob
          GD::Simple
          Getopt::Std
          Graph::Undirected
          GraphViz
          HTML::HeadParser
          HTML::TableExtract
          LWP
          LWP::Simple
          MIME::Base64
          Memoize
          PostScript::TextBlock
          SVG
          SVG::Graph
          SVG::Graph::Data
          SVG::Graph::Data::Node
          SVG::Graph::Data::Tree
          Sort::Naturally
          Spreadsheet::ParseExcel
          Term::ReadLine
          Text::NSP::Measures::2D::Fisher2::twotailed
          Text::ParseWords
          Time::Local
          Tree::DAG_Node
          URI::Escape
          WWW::Mechanize
          XML::Simple

    * The following is a new prerequisite:

          Test::RequiresInternet

    * The deobfuscator has been removed.

    * The emacs bioperl minor mode is no longer distributed as part of the
      perl module distributions.  See
      https://github.com/bioperl/emacs-bioperl-mode

(wiz)

doc: Updated converters/p5-Unicode-EastAsianWidth to 12.0

(wiz)

p5-Unicode-EastAsianWidth: update to 12.0.

[Changes for 12.0 - 2018-11-24]

* Update to Unicode v12.0.0.

(wiz)

doc: Updated converters/p5-Sereal to 4.018

(wiz)

p5-Sereal: update to 4.018.

4.018 Thurs Aug 3, 2020
    * Fix issue with gcc 10 with snappy compression.

4.017 Thurs July 9, 2020
    * The build fixes in 4.016 didn't work correctly, this should fix them.

4.016 Thurs July 9, 2020
    * Fix some dependency issues in build process

4.015 Weds  July 8, 2020
    * Build fixes (missing dependency)
    * Hardening against corrupted data
    * New thresholds to manage decoding process

(wiz)

doc: Updated converters/p5-Sereal-Encoder to 4.018

(wiz)

p5-Sereal-Encoder: update to 4.018.

4.018 Thurs Aug 3, 2020
    * Fix issue with gcc 10 with snappy compression.

4.017 Thurs July 9, 2020
    * The build fixes in 4.016 didn't work correctly, this should fix them.

4.016 Thurs July 9, 2020
    * Fix some dependency issues in build process

4.015 Weds  July 8, 2020
    * Build fixes (missing dependency)

(wiz)

doc: Updated converters/p5-Sereal-Decoder to 4.018

(wiz)

p5-Sereal-Decoder: update to 4.018.

4.018 Thurs Aug 3, 2020
    * Fix issue with gcc 10 with snappy compression.

4.017 Thurs July 9, 2020
    * The build fixes in 4.016 didn't work correctly, this should fix them.

4.016 Thurs July 9, 2020
    * Fix some dependency issues in build process

4.015 Weds  July 8, 2020
    * Build fixes (missing dependency)
    * Hardening against corrupted data
    * New thresholds to manage decoding process

(wiz)

doc: Updated converters/p5-JSON-MaybeXS to 1.004002

(wiz)

p5-JSON-MaybeXS: update to 1.004002.

1.004002 - 2020-05-17
- fix test that fails when JSON::XS is installed, but below version 3.0
  (RT#132578)

1.004001 - 2020-05-01
- document when is_bool became available
- now favouring Cpanel::JSON::XS over JSON::XS in more situations (the former
  is always added to prereqs when a compiler is available, although JSON::XS
  is still used at runtime if new enough and Cpanel::JSON::XS is not
  installed). This makes boolean handling more predictable and consistent.

(wiz)

doc: Updated converters/p5-Cpanel-JSON-XS to 4.23

(wiz)

p5-Cpanel-JSON-XS: update to 4.23.

4.23 2020-09-05 (rurban)
        - Fixup t/54_stringify change for JSON 2.09 (really use PR #169 madsen)

4.22 2020-09-04 (rurban)
        - Fix t/54_stringify needs JSON 2.09 for allow_unknown (PR #169 madsen)
        - Fix t/118_type.t for 5.6
        - Fix t/96_interop.t for missing JSON::XS (GH #83 ribasushi)
        - Possible fix for s390x with long double, untested (GH #83)

4.21 2020-08-13 (rurban)
        - Fix not enough HEK memory allocation for the new canonical tied hashes
          feature. (GH #168)
        - TODO broken JSON::PP::Boolean versions 2.9x - 4.0 with threads::shared in
          125_shared_boolean.t

4.20 2020-08-12 (rurban)
        - New feature: sort tied hashes with canonical. (GH #167)
        - Fix encode of threads::shared boolean (#166 Sam Bingner).
          This was broken with 4.00.
        - Fix some stringify overload cases via convert_blessed (GH #105)
        - Fix a compat case with JSON::XS, when convert_blessed is set, but
          allow_blessed not. (GH #105)
        - Improve blessed and stringify tests
        - Work on better inf/nan detection on AIX (#165 Peter Heuchert)
        - Fix documentation for booleans and their types (#162 by Karen Etheridge)

4.19 2020-02-06 (rurban)
        - Fix typed decode memory leak (#160 by Pali).

4.18 2019-12-13 (rurban)
        - Add new method ->type_all_string (#156 by Pali).
          When type_all_string is set then encode method produce stable deterministic
          string types in result JSON.
          This can be an alternative to Cpanel::JSON::XS::Type when having
          deterministic output is required but string JSON types are enough for any
          output.
        - Move SvGETMAGIC() from encode_av() and encode_hv() to encode_sv()
          (#156 by Pali)
        - Add Math::BigInt and Math::BigFloat as recommended dependences
          (#157 by Pali and Grinnz)

4.17 2019-11-04 (rurban)
        - Add Changes tests and fixups (see #155)

4.16 2019-11-04 (rurban)
        - Use Perl_strtod instead of self-made atof (via pow), to
          minimize differences from core string-to-float conversions.
          (#154). Fixes float representation regressions (in the 1e-6
          to 1e-16 range) since 5.22.

4.15 2019-10-21 (rurban)
        - Fix more tests for nvtype long double

4.14 2019-10-15 (rurban)
        - Fix tests for nvtype long double (#153)
        - Fix PREREQ's. E.g. CentOS 7 has not Test::More anymore. (#152 by Pali)

4.13 2019-10-14 (rurban)
        - For JSON_TYPE_INT and JSON_TYPE_FLOAT allow to encode numeric values
          above 2^64 in PV slot via Math::BigInt/Float (#145, #148, #149 by Pali)
        - For JSON_TYPE_INT and JSON_TYPE_FLOAT encoder allow to pass Math::BigInt
          and Math::BigFloat objects with allow_bignum. (#147 by Pali)
        - Fix encoding floating point values above 2^64 in PV slot to JSON_TYPE_INT
          (#148, #150 by Pali)
        - Do not allow serializing objects when convert_blessed is not enabled.
          (#146 by Pali)

4.12 2019-06-11 (rurban)
        - Make encoder independent on Math::BigInt version (#140 by Pali)
        - Rethrow error from eval_sv and eval_pv() (#138, #139 by Pali),
          e.g. when Math::BigInt/BigFloat fails.
        - Fix encoding Inf and NaN from PV and NV slots to JSON_TYPE_INT
          (#137 by Pali)
        - Fix memory corruption in sv_to_ivuv() function (#136 by Pali)
        - Add new method ->require_types (#135 by Pali)
        - Fix typed json encoder conversion from scalar's PV and NV slot to
          JSON_TYPE_INT (#133, #134 by Pali)
        - Fix inconsistency with warnings in typed json encoder (#131 by Pali)
        - Fix Perl 5.8.0 support (#130 by Pali)
        - Fixed minor pod typo (#129 by sheeit)
        - Document invalid recursive callbacks or overloads (#128)

4.11 2019-03-26 (rurban)
        - Fix unicode strings with BOM corrupt ->utf8 state (#125)
          The BOM encoding effects only its very own decode call,
          not its object.

4.10 2019-03-18 (rurban)
        - Fix incr_text refcounts (#123)
        - Add incr_rest testcase (#123)
        - Fix encode_stringify string-overload refcnt problem (#124)
          "Attempt to free unreferenced scalar" with convert_blessed and overload.

4.09 2019-02-15 (rurban)
        - Add seperate allow_dupkeys property, in relaxed (#122)
        - Fixed allow_dupkeys for the XS slow path
        - Silence 2 -Wunused-value warnings
        - Fix ->unblessed_bool to produce modifiable perl structures (PR #121 by Pali)

(wiz)

doc: Updated converters/p5-Convert-UUlib to 1.71

(wiz)

p5-Convert-UUlib: update to 1.710.

1.71 Tue Mar 17 00:54:06 CET 2020
- backport to c89 (patch by Paul Howarth).

1.7  Sat Feb 29 22:07:54 CET 2020
- new function: GetFileList.
- experimental perlmulticore support (see manpage).
        - Initialize is now a NOP and CleanUp automatically initializes again.
        - updated example decoder and documentation a bit.
- include ecb.h to deal with compiler builtins and endianness.
- some further 袖-optimisations in hot code, especially for yEnc.
        - replace crc32 function by slice-by-16 version by Stephan Brumme,
          which should speed up yEnc en-/decoding.
        - yEnc: do not calculate two crcs per part, instead, combine
          the part crcs together to form the file crc.
        - yEnc: allow pcrc= in addition to pcrc32= for yenc trailers, as
          some draft mentions both and it is actually in active use.
        - yEnc: ignore crc32= on multiparts, except on the last part,
          which avoids spurious corruption warnings.
        - be more precise in documenting code licenses in COPYING.
        - convert constant creation to the method I normally use.
        - use common::sense.

1.62 Mon Feb 17 23:19:42 CET 2020
- major performance improvement by simplifying code in _FP_gets
          to not use fscanf. This might slow things down on platforms
          with very slow fgetc.

1.61 Sun Feb  9 18:38:29 CET 2020
- lint uulib: fix some format string type mismatches
          and some other minor issues.

1.6  Thu Oct 24 17:11:54 CEST 2019
- fix heap overflow (testcase by Noel Duffy, reported
          by Robert Scheck). The defense-in-depth mechanism based
          on mmap should make this unexploitable for other than denial
          of service, on systems supporting mmap/mprotect.

(wiz)

doc: Updated comms/p5-Device-Modem to 1.59

(wiz)

p5-Device-Modem: update to 1.59.

1.59  Mon Jun 15 08:17:54 CEST 2020
    - Merged pull request #6 from ghciv6/fix_multi_instance_log
    fixed log handling with multi instances and typo in close().
    Thanks to @ghciv6 !

1.58
    - Updated test suite a bit.
    - Added the tests to the manifest.
    - Got rid of indirect object syntax.
    - Moved test.pl to the actual test suite.
    - Updated $VERSION declarations according to:
      http://www.dagolden.com/index.php/369/version-numbers-should-be-boring/
    - Added some extra tests (xt/author, xt/release).
    - Fixed some spelling.

(wiz)

doc: Updated biology/p5-Bio-ASN1-EntrezGene to 1.73

(wiz)

p5-Bio-ASN1-EntrezGene: update to 1.73.

1.73      2018-09-24 21:31:26-05:00 America/Chicago
  * Fix regex warnings for Perl 5.28.
  * New module 'Bio::SeqIO::entrezgene' imported from the BioPerl
    distribution.  This means Bio-ASN1-Entrezgene now "Enhances"
    BioPerl's Bio::SeqIO instead of being a hard dependency of
    BioPerl.

(wiz)

doc: Updated audio/p5-MPEG-Audio-Frame to 0.10

(wiz)

p5-MPEG-Audio-Frame: update to 0.10.

0.10 Sa, Oct 12 12:00:00 2019
- Now using `binmode` to make the module compatible with Windows

(wiz)

doc: Updated audio/p5-MP3-Tag to 1.15

(wiz)

p5-MP3-Tag: update to 1.15.

Release Name: 1.15
====================

Tag.pm: Fix more unescaped-{ warnings (thanks to Christian Walde etc).

(wiz)

doc: Updated archivers/p5-Compress-Bzip2 to 2.28

(wiz)

p5-Compress-Bzip2: update to 2.28.

Changes: not found.

(wiz)

syncthing: hardcode Go 1.14 for now, bump revision

syncthing builds with Go 1.15 but panics on startup, which is why my bulk
build has not found this. This will be fixed in the next upstream version.

Discussed with tnn@ and gdt@

(bsiegert)

Update tldr to 1.4.1.

v1.4.1 (2020-09-04)

- [fixed] Syntax error in zsh completion file

v1.4.0 (2020-09-03)

- [added] Configurable automatic cache updates
- [added] Improved color detection and support for `--color` argument and
  `NO_COLOR` env variable
- [changed] Make `--list` option comply with official spec
- [changed] Move cache age warning to stderr

(bsiegert)

doc: Updated net/dhcpcd to 9.2.0

(roy)

Update to dhcpcd-9.2.0 with the following changes:

* route: ensure IPv4LL routes come last in priority
* DHCP: fix many issues with extending the last lease
* privsep: don't read control group from config in privsep
* privsep: only the master process responds to signals
* privsep: use a socketpair for stderr/stdin rather than dupping /dev/null
* privsep: right limit stdin/stderr/stdout
* privsep: dumping a lease is now run in a sandbox
* options: check if kernel supports INET or INET6 before enabling default
* options: let clientid override a prior duid
* options: allow -1 to represent infinity for requested lease time
* dhcpcd: fix a crash initing a new interface after route overflow
* Linux: fix reading the IPv6 forwarding proc entry

(roy)

nginx-devel: add checksum for njs; fix checksum for lua-nginx-module (to match nginx)

(wiz)

graphene: simplify download URL

(wiz)

doc: Updated archivers/p5-Archive-Zip to 1.68

(wiz)

p5-Archive-Zip: update to 1.68.

1.68 Thr 12 Mar 2020
    - Switched to GitHub as issue tracker
    - Replaced references to Test::MockModule in
      t/23_closed_handle.t with code from PR #32, RT #110087
    - Unixified line endings in t/23_closed_handle.t
    - Added documentation for Archive::Zip::Member::isSymbolicLink,
      RT #130524
    - Implemented other, unrelated doc fixes
    - Fixed examples/zipcheck.pl to skip symbolic links, RT #130525
    - Described version 1.59, RT #117371 (tagged important!)

    - Completely re-did test suite:
      . Created new test APIs in t/common.pm and documented them in
        t/README.md
      . Changed tests to be less dependent on OS-specific quirks of "unzip -t"
      . Changed tests to write more diagnostic information if executed in
        automated test environments
      . Normalized access to test data and to temporary results.  Removed
        references to obsolete temporary results (for example, those to
        directory "extracted").
      . Normalized test headers and brushed up tests in general

1.67 Sun 06 Oct 2019
    - Fixed compatibility issues with zip64 format (defined-or, pack)
    - Fixed hard-coded version fields introduced in version 1.66
    - Fixed merge glitch with tests 26 and 27
    - Fixed merge glitch with bzip passthrough
    - Updated bzip test file to avoid zip bomb detection

1.66 Mon 16 Sep 2019
    - Refactored low-level methods for reading and writing zip files
      in zip64 format.  Added new parameters and return values to
      most of these.  Extended constants in Archive::Zip to cover
      zip64 formats and lengths.
    - Added public APIs
        Archive::Zip::Archive::zip64
        Archive::Zip::Archive::desiredZip64Mode
        Archive::Zip::Archive::versionMadeBy
        Archive::Zip::Archive::versionNeededToExtract
        Archive::Zip::Member::zip64
        Archive::Zip::Member::desiredZip64Mode
      and constants
        Archive::Zip::ZIP64_AS_NEEDED
        Archive::Zip::ZIP64_EOCD
        Archive::Zip::ZIP64_HEADERS
      plus POD on these.
    - Added tests for zip64 format in t/21_zip64.t and more test zip
      files below t/data.  Extended tests in t/02_main.t to perform
      all existing tests in all possible desired zip64 modes.
    - Extended methods
        Archive::Zip::Member::localExtraField
        Archive::Zip::Member::cdExtraField
      to perform format checks when called as setters and to reject
      any zip64 extended information extra fields passed by the user.
      Extended POD and tests in t/02_main.t accordingly.
    - Setting {'compressedSize'} after writing central directory
      header.
    - Added new optional parameter $noFormatError to method
      Archive::Zip::_readSignature to silence any format errros when
      testing for signatures.
    - Added error handling for potentially failed object conversion
      after calling method Archive::Zip::Member::_become.  Factored
      in method Archive::Zip::Member::_becomeDirectoryIfNecessary
      into caller.
    - Changed methods
        Archive::Zip::Archive::contents
        Archive::Zip::Member::contents
      (and all inheriting from these) to consistently return a pair
      ($contents, $status) when called in list context and a scalar
      $contents when called in scalar context.  Extended tests in
      t/02_main.t accordingly.
    - Changed method Archive::Zip::Member::extractToFileHandle to
      accept a file name instead of a file handle when extracting
      symbolic links.  Changed lower-level and higher-level methods
      to use that feature.  Cleaned up code related to the handling
      of symbolic links.  Added creation of intermediate directories
      in method Archive::Zip::Member::extractToFileNamed for symbolic
      links as well.  Reporting errors from symlink call as AZ-error.
      Added POD and test zip file t/data/symlink.zip and tests in
      t/26_symlinks.t for these changes.
    - Cleaned up code and added comment related to that highly
      dubious (?) {'wasWritten'} logic.

1.65 Sat 7 Sep 2019
    - Fix for members using bzip compression [github/pmqs]
    - NetBSD doesn't mind empty zips [github/pmqs]
    - Solaris test failure, Add diag to failing test to collect data [github/pmqs]
    - Test for presence of Test::MockModule [github/pmqs]
    - Fix skip line for Windows [github/pmqs]
    - Skip tests that assume /tmp on Windows [github/pmqs]

(wiz)

doc: Updated mail/sieve-connect to 0.89nb5

(wiz)

sieve-connect: depend on p5-Term-ReadLine-Gnu.

Bump PKGREVISION.

(wiz)

doc: Updated devel/p5-Reply to 0.42nb9

(wiz)

p5-Reply: depend on p5-Term-ReadLine-Gnu.

Bump PKGREVISION.

(wiz)

doc: Updated security/kpcli to 3.3nb4

(wiz)

kpcli: depend on p5-Term-ReadLine-Gnu.

Bump PKGREVISION.

(wiz)

doc: Added devel/p5-Term-ReadLine-Gnu version 1.36

(wiz)

devel/Makefile: + p5-Term-ReadLine-Gnu

(wiz)

devel/p5-Term-ReadLine-Gnu: import p5-Term-ReadLine-Gnu-1.36

This is an implementation of Term::ReadLine using the GNU
Readline/History Library.

(wiz)

doc: Updated net/youtube-dl to 20200906

(leot)

youtube-dl: Update to 20200906

pkgsrc changes:
* Update patch for the [rai] extractor (only related to tests)

Changes:
20200906
--------
Core
+ [utils] Recognize wav mimetype (#26463)

Extractors
* [nrktv:episode] Improve video id extraction (#25594, #26369, #26409)
* [youtube] Fix age gate content detection (#26100, #26152, #26311, #26384)
* [youtube:user] Extend URL regular expression (#26443)
* [xhamster] Improve initials regular expression (#26526, #26353)
* [svtplay] Fix video id extraction (#26425, #26428, #26438)
* [twitch] Rework extractors (#12297, #20414, #20604, #21811, #21812, #22979,
  #24263, #25010, #25553, #25606)
    * Switch to GraphQL
    + Add support for collections
    + Add support for clips and collections playlists
* [biqle] Improve video ext extraction
* [xhamster] Fix extraction (#26157, #26254)
* [xhamster] Extend URL regular expression (#25789, #25804, #25927))

(leot)

doc: Updated lang/yabasic to 2.87.0

(fcambus)

yabasic: update to 2.87.0.

ChangeLog:

Version 2.87.0 (August 12, 2020)
  - Fixed an edge-case in for-loops
  - Allow eof(0) and peek(0) to refer to standard input

(fcambus)

doc/TODO: add some

+ cantata-2.4.1, enchant2-2.2.10, fontforge-20200314, gnutls-3.6.15,
  libspiro-1.1.0.20200505, libuninameslist-20200413, libv4l-1.20.0,
  p11-kit-0.23.21, poppler-20.09.0, py-mercurial-5.5.1, redis-6.0.7,
  strawberry-0.7.2, wxGTK30-3.1.4.

(wiz)