textproc/xerces-c3: Update to 3.3.0

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=10510&version=12355023

biology/libsbml: Update to 5.20.4

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/libsbml: Fix build with libxml2 2.12.0+

PR:		279752
Obtained
from:	https://github.com/sbmlteam/libsbml/commit/a3e217851f18d3c5e8e2b0082fb98176738491e8

biology/libsbml: Update to 5.20.2

Changes:	https://github.com/sbmlteam/libsbml/releases

all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>

biology/libsbml: Update to 5.20.0

- Update MASTER_SITES
- Update WWW
- Sort PLIST

Changes:	https://github.com/sbmlteam/libsbml/releases

biology/libsbml: Update WWW and clean up pkg-descr

biology/libsbml: unbreak build after 18c6e1827669 (+)

Changes in framework need adjustment for declared options.

*_USE=ruby now became as *_USES=ruby

Approved by:	portmgr blanket

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>

textproc/libxml2: bump all LIB_DEPENDS consumers

This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)

textproc/libxml2: bump all dependencies

This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd733f67a9fc0dc00ab45268bdc236246

biology/libsbml: Update WWW

biology/libsbml: Fix build with Python 3.10

Obtained
from:	https://github.com/sbmlteam/libsbml/commit/4f01a15fde1d8afa9eaffb4c13dfc83a3404f183
(based on)

biology/libsbml: limit supported python versions

  File
"/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.19.0/src/bindings/python/doc-converter/rewrite_pydoc.py",
line 121, in <module>
    from formatter import NullWriter, AbstractFormatter
ModuleNotFoundError: No module named 'formatter'

Approved by:	portmgr blanket

biology/libsbml: Rename LIBXML option to LIBXML2

Remove # $FreeBSD$ from Makefiles.

Set CMAKE options explicitly

Add EXPAT, LIBXML and XERCES options

It allows choosing XML parser library.

Update to 5.19.0

Changes:	https://github.com/sbmlteam/libsbml/releases

Convert REINPLACE_CMD to patch file

Update PYTHON option to use Python 3

Move devel/swig30 to devel/swig and update to 4.0.1

- Do not silence installation message
- Update dependent ports:
  - Fix build with swig 4.0.1
  - Update *_DEPENDS
  - Remove BINARY_ALIAS

Changes:	http://www.swig.org/news.php
PR:		246613
Exp-run by:	antoine

Clean up Makefile

Use USES=pathfix

- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership

- Update to 5.18.0

Change cmake default behaviour to outsource.

Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".

I tried to only set insource where explictely needed.

PR:		232038
Exp-run by:	antoine

biology/libsbml: Fix build with Clang 6

In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/Model.cpp:41:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLDocument.h:298:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBMLTransforms.h:48:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/FunctionDefinition.h:129:
In file included from
/wrkdirs/usr/ports/biology/libsbml/work/libsbml-5.17.0/src/sbml/SBO.h:207:
/usr/include/c++/v1/map:629:15: error: object of type
'std::__1::pair<std::__1::pair<const std::__1::basic_string<char>, int>,
FormulaUnitsData *>' cannot be assigned because its copy assignment operator is
implicitly deleted
        {__nc = __v.__cc; return *this;}
              ^

http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/libsbml-5.17.0.log

Mark as broken with clang6 after r473289.

- Update to 5.17.0

- Update to 5.16.0

Switch from swig 2.0 to swig 3.0

Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the

- Update to 5.15.0

Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight

Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:

	https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78

Notified by:	portscout

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

- Update to 5.12.0

- Add LICENSE_FILE
- Switch to options helpers

Switch to USES=iconv:build.

The port does not use iconv on its own, the only dependency comes via
libxml2, which has one header that includes iconv.h.

- Update to 5.11.4

- Convert USE_PYTHON -> USES leftovers missed in the previous commits

Spotted by:	antoine
With hat:	python

- Update to 5.11.0

PR:		196377
Submitted by:	koue@chaosophia.net

Cleanup plist

- Update to 5.10.2

PR:		192198
Submitted by:	tkato432@yahoo.com

Convert the Python framework bits to USES=python.

Please use USES=python instead of USE_PYTHON.

  USE_PYTHON=yes becomes USES=python
  USE_PYTHON=2.7+ becomes USES=python:2.7+
  USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build
  ...

A new PYTHON_FEATURES variable was added, which enables certain features for a
port and replaces some knobs at the same time;

  PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS
  PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST
  PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK

- Update to 5.10.0

- Update to 5.9.0 [1]
- Stage support [1]
- Add LICENSE [1]
- Reset maintainer to port@

PR:		188554 [1]
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com> [1]

The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well

Convert b* to USES=zip

Reduce over inclusion of bsd.port.mk

In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology

- Fix build on head

- Switch to build with lang/ruby19
- No PORTREVISION bump, option is off by default

With hat:	portmgr

Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)

- adoption of optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)

- Get Rid MD5 support

- Update to 4.2.0

- Update to 4.1.0

- Update to 4.0.1

- Mark MAKE_JOBS_UNSAFE

Reported by:    pointyhat

- Update to 4.0.0
- Update my mail address to FreeBSD

PR:             ports/137652
Submitted by:   wenheping@gmail.com(myself)
Approved by:    miwi(mentor)
Feature safe:   yes

- Switch SourceForge ports to the new File Release System: categories starting
with B,C

LibSBML is an open-source programming library to help you read, write,
manipulate, translate, and validate SBML files and data streams. It is
not an application itself (though it does come with example programs),
but rather a library you can embed in your own applications.

LibSBML understands all Levels and Versions of SBML, as well as the
SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in
ISO C and C++ but can be used from all the languages listed in the
right-hand box.

WWW: http://www.sbml.org/

PR:             ports/135022
Submitted by:   Wen Heping <wenheping at gmail.com>