00:44 Po-Chuan Hsieh (sunpoet) 

biology/libsbml: Update to 5.20.2

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

    4c14d7a

19:34 Rene Ladan (rene) 

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>

    3d9a815

04:07 Po-Chuan Hsieh (sunpoet) 

biology/libsbml: Update to 5.20.0

- Update MASTER_SITES
- Update WWW
- Sort PLIST

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

    f98de8b

17:29 Po-Chuan Hsieh (sunpoet) 

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

    02db5c9

14:47 Dima Panov (fluffy) 

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

    4dc157d

21:10 Stefan Eßer (se) 

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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

    b7f0544

14:20 Tobias C. Berner (tcberner) 

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>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

    37526bb

19:11 Charlie Li (vishwin) 

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)

    d63665f

08:27 Matthias Fechner (mfechner) 

textproc/libxml2: bump all dependencies

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

    247c7db

21:28 Po-Chuan Hsieh (sunpoet) 

biology/libsbml: Fix build with Python 3.10

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

    8ad9338

15:28 Dmitry Marakasov (amdmi3) 

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

    893daf4

21:46 Po-Chuan Hsieh (sunpoet) 

biology/libsbml: Rename LIBXML option to LIBXML2

    f747a64

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

15:23 sunpoet 

Set CMAKE options explicitly

 

20:05 sunpoet 

Add EXPAT, LIBXML and XERCES options

It allows choosing XML parser library.

 

21:30 sunpoet 

Update to 5.19.0

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

 

18:23 sunpoet 

Convert REINPLACE_CMD to patch file

 

19:30 sunpoet 

Update PYTHON option to use Python 3

 

18:17 sunpoet 

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

 

19:01 sunpoet 

Clean up Makefile

 

21:48 sunpoet 

Use USES=pathfix

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

 

09:12 wen 

- Update to 5.18.0

 

20:25 tcberner 

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

 

03:31 tobik 

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

 

06:24 linimon 

Mark as broken with clang6 after r473289.

 

01:37 wen 

- Update to 5.17.0

 

08:24 wen 

- Update to 5.16.0

 

19:34 bapt 

Switch from swig 2.0 to swig 3.0

 

15:50 mat 

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
  current python flavor.  It can be used in dependency lines when the
  port itself is not python flavored.  For example, deskutils/calibre.

  By default, all the flavors are generated.  To only generate flavors
  for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
  BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.

  In all the ports with Python dependencies, the *_DEPENDS entries MUST
  end with the flavor so that the framework knows which to build/use.
  This is done by appending '@${PY_FLAVOR}' after the origin (or
  @${FLAVOR} if in a Python module with Python flavors, as the content
  will be the same).  For example:

    RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}

PR:		223071
Reviewed by:	portmgr, python
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D12464

 

02:22 wen 

- Update to 5.15.0

 

22:45 mat 

Cleanup no longer needed CHMOD usage after r424898.

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

 

01:54 mi 

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

 

13:29 mat 

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

With hat:	portmgr
Sponsored by:	Absolight

 

07:09 wen 

- Update to 5.12.0

 

23:51 amdmi3 

- Add LICENSE_FILE
- Switch to options helpers

 

13:15 rakuco 

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.

 

08:58 wen 

- Update to 5.11.4

 

08:23 mva 

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

Spotted by:	antoine
With hat:	python

 

12:57 wen 

- Update to 5.11.0

PR:		196377
Submitted by:	koue@chaosophia.net

 

06:21 wen 

- Update to 5.10.2

PR:		192198
Submitted by:	tkato432@yahoo.com

 

15:44 mva 

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
  PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO
  PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL
  PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX

Some knobs have been deprecated and are to be removed in the near future:

  PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead
  PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead
  PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement

Some knobs have been removed completely:

  PYTHON_MASTER_SITE_SUBDIR
  PYTHON_DISTNAME
  PYTHON_WRKSRC

Several variables specific to the Python framework are no longer passed to the
build environment to avoid polluting dependency builds.

  PYTHON_VERSION is not passed to .MAKEFLAGS anymore
  PYTHON_DEFAULT_VERSION,
  PYTHON_DEFAULT_PORTVERSION and
  PYTHONBASE are not passed to the make environment anymore

The conversion required a couple of ports to be updated to fit the changes and
new requirements. Those included "bsd.python.mk" directly or contained checks
in places, for which the USES framework would fail to provide correct values.

Python modules directly using the upstream Python package (such as py-tkinter
or py-sqlite3) were updated to avoid using the now unnecessary and remmoved
knobs from "bsd.python.mk".

Phabric:	D399
exp-run:	167368 192357
PR:		167368 192357
Reviewed by:	antoine, wg
Exp-run award:	antoine
With hat:	python@
Approved by:	portmgr

 

07:04 wen 

- Update to 5.10.0

 

02:46 wen 

- 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]

 

18:28 zeising 

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
as some drivers and utilities.

Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.

Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.

Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.

Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics

Thanks to:	all testers, bdrewery and the FreeBSD x11@ team
exp-run by:	bdrewery [1]
PR:		ports/187602 [1]
Approved by:	portmgr (bdrewery), core (jhb)

 

15:52 bapt 

Convert b* to USES=zip

 

22:50 bapt 

Reduce over inclusion of bsd.port.mk

 

14:43 bapt 

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

 

01:58 wen 

- Fix build on head

 

18:08 tabthorpe 

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

With hat:	portmgr

 

15:55 bapt 

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

 

06:50 jgh 

- adoption of optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)

 

02:06 wen 

- Update to 4.2.0

03:31 wen 

- Update to 4.1.0

07:19 wen 

- Update to 4.0.1

22:53 pav 

- Mark MAKE_JOBS_UNSAFE

Reported by:    pointyhat

01:06 wen 

- 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

00:15 amdmi3 

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

23:36 miwi 

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>