Commit graph

51 commits

Author SHA1 Message Date
Po-Chuan Hsieh
8ad9338b22
biology/libsbml: Fix build with Python 3.10
Obtained from:	4f01a15fde (based on)
2021-11-02 05:28:40 +08:00
Dmitry Marakasov
893daf4fbc 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
2021-11-01 18:28:24 +03:00
Po-Chuan Hsieh
f747a647a1
biology/libsbml: Rename LIBXML option to LIBXML2 2021-05-12 05:46:56 +08:00
Mathieu Arnold
305f148f48
Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Sunpoet Po-Chuan Hsieh
6b24a39b63 Set CMAKE options explicitly 2020-12-20 15:23:50 +00:00
Sunpoet Po-Chuan Hsieh
cf864357a8 Add EXPAT, LIBXML and XERCES options
It allows choosing XML parser library.
2020-12-19 20:05:55 +00:00
Sunpoet Po-Chuan Hsieh
1b255e1ef8 Update to 5.19.0
Changes:	https://github.com/sbmlteam/libsbml/releases
2020-12-10 21:30:19 +00:00
Sunpoet Po-Chuan Hsieh
4453cd341c Convert REINPLACE_CMD to patch file 2020-09-29 18:23:04 +00:00
Sunpoet Po-Chuan Hsieh
7d33b22118 Update PYTHON option to use Python 3 2020-09-27 19:30:20 +00:00
Sunpoet Po-Chuan Hsieh
cb333cf1ec 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
2020-06-17 18:17:45 +00:00
Sunpoet Po-Chuan Hsieh
32be5bcc79 Clean up Makefile 2020-02-08 19:01:40 +00:00
Sunpoet Po-Chuan Hsieh
47c6c8bc57 Use USES=pathfix
- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership
2019-06-22 21:48:14 +00:00
Wen Heping
6779cec238 - Update to 5.18.0 2019-05-20 09:12:41 +00:00
Tobias C. Berner
707c6bf295 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
2018-12-25 20:25:39 +00:00
Tobias Kortkamp
862bfe924c 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
2018-08-25 03:31:43 +00:00
Mark Linimon
3d51529fe8 Mark as broken with clang6 after r473289. 2018-08-24 06:24:30 +00:00
Wen Heping
18d5a5524f - Update to 5.17.0 2018-06-25 01:37:52 +00:00
Wen Heping
8cc87f5485 - Update to 5.16.0 2018-01-01 08:24:53 +00:00
Baptiste Daroussin
2e9911f602 Switch from swig 2.0 to swig 3.0 2017-12-20 19:34:11 +00:00
Mathieu Arnold
551be3c723 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
2017-11-30 15:50:30 +00:00
Wen Heping
b60a5c5e56 - Update to 5.15.0 2017-05-18 02:22:18 +00:00
Mathieu Arnold
d26ef18700 Cleanup no longer needed CHMOD usage after r424898.
PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
2016-11-02 22:45:14 +00:00
Mikhail Teterin
ce33766b1f 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
2016-04-16 01:54:15 +00:00
Mathieu Arnold
7f4572eae4 Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat:	portmgr
Sponsored by:	Absolight
2016-04-01 13:29:15 +00:00
Wen Heping
389b0168c4 - Update to 5.12.0 2016-03-27 07:09:34 +00:00
Dmitry Marakasov
1cda3966bb - Add LICENSE_FILE
- Switch to options helpers
2015-10-14 23:51:20 +00:00
Raphael Kubo da Costa
3705667db1 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.
2015-08-25 13:15:17 +00:00
Wen Heping
e277ea8c7b - Update to 5.11.4 2015-05-12 08:58:14 +00:00
Marcus von Appen
49cb3686eb - Convert USE_PYTHON -> USES leftovers missed in the previous commits
Spotted by:	antoine
With hat:	python
2015-01-04 08:23:23 +00:00
Wen Heping
6453105b31 - Update to 5.11.0
PR:		196377
Submitted by:	koue@chaosophia.net
2014-12-30 12:57:53 +00:00
Baptiste Daroussin
99a3e8559c Cleanup plist 2014-10-20 07:10:48 +00:00
Wen Heping
f6912d8c17 - Update to 5.10.2
PR:		192198
Submitted by:	tkato432@yahoo.com
2014-08-10 06:21:53 +00:00
Marcus von Appen
900db324a3 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
2014-08-09 15:44:27 +00:00
Wen Heping
06e1e7ab8b - Update to 5.10.0 2014-05-13 07:04:17 +00:00
Wen Heping
f6d9105f6a - 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]
2014-05-13 02:46:25 +00:00
Niclas Zeising
39fc32e828 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)
2014-04-16 18:28:47 +00:00
Baptiste Daroussin
d574c51a4f Convert b* to USES=zip 2014-03-07 15:52:40 +00:00
Baptiste Daroussin
3b82ca9795 Reduce over inclusion of bsd.port.mk 2014-01-15 22:50:50 +00:00
Baptiste Daroussin
a2275161bd In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
2013-12-11 14:43:51 +00:00
Wen Heping
7c42586279 - Fix build on head 2013-12-01 01:58:31 +00:00
Thomas Abthorpe
84e9967fe5 - Switch to build with lang/ruby19
- No PORTREVISION bump, option is off by default

With hat:	portmgr
2013-10-10 18:08:34 +00:00
Baptiste Daroussin
7055ff02f1 Add NO_STAGE all over the place in preparation for the staging support (cat: biology) 2013-09-20 15:55:44 +00:00
Jason Helfman
21ff3eb3b7 - adoption of optionsNG
- trim historical header
- tighten COMMENT

Approved by:	portmgr (miwi)
2013-03-18 06:50:12 +00:00
Martin Wilke
a9481afc8a - Get Rid MD5 support 2011-03-19 12:38:54 +00:00
Wen Heping
34df475911 - Update to 4.2.0 2010-10-08 02:06:53 +00:00
Wen Heping
aa10f7a2b8 - Update to 4.1.0 2010-09-16 03:31:29 +00:00
Wen Heping
b77703b9d2 - Update to 4.0.1 2010-05-24 07:19:35 +00:00
Pav Lucistnik
38eb8c5339 - Mark MAKE_JOBS_UNSAFE
Reported by:	pointyhat
2009-11-20 22:53:09 +00:00
Wen Heping
9c55d004d3 - 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
2009-09-23 01:06:29 +00:00
Dmitry Marakasov
c926af277e - Switch SourceForge ports to the new File Release System: categories starting with B,C 2009-08-22 00:15:15 +00:00