non port: biology/libsbml/Makefile |
Number of commits found: 58 |
Saturday, 30 Sep 2023
|
00:44 Po-Chuan Hsieh (sunpoet)
biology/libsbml: Update to 5.20.2
Changes: https://github.com/sbmlteam/libsbml/releases
4c14d7a |
Tuesday, 27 Jun 2023
|
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 |
Saturday, 27 May 2023
|
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 |
Wednesday, 5 Apr 2023
|
17:29 Po-Chuan Hsieh (sunpoet)
biology/libsbml: Update WWW and clean up pkg-descr
02db5c9 |
Wednesday, 18 Jan 2023
|
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 |
Wednesday, 7 Sep 2022
|
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 |
Wednesday, 20 Jul 2022
|
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 |
Sunday, 10 Apr 2022
|
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 |
Saturday, 26 Mar 2022
|
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 |
Monday, 1 Nov 2021
|
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 |
Tuesday, 11 May 2021
|
21:46 Po-Chuan Hsieh (sunpoet)
biology/libsbml: Rename LIBXML option to LIBXML2
f747a64 |
Tuesday, 6 Apr 2021
|
14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Sunday, 20 Dec 2020
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15:23 sunpoet
Set CMAKE options explicitly
 |
Saturday, 19 Dec 2020
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20:05 sunpoet
Add EXPAT, LIBXML and XERCES options
It allows choosing XML parser library.
 |
Thursday, 10 Dec 2020
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21:30 sunpoet
Update to 5.19.0
Changes: https://github.com/sbmlteam/libsbml/releases
 |
Tuesday, 29 Sep 2020
|
18:23 sunpoet
Convert REINPLACE_CMD to patch file
 |
Sunday, 27 Sep 2020
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19:30 sunpoet
Update PYTHON option to use Python 3
 |
Wednesday, 17 Jun 2020
|
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
 |
Saturday, 8 Feb 2020
|
19:01 sunpoet
Clean up Makefile
 |
Saturday, 22 Jun 2019
|
21:48 sunpoet
Use USES=pathfix
- Add USES=gnome
- Use = instead of += for PLIST_SUB
- Use CMAKE_BOOL
- Cosmetic change
- Take maintainership
 |
Monday, 20 May 2019
|
09:12 wen
- Update to 5.18.0
 |
Tuesday, 25 Dec 2018
|
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
 |
Saturday, 25 Aug 2018
|
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
 |
Friday, 24 Aug 2018
|
06:24 linimon
Mark as broken with clang6 after r473289.
 |
Monday, 25 Jun 2018
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01:37 wen
- Update to 5.17.0
 |
Monday, 1 Jan 2018
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08:24 wen
- Update to 5.16.0
 |
Wednesday, 20 Dec 2017
|
19:34 bapt
Switch from swig 2.0 to swig 3.0
 |
Thursday, 30 Nov 2017
|
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
 |
Thursday, 18 May 2017
|
02:22 wen
- Update to 5.15.0
 |
Wednesday, 2 Nov 2016
|
22:45 mat
Cleanup no longer needed CHMOD usage after r424898.
PR: 213743
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
 |
Saturday, 16 Apr 2016
|
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
 |
Friday, 1 Apr 2016
|
13:29 mat
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
 |
Sunday, 27 Mar 2016
|
07:09 wen
- Update to 5.12.0
 |
Wednesday, 14 Oct 2015
|
23:51 amdmi3
- Add LICENSE_FILE
- Switch to options helpers
 |
Tuesday, 25 Aug 2015
|
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.
 |
Tuesday, 12 May 2015
|
08:58 wen
- Update to 5.11.4
 |
Sunday, 4 Jan 2015
|
08:23 mva
- Convert USE_PYTHON -> USES leftovers missed in the previous commits
Spotted by: antoine
With hat: python
 |
Tuesday, 30 Dec 2014
|
12:57 wen
- Update to 5.11.0
PR: 196377
Submitted by: koue@chaosophia.net
 |
Sunday, 10 Aug 2014
|
06:21 wen
- Update to 5.10.2
PR: 192198
Submitted by: tkato432@yahoo.com
 |
Saturday, 9 Aug 2014
|
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
 |
Tuesday, 13 May 2014
|
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]
 |
Wednesday, 16 Apr 2014
|
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)
 |
Friday, 7 Mar 2014
|
15:52 bapt
Convert b* to USES=zip
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Wednesday, 15 Jan 2014
|
22:50 bapt
Reduce over inclusion of bsd.port.mk
 |
Wednesday, 11 Dec 2013
|
14:43 bapt
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
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Sunday, 1 Dec 2013
|
01:58 wen
- Fix build on head
 |
Thursday, 10 Oct 2013
|
18:08 tabthorpe
- Switch to build with lang/ruby19
- No PORTREVISION bump, option is off by default
With hat: portmgr
 |
Friday, 20 Sep 2013
|
15:55 bapt
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Monday, 18 Mar 2013
|
06:50 jgh
- adoption of optionsNG
- trim historical header
- tighten COMMENT
Approved by: portmgr (miwi)
 |
Friday, 8 Oct 2010
|
02:06 wen
- Update to 4.2.0
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Thursday, 16 Sep 2010
|
03:31 wen
- Update to 4.1.0
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Monday, 24 May 2010
|
07:19 wen
- Update to 4.0.1
 |
Friday, 20 Nov 2009
|
22:53 pav
- Mark MAKE_JOBS_UNSAFE
Reported by: pointyhat
 |
Wednesday, 23 Sep 2009
|
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
 |
Saturday, 22 Aug 2009
|
00:15 amdmi3
- Switch SourceForge ports to the new File Release System: categories starting
with B,C
 |
Thursday, 28 May 2009
|
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>
 |
Number of commits found: 58 |