| non port: biology/py-biopython/Makefile |
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SVNWeb
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Number of commits found: 70 |
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Tue, 27 Jun 2023
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[ 19:34 Rene Ladan (rene)  ]    3d9a815 (Only the first 10 of 4481 ports in this commit are shown above.  )
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>
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Sun, 23 Apr 2023
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[ 09:09 Gerald Pfeifer (gerald) ] 8d3e020 (Only the first 10 of 2091 ports in this commit are shown above. )
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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Thu, 9 Mar 2023
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[ 22:13 Wen Heping (wen) ] 191db1b
biology/py-biopython: Update to 1.81
PR: 269995
Reported by: wen@
Approved by: maintainer
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Mon, 5 Dec 2022
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[ 11:45 Wen Heping (wen) ] db114d7
biology/py-biopython: Update to 1.80
PR: 268106
Reported by: wen@
Approved by: maintainer
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above. )
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.
(Only the first 15 lines of the commit message are shown above )
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Wed, 20 Jul 2022
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[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
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> (Only the first 15 lines of the commit message are shown above )
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Tue, 12 Oct 2021
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[ 06:43 Wen Heping (wen) ] 112c183
biology/py-biopython: Update to 1.79
PR: 259046
Reported by: wen@
Approved by: maintainer
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Fri, 16 Oct 2020
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[ 19:12 jwb ]  
biology/py-biopython: Upgrade to 1.78
Eliminates Bio.Alphabet
Other minor improvements
PR: ports/250324
Submitted by: Mauricio Herrera Cuadra
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Sat, 13 Jun 2020
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[ 13:42 jwb ]
biology/py-biopython: Set python requirement to 3.6+
New requirement for v1.77 overlooked during upgrade
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Fri, 29 May 2020
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[ 02:03 jwb ]
biology/py-biopython: Upgrade to 1.77
Upstream support for python 3
PR: ports/246763
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
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Fri, 26 Jul 2019
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[ 20:46 gerald ] (Only the first 10 of 3853 ports in this commit are shown above. )
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330
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Sat, 22 Dec 2018
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[ 04:54 wen ]
- Update to 1.73
PR: 234154
Submitted by: wenheping2000@hotmail.com(myself)
Approved by: maintainer
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Wed, 12 Dec 2018
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[ 01:35 gerald ] (Only the first 10 of 3168 ports in this commit are shown above. )
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590
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Fri, 24 Aug 2018
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[ 00:12 wen ]
- Update to 1.72
PR: 230723
Submitted by: wen@(myself)
Approved by: maintainer
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Wed, 20 Jun 2018
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[ 17:05 mat ] (Only the first 10 of 1617 ports in this commit are shown above. )
Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.
Sponsored by: Absolight
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Sun, 13 May 2018
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[ 22:30 yuri ]
biology/py-biopython: Unbreak on python3; Add license
Two items prevented python3 compatibility:
* Breakage of ASCII codec due to non-ascii characters in README:
https://github.com/biopython/biopython/issues/1649
* The outdated dependency: print/py-reportlab1 instead of the modern version 3.X
print/py-reportlab
Port changes:
* USES=python:2.7 -> USES=python
* Add pre-configure that clears the README file
* Add LICENSE/LICENSE_FILE
Testing:
* Ran the tutorial testcase
http://biopython.org/DIST/docs/tutorial/Tutorial.html,
particularly pdf writing through print/py-reportlab worked fine.
Asked the upstream to clarify the acceptable dependency version:
https://github.com/biopython/biopython/issues/1650
Approved by: portmgr blanket (unbreak for python3; add license)
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Mon, 9 Apr 2018
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[ 06:26 wen ]
- Update to 1.71
Approved by: mauricio@arareko.net(maintainer, via email)
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Sat, 10 Mar 2018
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[ 17:46 gerald ] (Only the first 10 of 1104 ports in this commit are shown above. )
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
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Mon, 19 Feb 2018
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[ 11:10 antoine ] (Only the first 10 of 442 ports in this commit are shown above. )
Reduce dependency on the python2 metaport
PR: 225752
Submitted by: Yasuhiro KIMURA
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Thu, 30 Nov 2017
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[ 15:50 mat ] (Only the first 10 of 2423 ports in this commit are shown above. )
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 (Only the first 15 lines of the commit message are shown above )
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Fri, 18 Aug 2017
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[ 12:57 wen ]
- update to 1.70
PR: 221443
Submitted by: wen@(myself)
Approved by: maintainer
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Wed, 3 May 2017
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[ 12:39 wen ]
- Update to 1.69
PR: 218903
Submitted by: wen@
Approved by: maintainer
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Fri, 23 Sep 2016
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[ 01:54 wen ]
- Update to 1.68
PR: 212874
Submitted by: wen@(myself)
Approved by: maintainer
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Sun, 17 Apr 2016
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[ 03:55 wen ]
- Update to 1.66
PR: 208825
Submitted by: wen@
Approved by: maintainer
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Fri, 1 Apr 2016
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[ 13:29 mat ] (Only the first 10 of 1009 ports in this commit are shown above. )
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
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Wed, 5 Aug 2015
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[ 10:32 mat ]
Update to 1.65.
PR: 201888
Submitted by: brueffer
Approved by: maintainer
Sponsored by: Absolight
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Mon, 19 Jan 2015
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[ 20:21 makc ]
biology/py-biopython:
- Convert to options framework
Approved by: portmgr blanket
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Sun, 19 Oct 2014
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[ 07:38 mva ]
- Convert ports from benchmarks/ and biology/ to new USES=python
Approved by: portmgr (implicit)
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Wed, 10 Sep 2014
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[ 20:50 gerald ] (Only the first 10 of 3171 ports in this commit are shown above. )
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.
Part II, Bump PORTREVISIONs.
PR: 192025
Tested by: antoine (-exp runs)
Approved by: portmgr (implicit)
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Sun, 27 Apr 2014
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[ 01:59 swills ]
- Stage
- Drop easy_install
- Use auto pkg-plist
- Delete pkg-plist
PR: ports/188818
Submitted by: Bartek Rutkowski <ports@robakdesign.com>
Approved by: portmgr@ (blanket)
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Mon, 10 Mar 2014
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[ 20:55 gerald ] (Only the first 10 of 1081 ports in this commit are shown above. )
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs)
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Tue, 25 Feb 2014
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[ 12:44 tota ] (Only the first 10 of 22 ports in this commit are shown above. )
- Repocopy print/py-reportlab to print/py-reportlab1
to preserve version 1.x and to update to 3.0
print/py-reportlab:
- Update print/py-reportlab to 3.0 based on print/py-reportlab2
- Support STAGEDIR
- Use PYDISTUTILS_AUTOPLIST
* Remove pkg-plist, accordingly
- Set CONFLICTS
- Add PORTSCOUT
- Replace tab with a single space after WWW: in pkg-descr
print/py-reportlab1:
- Support STAGEDIR
- Add PKGNAMESUFFIX not to duplicate ports with the same name(Only the first 15 lines of the commit message are shown above )
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Mon, 13 Jan 2014
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[ 21:00 rene ] (Only the first 10 of 702 ports in this commit are shown above. )
Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by: python (mva, rm)
Approved by: portmgr-lurkers (mat)
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Sat, 26 Oct 2013
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[ 00:52 gerald ] (Only the first 10 of 1147 ports in this commit are shown above. )
Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui (Only the first 15 lines of the commit message are shown above )
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Fri, 20 Sep 2013
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[ 15:55 bapt ] (Only the first 10 of 94 ports in this commit are shown above. )
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Tue, 25 Sep 2012
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[ 08:06 rm ]
- update to 1.60
while here:
- convert Makefile header into two-line format
- update COMMENT (indefinite article removed)
- change USE_PYTHON to just -2.7
- remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there
- tab -> space change in pkg-descr:WWW
PR: 171115
Submitted by: wen
Approved by: Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer)
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Tue, 6 Mar 2012
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[ 06:40 wen ]
- Update to 1.59
PR: ports/165582
Submitted by: wen@ (myself)
Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer, via
email)
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Tue, 24 May 2011
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[ 09:06 wen ]
- Update to 1.57
PR: ports/156329
Submitted by: Wen Heping (myself)
Approved by: maintainer
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Thu, 24 Feb 2011
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[ 23:25 miwi ] (Only the first 10 of 20 ports in this commit are shown above. )
- Move over to python2.5 or higher
- While here kick md5
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Fri, 2 Jul 2010
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[ 02:57 wen ]
- Update to 1.54
PR: ports/148274
Submitted by: Ju Pengfei <jupengfei@gmail.com>
Approved by: maintainer
Feature safe: yes
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Wed, 6 Jan 2010
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[ 00:29 wen ]
- Update to 1.53
PR: ports/142221
Submitted by: Wen Heping (myself)
Approved by: maintainer
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Fri, 4 Sep 2009
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[ 20:41 miwi ]
- Update to 138038
PR: 138038
Submitted by: Wen Heping <wenheping@gmail.com>
Approved by: maintainer
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Sat, 11 Oct 2008
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[ 15:26 miwi ]
- Update to 1.48
PR: 127776
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer
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Mon, 11 Aug 2008
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[ 22:06 miwi ]
- Update to 1.47
PR: 125912
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer timeout
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Fri, 4 Jul 2008
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[ 02:53 beech ]
- Update to 1.45
PR: ports/125134
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
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Thu, 31 May 2007
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[ 03:49 miwi ]
- Fix typos.
Reported by: stas@
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Wed, 30 May 2007
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[ 06:57 miwi ]
- Update to 1.43
PR: 111817
Submitted by: "P.BandieraPaiva" <paiva@unifesp.br>
Approved by: maintainer
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Tue, 31 Oct 2006
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[ 13:25 miwi ]
- Update to 1.42
PR: ports/104635
Submitted by: Thomas Abthorpe <thomas@goodking.ca>
Approved by: maintainer
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Fri, 11 Nov 2005
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[ 01:15 mnag ]
Update to 1.41
Take MAINTAINER
Add SHA256
PR: 88792
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
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Sat, 20 Nov 2004
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[ 08:09 linimon ] (Only the first 10 of 33 ports in this commit are shown above. )
With portmgr hat on, reset inactive maintainer. These ports are now up
for adoption.
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Wed, 27 Oct 2004
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[ 20:39 pav ]
- Update to 1.30
PR: ports/71400
Submitted by: Stefan Walter <sw@gegenunendlich.de>
Approved by: maintainer timeout (2 months)
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Fri, 2 Jul 2004
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[ 08:20 kris ]
BROKEN: Does not build
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Mon, 9 Feb 2004
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[ 21:40 des ]
Upgrade to 1.23.
Approved by: maintainer timeout
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Thu, 20 Nov 2003
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[ 15:06 trevor ] (Only the first 10 of 111 ports in this commit are shown above. )
Define USE_PERL5_BUILD, not erroneous USE_PERL.
Submitted by: Oliver Eikemeier
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[ 13:51 trevor ] (Only the first 10 of 111 ports in this commit are shown above. )
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
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Thu, 13 Nov 2003
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[ 14:45 trevor ] (Only the first 10 of 81 ports in this commit are shown above. )
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
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Fri, 7 Mar 2003
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[ 05:56 ade ] (Only the first 10 of 28 ports in this commit are shown above. )
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.
E Nomini Patri, E Fili, E Spiritu Sancti.
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Mon, 15 Jul 2002
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[ 11:37 tg ]
Use $PYNUMERIC in the dependencies.
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Tue, 22 Jan 2002
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[ 10:54 wjv ]
- Update to version 1.00a4
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Tue, 2 Oct 2001
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[ 09:31 wjv ]
- Update the included (optional) Biopython-CORBA pacakge to version 0.3.0 - If
CORBA support is included, the default ORB has changed from omniORB to ORBit
- PORTREVISION bump
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Thu, 6 Sep 2001
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[ 13:42 wjv ]
- Update to version 1.00.a3 - Use pkg-req to check the installed version of
Python
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Mon, 9 Jul 2001
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[ 10:57 wjv ]
Update to version 1.00.a2
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Fri, 29 Jun 2001
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[ 16:04 wjv ]
Use $FILESDIR rather than hard-coded path.
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Fri, 15 Jun 2001
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[ 14:25 wjv ]
Update to 1.00.a1; change MAINTAINER to my new address. Many changes to port,
including addition of CORBA functionality.
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Tue, 29 May 2001
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[ 13:50 sobomax ]
math/numpy was renamed to math/py-numeric.
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Mon, 11 Sep 2000
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[ 15:56 nbm ]
Update to 0.90.d03
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Fri, 8 Sep 2000
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[ 13:24 tg ] (Only the first 10 of 26 ports in this commit are shown above. )
Don't break package building on Satoshi's cluster. Explicitly depend on
python1.5:lang/python15.
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Sat, 5 Aug 2000
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[ 17:01 will ]
Upgrade to 0.90.d02.
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Mon, 31 Jul 2000
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[ 13:12 nbm ]
Add py-biopython, is a collection of Python packages and modules created by
the Biopython Project, intended to provide the basis for building
bioinformatics applications in the Python language.
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Number of commits found: 70 |
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