non port: biology/py-biopython/Makefile |
Number of commits found: 70 |
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 |
Sunday, 23 Apr 2023
|
09:09 Gerald Pfeifer (gerald)
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
8d3e020 |
Thursday, 9 Mar 2023
|
22:13 Wen Heping (wen)
biology/py-biopython: Update to 1.81
PR: 269995
Reported by: wen@
Approved by: maintainer
191db1b |
Monday, 5 Dec 2022
|
11:45 Wen Heping (wen)
biology/py-biopython: Update to 1.80
PR: 268106
Reported by: wen@
Approved by: maintainer
db114d7 |
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 |
Tuesday, 12 Oct 2021
|
06:43 Wen Heping (wen)
biology/py-biopython: Update to 1.79
PR: 259046
Reported by: wen@
Approved by: maintainer
112c183 |
Tuesday, 6 Apr 2021
|
14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Friday, 16 Oct 2020
|
19:12 jwb
biology/py-biopython: Upgrade to 1.78
Eliminates Bio.Alphabet
Other minor improvements
PR: ports/250324
Submitted by: Mauricio Herrera Cuadra
|
Saturday, 13 Jun 2020
|
13:42 jwb
biology/py-biopython: Set python requirement to 3.6+
New requirement for v1.77 overlooked during upgrade
|
Friday, 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>
|
Friday, 26 Jul 2019
|
20:46 gerald
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
|
Saturday, 22 Dec 2018
|
04:54 wen
- Update to 1.73
PR: 234154
Submitted by: wenheping2000@hotmail.com(myself)
Approved by: maintainer
|
Wednesday, 12 Dec 2018
|
01:35 gerald
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
|
Friday, 24 Aug 2018
|
00:12 wen
- Update to 1.72
PR: 230723
Submitted by: wen@(myself)
Approved by: maintainer
|
Wednesday, 20 Jun 2018
|
17:05 mat
Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.
Sponsored by: Absolight
|
Sunday, 13 May 2018
|
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)
|
Monday, 9 Apr 2018
|
06:26 wen
- Update to 1.71
Approved by: mauricio@arareko.net(maintainer, via email)
|
Saturday, 10 Mar 2018
|
17:46 gerald
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
|
Monday, 19 Feb 2018
|
11:10 antoine
Reduce dependency on the python2 metaport
PR: 225752
Submitted by: Yasuhiro KIMURA
|
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
|
Friday, 18 Aug 2017
|
12:57 wen
- update to 1.70
PR: 221443
Submitted by: wen@(myself)
Approved by: maintainer
|
Wednesday, 3 May 2017
|
12:39 wen
- Update to 1.69
PR: 218903
Submitted by: wen@
Approved by: maintainer
|
Friday, 23 Sep 2016
|
01:54 wen
- Update to 1.68
PR: 212874
Submitted by: wen@(myself)
Approved by: maintainer
|
Sunday, 17 Apr 2016
|
03:55 wen
- Update to 1.66
PR: 208825
Submitted by: wen@
Approved by: maintainer
|
Friday, 1 Apr 2016
|
13:29 mat
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
|
Wednesday, 5 Aug 2015
|
10:32 mat
Update to 1.65.
PR: 201888
Submitted by: brueffer
Approved by: maintainer
Sponsored by: Absolight
|
Monday, 19 Jan 2015
|
20:21 makc
biology/py-biopython:
- Convert to options framework
Approved by: portmgr blanket
|
Sunday, 19 Oct 2014
|
07:38 mva
- Convert ports from benchmarks/ and biology/ to new USES=python
Approved by: portmgr (implicit)
|
Wednesday, 10 Sep 2014
|
20:50 gerald
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)
|
Sunday, 27 Apr 2014
|
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)
|
Monday, 10 Mar 2014
|
20:55 gerald
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)
|
Tuesday, 25 Feb 2014
|
12:44 tota
- 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
- Set CONFLICTS
- Use PYDISTUTILS_AUTOPLIST
* Remove pkg-plist, accordingly
- Make use of PORTDOCS
- Set OPTIONS_DEFINE explicitly
- Fix include statement
- Make docs unconditional to stage
- Replace tab with a single space after WWW: in pkg-descr
print/py-reportlab2:
- Update CONFLICTS
- Set PORTSCOUT
dependent ports:
- Switch dependency from print/py-reportlab to print/py-reportlab1
* biology/py-biopython
* deskutils/gourmet
* deskutils/griffith
* games/pythonsudoku
* misc/pdfmap
* print/py-trml2pdf
* www/py-satchmo
PR: ports/186970
Submitted by: tota (myself)
Approved by: Muhammad Moinur Rahman (maintainer)
|
Monday, 13 Jan 2014
|
21:00 rene
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)
|
Saturday, 26 Oct 2013
|
00:52 gerald
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
- 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
- Removed compatibility with K&R compilers, which was untestable due
to lack of such compilers.
- New functions
. mpc_log10
. mpc_mul_2si, mpc_div_2si
- Speed-ups
. mpc_fma
- Bug fixes
. mpc_div and mpc_norm now return a value indicating the effective
rounding direction, as the other functions.
. mpc_mul, mpc_sqr and mpc_norm now return correct results even if
there are over- or underflows during the computation.
. mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
infinite part and equals output variable is corrected.
. mpc_fr_sub: Wrong return value for imaginary part is corrected.
Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.
Bump PORTREVISIONS of all dependent ports.
PR: 183141
Approved by: portmgr (bdrewery)
|
Friday, 20 Sep 2013
|
15:55 bapt
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
|
Tuesday, 25 Sep 2012
|
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)
|
Tuesday, 6 Mar 2012
|
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)
|
Tuesday, 24 May 2011
|
09:06 wen
- Update to 1.57
PR: ports/156329
Submitted by: Wen Heping (myself)
Approved by: maintainer
|
Thursday, 24 Feb 2011
|
23:25 miwi
- Move over to python2.5 or higher
- While here kick md5
|
Friday, 2 Jul 2010
|
02:57 wen
- Update to 1.54
PR: ports/148274
Submitted by: Ju Pengfei <jupengfei@gmail.com>
Approved by: maintainer
Feature safe: yes
|
Wednesday, 6 Jan 2010
|
00:29 wen
- Update to 1.53
PR: ports/142221
Submitted by: Wen Heping (myself)
Approved by: maintainer
|
Friday, 4 Sep 2009
|
20:41 miwi
- Update to 138038
PR: 138038
Submitted by: Wen Heping <wenheping@gmail.com>
Approved by: maintainer
|
Saturday, 11 Oct 2008
|
15:26 miwi
- Update to 1.48
PR: 127776
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer
|
Monday, 11 Aug 2008
|
22:06 miwi
- Update to 1.47
PR: 125912
Submitted by: Wen heping <wenheping@gmail.com>
Approved by: maintainer timeout
|
Friday, 4 Jul 2008
|
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)
|
Thursday, 31 May 2007
|
03:49 miwi
- Fix typos.
Reported by: stas@
|
Wednesday, 30 May 2007
|
06:57 miwi
- Update to 1.43
PR: 111817
Submitted by: "P.BandieraPaiva" <paiva@unifesp.br>
Approved by: maintainer
|
Tuesday, 31 Oct 2006
|
13:25 miwi
- Update to 1.42
PR: ports/104635
Submitted by: Thomas Abthorpe <thomas@goodking.ca>
Approved by: maintainer
|
Friday, 11 Nov 2005
|
01:15 mnag
Update to 1.41
Take MAINTAINER
Add SHA256
PR: 88792
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
|
Saturday, 20 Nov 2004
|
08:09 linimon
With portmgr hat on, reset inactive maintainer. These ports are now up
for adoption.
|
Wednesday, 27 Oct 2004
|
20:39 pav
- Update to 1.30
PR: ports/71400
Submitted by: Stefan Walter <sw@gegenunendlich.de>
Approved by: maintainer timeout (2 months)
|
Friday, 2 Jul 2004
|
08:20 kris
BROKEN: Does not build
|
Monday, 9 Feb 2004
|
21:40 des
Upgrade to 1.23.
Approved by: maintainer timeout
|
Thursday, 20 Nov 2003
|
15:06 trevor
Define USE_PERL5_BUILD, not erroneous USE_PERL.
Submitted by: Oliver Eikemeier
|
13:51 trevor
Define USE_PERL to make Perl available for (mostly deprecated)
"perl -pi -e" construction.
|
Thursday, 13 Nov 2003
|
14:45 trevor
Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.
|
Friday, 7 Mar 2003
|
05:56 ade
Clear moonlight beckons.
Requiem mors pacem pkg-comment,
And be calm ports tree.
E Nomini Patri, E Fili, E Spiritu Sancti.
|
Monday, 15 Jul 2002
|
11:37 tg
Use $PYNUMERIC in the dependencies.
|
Tuesday, 22 Jan 2002
|
10:54 wjv
- Update to version 1.00a4
|
Tuesday, 2 Oct 2001
|
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
|
Thursday, 6 Sep 2001
|
13:42 wjv
- Update to version 1.00.a3 - Use pkg-req to check the installed version of
Python
|
Monday, 9 Jul 2001
|
10:57 wjv
Update to version 1.00.a2
|
Friday, 29 Jun 2001
|
16:04 wjv
Use $FILESDIR rather than hard-coded path.
|
Friday, 15 Jun 2001
|
14:25 wjv
Update to 1.00.a1; change MAINTAINER to my new address. Many changes to port,
including addition of CORBA functionality.
|
Tuesday, 29 May 2001
|
13:50 sobomax
math/numpy was renamed to math/py-numeric.
|
Monday, 11 Sep 2000
|
15:56 nbm
Update to 0.90.d03
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Friday, 8 Sep 2000
|
13:24 tg
Don't break package building on Satoshi's cluster. Explicitly depend on
python1.5:lang/python15.
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Saturday, 5 Aug 2000
|
17:01 will
Upgrade to 0.90.d02.
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Monday, 31 Jul 2000
|
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.
|
Number of commits found: 70 |