| non port: biology/py-biopython/Makefile |
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SVNWeb
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Number of commits found: 64 |
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Tue, 12 Oct 2021
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[ 06:43 wen (Wen Heping) ]  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 mat (Mathieu Arnold) ] 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: 64 |
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