| non port: biology/hyphy/Makefile |
Number of commits found: 64 |
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Sunday, 14 Apr 2024
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21:14 Joseph Mingrone (jrm) 
biology/hyphy: Update to 2.5.60
Changes: https://github.com/veg/hyphy/compare/2.5.59...2.5.60
https://github.com/veg/hyphy/compare/2.5.58...2.5.59
Sponsored by: The FreeBSD Foundation
    ce15321 |
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Saturday, 23 Dec 2023
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17:28 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.58
Changes: https://github.com/veg/hyphy/releases/tag/2.5.58
Sponsored by: The FreeBSD Foundation
3b90027 |
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Wednesday, 15 Nov 2023
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00:09 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.57
Changes: https://github.com/veg/hyphy/releases/tag/2.5.57
Sponsored by: The FreeBSD Foundation
0bb4adb |
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Tuesday, 7 Nov 2023
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14:46 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.56
Changes: https://github.com/veg/hyphy/releases/tag/2.5.56
https://github.com/veg/hyphy/releases/tag/2.5.55
Sponsored by: The FreeBSD Foundation
82a2407 |
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Tuesday, 5 Sep 2023
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14:49 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.53
Changes: https://github.com/veg/hyphy/releases/tag/2.5.53
Sponsored by: The FreeBSD Foundation
5d6c87d |
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Wednesday, 9 Aug 2023
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17:39 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.52
- FEL test is now passing, so remove comment about it failing.
- Remove armv7 support since most tests are segfaulting.
Changes: https://github.com/veg/hyphy/releases/tag/2.5.52
Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D41393
Tested by: fuz (armv7)
8d0b797 |
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Monday, 29 May 2023
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00:09 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.51hf
FEL test still fails. See https://github.com/veg/hyphy/issues/1585.
Sponsored by: The FreeBSD Foundation
5a78e2b |
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Wednesday, 19 Apr 2023
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16:30 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.50
This release fixes a bug when not using openmp.
https://github.com/veg/hyphy/compare/2.5.49...2.5.50
Sponsored by: The FreeBSD Foundation
947a366 |
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Friday, 24 Mar 2023
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15:54 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.49
Sponsored by: The FreeBSD Foundation
68b8e00 |
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Sunday, 5 Mar 2023
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15:51 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.48
Changes: https://github.com/veg/hyphy/releases/tag/2.5.48
Sponsored by: The FreeBSD Foundation
99d4dc3 |
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Saturday, 4 Feb 2023
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03:36 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.47
Changes: https://github.com/veg/hyphy/releases/tag/2.5.47
Sponsored by: The FreeBSD Foundation
048831e |
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Tuesday, 10 Jan 2023
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02:05 Joseph Mingrone (jrm)
biology/hyphy: Update to upstream tag 2.5.46hf1
Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D37975
c6a8b4e |
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Monday, 26 Dec 2022
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00:17 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.43
Sponsored by: The FreeBSD Foundation
f0ad33c |
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Saturday, 1 Oct 2022
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20:59 Yuri Victorovich (yuri)
biology/hyphy: Add tests; Fix ONLY_FOR_ARCHS order
d6b3e9f |
20:59 Yuri Victorovich (yuri)
biology/hyphy: Not broken on systems where OpenMP isn't available
PR: 265677
Reported by: Robert Clausecker <fuz@fuz.su>
e2b35d7 |
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Monday, 19 Sep 2022
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21:10 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.42
https://github.com/veg/hyphy/compare/2.5.41...2.5.42
Sponsored by: The FreeBSD Foundation
e7ac026 |
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Wednesday, 7 Sep 2022
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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 |
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Saturday, 6 Aug 2022
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22:23 Yuri Victorovich (yuri)
biology/hyphy: Update 2.5.40 -> 2.5.41
PR: 265677
Approved by: jrm@ (maintainer)
425afd9 |
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Thursday, 4 Aug 2022
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16:21 Yuri Victorovich (yuri)
biology/hyphy: Correct BROKEN message
36aeef9 |
07:41 Yuri Victorovich (yuri)
biology/hyphy: Broken on systems where OpenMP isn't enabled
Reported by: fallout
Approved by: portmgr (blanket)
6a6938e |
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Monday, 18 Jul 2022
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15:40 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.40
https://github.com/veg/hyphy/releases/tag/2.5.40
https://github.com/veg/hyphy/compare/2.5.39...2.5.40
Sponsored by: The FreeBSD Foundation
c886234 |
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Friday, 27 May 2022
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02:38 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.39
https://github.com/veg/hyphy/releases/tag/2.5.39hf1
Sponsored by: The FreeBSD Foundation
f519fe6 |
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Sunday, 24 Apr 2022
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18:24 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.38
Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38
Sponsored by: The FreeBSD Foundation
e2c4d38 |
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Thursday, 3 Feb 2022
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05:42 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.36
https://github.com/veg/hyphy/releases/tag/2.5.36
Sponsored by: The FreeBSD Foundation
f557264 |
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Wednesday, 17 Nov 2021
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11:51 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.33
https://github.com/veg/hyphy/releases/tag/2.5.33
913c9fb |
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Friday, 12 Nov 2021
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14:48 Piotr Kubaj (pkubaj)
biology/hyphy: enable on armv7
40dbbdf |
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Monday, 8 Nov 2021
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16:49 Piotr Kubaj (pkubaj)
biology/hyphy: enable on powerpc64le
6a7fc8d |
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Sunday, 7 Nov 2021
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12:14 Piotr Kubaj (pkubaj)
biology/hyphy: enable on powerpc and powerpc64
123f5e1 |
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Friday, 8 Oct 2021
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16:27 Mikael Urankar (mikael)
biology/hyphy: Enable on aarch64.
46ed8da |
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Friday, 20 Aug 2021
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13:56 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.4.32
https://github.com/veg/hyphy/releases/tag/2.5.32
Port changes:
- Remove USES=ssl since it's an indirect dependency from curl
- Remove patch that was upstreamed
dab99da |
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Saturday, 5 Jun 2021
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23:00 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.31
https://github.com/veg/hyphy/releases/tag/2.5.31
c33cf04 |
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Thursday, 8 Apr 2021
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01:54 Joseph Mingrone (jrm)
biology/hyphy: Update to 2.5.30
ac46e01 |
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Wednesday, 7 Apr 2021
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08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
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Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
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Thursday, 25 Feb 2021
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01:39 jrm
biology/hyphy: Update to 2.5.29
https://github.com/veg/hyphy/releases/tag/2.5.29
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Tuesday, 23 Feb 2021
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19:09 jrm
biology/hyphy: Update to 2.5.28
https://github.com/veg/hyphy/releases/tag/2.5.28
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Wednesday, 27 Jan 2021
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11:33 jrm
biology/hyphy: Update to version 2.5.27
https://github.com/veg/hyphy/releases/tag/2.5.27
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Friday, 15 Jan 2021
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20:09 jrm
biology/hyphy: Update to version 2.5.26
https://github.com/veg/hyphy/releases/tag/2.5.26
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Monday, 11 Jan 2021
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17:54 jrm
biology/hyphy: Remove USES=compiler:openmp
USES=compiler:openmp still forces building with GCC. This is no longer
necessary on tier 1 platforms, which have openmp in the base system.
PR: 247753, 252379
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02:51 jrm
biology/hyphy: Update to version 2.5.25
https://github.com/veg/hyphy/releases/tag/2.5.25
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Sunday, 20 Dec 2020
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20:21 jrm
biology/hyphy: Update to version 2.5.24
https://github.com/veg/hyphy/releases/tag/2.5.24
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Thursday, 19 Nov 2020
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10:53 jrm
biology/hyphy: Update to version 2.5.23
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.23
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Wednesday, 18 Nov 2020
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10:54 jrm
biology/hyphy: Update to version 2.5.22
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.22hf
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Friday, 30 Oct 2020
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14:05 jrm
biology/hyphy: Update to version 2.5.21
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Friday, 16 Oct 2020
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23:43 jrm
biology/hyphy: Update to version 2.5.20
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Tuesday, 13 Oct 2020
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01:05 jrm
biology/hyphy: Update to version 2.5.19
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.19
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Wednesday, 2 Sep 2020
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17:47 jrm
biology/hyphy: Update to version 2.5.18 and add AVX option
The AVX option is off by default, because hyphy will crash on systems
without advanced vector extensions support.
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Thursday, 20 Aug 2020
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16:15 jrm
biology/hyphy: Update to version 2.5.17
Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.16
https://github.com/veg/hyphy/releases/tag/2.5.17
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Sunday, 28 Jun 2020
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16:40 jrm
biology/hyphy: Update to version 2.5.15
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15
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Saturday, 30 May 2020
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19:39 jrm
biology/hyphy: Update to version 2.5.14
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
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Sunday, 3 May 2020
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02:08 jrm
biology/hyphy: Update to version 2.5.12
Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.11
https://github.com/veg/hyphy/releases/tag/2.5.12
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Saturday, 25 Apr 2020
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00:33 jrm
biology/hyphy: Update to version 2.5.10
Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.9
https://github.com/veg/hyphy/releases/tag/2.5.10
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Saturday, 28 Mar 2020
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12:27 jrm
biology/hyphy: Update to version 2.5.8
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8
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Friday, 20 Mar 2020
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01:30 jrm
biology/hyphy: Update to version 2.5.7
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7
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Tuesday, 17 Mar 2020
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18:17 jrm
biology/hyphy: Update to version 2.5.6
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6
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Monday, 2 Mar 2020
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01:31 jrm
biology/hyphy: Update to version 2.5.5
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5
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Friday, 21 Feb 2020
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12:22 jrm
biology/hyphy: Update to version 2.5.4
Upstream changes: https://github.com/veg/hyphy/releases
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Friday, 26 Jul 2019
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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
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Tuesday, 25 Dec 2018
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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
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Wednesday, 12 Dec 2018
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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
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Saturday, 20 Oct 2018
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12:21 jrm
biology/hyphy: Update to version 2.3.14.16
This pulls in fixes after the 2.3.14 release.
Upstream changes for version 2.3.14:
https://github.com/veg/hyphy/releases/tag/2.3.14
Subsequent fixes:
https://github.com/veg/hyphy/commit/1ecac31
https://github.com/veg/hyphy/commit/bec6833
https://github.com/veg/hyphy/commit/9847438
https://github.com/veg/hyphy/commit/02dcedd
https://github.com/veg/hyphy/commit/8f44d3c
https://github.com/veg/hyphy/commit/5297c30
https://github.com/veg/hyphy/commit/3d88d3e
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Tuesday, 22 May 2018
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22:55 jrm
biology/hyphy: Update to version 2.3.13
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Monday, 14 May 2018
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16:52 jrm
biology/hyphy: Bump PORTREVISION after upstream rerolled release
Also, remove patch that upstream incorporated in new tarball.
Upstream issue: https://github.com/veg/hyphy/issues/796
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Friday, 11 May 2018
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00:05 jrm
New port, biology/hyphy: Hypothesis testing using Phylogenies
WWW: http://www.hyphy.org/
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Number of commits found: 64 |
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