Joseph Mingrone
3b90027c76
biology/hyphy: Update to 2.5.58
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.58
Sponsored by: The FreeBSD Foundation
2023-12-23 13:28:25 -04:00
Joseph Mingrone
0bb4adb204
biology/hyphy: Update to 2.5.57
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.57
Sponsored by: The FreeBSD Foundation
2023-11-14 20:09:46 -04:00
Joseph Mingrone
82a2407a5c
biology/hyphy: Update to 2.5.56
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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
2023-11-07 10:46:41 -04:00
Joseph Mingrone
5d6c87d761
biology/hyphy: Update to 2.5.53
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.53
Sponsored by: The FreeBSD Foundation
2023-09-05 11:49:35 -03:00
Joseph Mingrone
8d0b7976cd
biology/hyphy: Update to 2.5.52
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- 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)
2023-08-09 14:39:17 -03:00
Robert Clausecker
b27d05a94c
biology/hyphy: fix build on armv7
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With OpenMP not present, the code had a duplicate function definition.
Get rid of one of the two to enable a build on armv7.
Approved by: portmgr (build fix blanket)
2023-06-30 14:00:28 +02:00
Joseph Mingrone
5a78e2be91
biology/hyphy: Update to 2.5.51hf
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FEL test still fails. See https://github.com/veg/hyphy/issues/1585 .
Sponsored by: The FreeBSD Foundation
2023-05-28 21:09:56 -03:00
Joseph Mingrone
947a366e11
biology/hyphy: Update to 2.5.50
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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
2023-04-19 13:30:57 -03:00
Joseph Mingrone
68b8e0027d
biology/hyphy: Update to 2.5.49
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Sponsored by: The FreeBSD Foundation
2023-03-24 12:54:30 -03:00
Joseph Mingrone
99d4dc3c2b
biology/hyphy: Update to 2.5.48
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.48
Sponsored by: The FreeBSD Foundation
2023-03-05 11:51:37 -04:00
Joseph Mingrone
048831ec57
biology/hyphy: Update to 2.5.47
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Changes: https://github.com/veg/hyphy/releases/tag/2.5.47
Sponsored by: The FreeBSD Foundation
2023-02-03 23:36:47 -04:00
Joseph Mingrone
c6a8b4ea40
biology/hyphy: Update to upstream tag 2.5.46hf1
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Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D37975
2023-01-09 22:05:57 -04:00
Joseph Mingrone
f0ad33c970
biology/hyphy: Update to 2.5.43
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Sponsored by: The FreeBSD Foundation
2022-12-25 20:17:42 -04:00
Yuri Victorovich
e2b35d7147
biology/hyphy: Not broken on systems where OpenMP isn't available
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PR: 265677
Reported by: Robert Clausecker <fuz@fuz.su>
2022-10-01 13:59:13 -07:00
Yuri Victorovich
d6b3e9f9c4
biology/hyphy: Add tests; Fix ONLY_FOR_ARCHS order
2022-10-01 13:59:13 -07:00
Joseph Mingrone
e7ac0267cd
biology/hyphy: Update to 2.5.42
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https://github.com/veg/hyphy/compare/2.5.41...2.5.42
Sponsored by: The FreeBSD Foundation
2022-09-19 18:10:39 -03:00
Stefan Eßer
fb16dfecae
Remove WWW entries moved into port Makefiles
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Commit b7f05445c0
2022-09-07 23:58:51 +02:00
Stefan Eßer
b7f05445c0
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)
2022-09-07 23:10:59 +02:00
Yuri Victorovich
425afd9918
biology/hyphy: Update 2.5.40 -> 2.5.41
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PR: 265677
Approved by: jrm@ (maintainer)
2022-08-06 15:23:11 -07:00
Yuri Victorovich
36aeef9b99
biology/hyphy: Correct BROKEN message
2022-08-04 09:21:46 -07:00
Yuri Victorovich
6a6938ea10
biology/hyphy: Broken on systems where OpenMP isn't enabled
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Reported by: fallout
Approved by: portmgr (blanket)
2022-08-04 00:41:22 -07:00
Joseph Mingrone
c886234c5a
biology/hyphy: Update to 2.5.40
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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
2022-07-18 12:40:25 -03:00
Joseph Mingrone
f519fe65ca
biology/hyphy: Update to 2.5.39
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https://github.com/veg/hyphy/releases/tag/2.5.39hf1
Sponsored by: The FreeBSD Foundation
2022-05-26 23:38:12 -03:00
Joseph Mingrone
e2c4d38d48
biology/hyphy: Update to 2.5.38
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Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38
Sponsored by: The FreeBSD Foundation
2022-04-24 15:24:30 -03:00
Joseph Mingrone
73b83478c1
biology/hyphy: Fix build with clang 13.0.0
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clang 13 complains about duplicate loop unrolling pragmas for clang and
CGG. According to [1], clang supports #pragma GCC unroll with identical
semantics to #pragma clang loop unroll, so remove instances of #pragma
clang loop unroll and #pragma unroll when they appear with #pragma GCC
unroll for the same loop.
[1]
https://clang.llvm.org/docs/AttributeReference.html#pragma-unroll-pragma-nounroll
Sponsored by: The FreeBSD Foundation
2022-02-21 16:13:16 -04:00
Joseph Mingrone
f557264ccc
biology/hyphy: Update to 2.5.36
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https://github.com/veg/hyphy/releases/tag/2.5.36
Sponsored by: The FreeBSD Foundation
2022-02-03 01:42:15 -04:00
Joseph Mingrone
913c9fbc40
biology/hyphy: Update to 2.5.33
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https://github.com/veg/hyphy/releases/tag/2.5.33
2021-11-17 07:51:41 -04:00
Piotr Kubaj
40dbbdf79c
biology/hyphy: enable on armv7
2021-11-12 14:48:47 +00:00
Piotr Kubaj
6a7fc8ddc2
biology/hyphy: enable on powerpc64le
2021-11-08 16:49:37 +00:00
Piotr Kubaj
123f5e1c0c
biology/hyphy: enable on powerpc and powerpc64
2021-11-07 12:14:59 +00:00
Mikael Urankar
46ed8da916
biology/hyphy: Enable on aarch64.
2021-10-08 18:27:33 +02:00
Joseph Mingrone
dab99da055
biology/hyphy: Update to 2.4.32
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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
2021-08-20 10:56:52 -03:00
Joseph Mingrone
c33cf04fe5
biology/hyphy: Update to 2.5.31
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https://github.com/veg/hyphy/releases/tag/2.5.31
2021-06-05 20:00:24 -03:00
Joseph Mingrone
ac46e01537
biology/hyphy: Update to 2.5.30
2021-04-07 22:54:50 -03:00
Mathieu Arnold
cf118ccf87
One more small cleanup, forgotten yesterday.
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Reported by: lwhsu
2021-04-07 10:09:01 +02:00
Mathieu Arnold
305f148f48
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
Joseph Mingrone
f07f561c0c
biology/hyphy: Update to 2.5.29
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https://github.com/veg/hyphy/releases/tag/2.5.29
2021-02-25 01:39:51 +00:00
Joseph Mingrone
97d3e19474
biology/hyphy: Update to 2.5.28
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https://github.com/veg/hyphy/releases/tag/2.5.28
2021-02-23 19:09:01 +00:00
Joseph Mingrone
059ebf3da7
biology/hyphy: Update to version 2.5.27
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https://github.com/veg/hyphy/releases/tag/2.5.27
2021-01-27 11:33:53 +00:00
Joseph Mingrone
3d9e4abbe0
biology/hyphy: Update to version 2.5.26
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https://github.com/veg/hyphy/releases/tag/2.5.26
2021-01-15 20:09:29 +00:00
Joseph Mingrone
56dac58885
biology/hyphy: Remove USES=compiler:openmp
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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
2021-01-11 17:54:42 +00:00
Joseph Mingrone
959aa35d1a
biology/hyphy: Update to version 2.5.25
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https://github.com/veg/hyphy/releases/tag/2.5.25
2021-01-11 02:51:29 +00:00
Joseph Mingrone
a2869b87e2
biology/hyphy: Update to version 2.5.24
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https://github.com/veg/hyphy/releases/tag/2.5.24
2020-12-20 20:21:52 +00:00
Joseph Mingrone
acaba2fd81
biology/hyphy: Update to version 2.5.23
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Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.23
2020-11-19 10:53:55 +00:00
Joseph Mingrone
9764ff1c09
biology/hyphy: Update to version 2.5.22
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Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.22hf
2020-11-18 10:54:03 +00:00
Joseph Mingrone
c0b2681b80
biology/hyphy: Update to version 2.5.21
2020-10-30 14:05:47 +00:00
Joseph Mingrone
9c9a2cecb6
biology/hyphy: Update to version 2.5.20
2020-10-16 23:43:17 +00:00
Joseph Mingrone
520d533f8b
biology/hyphy: Update to version 2.5.19
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Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.19
2020-10-13 01:05:45 +00:00
Joseph Mingrone
3a2ec6d491
biology/hyphy: Update to version 2.5.18 and add AVX option
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The AVX option is off by default, because hyphy will crash on systems
without advanced vector extensions support.
2020-09-02 17:47:10 +00:00
Joseph Mingrone
9c4faf08b0
biology/hyphy: Update to version 2.5.17
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Upstream changes:
https://github.com/veg/hyphy/releases/tag/2.5.16
https://github.com/veg/hyphy/releases/tag/2.5.17
2020-08-20 16:15:22 +00:00
