| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
2.5.68
28 Jan 2025 20:48:19
     |
Joseph Mingrone (jrm)  |
biology/hyphy: Update to 2.5.68
This update fixes some broken tests. See
https://github.com/veg/hyphy/issues/1779 for details.
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.68
Sponsored by: The FreeBSD Foundation |
2.5.67
28 Jan 2025 20:48:19
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.67
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.67
Sponsored by: The FreeBSD Foundation |
2.5.66
28 Jan 2025 20:48:11
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.66
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.66
Sponsored by: The FreeBSD Foundation |
2.5.65
28 Jan 2025 20:44:25
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.65
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.65.actual
PR: 283452, 284161
Sponsored by: The FreeBSD Foundation
Co-authored-by: Älven <alster@vinterdalen.se> |
2.5.64
10 Dec 2024 20:31:58
|
Joseph Mingrone (jrm)
Author: Älven |
biology/hyphy: Update to 2.5.64
PR: 283028 |
2.5.63
25 Oct 2024 16:20:53
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.62
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.63
Sponsored by: The FreeBSD Foundation |
2.5.62
21 Jun 2024 16:58:09
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.62
Commit log: https://github.com/veg/hyphy/compare/2.5.61...2.5.62
Sponsored by: The FreeBSD Foundation |
2.5.61
16 May 2024 16:08:06
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.61
Release notes: https://github.com/veg/hyphy/releases/tag/2.5.61
Commit log: https://github.com/veg/hyphy/compare/2.5.56...2.5.61
Sponsored by: The FreeBSD Foundation |
2.5.60
14 Apr 2024 21:14:19
|
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 |
2.5.58
23 Dec 2023 17:28:25
|
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 |
2.5.57
15 Nov 2023 00:09:46
|
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 |
2.5.56
07 Nov 2023 14:46:41
|
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 |
2.5.53
05 Sep 2023 14:49:35
|
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 |
2.5.52
09 Aug 2023 17:39:17
|
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) |
2.5.51.h
30 Jun 2023 12:00:28
|
Robert Clausecker (fuz) |
biology/hyphy: fix build on armv7
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) |
2.5.51.h
29 May 2023 00:09:56
|
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 |
2.5.50
19 Apr 2023 16:30:57
|
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 |
2.5.49
24 Mar 2023 15:54:30
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.49
Sponsored by: The FreeBSD Foundation |
2.5.48
05 Mar 2023 15:51:37
|
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 |
2.5.47
04 Feb 2023 03:36:47
|
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 |
2.5.46.h1
10 Jan 2023 02:05:57
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to upstream tag 2.5.46hf1
Sponsored by: The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D37975 |
2.5.43
26 Dec 2022 00:17:42
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.43
Sponsored by: The FreeBSD Foundation |
2.5.42
01 Oct 2022 20:59:13
|
Yuri Victorovich (yuri) |
biology/hyphy: Not broken on systems where OpenMP isn't available
PR: 265677
Reported by: Robert Clausecker <fuz@fuz.su> |
2.5.42
01 Oct 2022 20:59:13
|
Yuri Victorovich (yuri) |
biology/hyphy: Add tests; Fix ONLY_FOR_ARCHS order |
2.5.42
19 Sep 2022 21:10:39
|
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 |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
2.5.41
07 Sep 2022 21:10:59
|
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.
(Only the first 15 lines of the commit message are shown above  ) |
2.5.41
06 Aug 2022 22:23:11
|
Yuri Victorovich (yuri) |
biology/hyphy: Update 2.5.40 -> 2.5.41
PR: 265677
Approved by: jrm@ (maintainer) |
2.5.40
04 Aug 2022 16:21:46
|
Yuri Victorovich (yuri) |
biology/hyphy: Correct BROKEN message |
2.5.40
04 Aug 2022 07:41:22
|
Yuri Victorovich (yuri) |
biology/hyphy: Broken on systems where OpenMP isn't enabled
Reported by: fallout
Approved by: portmgr (blanket) |
2.5.40
18 Jul 2022 15:40:25
|
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 |
2.5.39
27 May 2022 02:38:12
|
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 |
2.5.38
24 Apr 2022 18:24:30
|
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 |
2.5.36
21 Feb 2022 20:13:16
|
Joseph Mingrone (jrm) |
biology/hyphy: Fix build with clang 13.0.0
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 |
2.5.36
03 Feb 2022 05:42:15
|
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 |
2.5.33
17 Nov 2021 11:51:41
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.33
https://github.com/veg/hyphy/releases/tag/2.5.33 |
2.5.32
12 Nov 2021 14:48:47
|
Piotr Kubaj (pkubaj) |
biology/hyphy: enable on armv7 |
2.5.32
08 Nov 2021 16:49:37
|
Piotr Kubaj (pkubaj) |
biology/hyphy: enable on powerpc64le |
2.5.32
07 Nov 2021 12:14:59
|
Piotr Kubaj (pkubaj) |
biology/hyphy: enable on powerpc and powerpc64 |
2.5.32
08 Oct 2021 16:27:33
|
Mikael Urankar (mikael) |
biology/hyphy: Enable on aarch64. |
2.5.32
20 Aug 2021 13:56:52
|
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 |
2.5.31
05 Jun 2021 23:00:24
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.31
https://github.com/veg/hyphy/releases/tag/2.5.31 |
2.5.30
08 Apr 2021 01:54:50
|
Joseph Mingrone (jrm) |
biology/hyphy: Update to 2.5.30 |
2.5.29
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.5.29
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.5.29
25 Feb 2021 01:39:51
  |
jrm |
biology/hyphy: Update to 2.5.29
https://github.com/veg/hyphy/releases/tag/2.5.29 |
2.5.28
23 Feb 2021 19:09:02
|
jrm |
biology/hyphy: Update to 2.5.28
https://github.com/veg/hyphy/releases/tag/2.5.28 |
2.5.27
27 Jan 2021 11:33:53
|
jrm |
biology/hyphy: Update to version 2.5.27
https://github.com/veg/hyphy/releases/tag/2.5.27 |
2.5.26
15 Jan 2021 20:09:29
|
jrm |
biology/hyphy: Update to version 2.5.26
https://github.com/veg/hyphy/releases/tag/2.5.26 |
2.5.25_1
11 Jan 2021 17:54:42
|
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 |
2.5.25
11 Jan 2021 02:51:30
|
jrm |
biology/hyphy: Update to version 2.5.25
https://github.com/veg/hyphy/releases/tag/2.5.25 |
2.5.24
20 Dec 2020 20:21:53
|
jrm |
biology/hyphy: Update to version 2.5.24
https://github.com/veg/hyphy/releases/tag/2.5.24 |
2.5.23
19 Nov 2020 10:53:56
|
jrm |
biology/hyphy: Update to version 2.5.23
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.23 |
2.5.22
18 Nov 2020 10:54:04
|
jrm |
biology/hyphy: Update to version 2.5.22
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.22hf |
2.5.21
30 Oct 2020 14:05:47
|
jrm |
biology/hyphy: Update to version 2.5.21 |
2.5.20
16 Oct 2020 23:43:17
|
jrm |
biology/hyphy: Update to version 2.5.20 |
2.5.19
13 Oct 2020 01:05:45
|
jrm |
biology/hyphy: Update to version 2.5.19
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.19 |
2.5.18
02 Sep 2020 17:47:10
|
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. |
2.5.17
20 Aug 2020 16:15:22
|
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 |
2.5.15
28 Jun 2020 16:40:34
|
jrm |
biology/hyphy: Update to version 2.5.15
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15 |
2.5.14
30 May 2020 19:39:11
|
jrm |
biology/hyphy: Update to version 2.5.14
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14 |
2.5.12
03 May 2020 02:08:20
|
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 |
2.5.10
25 Apr 2020 00:33:17
|
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 |
2.5.8
28 Mar 2020 12:27:11
|
jrm |
biology/hyphy: Update to version 2.5.8
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8 |
2.5.7
20 Mar 2020 01:30:46
|
jrm |
biology/hyphy: Update to version 2.5.7
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7 |
2.5.6
17 Mar 2020 18:17:16
|
jrm |
biology/hyphy: Update to version 2.5.6
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6 |
2.5.5
02 Mar 2020 01:31:57
|
jrm |
biology/hyphy: Update to version 2.5.5
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5 |
2.5.4
21 Feb 2020 12:22:17
|
jrm |
biology/hyphy: Update to version 2.5.4
Upstream changes: https://github.com/veg/hyphy/releases |
2.3.14.16_2
26 Jul 2019 20:46:57
|
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 |
2.3.14.16_1
25 Dec 2018 20:25:40
|
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 |
2.3.14.16_1
12 Dec 2018 01:35:36
|
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 |
2.3.14.16
20 Oct 2018 12:21:15
|
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 |
2.3.13
22 May 2018 22:55:18
|
jrm |
biology/hyphy: Update to version 2.3.13 |
2.3.12_1
14 May 2018 16:52:40
|
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 |
2.3.12
11 May 2018 00:05:16
|
jrm |
New port, biology/hyphy: Hypothesis testing using Phylogenies
WWW: http://www.hyphy.org/ |
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