Commit graph

53 commits

Author SHA1 Message Date
Yuri Victorovich
e2b35d7147 biology/hyphy: Not broken on systems where OpenMP isn't available
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
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
Commit b7f05445c0 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)
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
Joseph Mingrone
26bcffc642 biology/hyphy: Update to version 2.5.15
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.15
2020-06-28 16:40:33 +00:00
Joseph Mingrone
e677d43938 biology/hyphy: Update to version 2.5.14
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.14
2020-05-30 19:39:11 +00:00
Joseph Mingrone
e743846843 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
2020-05-03 02:08:19 +00:00
Joseph Mingrone
c20d5fb7fb 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
2020-04-25 00:33:16 +00:00
Joseph Mingrone
263987970a biology/hyphy: Update to version 2.5.8
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8
2020-03-28 12:27:11 +00:00
Joseph Mingrone
22c22dff73 biology/hyphy: Update to version 2.5.7
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7
2020-03-20 01:30:46 +00:00
Joseph Mingrone
fe591bd88b biology/hyphy: Update to version 2.5.6
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6
2020-03-17 18:17:16 +00:00
Joseph Mingrone
aef8ee9db0 biology/hyphy: Update to version 2.5.5
Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5
2020-03-02 01:31:56 +00:00
Joseph Mingrone
6bb8f81a44 biology/hyphy: Update to version 2.5.4
Upstream changes: https://github.com/veg/hyphy/releases
2020-02-21 12:22:17 +00:00
Gerald Pfeifer
ea8c8ec7da 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
2019-07-26 20:46:53 +00:00
Tobias C. Berner
707c6bf295 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
2018-12-25 20:25:39 +00:00
Gerald Pfeifer
a9f015d155 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
2018-12-12 01:35:33 +00:00
Joseph Mingrone
6c672c455f 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
2018-10-20 12:21:15 +00:00