notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Want a good monitor light? See my photosAll times are UTC
Ukraine
non port: biology/hhsuite/Makefile

Number of commits found: 24

Sunday, 18 Feb 2024
09:29 Thierry Thomas (thierry) search for other commits by this committer
*/*: bump PORTREVISION after OpenMPI upgrade
commit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373a commit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373a commit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373a commit hash: 9eba6162f8f63de2b89ae35eef90e7c296f2373a 9eba616
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Saturday, 1 Oct 2022
18:16 Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Disable on 32-bit architectures following upstream advice
commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64 commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64 commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64 commit hash: e7cb6b0a685d45e861be55d1925b9101e88a9e64 e7cb6b0
15:08 Yuri Victorovich (yuri) search for other commits by this committer Author: Robert Clausecker
biology/hhsuite: fix build on armv7

PR:		266736
commit hash: 75d814716539317715472ded1bb11b3c6ccb72bc commit hash: 75d814716539317715472ded1bb11b3c6ccb72bc commit hash: 75d814716539317715472ded1bb11b3c6ccb72bc commit hash: 75d814716539317715472ded1bb11b3c6ccb72bc 75d8147
Friday, 9 Sep 2022
21:49 Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Broken on armv7

Reported by:	fallout
commit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fceb commit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fceb commit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fceb commit hash: 65b542d259ee8de09ae6802dd2e3ed811ea8fceb 65b542d
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Thursday, 4 Aug 2022
16:21 Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Revert commit "Broken on systems where OpenMP isn't enabled"

IT was added by mistake.
The failures on armv7 are due to -march=native.

This reverts commit 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45.

Reported by:	pkubaj@
commit hash: bd8b68e6415a3671c144baa10871ef3f19f26eab commit hash: bd8b68e6415a3671c144baa10871ef3f19f26eab commit hash: bd8b68e6415a3671c144baa10871ef3f19f26eab commit hash: bd8b68e6415a3671c144baa10871ef3f19f26eab bd8b68e
07:41 Yuri Victorovich (yuri) search for other commits by this committer
biology/hhsuite: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45 commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45 commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45 commit hash: 0f20e25bb0c89821c657ce7d8424f6e6ad1c9a45 0f20e25
Wednesday, 27 Apr 2022
13:22 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: check for omp.h on all architectures
commit hash: e7af5e32b40796da3f0c252941d5f427f7519234 commit hash: e7af5e32b40796da3f0c252941d5f427f7519234 commit hash: e7af5e32b40796da3f0c252941d5f427f7519234 commit hash: e7af5e32b40796da3f0c252941d5f427f7519234 e7af5e3
Thursday, 21 Apr 2022
17:11 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: drop HAVE_POWER8 on powerpc64

powerpc64 uses PPC970 as a baseline.
commit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92a commit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92a commit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92a commit hash: 8a75ffbc9ffcdcf330104bfbbc95f5ad57fbf92a 8a75ffb
Tuesday, 16 Nov 2021
12:03 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: fix packaging on powerpc

pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such
file or directory
pkg-static: Unable to access file
/wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such
file or directory

powerpc doesn't have LLVM with libomp.
commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4 commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4 commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4 commit hash: f00588c63480bbe584bbfa766e5ca86cff893cf4 f00588c
Monday, 13 Sep 2021
15:47 Mikael Urankar (mikael) search for other commits by this committer
biology/hhsuite: Fix build on aarch64

Approved by:	portmgr (build fix blanket)
commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66 commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66 commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66 commit hash: e9f35d7e41d9f83d4212d4fe2d2e0410a3e90f66 e9f35d7
Thursday, 8 Jul 2021
13:13 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/hhsuite: fix build on powerpc64*

hhsuite now supports VSX.
commit hash: f1475a456c8257a759010ee0b949bde85ad6ad4f commit hash: f1475a456c8257a759010ee0b949bde85ad6ad4f commit hash: f1475a456c8257a759010ee0b949bde85ad6ad4f commit hash: f1475a456c8257a759010ee0b949bde85ad6ad4f f1475a4
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Thursday, 27 Aug 2020
04:28 yuri search for other commits by this committer
biology/hhsuite: Update 3.2.0 -> 3.3.0

Reported by:	portscout
Original commitRevision:546314 
Monday, 11 May 2020
19:33 pkubaj search for other commits by this committer
biology/hhsuite: fix build on powerpc64 elfv2

Use GCC instead of Clang:
/usr/lib/clang/10.0.0/include/mmintrin.h:216:19: error: use of undeclared
identifier '__builtin_ia32_punpckhbw'
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
Original commitRevision:534934 
Sunday, 19 Apr 2020
09:49 danilo search for other commits by this committer
- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)
- Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is
deprecated and will be removed)
- Fix science/gromacs plist when MPI option is enabled
- Bump PORTREVISION for all the consumers of net/openmpi
Original commitRevision:532095 
Sunday, 8 Mar 2020
21:56 jbeich search for other commits by this committer
Drop dependency on devel/openmp

- Drop if devel/llvm* was used as a substitute

Approved by:	yuri, rene (earlier version)
Differential Revision:	https://reviews.freebsd.org/D23020
Original commitRevision:528082 
Saturday, 21 Sep 2019
18:59 jbeich search for other commits by this committer
devel/openmp: update to 9.0.0

- Connect tests to the framework to help QA remaining patches
- Force rebuild all consumers after https://reviews.llvm.org/D59783

Changes:	http://llvm.org/viewvc/llvm-project/openmp/tags/RELEASE_900/final/?view=log
ABI:		https://abi-laboratory.pro/tracker/timeline/llvm_openmp/
Original commitRevision:512535 
Monday, 5 Aug 2019
14:23 pkubaj search for other commits by this committer
biology/hhsuite: fix build on powerpc64

This port can't use Altivec. Instead, it's possible to use GCC's translation
layer from SSE. Adjust build flags to do it.

PR:		239645
Approved by:	yuri (maintainer), tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D21160
Original commitRevision:508177 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
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
Original commitRevision:507372 
Wednesday, 22 May 2019
02:50 yuri search for other commits by this committer
biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist
or isn't detected.

It forces it to default to SSE2 on amd64/i386 and relaxes the SIMD requirement
on all other platforms.

Reported by:	fallout
Original commitRevision:502244 
Sunday, 19 May 2019
06:52 yuri search for other commits by this committer
New port: biology/hhsuite: Remote protein homology detection suite
Original commitRevision:502015 

Number of commits found: 24