09:29 Thierry Thomas (thierry) 

*/*: bump PORTREVISION after OpenMPI upgrade

    9eba616

09:09 Gerald Pfeifer (gerald) 

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

    8d3e020

18:16 Yuri Victorovich (yuri) 

biology/hhsuite: Disable on 32-bit architectures following upstream advice

    e7cb6b0

15:08 Yuri Victorovich (yuri)  Author: Robert Clausecker

biology/hhsuite: fix build on armv7

PR:		266736

    75d8147

21:49 Yuri Victorovich (yuri) 

biology/hhsuite: Broken on armv7

Reported by:	fallout

    65b542d

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

16:21 Yuri Victorovich (yuri) 

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@

    bd8b68e

07:41 Yuri Victorovich (yuri) 

biology/hhsuite: Broken on systems where OpenMP isn't enabled

Reported by:	fallout

    0f20e25

13:22 Piotr Kubaj (pkubaj) 

biology/hhsuite: check for omp.h on all architectures

    e7af5e3

17:11 Piotr Kubaj (pkubaj) 

biology/hhsuite: drop HAVE_POWER8 on powerpc64

powerpc64 uses PPC970 as a baseline.

    8a75ffb

12:03 Piotr Kubaj (pkubaj) 

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.

    f00588c

15:47 Mikael Urankar (mikael) 

biology/hhsuite: Fix build on aarch64

Approved by:	portmgr (build fix blanket)

    e9f35d7

13:13 Piotr Kubaj (pkubaj) 

biology/hhsuite: fix build on powerpc64*

hhsuite now supports VSX.

    f1475a4

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

04:28 yuri 

biology/hhsuite: Update 3.2.0 -> 3.3.0

Reported by:	portscout

 

19:33 pkubaj 

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);

 

09:49 danilo 

- 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

 

21:56 jbeich 

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

 

18:59 jbeich 

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/

 

14:23 pkubaj 

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

 

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

 

02:50 yuri 

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

 

06:52 yuri 

New port: biology/hhsuite: Remote protein homology detection suite