10:04 Nuno Teixeira (eduardo) 

biology/abyss: Move man pages to share/man

Approved by:	portmgr (blanket)

    dfc94f5

10:23 Thierry Thomas (thierry) 

*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2

    843da99

08:55 Yuri Victorovich (yuri) 

biology/abyss: Update 2.3.5 → 2.3.7

Reported by:	portscout

    97a754c

07:25 Muhammad Moinur Rahman (bofh) 

biology/abyss: Fix build with llvm15

Approved by:	portmgr (blanket)

    7be12eb

09:09 Gerald Pfeifer (gerald) 

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

    8d3e020

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

14:46 Dima Panov (fluffy) 

*/*: bump all consumers after recent boost upgrade

    4cf39de

07:34 Yuri Victorovich (yuri) 

biology/abyss: Add test target

    5c534ae

19:57 Yuri Victorovich (yuri) 

biology/abyss: Update 2.3.1 -> 2.3.5

    0a75283

19:23 Kevin Bowling (kbowling) 

devel/libffi: Bump deps PORTREVISION for shlib change

PR:		263764
Reported by:	VVD <vvd@unislabs.com>

    db78da8

21:23 Rene Ladan (rene) 

cleanup: drop support for EOL FreeBSD 11.X

Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index

    620968a

19:02 Yuri Victorovich (yuri) 

biology/abyss: Broken on 11

Reported by:	fallout

    9352bd7

17:18 Yuri Victorovich (yuri) 

biology/abyss: Update 2.3.0-3 -> 2.3.1

Reported by:	portscout

    8ec7f5d

20:19 Yuri Victorovich (yuri) 

biology/abyss: Update 2.2.5 -> 2.3.0-3

    8e65beb

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

05:17 yuri 

biology/abyss: Add PORTSCOUT line

 

06:59 yuri 

biology/abyss: Update 2.2.4 -> 2.2.5

Reported by:	portscout

 

18:11 zeising 

Chanse update of devel/libffi

Chase the devel/libffi update
Bump portrevision of all dependent ports to chace shard library version bump
in libffi.
Update LIB_DEPENDS lines where needed to not require a specific version of
libffi.so.

PR:		247028 (for tracking)

 

09:10 yuri 

biology/abyss: Update 2.2.3 -> 2.2.4

 

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

 

19:46 yuri 

biology/abyss: Broken on i386

Reported by:	fallout

 

04:06 yuri 

biology/abyss: Update 2.1.5 -> 2.2.3

Reported by:	portscout

 

17:53 jbeich 

devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136

 

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/

 

15:35 jbeich 

devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774

 

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

 

11:43 pkubaj 

biology/abyss: fix build on big-endian architectures

Use new GCC from ports on GCC architectures.

Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC
architectures.

Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at
https://github.com/bcgsc/abyss/pull/287 ).

PR:		238737
Approved by:	yuri (maintainer), mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D20717

 

16:05 jbeich 

devel/openmp: phase out

- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767

 

06:36 jbeich 

devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303

 

07:56 yuri 

New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end
sequence assembler