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3443 commits

Author SHA1 Message Date
Yuri Victorovich
0eb3b0314b biology/taxonkit: Update 0.12.0 -> 0.13.0 
Reported by:	portscout
 2022-09-24 19:45:15 -07:00
Yuri Victorovich
db4f1a6fea biology/py-mrcfile: Update 1.4.2 -> 1.4.3 
Reported by:	portscout
 2022-09-24 14:54:24 -07:00
Jason W. Bacon
001947d3e5 biology/vsearch: Update to 2.22.1 
Add the derep_smallmem command for dereplication with less memory usage
Changes:    https://github.com/torognes/vsearch/releases

Reported by:    portscout
 2022-09-21 11:24:14 -05:00
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
Jason W. Bacon
de24c3efe8 biology/vsearch: Update to 2.21.2 
Fix problems with the --lcaout option
Changes:        https://github.com/torognes/vsearch/tags

Reported by:    portscout
 2022-09-16 11:17:55 -05:00
Felix Palmen
ddae4e92d8 Mk/Uses: always use colon for build/run suffix 
Most USES use a colon for build/run(/test) suffixes. Change kde.mk,
qt.mk and pyqt.mk to do the same, and update all ports using that.

Document in CHANGES.

PR:			266034
Exp-run by:		antoine
Approved by:		tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D36349
 2022-09-11 12:20:14 +02:00
Yuri Victorovich
65b542d259 biology/hhsuite: Broken on armv7 
Reported by:	fallout
 2022-09-09 14:49:50 -07:00
Daniel Engberg
e942e560c4 */*: Update path set in BUILD_DEPENDS for CMake 
Commit b23ea4e2d2 changed its location to
devel/cmake-core

Approved by:	portmgr (blanket)
 2022-09-09 22:32:24 +02:00
Dmitri Goutnik
f05c98fffb all: Bump PORTREVISION after lang/go{118,119} update 2022-09-08 11:33:18 -05:00
Stefan Eßer
ade2a047e0 Remove WWW lines that have been moved into Makefiles 
Approved by:	portmgr (implicit)
 2022-09-08 17:46:38 +02:00
Stefan Eßer
986beaaabc Move more WWW entries from pkg-descr files into Makefiles 
The WWW: lines in the pkg-descr files of these ports where not at the
end of those files and have been missed in prior conversion runs.

Approved by:	portmgr (implicit)
 2022-09-08 17:43:21 +02:00
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
Tobias C. Berner
b86221feea cleanup: remove trailing whitepaces 2022-09-07 12:26:41 +02:00
Yuri Victorovich
cf9072d641 biology/seqkit: Update 2.2.0 -> 2.3.0 
Reported by:	portscout
 2022-09-04 15:15:19 -07:00
Wen Heping
026150563e biology/phyml: Update to 3.3.20220408 2022-09-02 07:57:11 +00:00
Yuri Victorovich
56003e73b8 biology/figtree: Update 1.4.4 -> 1.4.4-14 2022-08-27 22:52:00 -07:00
Joseph Mingrone
5aec6e4a19
biology/paml: Update to 4.10.5 
https://github.com/abacus-gene/paml/releases/tag/v4.10.0
https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8
https://github.com/abacus-gene/paml/releases/tag/v4.10.5

Sponsored by:	The FreeBSD Foundation
 2022-08-26 01:22:46 -03:00
Yuri Victorovich
cd42c21b03 biology/kmcp: Update 0.8.3 -> 0.8.4 2022-08-18 11:56:49 -07:00
Yuri Victorovich
98217ec7b7 biology/kmcp: Update 0.8.2 -> 0.8.3 2022-08-15 10:30:24 -07:00
Yuri Victorovich
a47d034514 biology/kmcp: Broken on i386 and arm64 
Reported by:	fallout
 2022-08-14 23:09:12 -07:00
Matthias Andree
875d7c7d19 *: bump PORTREVISION of all devel/xxhash users... 
...except archivers/py-borgbackup, which requires a more complete fix.
 2022-08-13 20:51:14 +02:00
Dima Panov
4cf39decb3 */*: bump all consumers after recent boost upgrade 2022-08-12 17:46:53 +03:00
Dmitry Marakasov
b28e6ccdb9 biology/gatk: mark BROKEN 
FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.2.6.1/build.gradle' line: 15

* What went wrong:
Plugin [id: 'de.undercouch.download', version: '4.1.2'] was not found in any of the following sources:

- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:4.1.2')
  Searched in the following repositories:
    Gradle Central Plugin Repository

Reported by:	pkg-fallout
Approved by:	portmgr blanket
 2022-08-11 21:33:41 +03:00
Yuri Victorovich
d17e67375d biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching 2022-08-07 13:30:47 -07:00
Yuri Victorovich
183ec5cd65 biology/ncbi-cxx-toolkit: Broken on armv6 
Reported by:	fallout
 2022-08-06 16:28:43 -07:00
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
a93cd97f3c biology/py-ete3: Add tests 2022-08-06 15:23:11 -07:00
Yuri Victorovich
5d1325cd1b biology/ugene: Correct BROKEN message 
Approved by:	portmgr (blanket)
 2022-08-04 09:35:24 -07:00
Yuri Victorovich
36aeef9b99 biology/hyphy: Correct BROKEN message 2022-08-04 09:21:46 -07:00
Yuri Victorovich
efc6565174 biology/hhsuite: Fix build on some architectures 
... by removing -march=native.

Reported by:	fallout
 2022-08-04 09:21:45 -07:00
Yuri Victorovich
bd8b68e641 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 0f20e25bb0.

Reported by:	pkubaj@
 2022-08-04 09:21:45 -07:00
Yuri Victorovich
34c51b63d7 biology/ugene: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-08-04 00:41:24 -07:00
Yuri Victorovich
0f20e25bb0 biology/hhsuite: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
 2022-08-04 00:41:24 -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
Dmitri Goutnik
4476f89764 all: Bump PORTREVISION after Go update 
Bump Go ports PORTREVISION after GO_DEFAULT and lang/go118 update.
 2022-08-03 16:35:13 -05:00
Yuri Victorovich
c7b296877c biology/viennarna: Update 2.5.0 -> 2.5.1 
Also add test target.
 2022-07-31 01:12:49 -07:00
Yuri Victorovich
5c534ae656 biology/abyss: Add test target 2022-07-30 00:34:34 -07:00
Po-Chuan Hsieh
8d5b2bc5bb
devel/grpc: Update to 1.48.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-07-30 13:57:09 +08:00
Yuri Victorovich
0a752832a5 biology/abyss: Update 2.3.1 -> 2.3.5 2022-07-29 12:57:36 -07:00
Yuri Victorovich
62ffe981e3 biology/py-mrcfile: Update 1.4.0 -> 1.4.2 2022-07-29 01:46:46 -07:00
Yuri Victorovich
8fd55d46d9 biology/cufflinks: Unbreak 2022-07-27 20:43:06 -07:00
Yuri Victorovich
8832ed3498 biology/star: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-07-23 18:24:10 -07:00
Yuri Victorovich
8dc7394ac8 biology/molden: Update 6.7 -> 7.1 
PR:		265245
Approved by:	jmd@ (maintainer)
 2022-07-23 13:00:53 -07:00
Yuri Victorovich
280dd32be2 biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-07-23 09:40:43 -07:00
Yuri Victorovich
768fb66f82 biology/ngs-sdk: Broken on armv6, armv7 
Reported by:	fallout
 2022-07-22 15:34:07 -07:00
Tobias C. Berner
11049e36cb cleanup: remove '$MCom' tag 
gnome@ no longer uses Marcusom as their staging ground.

Approved by:		gnome (nc)
Differential Revision:	https://reviews.freebsd.org/D35866
 2022-07-20 21:44:12 +02:00
Tobias C. Berner
5564b3b420 science/hdf5: bump PORTREVISION of consumers 
The SO-version increased in the update to 1.12.2 in
a43418b815 .

Reported by:	VVD <vvd@unislabs.com>
 2022-07-20 16:35:24 +02:00
Tobias C. Berner
37526bbd4e biology: remove 'Created by' lines 
A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr
 2022-07-20 16:20:57 +02:00
Yuri Victorovich
978fbbf602 biology/py-pysam: Remove BROKEN lines 2022-07-19 08:51:56 -07:00