Commit Graph

3460 Commits

Author SHA1 Message Date
Motomichi Matsuzaki
5a4350de94 biology/tRNAscan-SE: Update to 2.0.11
ChangeLog:	http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt
PR:		266966
2022-10-12 12:45:24 +01:00
Motomichi Matsuzaki
95b2e3a088 biology/infernal: Update to 1.1.4
ChangeLog:	http://eddylab.org/infernal/RELEASE-1.1.4.md
PR:		266967
2022-10-12 11:15:54 +01:00
Yuri Victorovich
3a7900f35a biology/jalview: Update 2.11.1.4 -> 2.11.2.5 2022-10-11 23:58:18 -07:00
Jason W. Bacon
b532c5dd96 biology/hmmer: Update to 3.3.2
No release notes.  See commits for changes:
https://github.com/EddyRivasLab/hmmer

PR:             266968
Reported by:    mzaki@e-mail.ne.jp
2022-10-11 15:13:01 -05:00
Yuri Victorovich
8ee88cf31b biology/biosoup: Update g20201216 -> 0.10.0-2 2022-10-10 23:10:56 -07:00
Yuri Victorovich
11f6ef1ffb biology/biosig: Update 2.4.2 -> 2.4.3
Reported by:	portscout
2022-10-09 12:02:15 -07:00
Dmitri Goutnik
bde51869ee all: Bump PORTREVISION after lang/go{118,119} update 2022-10-06 14:24:26 -05:00
Yuri Victorovich
f83007151d biology/py-valerius: New port: Python bioinformatics tools 2022-10-03 21:06:22 -07:00
Po-Chuan Hsieh
6df64aaff1
biology/rubygem-bio: Update to 2.0.4
Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
2022-10-03 10:17:49 +08:00
Po-Chuan Hsieh
b2b1773a80
devel/grpc: Update to 1.49.0
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
2022-10-03 10:14:06 +08:00
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
Yuri Victorovich
e7cb6b0a68 biology/hhsuite: Disable on 32-bit architectures following upstream advice 2022-10-01 11:16:04 -07:00
Robert Clausecker
75d8147165 biology/hhsuite: fix build on armv7
PR:		266736
2022-10-01 08:08:17 -07:00
Rene Ladan
f9f811816c all: deprecate ports depending on expired security/py-keyrings.alt 2022-09-30 22:06:28 +02:00
Yuri Victorovich
fdebc5b7b2 biology/py-PySCeS: Update 1.0.2 -> 1.0.3
Reported by:	portscout
2022-09-26 01:18:31 -07:00
Yuri Victorovich
420a6670b5 biology/seqkit: Update 2.3.0 -> 2.3.1
Reported by:	portscout
2022-09-24 19:45:15 -07:00
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