| non port: biology/diamond/Makefile |
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SVNWeb
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Number of commits found: 79 |
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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se)  ]    b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
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.
(Only the first 15 lines of the commit message are shown above )
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Sun, 24 Apr 2022
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[ 17:50 Joseph Mingrone (jrm) ] d9f5d5d
biology/diamond: Update to 2.0.15
https://github.com/bbuchfink/diamond/releases/tag/v2.0.15
Sponsored by: The FreeBSD Foundation
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Thu, 13 Jan 2022
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[ 17:42 Joseph Mingrone (jrm) ] 7c428e8
biology/diamond: Update to 2.0.14
https://github.com/bbuchfink/diamond/releases/tag/v2.0.14
Sponsored by: The FreeBSD Foundation
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Thu, 11 Nov 2021
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[ 17:17 Joseph Mingrone (jrm) ] 84e457e
biology/diamond: Update to 2.0.13
This update fixes a bug that caused invalid bit scores in frameshift
alignment mode.
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Tue, 12 Oct 2021
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[ 15:40 Joseph Mingrone (jrm) ] 523d253
biology/diamond: Update to 2.0.12
https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
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Sat, 9 Oct 2021
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[ 13:49 Piotr Kubaj (pkubaj) ] b6994df
biology/diamond: enable on powerpc64le
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Fri, 8 Oct 2021
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[ 18:19 Piotr Kubaj (pkubaj) ] 096fef4
biology/diamond: enable on powerpc64
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[ 16:25 Mikael Urankar (mikael) ] 63de6c3
biology/diamond: Enable on aarch64.
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Tue, 6 Jul 2021
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[ 13:15 Joseph Mingrone (jrm) ] d0bf21b
biology/diamond: Update to 2.0.11-1
Includes a build fix for 2.0.11 on FreeBSD
https://github.com/bbuchfink/diamond/releases/tag/v2.0.11
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Sat, 3 Jul 2021
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[ 16:25 Joseph Mingrone (jrm) ] 4335856
biology/diamond: Update to 2.0.10
https://github.com/bbuchfink/diamond/releases/tag/v2.0.10
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Tue, 13 Apr 2021
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[ 00:55 Joseph Mingrone (jrm) ] 46fc7df
biology/diamond: Update to 2.0.9
https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
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Wed, 7 Apr 2021
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[ 08:09 Mathieu Arnold (mat) ] cf118cc (Only the first 10 of 8873 ports in this commit are shown above. )
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Thu, 11 Mar 2021
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[ 12:41 jrm ]  
biology/diamond: Update to 2.0.8
https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
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Wed, 17 Feb 2021
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[ 16:43 jrm ]
biology/diamond: Update to 2.0.7
https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
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Sun, 20 Dec 2020
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[ 20:21 jrm ]
biology/diamond: Update to version 2.0.6
https://github.com/bbuchfink/diamond/releases/tag/v2.0.6
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Tue, 1 Dec 2020
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[ 22:27 jrm ]
biology/diamond: Update to version 2.0.5
https://github.com/bbuchfink/diamond/releases/tag/v2.0.5
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Sun, 30 Aug 2020
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[ 16:14 jrm ]
biology/diamond: Update to version 2.0.4
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.3
https://github.com/bbuchfink/diamond/releases/tag/v2.0.4
Port changes:
Remove a patch that was upstreamed:
https://github.com/bbuchfink/diamond/pull/378
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Fri, 7 Aug 2020
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[ 11:20 jrm ]
biology/diamond: Update to version 2.0.2
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.1
https://github.com/bbuchfink/diamond/releases/tag/v2.0.2
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Tue, 28 Jul 2020
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[ 02:39 jrm ]
biology/diamond: Update to version 2.0.0
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0
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Fri, 3 Jul 2020
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[ 11:22 jrm ]
biology/diamond: Update to version 0.9.36
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
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Sat, 27 Jun 2020
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[ 16:26 jrm ]
biology/diamond: Update to version 0.9.35
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
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Fri, 12 Jun 2020
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[ 12:12 jrm ]
biology/diamond: Update to version 0.9.34
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
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Wed, 3 Jun 2020
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[ 21:44 jrm ]
biology/diamond: Update to version 0.9.33
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
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Fri, 24 Apr 2020
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[ 23:04 jrm ]
biology/diamond: Update to version 0.9.32
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32
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Sat, 21 Mar 2020
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[ 22:11 jrm ]
biology/diamond: Update to version 0.9.31.2
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.31
Also include two additional commits that fix a build error.
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Mon, 3 Feb 2020
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[ 15:55 jrm ]
biology/diamond: Update to version 0.9.30
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
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Wed, 20 Nov 2019
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[ 17:14 jrm ]
biology/diamond: Update to v0.9.29
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
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Thu, 7 Nov 2019
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[ 14:12 jrm ]
biology/diamond: Update to version 0.9.28
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
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Sun, 3 Nov 2019
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[ 01:34 jrm ]
biology/diamond: Update to version 0.9.27 (plus one fix)
Since compiling from source no longer performs a native build, remove
-mtune=generic from CLFAGS when package building.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.27
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Wed, 18 Sep 2019
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[ 18:45 jrm ]
biology/diamond: Update to version 0.9.26
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
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Sun, 4 Aug 2019
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[ 23:35 jrm ]
biology/diamond: Update to version 0.9.25
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
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Mon, 31 Dec 2018
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[ 19:00 jrm ]
biology/diamond: Update to version 0.9.24
Port changes: Tune for package building based on the author's
recommendation.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24
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Tue, 25 Dec 2018
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[ 20:25 tcberner ] (Only the first 10 of 1277 ports in this commit are shown above. )
Change cmake default behaviour to outsource.
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine
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Mon, 17 Dec 2018
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[ 19:12 jrm ]
biology/diamond: Update to 0.9.23 plus fixes after release
Also:
- update license since upstream changed to GPLv3
- only build/package for amd64, since it is untested on other architectures
and currently does not build on i386
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23
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Mon, 14 May 2018
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[ 17:17 jrm ]
biology/diamond: Update to version 0.9.22
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
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Fri, 20 Apr 2018
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[ 21:23 jrm ]
biology/diamond: Update to version 0.9.21
Upstream changes: https://github.com/bbuchfink/diamond/releases
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Sat, 17 Mar 2018
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[ 15:29 jrm ]
biology/diamond: Update to version 0.9.19
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
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Thu, 15 Mar 2018
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[ 02:28 jrm ]
biology/diamond: Update to version 0.9.18-49
Pull in commits after the 0.9.18 release for build fixes.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.18
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Thu, 1 Feb 2018
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[ 19:20 jrm ]
biology/diamond: Update to version 0.9.17
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
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Wed, 13 Dec 2017
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[ 16:31 jrm ]
biology/diamond: Update to version 0.9.14
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
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Fri, 17 Nov 2017
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[ 20:11 jrm ]
biology/diamond: Update to version 0.9.13
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
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Wed, 8 Nov 2017
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[ 16:06 jrm ]
biology/diamond: Update to version 0.9.12
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
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Fri, 3 Nov 2017
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[ 03:45 jrm ]
biology/diamond: Update to 0.9.11
Upstream changes: https://github.com/bbuchfink/diamond/releases
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Tue, 15 Aug 2017
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[ 20:45 jrm ]
biology/diamond: Update to version 0.9.10
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
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Mon, 3 Jul 2017
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[ 19:12 jrm ]
biology/diamond: Update to version 0.9.9
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
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Fri, 16 Jun 2017
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[ 14:49 jrm ]
biology/diamond: Update to version 0.9.8
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Sat, 3 Jun 2017
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[ 12:32 jrm ]
biology/diamond: Update to version 0.9.4
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
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Mon, 29 May 2017
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[ 15:24 jrm ]
biology/diamond: Update to version 0.9.3
Upstream changes: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor, implicit)
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Tue, 23 May 2017
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[ 11:03 jrm ]
biology/diamond: Update to version 0.9.1
Upstream changes: https://github.com/bbuchfink/diamond/releases
- License has changed to AGPLv3
Approved by: swills (mentor, implicit)
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Fri, 21 Apr 2017
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[ 14:46 jrm ]
biology/diamond: Update to version 0.8.38
- The base compilers meet all of Diamond's requirements, so remove
compiler:c++11-lang from USES definition.
- Upstream release notes:
https://github.com/bbuchfink/diamond/releases/tag/v0.8.38
Approved by: swills (mentor, implicit)
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Sun, 2 Apr 2017
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[ 10:55 jrm ]
biology/diamond: Update to version 0.8.37
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.37
Approved by: swills (mentor, implicit)
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Sat, 1 Apr 2017
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[ 15:23 gerald ] (Only the first 10 of 1118 ports in this commit are shown above. )
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using using Mk/bsd.octave.mk which in turn has USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
c++11-lang, c++0x, c11, or gcc-c++11-lib.
PR: 216707
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Sun, 12 Feb 2017
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[ 14:04 jrm ]
biology/diamond: Update to version 0.8.36.
Approved by: swills (mentor, implicit)
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Sun, 5 Feb 2017
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[ 22:23 jrm ]
biology/diamond: Update to version 0.8.35.
Version 0.8.35 fixes a compiler error on i386.
Approved by: swills (mentor, implicit)
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Mon, 23 Jan 2017
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[ 13:19 jrm ]
biology/diamond: Update to version 0.8.34.
Upstream changelog: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9288
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Mon, 16 Jan 2017
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[ 13:38 jrm ]
biology/diamond: Update to version 0.8.32.
Upstream changes: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9197
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Thu, 12 Jan 2017
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[ 23:23 jrm ]
biology/diamond: Update to version 0.8.31.
Upstream changelog:
- Added compositional score adjustments (option --comp-based-stats
(0,1)). This is a useful feature for filtering false positive hits and
is enabled by default.
- Removed --single-domain option and replaced by --max-hsps, to set the
maximum number of Hsps per query/subject pair, to be consistent with
BLAST. This option is set to 1 by default as getting more than 1 Hsp
per subject seems to be confusing users.
- Added option --no-self-hits to filter identical self-hits.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D9134
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Fri, 30 Dec 2016
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[ 16:27 jrm ]
biology/diamond: Update to version 0.8.30
Upstream changes:
- slightly improved sensitivity
- added option to report unaligned queries: --unal (0=no, 1=yes)
- pairwise, XML and SAM format will report unaligned queries by default
- added option to filter alignments by subject cover (--subject-cover)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9000
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Sun, 18 Dec 2016
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[ 13:52 jrm ]
biology/diamond: Update to version 0.8.29
Upstream change: fixed an issue that could cause a crash when using view on
incomplete DAA files
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8832
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Mon, 28 Nov 2016
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[ 15:18 jrm ]
biology/diamond: Update to version 0.8.28
Correct LICENSE and set LICENSE_FILE
Upstream changelog:
- support for gzip compressed files containing multiple gzip streams
- support for the BLAST pairwise format (option -f 0)
- slightly improved sensitivity
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8652
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Sun, 6 Nov 2016
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[ 05:42 jrm ]
biology/diamond: Update to version 0.8.26
Release notes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.26
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8447
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Mon, 17 Oct 2016
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[ 14:17 jrm ]
biology/diamond: update to version 0.8.24
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8268
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Mon, 10 Oct 2016
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[ 04:33 jrm ]
biology/diamond: update to version 0.8.23
Upstream release notes:
Added option to change the genetic code used for translation of query in
blastx mode (option --query-gencode, see here for a list of possible values:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8202
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Fri, 23 Sep 2016
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[ 21:42 jrm ] (Only the first 10 of 16 ports in this commit are shown above. )
Update email address to jrm@FreeBSD.org for ports that I maintain
Reviewed by: mat, swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D7995
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Tue, 13 Sep 2016
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[ 17:50 amdmi3 ]
- Update to 0.8.22
PR: 212603
Submitted by: jrm@ftfl.ca (maintainer)
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Tue, 6 Sep 2016
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[ 06:34 wen ]
- Update to 0.8.20
PR: 212399
Submitted by: jrm@ftfl.ca(maintainer)
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Thu, 25 Aug 2016
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[ 18:49 pawel ]
Update to version 0.8.19
PR: 212145
Submitted by: Joseph Mingrone (maintainer)
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Sun, 14 Aug 2016
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[ 21:47 brd ]
Update biology/diamond to 0.8.18.
PR: 211845
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by: bdrewery (implicit)
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Fri, 5 Aug 2016
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[ 21:24 pawel ]
Update to version 0.8.17
PR: 211582
Submitted by: Joseph Mingrone (maintainer)
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Sun, 24 Jul 2016
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[ 18:06 riggs ]
Update to upstream release 0.8.16
PR: 211335
Submitted by: jrm@ftfl.ca (maintainer)
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Thu, 14 Jul 2016
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[ 16:53 pawel ]
Trim excess tabs, no-op change
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[ 16:49 pawel ]
Update to version 0.8.14
PR: 211078
Submitted by: Joseph Mingrone (maintainer)
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Thu, 7 Jul 2016
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[ 15:46 amdmi3 ]
- Update to 0.8.11
PR: 210877
Submitted by: jrm@ftfl.ca (maintainer)
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Thu, 30 Jun 2016
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[ 01:37 junovitch ]
biology/diamond: update 0.8.6 -> 0.8.9
PR: 210710
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
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Fri, 17 Jun 2016
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[ 19:53 rm ]
biology/diamond: update to 0.8.6
PR: 210345
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
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Thu, 9 Jun 2016
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[ 01:39 matthew ]
Update to 0.8.5
PR: 209611
Submitted by: jrm@ftfl.ca (maintainer)
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Wed, 18 May 2016
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[ 16:22 antoine ]
Fix DEPENDS
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Fri, 6 May 2016
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[ 08:45 wen ]
DNA query sequences against a protein reference database (BLASTP and BLASTX
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
PR: 208998
Submitted by: jrm@ftfl.ca
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Number of commits found: 79 |
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