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Get notified when packages are built

A new feature has been added. FreshPorts already tracks package built by the FreeBSD project. This information is displayed on each port page. You can now get an email when FreshPorts notices a new package is available for something on one of your watch lists. However, you must opt into that. Click on Report Subscriptions on the right, and New Package Notification box, and click on Update.

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non port: biology/diamond/Makefile

Number of commits found: 87

Sunday, 4 Feb 2024
19:41 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.9

Changelog:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.9
Sponsored by:	The FreeBSD Foundation
commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083 commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083 commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083 commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083 92b051a
Friday, 29 Dec 2023
18:57 Joseph Mingrone (jrm) search for other commits by this committer Author: Dimitry Andric
biology/diamond: Fix build on main after import of clang 17
commit hash: 96286fc8fdabb430731185b20409aba4e9f473fd commit hash: 96286fc8fdabb430731185b20409aba4e9f473fd commit hash: 96286fc8fdabb430731185b20409aba4e9f473fd commit hash: 96286fc8fdabb430731185b20409aba4e9f473fd 96286fc
Saturday, 8 Jul 2023
03:45 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.8

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.7
                https://github.com/bbuchfink/diamond/releases/tag/v2.1.8
Sponsored by:	The FreeBSD Foundation
commit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78af commit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78af commit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78af commit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78af 371eba1
Saturday, 18 Mar 2023
15:49 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.6

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.5
		https://github.com/bbuchfink/diamond/releases/tag/v2.1.6
Sponsored by:	The FreeBSD Foundation
commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6 commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6 commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6 commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6 43743a8
Sunday, 5 Mar 2023
15:33 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.4

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.4
Sponsored by:	The FreeBSD Foundation
commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124 commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124 commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124 commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124 d363e4b
Wednesday, 22 Feb 2023
11:48 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.3

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.3
Sponsored by:	The FreeBSD Foundation
commit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dc commit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dc commit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dc commit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dc 85920ea
Monday, 20 Feb 2023
14:35 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.2

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.2
Sponsored by:	The FreeBSD Foundation
commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5 commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5 commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5 commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5 89f956f
Friday, 10 Feb 2023
17:36 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.1.1

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.0
		https://github.com/bbuchfink/diamond/releases/tag/v2.1.1
Sponsored by:	The FreeBSD Foundation
commit hash: 056255445ec7f8fa17b551020b74d74905eaf753 commit hash: 056255445ec7f8fa17b551020b74d74905eaf753 commit hash: 056255445ec7f8fa17b551020b74d74905eaf753 commit hash: 056255445ec7f8fa17b551020b74d74905eaf753 0562554
Wednesday, 7 Sep 2022
21:10 Stefan Eßer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Sunday, 24 Apr 2022
17:50 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.15

https://github.com/bbuchfink/diamond/releases/tag/v2.0.15

Sponsored by:	The FreeBSD Foundation
commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8 commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8 commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8 commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8 d9f5d5d
Thursday, 13 Jan 2022
17:42 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.14

https://github.com/bbuchfink/diamond/releases/tag/v2.0.14

Sponsored by:	The FreeBSD Foundation
commit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8a commit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8a commit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8a commit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8a 7c428e8
Thursday, 11 Nov 2021
17:17 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.13

This update fixes a bug that caused invalid bit scores in frameshift
alignment mode.
commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767 commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767 commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767 commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767 84e457e
Tuesday, 12 Oct 2021
15:40 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.12

https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
commit hash: 523d2537b4a95a59e720f66d560529e1938c796f commit hash: 523d2537b4a95a59e720f66d560529e1938c796f commit hash: 523d2537b4a95a59e720f66d560529e1938c796f commit hash: 523d2537b4a95a59e720f66d560529e1938c796f 523d253
Saturday, 9 Oct 2021
13:49 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/diamond: enable on powerpc64le
commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03 commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03 commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03 commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03 b6994df
Friday, 8 Oct 2021
18:19 Piotr Kubaj (pkubaj) search for other commits by this committer
biology/diamond: enable on powerpc64
commit hash: 096fef40c53a0bcc585624139de0109511580649 commit hash: 096fef40c53a0bcc585624139de0109511580649 commit hash: 096fef40c53a0bcc585624139de0109511580649 commit hash: 096fef40c53a0bcc585624139de0109511580649 096fef4
16:25 Mikael Urankar (mikael) search for other commits by this committer
biology/diamond: Enable on aarch64.
commit hash: 63de6c3db611788a528afe985cd46fbe055b439a commit hash: 63de6c3db611788a528afe985cd46fbe055b439a commit hash: 63de6c3db611788a528afe985cd46fbe055b439a commit hash: 63de6c3db611788a528afe985cd46fbe055b439a 63de6c3
Tuesday, 6 Jul 2021
13:15 Joseph Mingrone (jrm) search for other commits by this committer
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
commit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8db commit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8db commit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8db commit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8db d0bf21b
Saturday, 3 Jul 2021
16:25 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.10

https://github.com/bbuchfink/diamond/releases/tag/v2.0.10
commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3 commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3 commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3 commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3 4335856
Tuesday, 13 Apr 2021
00:55 Joseph Mingrone (jrm) search for other commits by this committer
biology/diamond: Update to 2.0.9

https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
commit hash: 46fc7df8540c256facd27c205897db46857d730e commit hash: 46fc7df8540c256facd27c205897db46857d730e commit hash: 46fc7df8540c256facd27c205897db46857d730e commit hash: 46fc7df8540c256facd27c205897db46857d730e 46fc7df
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Thursday, 11 Mar 2021
12:41 jrm search for other commits by this committer
biology/diamond: Update to 2.0.8

https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
Original commitRevision:568088 
Wednesday, 17 Feb 2021
16:43 jrm search for other commits by this committer
biology/diamond: Update to 2.0.7

https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
Original commitRevision:565520 
Sunday, 20 Dec 2020
20:21 jrm search for other commits by this committer
biology/diamond: Update to version 2.0.6

https://github.com/bbuchfink/diamond/releases/tag/v2.0.6
Original commitRevision:558772 
Tuesday, 1 Dec 2020
22:27 jrm search for other commits by this committer
biology/diamond: Update to version 2.0.5

https://github.com/bbuchfink/diamond/releases/tag/v2.0.5
Original commitRevision:556797 
Sunday, 30 Aug 2020
16:14 jrm search for other commits by this committer
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
Original commitRevision:547066 
Friday, 7 Aug 2020
11:20 jrm search for other commits by this committer
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
Original commitRevision:544321 
Tuesday, 28 Jul 2020
02:39 jrm search for other commits by this committer
biology/diamond: Update to version 2.0.0

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0
Original commitRevision:543567 
Friday, 3 Jul 2020
11:22 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.36

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
Original commitRevision:541097 
Saturday, 27 Jun 2020
16:26 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.35

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
Original commitRevision:540624 
Friday, 12 Jun 2020
12:12 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.34

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
Original commitRevision:538606 
Wednesday, 3 Jun 2020
21:44 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.33

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
Original commitRevision:537853 
Friday, 24 Apr 2020
23:04 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.32

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32
Original commitRevision:532906 
Saturday, 21 Mar 2020
22:11 jrm search for other commits by this committer
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.
Original commitRevision:528881 
Monday, 3 Feb 2020
15:55 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.30

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
Original commitRevision:525045 
Wednesday, 20 Nov 2019
17:14 jrm search for other commits by this committer
biology/diamond: Update to v0.9.29

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
Original commitRevision:518039 
Thursday, 7 Nov 2019
14:12 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.28

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
Original commitRevision:516974 
Sunday, 3 Nov 2019
01:34 jrm search for other commits by this committer
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
Original commitRevision:516379 
Wednesday, 18 Sep 2019
18:45 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.26

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
Original commitRevision:512282 
Sunday, 4 Aug 2019
23:35 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.25

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
Original commitRevision:508134 
Monday, 31 Dec 2018
19:00 jrm search for other commits by this committer
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
Original commitRevision:488819 
Tuesday, 25 Dec 2018
20:25 tcberner search for other commits by this committer
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
Original commitRevision:488341 
Monday, 17 Dec 2018
19:12 jrm search for other commits by this committer
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
Original commitRevision:487707 
Monday, 14 May 2018
17:17 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.22

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
Original commitRevision:469925 
Friday, 20 Apr 2018
21:23 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.21

Upstream changes: https://github.com/bbuchfink/diamond/releases
Original commitRevision:467847 
Saturday, 17 Mar 2018
15:29 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.19

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
Original commitRevision:464826 
Thursday, 15 Mar 2018
02:28 jrm search for other commits by this committer
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
Original commitRevision:464549 
Thursday, 1 Feb 2018
19:20 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.17

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
Original commitRevision:460624 
Wednesday, 13 Dec 2017
16:31 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.14

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
Original commitRevision:456220 
Friday, 17 Nov 2017
20:11 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.13

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
Original commitRevision:454383 
Wednesday, 8 Nov 2017
16:06 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.12

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
Original commitRevision:453752 
Friday, 3 Nov 2017
03:45 jrm search for other commits by this committer
biology/diamond: Update to 0.9.11

Upstream changes: https://github.com/bbuchfink/diamond/releases
Original commitRevision:453387 
Tuesday, 15 Aug 2017
20:45 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.10

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
Original commitRevision:448009 
Monday, 3 Jul 2017
19:12 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.9

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
Original commitRevision:444981 
Friday, 16 Jun 2017
14:49 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.8
Original commitRevision:443706 
Saturday, 3 Jun 2017
12:32 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.4

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
Original commitRevision:442478 
Monday, 29 May 2017
15:24 jrm search for other commits by this committer
biology/diamond: Update to version 0.9.3

Upstream changes: https://github.com/bbuchfink/diamond/releases

Approved by:	swills (mentor, implicit)
Original commitRevision:441991 
Tuesday, 23 May 2017
11:03 jrm search for other commits by this committer
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)
Original commitRevision:441513 
Friday, 21 Apr 2017
14:46 jrm search for other commits by this committer
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)
Original commitRevision:439081 
Sunday, 2 Apr 2017
10:55 jrm search for other commits by this committer
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)
Original commitRevision:437552 
Saturday, 1 Apr 2017
15:23 gerald search for other commits by this committer
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
Original commitRevision:437439 
Sunday, 12 Feb 2017
14:04 jrm search for other commits by this committer
biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)
Original commitRevision:433945 
Sunday, 5 Feb 2017
22:23 jrm search for other commits by this committer
biology/diamond: Update to version 0.8.35.

Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)
Original commitRevision:433463 
Monday, 23 Jan 2017
13:19 jrm search for other commits by this committer
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
Original commitRevision:432214 
Monday, 16 Jan 2017
13:38 jrm search for other commits by this committer
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
Original commitRevision:431644 
Thursday, 12 Jan 2017
23:23 jrm search for other commits by this committer
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
Original commitRevision:431331 
Friday, 30 Dec 2016
16:27 jrm search for other commits by this committer
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
Original commitRevision:429998 
Sunday, 18 Dec 2016
13:52 jrm search for other commits by this committer
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
Original commitRevision:428850 
Monday, 28 Nov 2016
15:18 jrm search for other commits by this committer
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
Original commitRevision:427328 
Sunday, 6 Nov 2016
05:42 jrm search for other commits by this committer
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
Original commitRevision:425464 
Monday, 17 Oct 2016
14:17 jrm search for other commits by this committer
biology/diamond: update to version 0.8.24

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8268
Original commitRevision:424118 
Monday, 10 Oct 2016
04:33 jrm search for other commits by this committer
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
Original commitRevision:423635 
Friday, 23 Sep 2016
21:42 jrm search for other commits by this committer
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
Original commitRevision:422697 
Tuesday, 13 Sep 2016
17:50 amdmi3 search for other commits by this committer
- Update to 0.8.22

PR:		212603
Submitted by:	jrm@ftfl.ca (maintainer)
Original commitRevision:422046 
Tuesday, 6 Sep 2016
06:34 wen search for other commits by this committer
- Update to 0.8.20

PR:		212399
Submitted by:	jrm@ftfl.ca(maintainer)
Original commitRevision:421406 
Thursday, 25 Aug 2016
18:49 pawel search for other commits by this committer
Update to version 0.8.19

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)
Original commitRevision:420873 
Sunday, 14 Aug 2016
21:47 brd search for other commits by this committer
Update biology/diamond to 0.8.18.

PR:		211845
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by:	bdrewery (implicit)
Original commitRevision:420200 
Friday, 5 Aug 2016
21:24 pawel search for other commits by this committer
Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)
Original commitRevision:419710 
Sunday, 24 Jul 2016
18:06 riggs search for other commits by this committer
Update to upstream release 0.8.16

PR:		211335
Submitted by:	jrm@ftfl.ca (maintainer)
Original commitRevision:419014 
Thursday, 14 Jul 2016
16:53 pawel search for other commits by this committer
Trim excess tabs, no-op change
Original commitRevision:418546 
16:49 pawel search for other commits by this committer
Update to version 0.8.14

PR:		211078
Submitted by:	Joseph Mingrone (maintainer)
Original commitRevision:418544 
Thursday, 7 Jul 2016
15:46 amdmi3 search for other commits by this committer
- Update to 0.8.11

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)
Original commitRevision:418187 
Thursday, 30 Jun 2016
01:37 junovitch search for other commits by this committer
biology/diamond: update 0.8.6 -> 0.8.9

PR:		210710
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Original commitRevision:417803 
Friday, 17 Jun 2016
19:53 rm search for other commits by this committer
biology/diamond: update to 0.8.6

PR:		210345
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Original commitRevision:417033 
Thursday, 9 Jun 2016
01:39 matthew search for other commits by this committer
Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)
Original commitRevision:416575 
Wednesday, 18 May 2016
16:22 antoine search for other commits by this committer
Fix DEPENDS
Original commitRevision:415454 
Friday, 6 May 2016
08:45 wen search for other commits by this committer
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
Original commitRevision:414686 

Number of commits found: 87