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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.

Finally, under Watch Lists, click on ABI Package Subscriptions to select your ABI (e.g. FreeBSD:14:amd64) & package set (latest/quarterly) combination for a given watch list. This is what FreshPorts will look for.

Port details
diamond BLAST-compatible local sequence aligner
2.1.9 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.1.9Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-05-06 08:45:09
Last Update: 2024-02-04 19:41:51
Commit Hash: 92b051a
License: GPLv3
WWW:
http://ab.inf.uni-tuebingen.de/software/diamond/
Description:
DIAMOND is a BLAST-compatible local aligner for mapping protein and translated 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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/diamond
  2. /usr/local/share/licenses/diamond-2.1.9/catalog.mk
  3. /usr/local/share/licenses/diamond-2.1.9/LICENSE
  4. /usr/local/share/licenses/diamond-2.1.9/GPLv3
Collapse this list.
Dependency lines:
  • diamond>0:biology/diamond
To install the port:
cd /usr/ports/biology/diamond/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/diamond
  • pkg install diamond
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: diamond
Flavors: there is no flavor information for this port.
ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le
distinfo:
TIMESTAMP = 1707069968 SHA256 (bbuchfink-diamond-v2.1.9_GH0.tar.gz) = 4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88 SIZE (bbuchfink-diamond-v2.1.9_GH0.tar.gz) = 5946668

Packages (timestamps in pop-ups are UTC):
diamond
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.1.92.1.9------
FreeBSD:13:quarterly2.1.92.1.9----2.1.8_12.1.8_1
FreeBSD:14:latest2.1.92.1.9-----2.1.6
FreeBSD:14:quarterly2.1.92.1.9----2.1.8_12.1.8_1
FreeBSD:15:latest2.1.92.1.9n/a-n/a-2.1.8_12.1.9
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. ninja : devel/ninja
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_diamond
USES:
cmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/bbuchfink/diamond/tar.gz/v2.1.9?dummy=/
Collapse this list.

Number of commits found: 89

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.1.9
04 Feb 2024 19:41:51
commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083commit hash: 92b051a2909f68d74d1bb641a08bdc09365e5083 files touched by this commit
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
2.1.8_1
29 Dec 2023 18:57:14
commit hash: 96286fc8fdabb430731185b20409aba4e9f473fdcommit hash: 96286fc8fdabb430731185b20409aba4e9f473fdcommit hash: 96286fc8fdabb430731185b20409aba4e9f473fdcommit hash: 96286fc8fdabb430731185b20409aba4e9f473fd files touched by this commit
Joseph Mingrone (jrm) search for other commits by this committer
Author: Dimitry Andric
biology/diamond: Fix build on main after import of clang 17
2.1.8
08 Jul 2023 03:45:48
commit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78afcommit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78afcommit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78afcommit hash: 371eba15ec720da1d7f85c6282e58dc9d30c78af files touched by this commit
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
2.1.6
18 Mar 2023 15:49:03
commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6commit hash: 43743a89d4d88202fa2e6aa72bcb7459a207baa6 files touched by this commit
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
2.1.4
05 Mar 2023 15:33:44
commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124commit hash: d363e4b4eb6517530e4a47ed92a914b7b27ac124 files touched by this commit
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
2.1.3
22 Feb 2023 11:48:44
commit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dccommit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dccommit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dccommit hash: 85920ea2cc8e2c2802a8bc4281f703f5993942dc files touched by this commit
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
2.1.2
20 Feb 2023 14:35:05
commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5commit hash: 89f956fe5f0cb338aca973b8651b048606be8fb5 files touched by this commit
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
2.1.1
10 Feb 2023 17:36:10
commit hash: 056255445ec7f8fa17b551020b74d74905eaf753commit hash: 056255445ec7f8fa17b551020b74d74905eaf753commit hash: 056255445ec7f8fa17b551020b74d74905eaf753commit hash: 056255445ec7f8fa17b551020b74d74905eaf753 files touched by this commit
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
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f 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)
2.0.15
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0.15
24 Apr 2022 17:50:21
commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8commit hash: d9f5d5d949ea138ba4d965dd7d84c51758ea0ed8 files touched by this commit
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
2.0.14
13 Jan 2022 17:42:38
commit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8acommit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8acommit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8acommit hash: 7c428e83c0070adce767c19a0e806d1793d4ad8a files touched by this commit
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
2.0.13
11 Nov 2021 17:17:24
commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767commit hash: 84e457ed42919d5b23eb4e23f75314dad9f1f767 files touched by this commit
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.
2.0.12
12 Oct 2021 15:40:55
commit hash: 523d2537b4a95a59e720f66d560529e1938c796fcommit hash: 523d2537b4a95a59e720f66d560529e1938c796fcommit hash: 523d2537b4a95a59e720f66d560529e1938c796fcommit hash: 523d2537b4a95a59e720f66d560529e1938c796f files touched by this commit
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
2.0.11.1
09 Oct 2021 13:49:00
commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03commit hash: b6994dfc3e9f38415b9f699e35cd788e7d36bc03 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/diamond: enable on powerpc64le
2.0.11.1
08 Oct 2021 18:19:23
commit hash: 096fef40c53a0bcc585624139de0109511580649commit hash: 096fef40c53a0bcc585624139de0109511580649commit hash: 096fef40c53a0bcc585624139de0109511580649commit hash: 096fef40c53a0bcc585624139de0109511580649 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/diamond: enable on powerpc64
2.0.11.1
08 Oct 2021 16:25:09
commit hash: 63de6c3db611788a528afe985cd46fbe055b439acommit hash: 63de6c3db611788a528afe985cd46fbe055b439acommit hash: 63de6c3db611788a528afe985cd46fbe055b439acommit hash: 63de6c3db611788a528afe985cd46fbe055b439a files touched by this commit
Mikael Urankar (mikael) search for other commits by this committer
biology/diamond: Enable on aarch64.
2.0.11.1
06 Jul 2021 13:15:24
commit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8dbcommit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8dbcommit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8dbcommit hash: d0bf21ba1d9d8c8270615f788349a51586c1e8db files touched by this commit
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
2.0.10
03 Jul 2021 16:25:00
commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3commit hash: 43358569be1f5f0766b93f49dbb91e0eb8ed1fd3 files touched by this commit
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
2.0.9
13 Apr 2021 00:55:49
commit hash: 46fc7df8540c256facd27c205897db46857d730ecommit hash: 46fc7df8540c256facd27c205897db46857d730ecommit hash: 46fc7df8540c256facd27c205897db46857d730ecommit hash: 46fc7df8540c256facd27c205897db46857d730e files touched by this commit
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
2.0.8
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.0.8
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.0.8
11 Mar 2021 12:41:20
Revision:568088Original commit files touched by this commit
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
2.0.7
17 Feb 2021 16:43:27
Revision:565520Original commit files touched by this commit
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
2.0.6
20 Dec 2020 20:21:42
Revision:558772Original commit files touched by this commit
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
2.0.5
01 Dec 2020 22:27:24
Revision:556797Original commit files touched by this commit
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
2.0.4
30 Aug 2020 16:14:22
Revision:547066Original commit files touched by this commit
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
2.0.2
07 Aug 2020 11:20:11
Revision:544321Original commit files touched by this commit
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
2.0.0
28 Jul 2020 02:39:00
Revision:543567Original commit files touched by this commit
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
0.9.36
03 Jul 2020 11:22:49
Revision:541097Original commit files touched by this commit
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
0.9.35
27 Jun 2020 16:26:54
Revision:540624Original commit files touched by this commit
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
0.9.34
12 Jun 2020 12:12:12
Revision:538606Original commit files touched by this commit
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
0.9.33
03 Jun 2020 21:44:36
Revision:537853Original commit files touched by this commit
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
0.9.32
24 Apr 2020 23:04:14
Revision:532906Original commit files touched by this commit
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
0.9.31.2
21 Mar 2020 22:11:26
Revision:528881Original commit files touched by this commit
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.
0.9.30
03 Feb 2020 15:55:05
Revision:525045Original commit files touched by this commit
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
0.9.29
20 Nov 2019 17:14:29
Revision:518039Original commit files touched by this commit
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
0.9.28
07 Nov 2019 14:12:08
Revision:516974Original commit files touched by this commit
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
0.9.27.1
03 Nov 2019 01:34:11
Revision:516379Original commit files touched by this commit
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
0.9.26
18 Sep 2019 18:45:09
Revision:512282Original commit files touched by this commit
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
0.9.25
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
0.9.25
04 Aug 2019 23:35:15
Revision:508134Original commit files touched by this commit
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
0.9.24
31 Dec 2018 19:00:00
Revision:488819Original commit files touched by this commit
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
0.9.23.6
25 Dec 2018 20:25:40
Revision:488341Original commit files touched by this commit
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
0.9.23.6
17 Dec 2018 19:12:38
Revision:487707Original commit files touched by this commit
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
0.9.22
14 May 2018 17:17:12
Revision:469925Original commit files touched by this commit
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
0.9.21
20 Apr 2018 21:23:27
Revision:467847Original commit files touched by this commit
jrm search for other commits by this committer
biology/diamond: Update to version 0.9.21

Upstream changes: https://github.com/bbuchfink/diamond/releases
0.9.19
17 Mar 2018 15:29:13
Revision:464826Original commit files touched by this commit
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
0.9.18.49
15 Mar 2018 02:28:09
Revision:464549Original commit files touched by this commit
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
0.9.17
01 Feb 2018 19:20:07
Revision:460624Original commit files touched by this commit
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
0.9.14
13 Dec 2017 16:31:53
Revision:456220Original commit files touched by this commit
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biology/diamond: Update to version 0.9.14

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
0.9.13
17 Nov 2017 20:11:05
Revision:454383Original commit files touched by this commit
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biology/diamond: Update to version 0.9.13

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
0.9.12
08 Nov 2017 16:06:50
Revision:453752Original commit files touched by this commit
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biology/diamond: Update to version 0.9.12

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
0.9.11
03 Nov 2017 03:45:01
Revision:453387Original commit files touched by this commit
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biology/diamond: Update to 0.9.11

Upstream changes: https://github.com/bbuchfink/diamond/releases
0.9.10
15 Aug 2017 20:45:08
Revision:448009Original commit files touched by this commit
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biology/diamond: Update to version 0.9.10

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
0.9.9
03 Jul 2017 19:12:18
Revision:444981Original commit files touched by this commit
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biology/diamond: Update to version 0.9.9

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
0.9.8
16 Jun 2017 14:49:19
Revision:443706Original commit files touched by this commit
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biology/diamond: Update to version 0.9.8
0.9.4
03 Jun 2017 12:32:16
Revision:442478Original commit files touched by this commit
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biology/diamond: Update to version 0.9.4

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
0.9.3
29 May 2017 15:24:01
Revision:441991Original commit files touched by this commit
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biology/diamond: Update to version 0.9.3

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

Approved by:	swills (mentor, implicit)
0.9.1
23 May 2017 11:03:09
Revision:441513Original commit files touched by this commit
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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)
0.8.38
21 Apr 2017 14:46:07
Revision:439081Original commit files touched by this commit
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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)
0.8.37
02 Apr 2017 10:55:31
Revision:437552Original commit files touched by this commit
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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)
0.8.36_1
01 Apr 2017 15:23:32
Revision:437439Original commit files touched by this commit
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
0.8.36
12 Feb 2017 14:04:57
Revision:433945Original commit files touched by this commit
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biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)
0.8.35
05 Feb 2017 22:23:32
Revision:433463Original commit files touched by this commit
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biology/diamond: Update to version 0.8.35.

Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)
0.8.34
23 Jan 2017 13:19:18
Revision:432214Original commit files touched by this commit
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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
0.8.32
16 Jan 2017 13:38:12
Revision:431644Original commit files touched by this commit
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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
0.8.31
12 Jan 2017 23:23:19
Revision:431331Original commit files touched by this commit
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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
0.8.30
30 Dec 2016 16:27:25
Revision:429998Original commit files touched by this commit
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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
0.8.29
18 Dec 2016 13:52:32
Revision:428850Original commit files touched by this commit
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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
0.8.28
28 Nov 2016 15:18:15
Revision:427328Original commit files touched by this commit
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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
0.8.26
06 Nov 2016 05:42:32
Revision:425464Original commit files touched by this commit
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
0.8.24
17 Oct 2016 14:17:19
Revision:424118Original commit files touched by this commit
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
0.8.23
10 Oct 2016 04:33:16
Revision:423635Original commit files touched by this commit
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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
0.8.22
23 Sep 2016 21:42:02
Revision:422697Original commit files touched by this commit
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
0.8.22
13 Sep 2016 17:50:31
Revision:422046Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Update to 0.8.22

PR:		212603
Submitted by:	jrm@ftfl.ca (maintainer)
0.8.20
06 Sep 2016 06:34:59
Revision:421406Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.8.20

PR:		212399
Submitted by:	jrm@ftfl.ca(maintainer)
0.8.19
25 Aug 2016 18:49:12
Revision:420873Original commit files touched by this commit
pawel search for other commits by this committer
Update to version 0.8.19

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)
0.8.18
14 Aug 2016 21:47:57
Revision:420200Original commit files touched by this commit
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)
0.8.17
05 Aug 2016 21:24:06
Revision:419710Original commit files touched by this commit
pawel search for other commits by this committer
Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)
0.8.16
24 Jul 2016 18:06:21
Revision:419014Original commit files touched by this commit
riggs search for other commits by this committer
Update to upstream release 0.8.16

PR:		211335
Submitted by:	jrm@ftfl.ca (maintainer)
0.8.14
14 Jul 2016 16:53:06
Revision:418546Original commit files touched by this commit
pawel search for other commits by this committer
Trim excess tabs, no-op change
0.8.14
14 Jul 2016 16:49:41
Revision:418544Original commit files touched by this commit
pawel search for other commits by this committer
Update to version 0.8.14

PR:		211078
Submitted by:	Joseph Mingrone (maintainer)
0.8.11
07 Jul 2016 15:46:12
Revision:418187Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Update to 0.8.11

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)
0.8.9
30 Jun 2016 01:37:22
Revision:417803Original commit files touched by this commit
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)
0.8.6
17 Jun 2016 19:53:46
Revision:417033Original commit files touched by this commit
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)
0.8.5
09 Jun 2016 01:39:58
Revision:416575Original commit files touched by this commit
matthew search for other commits by this committer
Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)
0.7.12_1
18 May 2016 16:22:07
Revision:415454Original commit files touched by this commit
antoine search for other commits by this committer
Fix DEPENDS
0.7.12
06 May 2016 08:45:02
Revision:414686Original commit files touched by this commit
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

Number of commits found: 89