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Current status

The server has been repaired, with a new power supply, for $23. I am waiting for lower COVID rates before visiting the datacenter to return it.
non port: biology/diamond/Makefile
SVNWeb

Number of commits found: 69

Tue, 13 Apr 2021
[ 00:55 jrm (Joseph Mingrone) ]    commit hash:46fc7df8540c256facd27c205897db46857d730e  46fc7df 
biology/diamond: Update to 2.0.9

https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
Wed, 7 Apr 2021
[ 08:09 mat (Mathieu Arnold) ]    commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  cf118cc (Only the first 10 of 8873 ports in this commit are shown above. View all ports for this commit)
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
Tue, 6 Apr 2021
[ 14:31 mat (Mathieu Arnold) ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148 (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Thu, 11 Mar 2021
[ 12:41 jrm ] Original commit   Revision:568088
biology/diamond: Update to 2.0.8

https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
Wed, 17 Feb 2021
[ 16:43 jrm ] Original commit   Revision:565520
biology/diamond: Update to 2.0.7

https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
Sun, 20 Dec 2020
[ 20:21 jrm ] Original commit   Revision:558772
biology/diamond: Update to version 2.0.6

https://github.com/bbuchfink/diamond/releases/tag/v2.0.6
Tue, 1 Dec 2020
[ 22:27 jrm ] Original commit   Revision:556797
biology/diamond: Update to version 2.0.5

https://github.com/bbuchfink/diamond/releases/tag/v2.0.5
Sun, 30 Aug 2020
[ 16:14 jrm ] Original commit   Revision:547066
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
Fri, 7 Aug 2020
[ 11:20 jrm ] Original commit   Revision:544321
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
Tue, 28 Jul 2020
[ 02:39 jrm ] Original commit   Revision:543567
biology/diamond: Update to version 2.0.0

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0
Fri, 3 Jul 2020
[ 11:22 jrm ] Original commit   Revision:541097
biology/diamond: Update to version 0.9.36

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
Sat, 27 Jun 2020
[ 16:26 jrm ] Original commit   Revision:540624
biology/diamond: Update to version 0.9.35

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
Fri, 12 Jun 2020
[ 12:12 jrm ] Original commit   Revision:538606
biology/diamond: Update to version 0.9.34

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
Wed, 3 Jun 2020
[ 21:44 jrm ] Original commit   Revision:537853
biology/diamond: Update to version 0.9.33

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
Fri, 24 Apr 2020
[ 23:04 jrm ] Original commit   Revision:532906
biology/diamond: Update to version 0.9.32

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32
Sat, 21 Mar 2020
[ 22:11 jrm ] Original commit   Revision:528881
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.
Mon, 3 Feb 2020
[ 15:55 jrm ] Original commit   Revision:525045
biology/diamond: Update to version 0.9.30

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
Wed, 20 Nov 2019
[ 17:14 jrm ] Original commit   Revision:518039
biology/diamond: Update to v0.9.29

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
Thu, 7 Nov 2019
[ 14:12 jrm ] Original commit   Revision:516974
biology/diamond: Update to version 0.9.28

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
Sun, 3 Nov 2019
[ 01:34 jrm ] Original commit   Revision:516379
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
Wed, 18 Sep 2019
[ 18:45 jrm ] Original commit   Revision:512282
biology/diamond: Update to version 0.9.26

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
Sun, 4 Aug 2019
[ 23:35 jrm ] Original commit   Revision:508134
biology/diamond: Update to version 0.9.25

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
Mon, 31 Dec 2018
[ 19:00 jrm ] Original commit   Revision:488819
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
Tue, 25 Dec 2018
[ 20:25 tcberner ] Original commit   Revision:488341(Only the first 10 of 1277 ports in this commit are shown above. View all ports for this commit)
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
Mon, 17 Dec 2018
[ 19:12 jrm ] Original commit   Revision:487707
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
Mon, 14 May 2018
[ 17:17 jrm ] Original commit   Revision:469925
biology/diamond: Update to version 0.9.22

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
Fri, 20 Apr 2018
[ 21:23 jrm ] Original commit   Revision:467847
biology/diamond: Update to version 0.9.21

Upstream changes: https://github.com/bbuchfink/diamond/releases
Sat, 17 Mar 2018
[ 15:29 jrm ] Original commit   Revision:464826
biology/diamond: Update to version 0.9.19

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
Thu, 15 Mar 2018
[ 02:28 jrm ] Original commit   Revision:464549
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
Thu, 1 Feb 2018
[ 19:20 jrm ] Original commit   Revision:460624
biology/diamond: Update to version 0.9.17

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
Wed, 13 Dec 2017
[ 16:31 jrm ] Original commit   Revision:456220
biology/diamond: Update to version 0.9.14

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
Fri, 17 Nov 2017
[ 20:11 jrm ] Original commit   Revision:454383
biology/diamond: Update to version 0.9.13

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
Wed, 8 Nov 2017
[ 16:06 jrm ] Original commit   Revision:453752
biology/diamond: Update to version 0.9.12

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
Fri, 3 Nov 2017
[ 03:45 jrm ] Original commit   Revision:453387
biology/diamond: Update to 0.9.11

Upstream changes: https://github.com/bbuchfink/diamond/releases
Tue, 15 Aug 2017
[ 20:45 jrm ] Original commit   Revision:448009
biology/diamond: Update to version 0.9.10

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
Mon, 3 Jul 2017
[ 19:12 jrm ] Original commit   Revision:444981
biology/diamond: Update to version 0.9.9

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
Fri, 16 Jun 2017
[ 14:49 jrm ] Original commit   Revision:443706
biology/diamond: Update to version 0.9.8
Sat, 3 Jun 2017
[ 12:32 jrm ] Original commit   Revision:442478
biology/diamond: Update to version 0.9.4

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
Mon, 29 May 2017
[ 15:24 jrm ] Original commit   Revision:441991
biology/diamond: Update to version 0.9.3

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

Approved by:	swills (mentor, implicit)
Tue, 23 May 2017
[ 11:03 jrm ] Original commit   Revision:441513
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)
Fri, 21 Apr 2017
[ 14:46 jrm ] Original commit   Revision:439081
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)
Sun, 2 Apr 2017
[ 10:55 jrm ] Original commit   Revision:437552
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)
Sat, 1 Apr 2017
[ 15:23 gerald ] Original commit   Revision:437439(Only the first 10 of 1118 ports in this commit are shown above. View all ports for this commit)
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
Sun, 12 Feb 2017
[ 14:04 jrm ] Original commit   Revision:433945
biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)
Sun, 5 Feb 2017
[ 22:23 jrm ] Original commit   Revision:433463
biology/diamond: Update to version 0.8.35.

Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)
Mon, 23 Jan 2017
[ 13:19 jrm ] Original commit   Revision:432214
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
Mon, 16 Jan 2017
[ 13:38 jrm ] Original commit   Revision:431644
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
Thu, 12 Jan 2017
[ 23:23 jrm ] Original commit   Revision:431331
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
Fri, 30 Dec 2016
[ 16:27 jrm ] Original commit   Revision:429998
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
Sun, 18 Dec 2016
[ 13:52 jrm ] Original commit   Revision:428850
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
Mon, 28 Nov 2016
[ 15:18 jrm ] Original commit   Revision:427328
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
Sun, 6 Nov 2016
[ 05:42 jrm ] Original commit   Revision:425464
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
Mon, 17 Oct 2016
[ 14:17 jrm ] Original commit   Revision:424118
biology/diamond: update to version 0.8.24

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8268
Mon, 10 Oct 2016
[ 04:33 jrm ] Original commit   Revision:423635
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
Fri, 23 Sep 2016
[ 21:42 jrm ] Original commit   Revision:422697(Only the first 10 of 16 ports in this commit are shown above. View all ports for this commit)
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
Tue, 13 Sep 2016
[ 17:50 amdmi3 ] Original commit   Revision:422046
- Update to 0.8.22

PR:		212603
Submitted by:	jrm@ftfl.ca (maintainer)
Tue, 6 Sep 2016
[ 06:34 wen ] Original commit   Revision:421406
- Update to 0.8.20

PR:		212399
Submitted by:	jrm@ftfl.ca(maintainer)
Thu, 25 Aug 2016
[ 18:49 pawel ] Original commit   Revision:420873
Update to version 0.8.19

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)
Sun, 14 Aug 2016
[ 21:47 brd ] Original commit   Revision:420200
Update biology/diamond to 0.8.18.

PR:		211845
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by:	bdrewery (implicit)
Fri, 5 Aug 2016
[ 21:24 pawel ] Original commit   Revision:419710
Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)
Sun, 24 Jul 2016
[ 18:06 riggs ] Original commit   Revision:419014
Update to upstream release 0.8.16

PR:		211335
Submitted by:	jrm@ftfl.ca (maintainer)
Thu, 14 Jul 2016
[ 16:53 pawel ] Original commit   Revision:418546
Trim excess tabs, no-op change
[ 16:49 pawel ] Original commit   Revision:418544
Update to version 0.8.14

PR:		211078
Submitted by:	Joseph Mingrone (maintainer)
Thu, 7 Jul 2016
[ 15:46 amdmi3 ] Original commit   Revision:418187
- Update to 0.8.11

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)
Thu, 30 Jun 2016
[ 01:37 junovitch ] Original commit   Revision:417803
biology/diamond: update 0.8.6 -> 0.8.9

PR:		210710
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Fri, 17 Jun 2016
[ 19:53 rm ] Original commit   Revision:417033
biology/diamond: update to 0.8.6

PR:		210345
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Thu, 9 Jun 2016
[ 01:39 matthew ] Original commit   Revision:416575
Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)
Wed, 18 May 2016
[ 16:22 antoine ] Original commit   Revision:415454
Fix DEPENDS
Fri, 6 May 2016
[ 08:45 wen ] Original commit   Revision:414686
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: 69