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non port: biology/diamond/Makefile
SVNWeb

Number of commits found XX: 56

Wed, 3 Jun 2020
[ 21:44 jrm ] Original commit   Revision:537853
537853 biology/diamond/Makefile
537853 biology/diamond/distinfo
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
532906 biology/diamond/Makefile
532906 biology/diamond/distinfo
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
528881 biology/diamond/Makefile
528881 biology/diamond/distinfo
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
525045 biology/diamond/Makefile
525045 biology/diamond/distinfo
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
518039 biology/diamond/Makefile
518039 biology/diamond/distinfo
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
516974 biology/diamond/Makefile
516974 biology/diamond/distinfo
516974 biology/diamond/pkg-message
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
516379 biology/diamond/Makefile
516379 biology/diamond/distinfo
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
512282 biology/diamond/Makefile
512282 biology/diamond/distinfo
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
508134 biology/diamond/Makefile
508134 biology/diamond/distinfo
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
488819 biology/diamond/Makefile
488819 biology/diamond/distinfo
488819 biology/diamond/files
488819 biology/diamond/pkg-message
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
488341 CHANGES
488341 Mk/Uses/cmake.mk
488341 accessibility/jovie-kde4/Makefile
488341 accessibility/kaccessible-kde4/Makefile
488341 accessibility/kmag-kde4/Makefile
488341 accessibility/kmag/Makefile
488341 accessibility/kmousetool-kde4/Makefile
488341 accessibility/kmousetool/Makefile
488341 accessibility/kmouth-kde4/Makefile
488341 accessibility/kmouth/Makefile

(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
487707 biology/diamond/Makefile
487707 biology/diamond/distinfo
487707 biology/diamond/files/patch-CMakeLists.txt
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
469925 biology/diamond/Makefile
469925 biology/diamond/distinfo
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
467847 biology/diamond/Makefile
467847 biology/diamond/distinfo
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
464826 biology/diamond/Makefile
464826 biology/diamond/distinfo
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
464549 biology/diamond/Makefile
464549 biology/diamond/distinfo
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
460624 biology/diamond/Makefile
460624 biology/diamond/distinfo
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
456220 biology/diamond/Makefile
456220 biology/diamond/distinfo
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
454383 biology/diamond/Makefile
454383 biology/diamond/distinfo
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
453752 biology/diamond/Makefile
453752 biology/diamond/distinfo
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
453387 biology/diamond/Makefile
453387 biology/diamond/distinfo
453387 biology/diamond/files/patch-CMakeLists.txt
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
448009 biology/diamond/Makefile
448009 biology/diamond/distinfo
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
444981 biology/diamond/Makefile
444981 biology/diamond/distinfo
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
443706 biology/diamond/Makefile
443706 biology/diamond/distinfo
biology/diamond: Update to version 0.9.8
Sat, 3 Jun 2017
[ 12:32 jrm ] Original commit   Revision:442478
442478 biology/diamond/Makefile
442478 biology/diamond/distinfo
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
441991 biology/diamond/Makefile
441991 biology/diamond/distinfo
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
441513 biology/diamond/Makefile
441513 biology/diamond/distinfo
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
439081 biology/diamond/Makefile
439081 biology/diamond/distinfo
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
437552 biology/diamond/Makefile
437552 biology/diamond/distinfo
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
437439 archivers/kf5-karchive/Makefile
437439 archivers/paq/Makefile
437439 archivers/pxz/Makefile
437439 archivers/py-brotli/Makefile
437439 archivers/rvm/Makefile
437439 astro/geographiclib/Makefile
437439 astro/gpstk/Makefile
437439 astro/kstars/Makefile
437439 astro/libosmium/Makefile
437439 astro/nightfall/Makefile

(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
433945 biology/diamond/Makefile
433945 biology/diamond/distinfo
biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)
Sun, 5 Feb 2017
[ 22:23 jrm ] Original commit   Revision:433463
433463 biology/diamond/Makefile
433463 biology/diamond/distinfo
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
432214 biology/diamond/Makefile
432214 biology/diamond/distinfo
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
431644 biology/diamond/Makefile
431644 biology/diamond/distinfo
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
431331 biology/diamond/Makefile
431331 biology/diamond/distinfo
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
429998 biology/diamond/Makefile
429998 biology/diamond/distinfo
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
428850 biology/diamond/Makefile
428850 biology/diamond/distinfo
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
427328 biology/diamond/Makefile
427328 biology/diamond/distinfo
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
425464 biology/diamond/Makefile
425464 biology/diamond/distinfo
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
424118 biology/diamond/Makefile
424118 biology/diamond/distinfo
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
423635 biology/diamond/Makefile
423635 biology/diamond/distinfo
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
422697 biology/diamond/Makefile
422697 biology/paml/Makefile
422697 biology/py-biom-format/Makefile
422697 databases/py-psycopg2cffi/Makefile
422697 deskutils/clipit/Makefile
422697 devel/py-pyqi/Makefile
422697 devel/py-simpleeval/Makefile
422697 mail/getmail/Makefile
422697 math/R/Makefile
422697 print/foomatic-filters/Makefile

(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
422046 biology/diamond/Makefile
422046 biology/diamond/distinfo
- Update to 0.8.22

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

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

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)
Sun, 14 Aug 2016
[ 21:47 brd ] Original commit   Revision:420200
420200 biology/diamond/Makefile
420200 biology/diamond/distinfo
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
419710 biology/diamond/Makefile
419710 biology/diamond/distinfo
Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)
Sun, 24 Jul 2016
[ 18:06 riggs ] Original commit   Revision:419014
419014 biology/diamond/Makefile
419014 biology/diamond/distinfo
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
418546 biology/diamond/Makefile
Trim excess tabs, no-op change
[ 16:49 pawel ] Original commit   Revision:418544
418544 biology/diamond/Makefile
418544 biology/diamond/distinfo
Update to version 0.8.14

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

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)
Thu, 30 Jun 2016
[ 01:37 junovitch ] Original commit   Revision:417803
417803 biology/diamond/Makefile
417803 biology/diamond/distinfo
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
417033 biology/diamond/Makefile
417033 biology/diamond/distinfo
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
416575 biology/diamond/Makefile
416575 biology/diamond/distinfo
416575 biology/diamond/files/patch-CMakeLists.txt
Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)
Wed, 18 May 2016
[ 16:22 antoine ] Original commit   Revision:415454
415454 biology/diamond/Makefile
Fix DEPENDS
Fri, 6 May 2016
[ 08:45 wen ] Original commit   Revision:414686
414686 biology/Makefile
414686 biology/diamond
414686 biology/diamond/Makefile
414686 biology/diamond/distinfo
414686 biology/diamond/files
414686 biology/diamond/files/patch-CMakeLists.txt
414686 biology/diamond/pkg-descr
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 XX: 56

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