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non port: biology/iqtree/Makefile

Number of commits found: 40

Sunday, 14 Apr 2024
19:38 Joseph Mingrone (jrm) search for other commits by this committer
biology/iqtree: Update to 2.3.2

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.3.2
                https://github.com/iqtree/iqtree2/releases/tag/v2.3.1
Sponsored by:	The FreeBSD Foundation
commit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985d commit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985d commit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985d commit hash: 1d8536b7d6e6741a33909e46fe9075b12f67985d 1d8536b
Tuesday, 5 Sep 2023
02:45 Joseph Mingrone (jrm) search for other commits by this committer
biology/iqtree: Update to 2.2.2.7

Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7
Sponsored by:	The FreeBSD Foundation
commit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aed commit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aed commit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aed commit hash: 8a1ec0de6bd5a7f16bd4967023f46d50fcd13aed 8a1ec0d
Sunday, 23 Apr 2023
09:09 Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b 8d3e020
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (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
Friday, 12 Aug 2022
14:46 Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed 4cf39de
Sunday, 22 May 2022
20:17 Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd b082b3d
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
Tuesday, 12 Jan 2021
18:12 jrm search for other commits by this committer
biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build

- USES=compiler:openmp still forces building with GCC.  This is no longer
  necessary on tier 1 platforms, which have openmp in base.

- Mark broken on i386, because base clang doesn't have 64 bit atomic
  functions for i386 (see bug 230888).

PR:		247753, 252379
Submitted by:	cmt (based on)
Original commitRevision:561368 
Saturday, 12 Dec 2020
17:04 thierry search for other commits by this committer
- Upgrade math/eigen3 to 3.3.8;

- Add some dependencies which might be detected by Find_Package but not
registered;

- Bump PORTREVISION of consumers.

PR:		250833
Submitted by:	/me
Approved by:	tcberner@ (KDE / maintainer) + exp-run
Original commitRevision:557839 
Saturday, 30 May 2020
18:43 jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6
Original commitRevision:537101 
Thursday, 28 May 2020
00:27 jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5

While here, incorporate portfmt suggestions.
Original commitRevision:536729 
Saturday, 2 May 2020
20:32 jrm search for other commits by this committer
biology/iqtree: Update to version 2.0.4
Original commitRevision:533706 
Tuesday, 27 Aug 2019
01:19 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.12

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12
Original commitRevision:509979 
Friday, 26 Jul 2019
20:46 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
Original commitRevision:507372 
Monday, 24 Jun 2019
21:47 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.11

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11
Original commitRevision:505061 
Thursday, 21 Feb 2019
14:33 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.10

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10
Original commitRevision:493504 
Thursday, 27 Dec 2018
18:34 jrm search for other commits by this committer
biology/iqtree: switch to outsource cmake build
Original commitRevision:488558 
Wednesday, 26 Dec 2018
09:06 tcberner search for other commits by this committer
Update math/eigen3 to 3.3.7

- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6
- http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
Original commitRevision:488363 
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 
Sunday, 23 Dec 2018
13:21 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.9

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
Original commitRevision:488217 
Wednesday, 12 Dec 2018
01:35 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
Original commitRevision:487272 
Sunday, 28 Oct 2018
22:00 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.8

Upstream release notes:
https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
Original commitRevision:483358 
Tuesday, 16 Oct 2018
13:49 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.7.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
Original commitRevision:482228 
Monday, 27 Aug 2018
01:20 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.7

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
Original commitRevision:478170 
Sunday, 29 Jul 2018
22:18 gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
Original commitRevision:475857 
Sunday, 8 Jul 2018
21:15 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.6

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6
Original commitRevision:474201 
Monday, 18 Jun 2018
01:48 linimon search for other commits by this committer
Mark ports broken on powerpc64, categories a-c.

While here, pet portlint and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:472665 
Friday, 11 May 2018
16:57 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.5

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5
Original commitRevision:469673 
Monday, 30 Apr 2018
16:37 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.4

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4
Original commitRevision:468714 
Friday, 23 Mar 2018
01:22 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.3

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3
Original commitRevision:465330 
Saturday, 10 Mar 2018
17:46 gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
Original commitRevision:464084 
Saturday, 3 Mar 2018
03:15 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.2

Upstream changes: http://www.iqtree.org/release/v1.6.2
Original commitRevision:463462 
Tuesday, 2 Jan 2018
16:49 tcberner search for other commits by this committer
New USES=eigen

  Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it
to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702
Original commitRevision:457914 
Friday, 29 Dec 2017
17:14 jrm search for other commits by this committer
biology/iqtree: Fix distinfo after upstream re-released v1.6.1
Original commitRevision:457516 
Thursday, 28 Dec 2017
18:37 jrm search for other commits by this committer
biology/iqtree: Update to version 1.6.1

Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
Original commitRevision:457467 
Monday, 11 Dec 2017
07:18 linimon search for other commits by this committer
Mark several ports newly broken on arm.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:455927 
Monday, 6 Nov 2017
14:24 mat search for other commits by this committer
Fix USE_GITHUB usage.

Sponsored by:	Absolight
Original commitRevision:453620 
Saturday, 21 Oct 2017
17:40 jrm search for other commits by this committer
biology/iqtree: Add EXAMPLES option and fix mess with installation of
example files in first commit
Original commitRevision:452596 
16:57 jrm search for other commits by this committer
New port, biology/iqtree: Efficient phylogenomic software

WWW: http://www.iqtree.org/
Original commitRevision:452595 

Number of commits found: 40