Commit graph

24 commits

Author SHA1 Message Date
Joseph Mingrone
09ba90a645 biology/iqtree: Update to version 1.6.10
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10
2019-02-21 14:33:43 +00:00
Joseph Mingrone
8e9f700daa biology/iqtree: switch to outsource cmake build 2018-12-27 18:34:44 +00:00
Tobias C. Berner
8a4ab05d84 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
2018-12-26 09:06:34 +00:00
Tobias C. Berner
707c6bf295 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
2018-12-25 20:25:39 +00:00
Joseph Mingrone
04ee035998 biology/iqtree: Update to version 1.6.9
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
2018-12-23 13:21:11 +00:00
Gerald Pfeifer
a9f015d155 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
2018-12-12 01:35:33 +00:00
Joseph Mingrone
97a4339219 biology/iqtree: Update to version 1.6.8
Upstream release notes:
https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
2018-10-28 22:00:18 +00:00
Joseph Mingrone
53a7170018 biology/iqtree: Update to version 1.6.7.1
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
2018-10-16 13:49:54 +00:00
Joseph Mingrone
a0b1ec7ab5 biology/iqtree: Update to version 1.6.7
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
2018-08-27 01:20:28 +00:00
Gerald Pfeifer
09f9633cb6 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
2018-07-29 22:18:44 +00:00
Joseph Mingrone
4d60e6a139 biology/iqtree: Update to version 1.6.6
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6
2018-07-08 21:15:47 +00:00
Mark Linimon
a875dccebc Mark ports broken on powerpc64, categories a-c.
While here, pet portlint and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)
2018-06-18 01:48:46 +00:00
Joseph Mingrone
52a0e92673 biology/iqtree: Update to version 1.6.5
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5
2018-05-11 16:57:09 +00:00
Joseph Mingrone
ae88b95de5 biology/iqtree: Update to version 1.6.4
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4
2018-04-30 16:37:22 +00:00
Joseph Mingrone
c7d08fd55f biology/iqtree: Update to version 1.6.3
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3
2018-03-23 01:22:47 +00:00
Gerald Pfeifer
c2a92a1aea Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
2018-03-10 17:46:04 +00:00
Joseph Mingrone
d0542b46be biology/iqtree: Update to version 1.6.2
Upstream changes: http://www.iqtree.org/release/v1.6.2
2018-03-03 03:15:24 +00:00
Tobias C. Berner
51d04637cb 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
2018-01-02 16:49:24 +00:00
Joseph Mingrone
e84339cb2b biology/iqtree: Fix distinfo after upstream re-released v1.6.1 2017-12-29 17:14:07 +00:00
Joseph Mingrone
3baf04725e biology/iqtree: Update to version 1.6.1
Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
2017-12-28 18:37:06 +00:00
Mark Linimon
5324a23092 Mark several ports newly broken on arm.
While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
2017-12-11 07:18:48 +00:00
Mathieu Arnold
6d9a5c87be Fix USE_GITHUB usage.
Sponsored by:	Absolight
2017-11-06 14:24:39 +00:00
Joseph Mingrone
f371e4713e biology/iqtree: Add EXAMPLES option and fix mess with installation of
example files in first commit
2017-10-21 17:40:18 +00:00
Joseph Mingrone
1027ca2f40 New port, biology/iqtree: Efficient phylogenomic software
WWW: http://www.iqtree.org/
2017-10-21 16:57:53 +00:00