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* biology/iqtree: switch to outsource cmake buildjrm2018-12-281-2/+2
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* Update math/eigen3 to 3.3.7tcberner2018-12-261-0/+1
| | | | | - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.6 - http://eigen.tuxfamily.org/index.php?title=ChangeLog#Eigen_3.3.7
* Change cmake default behaviour to outsource.tcberner2018-12-261-1/+1
| | | | | | | | | | | 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
* biology/iqtree: Update to version 1.6.9jrm2018-12-231-2/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-12-121-0/+1
| | | | | | | | | | | | | | | 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
* biology/iqtree: Update to version 1.6.8jrm2018-10-291-1/+1
| | | | | Upstream release notes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8
* biology/iqtree: Update to version 1.6.7.1jrm2018-10-161-1/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1
* biology/iqtree: Update to version 1.6.7jrm2018-08-271-2/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-07-301-0/+1
| | | | | | | | | | | | | | 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
* biology/iqtree: Update to version 1.6.6jrm2018-07-091-1/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6
* Mark ports broken on powerpc64, categories a-c.linimon2018-06-181-3/+4
| | | | | | While here, pet portlint and do some other cleanup. Approved by: portmgr (tier-2 blanket)
* biology/iqtree: Update to version 1.6.5jrm2018-05-121-1/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5
* biology/iqtree: Update to version 1.6.4jrm2018-05-011-1/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4
* biology/iqtree: Update to version 1.6.3jrm2018-03-231-2/+1
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3
* Bump PORTREVISIONs of all users of math/mpc that we just updated togerald2018-03-111-0/+1
| | | | version 1.1.0 (via revision 464079).
* biology/iqtree: Update to version 1.6.2jrm2018-03-031-2/+1
| | | | Upstream changes: http://www.iqtree.org/release/v1.6.2
* New USES=eigentcberner2018-01-031-5/+2
| | | | | | | | | | | | | | | | | | | | | | 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
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1jrm2017-12-301-0/+1
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* biology/iqtree: Update to version 1.6.1jrm2017-12-291-6/+5
| | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases
* Mark several ports newly broken on arm.linimon2017-12-111-0/+4
| | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket)
* Fix USE_GITHUB usage.mat2017-11-061-2/+1
| | | | Sponsored by: Absolight
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofjrm2017-10-221-1/+13
| | | | example files in first commit
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2017-10-221-0/+24
WWW: http://www.iqtree.org/
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