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* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ buildJoseph Mingrone2021-01-122-2/+14
| | | | | | | | | | | | | | - 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) Notes: svn path=/head/; revision=561368
* - Upgrade math/eigen3 to 3.3.8;Thierry Thomas2020-12-121-0/+1
| | | | | | | | | | | | | - 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 Notes: svn path=/head/; revision=557839
* biology/iqtree: Update to version 2.0.6Joseph Mingrone2020-05-302-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.6 Notes: svn path=/head/; revision=537101
* biology/iqtree: Update to version 2.0.5Joseph Mingrone2020-05-282-7/+7
| | | | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v2.0.5 While here, incorporate portfmt suggestions. Notes: svn path=/head/; revision=536729
* biology/iqtree: Update to version 2.0.4Joseph Mingrone2020-05-022-5/+7
| | | | Notes: svn path=/head/; revision=533706
* biology/iqtree: Update to version 1.6.12Joseph Mingrone2019-08-272-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.12 Notes: svn path=/head/; revision=509979
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-0/+1
| | | | | | | | | | | | | | | | | | 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 Notes: svn path=/head/; revision=507372
* biology/iqtree: Update to version 1.6.11Joseph Mingrone2019-06-242-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.11 Notes: svn path=/head/; revision=505061
* biology/iqtree: Update to version 1.6.10Joseph Mingrone2019-02-212-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.10 Notes: svn path=/head/; revision=493504
* biology/iqtree: switch to outsource cmake buildJoseph Mingrone2018-12-271-2/+2
| | | | Notes: svn path=/head/; revision=488558
* Update math/eigen3 to 3.3.7Tobias C. Berner2018-12-261-0/+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 Notes: svn path=/head/; revision=488363
* Change cmake default behaviour to outsource.Tobias C. Berner2018-12-251-1/+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 Notes: svn path=/head/; revision=488341
* biology/iqtree: Update to version 1.6.9Joseph Mingrone2018-12-232-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.9 Notes: svn path=/head/; revision=488217
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-0/+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 Notes: svn path=/head/; revision=487272
* biology/iqtree: Update to version 1.6.8Joseph Mingrone2018-10-282-4/+4
| | | | | | | | Upstream release notes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.8 Notes: svn path=/head/; revision=483358
* biology/iqtree: Update to version 1.6.7.1Joseph Mingrone2018-10-162-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7.1 Notes: svn path=/head/; revision=482228
* biology/iqtree: Update to version 1.6.7Joseph Mingrone2018-08-272-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.7 Notes: svn path=/head/; revision=478170
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-291-0/+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 Notes: svn path=/head/; revision=475857
* biology/iqtree: Update to version 1.6.6Joseph Mingrone2018-07-082-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.6 Notes: svn path=/head/; revision=474201
* Mark ports broken on powerpc64, categories a-c.Mark Linimon2018-06-181-3/+4
| | | | | | | | | While here, pet portlint and do some other cleanup. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=472665
* biology/iqtree: Update to version 1.6.5Joseph Mingrone2018-05-112-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.5 Notes: svn path=/head/; revision=469673
* biology/iqtree: Update to version 1.6.4Joseph Mingrone2018-04-302-4/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.4 Notes: svn path=/head/; revision=468714
* biology/iqtree: Update to version 1.6.3Joseph Mingrone2018-03-232-5/+4
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases/tag/v1.6.3 Notes: svn path=/head/; revision=465330
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-101-0/+1
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* biology/iqtree: Update to version 1.6.2Joseph Mingrone2018-03-032-5/+4
| | | | | | | Upstream changes: http://www.iqtree.org/release/v1.6.2 Notes: svn path=/head/; revision=463462
* New USES=eigenTobias C. Berner2018-01-021-5/+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 Notes: svn path=/head/; revision=457914
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1Joseph Mingrone2017-12-292-3/+4
| | | | Notes: svn path=/head/; revision=457516
* biology/iqtree: Update to version 1.6.1Joseph Mingrone2017-12-282-9/+8
| | | | | | | Upstream changes: https://github.com/Cibiv/IQ-TREE/releases Notes: svn path=/head/; revision=457467
* Mark several ports newly broken on arm.Mark Linimon2017-12-111-0/+4
| | | | | | | | | While here, pet portlint. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=455927
* Fix USE_GITHUB usage.Mathieu Arnold2017-11-062-5/+4
| | | | | | | Sponsored by: Absolight Notes: svn path=/head/; revision=453620
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofJoseph Mingrone2017-10-211-1/+13
| | | | | | | example files in first commit Notes: svn path=/head/; revision=452596
* New port, biology/iqtree: Efficient phylogenomic softwareJoseph Mingrone2017-10-213-0/+42
WWW: http://www.iqtree.org/ Notes: svn path=/head/; revision=452595
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