| non port: biology/paml/pkg-plist |
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SVNWeb
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Number of commits found: 14 |
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Sun, 13 Nov 2022
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[ 02:35 Joseph Mingrone (jrm)  ]    a875dde
biology/paml: Update to 4.10.6
https://github.com/abacus-gene/paml/releases/tag/v4.10.6
Sponsored by: The FreeBSD Foundation
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Fri, 26 Aug 2022
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[ 04:22 Joseph Mingrone (jrm) ] 5aec6e4
biology/paml: Update to 4.10.5
https://github.com/abacus-gene/paml/releases/tag/v4.10.0
https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8
https://github.com/abacus-gene/paml/releases/tag/v4.10.5
Sponsored by: The FreeBSD Foundation
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Tue, 26 Feb 2019
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[ 15:12 jrm ]  
biology/paml: Update to version 4.9i
Upstream changes as described by the author:
- mcmctree: I have added an option (duplication = 1) for dating a tree with
both speciations and gene duplications, so that some nodes on the tree
share divergence times. Nodes sharing ages are identified using labels in
the tree file: #1, #2, .... I have yet to update the document about
specification of the model.
- mcmctree: The TipDate option was written for one locus or partition and
never worked for more than two loci/partitions. I have edited the code so
that it works for multiple partitions, some of which may be molecular and
the others morphological.
(Only the first 15 lines of the commit message are shown above  )
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Wed, 25 Apr 2018
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[ 20:36 jrm ]
biology/paml: Update to version 4.9h
Port Changes:
- Add EXAMPLES option and install most files under EXAMPLESDIR
- Add USES=dos2unix to fix DOS line endings
Upstream Changes:
Version 4.9h, March 2018
(*) mcmctree: gamma-Dirichlet versus conditional i.i.d. priors for
rates for loci. Since 4.9d, the program and the documentation are
inconsistent about the two priors, and which value (0 or 1) means
which prior. I have now checked the program and the documentation to
make sure that they are consistent:
(Only the first 15 lines of the commit message are shown above )
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Wed, 28 Sep 2016
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[ 02:30 jrm ]
biology/paml: update to version 4.9c and various improvements
- Update to version 4.9c
- Set LICENSE=GPLv3
- Use the variable PORTDOCS to automate the generation of the DOCS plist (as
suggested by mat@).
- Install dat/ examples/ and Technical/ directories as well as files in the root
directory of the distribution tarball.
- Fix broken permissions.
- Delete Windows executables.
- Build and install useful binaries not built by upstream's Makefile.
- Update pkg-descr.
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8040
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Mon, 20 Oct 2014
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[ 07:10 bapt ] (Only the first 10 of 36 ports in this commit are shown above. )
Cleanup plist
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Sat, 5 Apr 2014
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[ 10:56 wen ]
- Update to 4.8
- Reset maintainer to ports@
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Tue, 21 Jan 2014
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[ 23:18 bapt ] (Only the first 10 of 73 ports in this commit are shown above. )
Fix properties on pkg-plist
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Tue, 30 Sep 2008
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[ 08:54 miwi ]
- Update to 4.1
- Pass maintainership to submitter
PR: 127683
Submitted by: Wen heping <wenheping@gmail.com>
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Sat, 6 Nov 2004
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[ 03:55 kevlo ]
Update to 3.14
PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
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Wed, 22 Oct 2003
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[ 09:29 osa ] (Only the first 10 of 31 ports in this commit are shown above. )
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.
Submitted by: Oleg Karachevtsev <ok@etrust.ru>
A part of PR: 57992
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Fri, 14 Feb 2003
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[ 23:21 naddy ]
* Update to 3.13.
PR: 48255
Submitted by: David A. Bader <dbader@eece.unm.edu>
* Also honor CC/CFLAGS.
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Wed, 29 Aug 2001
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[ 13:00 wjv ]
- Update to version 3.1
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Tue, 3 Jul 2001
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[ 09:17 wjv ]
Update to version 3.04
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Number of commits found: 14 |
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