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SVNWeb
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Number of commits found XX: 12 |
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Tue, 26 Feb 2019
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[ 15:12 jrm ]  
493971 biology/paml/Makefile
493971 biology/paml/distinfo
493971 biology/paml/pkg-plist
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 ]
468297 biology/paml/Makefile
468297 biology/paml/distinfo
468297 biology/paml/pkg-plist
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 ]
422846 biology/paml/Makefile
422846 biology/paml/distinfo
422846 biology/paml/pkg-descr
422846 biology/paml/pkg-plist
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 ]
371237 biology/artemis/pkg-plist
371237 biology/biococoa/pkg-plist
371237 biology/crux/pkg-plist
371237 biology/emboss/pkg-plist
371237 biology/fasta3/pkg-plist
371237 biology/fastdnaml/pkg-plist
371237 biology/garlic/pkg-plist
371237 biology/hmmer/pkg-plist
371237 biology/iolib/pkg-plist
371237 biology/jalview/pkg-plist
(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 ]
350214 biology/paml/Makefile
350214 biology/paml/distinfo
350214 biology/paml/pkg-plist
- Update to 4.8
- Reset maintainer to ports@
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Tue, 21 Jan 2014
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[ 23:18 bapt ]
340671 benchmarks/flowgrind/pkg-plist
340671 biology/crux/pkg-plist
340671 biology/jalview/pkg-plist
340671 biology/libgenome/pkg-plist
340671 biology/paml/pkg-plist
340671 cad/alliance/pkg-plist
340671 cad/fidocadj/pkg-plist
340671 cad/pcb/pkg-plist
340671 chinese/FreeWnn-lib/pkg-plist
340671 chinese/FreeWnn-server/pkg-plist
(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 ]
1.10 biology/paml/Makefile
1.10 biology/paml/distinfo
1.7 biology/paml/pkg-plist
- 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 ]
1.6 biology/paml/Makefile
1.7 biology/paml/distinfo
1.6 biology/paml/pkg-plist
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 ]
1.4 biology/babel/pkg-plist
1.5 biology/biojava/pkg-plist
1.2 biology/coalesce/pkg-plist
1.2 biology/crimap/pkg-plist
1.2 biology/dna-qc/pkg-plist
1.2 biology/fasta/pkg-plist
1.2 biology/fasta3/pkg-plist
1.3 biology/fastdnaml/pkg-plist
1.2 biology/fluctuate/pkg-plist
1.2 biology/garlic/pkg-plist
(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 ]
1.5 biology/paml/Makefile
1.5 biology/paml/distinfo
1.2 biology/paml/files/patch-src::Makefile
1.2 biology/paml/pkg-comment
1.4 biology/paml/pkg-plist
* 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 ]
unknown biology/paml/Makefile
unknown biology/paml/distinfo
unknown biology/paml/files/patch-src::Makefile
unknown biology/paml/pkg-plist
- Update to version 3.1
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Tue, 3 Jul 2001
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[ 09:17 wjv ]
unknown biology/paml/Makefile
unknown biology/paml/distinfo
unknown biology/paml/pkg-plist
Update to version 3.04
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Number of commits found XX: 12 |
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