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non port: biology/paml/pkg-plist
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Number of commits found: 12

Tue, 26 Feb 2019
[ 15:12 jrm ] Original commit   Revision:493971
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 View all of this commit message)
Wed, 25 Apr 2018
[ 20:36 jrm ] Original commit   Revision:468297
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 View all of this commit message)
Wed, 28 Sep 2016
[ 02:30 jrm ] Original commit   Revision:422846
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
Mon, 20 Oct 2014
[ 07:10 bapt ] Original commit   Revision:371237
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. View all ports for this commit)
Cleanup plist
Sat, 5 Apr 2014
[ 10:56 wen ] Original commit   Revision:350214
350214 biology/paml/Makefile
350214 biology/paml/distinfo
350214 biology/paml/pkg-plist
- Update to 4.8
- Reset maintainer to ports@
Tue, 21 Jan 2014
[ 23:18 bapt ] Original commit   Revision:340671
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. View all ports for this commit)
Fix properties on pkg-plist
Tue, 30 Sep 2008
[ 08:54 miwi ] Original commit 
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>
Sat, 6 Nov 2004
[ 03:55 kevlo ] Original commit 
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>
Wed, 22 Oct 2003
[ 09:29 osa ] Original commit 
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. View all ports for this commit)
Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:   Oleg Karachevtsev <ok@etrust.ru>
A part of PR:   57992
Fri, 14 Feb 2003
[ 23:21 naddy ] Original commit 
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.
Wed, 29 Aug 2001
[ 13:00 wjv ] Original commit 
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    
Tue, 3 Jul 2001
[ 09:17 wjv ] Original commit 
unknown biology/paml/Makefile
unknown biology/paml/distinfo
unknown biology/paml/pkg-plist
Update to version 3.04    

Number of commits found: 12

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