notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
non port: biology/paml/distinfo
SVNWeb

Number of commits found: 23

Fri, 22 Nov 2019
[ 15:32 jrm search for other commits by this committer ] Original commit   Revision:518150
biology/paml: Update to version 4.9j

- Remove BROKEN=. Version 4.9i became unfetchable when the author pulled
  the tarball to prevent users from downloading a version with new, serious
  bugs.

Upstream changes described by the author:

  - mcmctree: Initial values have ages that are too old, exceeding max
    bounds.  In theory bounds in mcmctree are always soft so that the node
    ages will move to the area of posterior mode when burnin is long enough.
    In practice the poor starting values are problematic and requires long
    burn-in.  I have rewritten the code for generating initial values to
    respect the min and max bounds specified in the fossil calibrations.

  - codeml: A bug introduced in 4.9i caused the clade labels ($) to be
    ignored.  This affects the branch, branch-site and clade models.  If
    your tree has branch labels (#) only and no clade models, everything
    will be fine.  If you have used the clade label ($) in the tree with or
    without the branch label (#), either the program will abort or the
    results will be incorrect.  The clade label ($) is supposed to label
    all branches in the clade as well as the branch itself, but all clade
    labels in the tree are ignored in 4.9i.  Earlier versions are correct.
Tue, 26 Feb 2019
[ 15:12 jrm search for other commits by this committer ] Original commit   Revision:493971
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 search for other commits by this committer ] Original commit   Revision:468297
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)
Thu, 29 Sep 2016
[ 21:12 jrm search for other commits by this committer ] Original commit   Revision:422950
Update PORTREVISION and dinstinfo due to upstream tarball change

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8083
Wed, 28 Sep 2016
[ 02:30 jrm search for other commits by this committer ] Original commit   Revision:422846
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, 16 May 2016
[ 16:10 amdmi3 search for other commits by this committer ] Original commit   Revision:415338
- Update to 4.9a
- While here, simplify WRKSRC and use options helpers

PR:		209535
Submitted by:	jrm@ftfl.ca (maintainer)
Fri, 10 Apr 2015
[ 15:39 brd search for other commits by this committer ] Original commit   Revision:383736
Update biology/paml to 4.8a and unbreak.

PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)
Sat, 5 Apr 2014
[ 10:56 wen search for other commits by this committer ] Original commit   Revision:350214
- Update to 4.8
- Reset maintainer to ports@
Sat, 19 Mar 2011
[ 12:38 miwi search for other commits by this committer ] Original commit  (Only the first 10 of 4601 ports in this commit are shown above. View all ports for this commit)
- Get Rid MD5 support
Wed, 8 Sep 2010
[ 00:16 wen search for other commits by this committer ] Original commit 
- Update to 4.4c
Tue, 20 Apr 2010
[ 08:42 wen search for other commits by this committer ] Original commit 
- Update to 4.4a
- Update my mail address to FreeBSD
Thu, 13 Aug 2009
[ 17:00 miwi search for other commits by this committer ] Original commit 
- Update to 4.3

PR:             137625
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
Mon, 2 Mar 2009
[ 19:02 miwi search for other commits by this committer ] Original commit 
- Update to 4.2b

PR:             132249
Submitted by:   Wen Heping <wenheping@gmail.com>
Thu, 25 Dec 2008
[ 19:56 miwi search for other commits by this committer ] Original commit 
- Update to 4.2

PR:             129895
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
Tue, 30 Sep 2008
[ 08:54 miwi search for other commits by this committer ] Original commit 
- Update to 4.1
- Pass maintainership to submitter

PR:             127683
Submitted by:   Wen heping <wenheping@gmail.com>
Sat, 20 May 2006
[ 18:52 sem search for other commits by this committer ] Original commit 
- Update to 3.15

PR:             ports/96941
Submitted by:   Paul Schmehl <pauls@utdallas.edu>
Approved by:    maintainer timeout
Thu, 10 Nov 2005
[ 01:21 mnag search for other commits by this committer ] Original commit 
Update to 3.14b
Update MASTER_SITES
Add SHA256
Remove extra TABS

PR:             88007
Submitted by:   Jean Milanez Melo <jmelo@freebsdbrasil.com.br>
Approved by:    maintainer timeout, 14 days
Sat, 6 Nov 2004
[ 03:55 kevlo search for other commits by this committer ] Original commit 
Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
Wed, 31 Mar 2004
[ 03:12 trevor search for other commits by this committer ] Original commit  (Only the first 10 of 3024 ports in this commit are shown above. View all ports for this commit)
SIZEify (maintainer timeout)
Fri, 14 Feb 2003
[ 23:21 naddy search for other commits by this committer ] Original commit 
* 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 search for other commits by this committer ] Original commit 
- Update to version 3.1    
Tue, 3 Jul 2001
[ 09:17 wjv search for other commits by this committer ] Original commit 
Update to version 3.04    
Mon, 2 Apr 2001
[ 06:16 mharo search for other commits by this committer ] Original commit 
update to 3.03    

Number of commits found: 23