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non port: biology/paml/Makefile
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Number of commits found: 38

Tue, 6 Apr 2021
[ 14:31 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
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.
Wed, 6 Nov 2019
[ 12:48 antoine search for other commits by this committer ] Original commit   Revision:516880 (Only the first 10 of 268 ports in this commit are shown above. View all ports for this commit)
Mark a few ports BROKEN, unfetchable
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)
Thu, 26 Apr 2018
[ 15:36 jrm search for other commits by this committer ] Original commit   Revision:468355
biology/paml: Set PORTVERSION directly

Setting DISTVERSION= 4.9h in the last commit caused PORTVERSION to be translated
to 4.9.h, which was not correct.

Pointy-hat: jrm
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)
Wed, 2 Nov 2016
[ 22:45 mat search for other commits by this committer ] Original commit   Revision:425174 (Only the first 10 of 110 ports in this commit are shown above. View all ports for this commit)
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
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
Fri, 23 Sep 2016
[ 21:42 jrm search for other commits by this committer ] Original commit   Revision:422697 (Only the first 10 of 16 ports in this commit are shown above. View all ports for this commit)
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
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)
Sun, 5 Apr 2015
[ 17:55 bapt search for other commits by this committer ] Original commit   Revision:383309
Mark as broken unfetchable ports
Mon, 19 Jan 2015
[ 12:11 wen search for other commits by this committer ] Original commit   Revision:377397
- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>
Tue, 29 Jul 2014
[ 19:11 adamw search for other commits by this committer ] Original commit   Revision:363374 (Only the first 10 of 436 ports in this commit are shown above. View all ports for this commit)
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
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@
Fri, 14 Mar 2014
[ 12:59 ehaupt search for other commits by this committer ] Original commit   Revision:348221
Support staging
Thu, 13 Mar 2014
[ 07:41 miwi search for other commits by this committer ] Original commit   Revision:348042
- Convert USE_GMAKE to USES
Fri, 21 Feb 2014
[ 13:35 ehaupt search for other commits by this committer ] Original commit   Revision:345397
Remove trailing whitespaces from category biology
Mon, 10 Feb 2014
[ 13:54 ehaupt search for other commits by this committer ] Original commit   Revision:343634 (Only the first 10 of 581 ports in this commit are shown above. View all ports for this commit)
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)
Fri, 3 Jan 2014
[ 15:46 adamw search for other commits by this committer ] Original commit   Revision:338550 (Only the first 10 of 14 ports in this commit are shown above. View all ports for this commit)
Convert biology to MDOCS and MEXAMPLES
Fri, 20 Sep 2013
[ 15:55 bapt search for other commits by this committer ] Original commit   Revision:327709 (Only the first 10 of 94 ports in this commit are shown above. View all ports for this commit)
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Sat, 1 Jun 2013
[ 14:22 wen search for other commits by this committer ] Original commit   Revision:319570
- Trim Makefile headers
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>
Sun, 11 Mar 2007
[ 03:21 linimon search for other commits by this committer ] Original commit 
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr
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>
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    
Mon, 10 Jul 2000
[ 04:21 steve search for other commits by this committer ] Original commit 
Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    

Number of commits found: 38