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SVNWeb
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Number of commits found: 42 |
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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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Wed, 7 Sep 2022
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[ 21:10 Stefan Eßer (se) ] b7f0544 (Only the first 10 of 27931 ports in this commit are shown above.  )
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above )
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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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Wed, 20 Jul 2022
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[ 14:20 Tobias C. Berner (tcberner) ] 37526bb (Only the first 10 of 82 ports in this commit are shown above. )
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above )
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Tue, 6 Apr 2021
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[ 14:31 Mathieu Arnold (mat) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Fri, 22 Nov 2019
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[ 15:32 jrm ]  
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.
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Wed, 6 Nov 2019
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[ 12:48 antoine ] (Only the first 10 of 268 ports in this commit are shown above. )
Mark a few ports BROKEN, unfetchable
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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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Thu, 26 Apr 2018
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[ 15:36 jrm ]
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
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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, 2 Nov 2016
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[ 22:45 mat ] (Only the first 10 of 110 ports in this commit are shown above. )
Cleanup no longer needed CHMOD usage after r424898.
PR: 213743
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
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Thu, 29 Sep 2016
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[ 21:12 jrm ]
Update PORTREVISION and dinstinfo due to upstream tarball change
Reviewed by: swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8083
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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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Fri, 23 Sep 2016
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[ 21:42 jrm ] (Only the first 10 of 16 ports in this commit are shown above. )
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
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Mon, 16 May 2016
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[ 16:10 amdmi3 ]
- Update to 4.9a
- While here, simplify WRKSRC and use options helpers
PR: 209535
Submitted by: jrm@ftfl.ca (maintainer)
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Fri, 10 Apr 2015
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[ 15:39 brd ]
Update biology/paml to 4.8a and unbreak.
PR: 199264
Submitted by: Joseph Mingrone <jrm@ftfl.ca>
Approved by: bdrewery (mentor)
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Sun, 5 Apr 2015
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[ 17:55 bapt ]
Mark as broken unfetchable ports
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Mon, 19 Jan 2015
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[ 12:11 wen ]
- Pass maintainership to submitter
PR: 196859
Submitted by: Joseph Mingrone<jrm@ftfl.ca>
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Tue, 29 Jul 2014
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[ 19:11 adamw ] (Only the first 10 of 436 ports in this commit are shown above. )
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...
Approved by: portmgr (not really, but touches unstaged ports)
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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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Fri, 14 Mar 2014
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[ 12:59 ehaupt ]
Support staging
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Thu, 13 Mar 2014
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[ 07:41 miwi ]
- Convert USE_GMAKE to USES
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Fri, 21 Feb 2014
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[ 13:35 ehaupt ]
Remove trailing whitespaces from category biology
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Mon, 10 Feb 2014
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[ 13:54 ehaupt ] (Only the first 10 of 581 ports in this commit are shown above. )
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)
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Fri, 3 Jan 2014
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[ 15:46 adamw ] (Only the first 10 of 14 ports in this commit are shown above. )
Convert biology to MDOCS and MEXAMPLES
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Fri, 20 Sep 2013
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[ 15:55 bapt ] (Only the first 10 of 94 ports in this commit are shown above. )
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
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Sat, 1 Jun 2013
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[ 14:22 wen ]
- Trim Makefile headers
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Wed, 8 Sep 2010
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[ 00:16 wen ]
- Update to 4.4c
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Tue, 20 Apr 2010
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[ 08:42 wen ]
- Update to 4.4a
- Update my mail address to FreeBSD
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Thu, 13 Aug 2009
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[ 17:00 miwi ]
- Update to 4.3
PR: 137625
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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Mon, 2 Mar 2009
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[ 19:02 miwi ]
- Update to 4.2b
PR: 132249
Submitted by: Wen Heping <wenheping@gmail.com>
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Thu, 25 Dec 2008
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[ 19:56 miwi ]
- Update to 4.2
PR: 129895
Submitted by: Wen Heping <wenheping@gmail.com> (maintainer)
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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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Sun, 11 Mar 2007
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[ 03:21 linimon ]
Reset dbader@eece.unm.edu due to maintainer-timeouts.
Hat: portmgr
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Sat, 20 May 2006
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[ 18:52 sem ]
- Update to 3.15
PR: ports/96941
Submitted by: Paul Schmehl <pauls@utdallas.edu>
Approved by: maintainer timeout
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Thu, 10 Nov 2005
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[ 01:21 mnag ]
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
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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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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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Mon, 2 Apr 2001
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[ 06:16 mharo ]
update to 3.03
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Mon, 10 Jul 2000
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[ 04:21 steve ]
Add paml version 3.01. A set of utilities for performing Phylogenetic Analysis
by Maximum Likelihood (PAML).
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Number of commits found: 42 |
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