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non port: biology/paml/Makefile
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Number of commits found: 37

Fri, 22 Nov 2019
[ 15:32 jrm ] Original commit   Revision:518150
518150 biology/paml/Makefile
518150 biology/paml/distinfo
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 ] Original commit   Revision:516880
516880 archivers/xarchiver/Makefile
516880 astro/garmindev/Makefile
516880 astro/opencpn/Makefile
516880 astro/qmapshack/Makefile
516880 audio/carla/Makefile
516880 audio/decibel-audio-player/Makefile
516880 audio/festvox-czech/Makefile
516880 audio/gkrellmvolume2/Makefile
516880 audio/gnaural/Makefile
516880 audio/mixmos/Makefile

(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 ] 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)
Thu, 26 Apr 2018
[ 15:36 jrm ] Original commit   Revision:468355
468355 biology/paml/Makefile
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 ] 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, 2 Nov 2016
[ 22:45 mat ] Original commit   Revision:425174
425174 audio/festdoc/Makefile
425174 audio/festlex-oald/Makefile
425174 audio/festlex-ogi/Makefile
425174 audio/festvox-don/Makefile
425174 audio/festvox-el11/Makefile
425174 audio/festvox-kal8/Makefile
425174 audio/festvox-ked16/Makefile
425174 audio/festvox-ked8/Makefile
425174 audio/festvox-rab16/Makefile
425174 audio/festvox-rab8/Makefile

(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 ] Original commit   Revision:422950
422950 biology/paml/Makefile
422950 biology/paml/distinfo
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 ] 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
Fri, 23 Sep 2016
[ 21:42 jrm ] Original commit   Revision:422697
422697 biology/diamond/Makefile
422697 biology/paml/Makefile
422697 biology/py-biom-format/Makefile
422697 databases/py-psycopg2cffi/Makefile
422697 deskutils/clipit/Makefile
422697 devel/py-pyqi/Makefile
422697 devel/py-simpleeval/Makefile
422697 mail/getmail/Makefile
422697 math/R/Makefile
422697 print/foomatic-filters/Makefile

(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 ] Original commit   Revision:415338
415338 biology/paml/Makefile
415338 biology/paml/distinfo
- 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 ] Original commit   Revision:383736
383736 biology/paml/Makefile
383736 biology/paml/distinfo
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 ] Original commit   Revision:383309
383309 biology/consed/Makefile
383309 biology/migrate/Makefile
383309 biology/ncbi-blast+/Makefile
383309 biology/njplot/Makefile
383309 biology/ortep3/Makefile
383309 biology/p5-Bio-ASN1-EntrezGene/Makefile
383309 biology/paml/Makefile
383309 biology/platon/Makefile
383309 biology/povchem/Makefile
383309 biology/seaview/Makefile
Mark as broken unfetchable ports
Mon, 19 Jan 2015
[ 12:11 wen ] Original commit   Revision:377397
377397 biology/paml/Makefile
- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>
Tue, 29 Jul 2014
[ 19:11 adamw ] Original commit   Revision:363374
363374 archivers/ha/Makefile
363374 archivers/unalz/Makefile
363374 astro/gpsman/Makefile
363374 audio/amrcoder/Makefile
363374 audio/chordpack/Makefile
363374 audio/cmt/Makefile
363374 audio/enscribe/Makefile
363374 audio/funktrackergold/Makefile
363374 audio/ladspa/Makefile
363374 audio/libconvolve/Makefile

(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 ] 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@
Fri, 14 Mar 2014
[ 12:59 ehaupt ] Original commit   Revision:348221
348221 biology/paml/Makefile
Support staging
Thu, 13 Mar 2014
[ 07:41 miwi ] Original commit   Revision:348042
348042 biology/garlic/Makefile
348042 biology/mafft/Makefile
348042 biology/mopac/Makefile
348042 biology/mummer/Makefile
348042 biology/muscle/Makefile
348042 biology/paml/Makefile
348042 biology/phylip/Makefile
348042 biology/pymol/Makefile
348042 biology/velvet/Makefile
348042 biology/xmolwt/Makefile
- Convert USE_GMAKE to USES
Fri, 21 Feb 2014
[ 13:35 ehaupt ] Original commit   Revision:345397
345397 biology/biojava/Makefile
345397 biology/consed/Makefile
345397 biology/finchtv/Makefile
345397 biology/genpak/Makefile
345397 biology/mummer/Makefile
345397 biology/njplot/Makefile
345397 biology/p5-bioperl-run/Makefile
345397 biology/p5-bioperl/Makefile
345397 biology/paml/Makefile
345397 biology/velvet/Makefile
Remove trailing whitespaces from category biology
Mon, 10 Feb 2014
[ 13:54 ehaupt ] Original commit   Revision:343634
343634 archivers/aolserver-nszlib/Makefile
343634 archivers/dact/Makefile
343634 archivers/freeze/Makefile
343634 archivers/javatar/Makefile
343634 archivers/lha-ac/Makefile
343634 archivers/libpar2/Makefile
343634 archivers/lzo2/Makefile
343634 archivers/makeself/Makefile
343634 archivers/py-lzma/Makefile
343634 archivers/ruby-libarchive/Makefile

(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 ] Original commit   Revision:338550
338550 biology/biojava/Makefile
338550 biology/blast/Makefile
338550 biology/consed/Makefile
338550 biology/finchtv/Makefile
338550 biology/mafft/Makefile
338550 biology/mummer/Makefile
338550 biology/njplot/Makefile
338550 biology/p5-bioperl-run/Makefile
338550 biology/p5-bioperl/Makefile
338550 biology/paml/Makefile

(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 ] Original commit   Revision:327709
327709 biology/ariadne/Makefile
327709 biology/artemis/Makefile
327709 biology/avida/Makefile
327709 biology/babel/Makefile
327709 biology/biococoa/Makefile
327709 biology/biojava/Makefile
327709 biology/blast/Makefile
327709 biology/blat/Makefile
327709 biology/boinc-simap/Makefile
327709 biology/chemeq/Makefile

(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 ] Original commit   Revision:319570
319570 astro/p5-GPS-OID/Makefile
319570 astro/p5-Starlink-AST/Makefile
319570 astro/py-aipy/Makefile
319570 astro/pyephem/Makefile
319570 audio/py-pyliblo/Makefile
319570 biology/p5-Bio-SCF/Makefile
319570 biology/paml/Makefile
319570 biology/pyfasta/Makefile
- Trim Makefile headers
Wed, 8 Sep 2010
[ 00:16 wen ] Original commit 
1.15 biology/paml/Makefile
1.15 biology/paml/distinfo
- Update to 4.4c
Tue, 20 Apr 2010
[ 08:42 wen ] Original commit 
1.14 biology/paml/Makefile
1.14 biology/paml/distinfo
- Update to 4.4a
- Update my mail address to FreeBSD
Thu, 13 Aug 2009
[ 17:00 miwi ] Original commit 
1.13 biology/paml/Makefile
1.13 biology/paml/distinfo
- Update to 4.3

PR:             137625
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
Mon, 2 Mar 2009
[ 19:02 miwi ] Original commit 
1.12 biology/paml/Makefile
1.12 biology/paml/distinfo
- Update to 4.2b

PR:             132249
Submitted by:   Wen Heping <wenheping@gmail.com>
Thu, 25 Dec 2008
[ 19:56 miwi ] Original commit 
1.11 biology/paml/Makefile
1.11 biology/paml/distinfo
- Update to 4.2

PR:             129895
Submitted by:   Wen Heping <wenheping@gmail.com> (maintainer)
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>
Sun, 11 Mar 2007
[ 03:21 linimon ] Original commit 
1.9 biology/paml/Makefile
1.11 print/bibview/Makefile
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr
Sat, 20 May 2006
[ 18:52 sem ] Original commit 
1.8 biology/paml/Makefile
1.9 biology/paml/distinfo
- 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 ] Original commit 
1.7 biology/paml/Makefile
1.8 biology/paml/distinfo
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 ] 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>
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    
Mon, 2 Apr 2001
[ 06:16 mharo ] Original commit 
unknown biology/paml/Makefile
unknown biology/paml/distinfo
unknown biology/paml/files/patch-aa
unknown biology/paml/files/patch-ab
update to 3.03    
Mon, 10 Jul 2000
[ 04:21 steve ] Original commit 
unknown biology/paml/Makefile
unknown biology/paml/files/md5
unknown biology/paml/patches/patch-aa
unknown biology/paml/patches/patch-ab
unknown biology/paml/pkg/COMMENT
unknown biology/paml/pkg/DESCR
unknown biology/paml/pkg/PLIST
Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    

Number of commits found: 37

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