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non port: biology/paml/Makefile

Number of commits found: 43

Saturday, 8 Jul 2023
03:46 Joseph Mingrone (jrm) search for other commits by this committer
biology/paml: Update to 4.10.7

Remove -Wmemset-elt-size from CFLAGS.  The warning is only applicable to
gcc and is already enabled with -Wall.

Changes:	https://github.com/abacus-gene/paml/releases/tag/4.10.7
Sponsored by:	The FreeBSD Foundation
commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3 commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3 commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3 commit hash: 5fc301443c77a4952c42153f12a7520f913f60a3 5fc3014
Sunday, 13 Nov 2022
02:35 Joseph Mingrone (jrm) search for other commits by this committer
biology/paml: Update to 4.10.6

https://github.com/abacus-gene/paml/releases/tag/v4.10.6

Sponsored by:	The FreeBSD Foundation
commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3 commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3 commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3 commit hash: a875dde83e05c32752b096808e6b3ca50088a8a3 a875dde
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Friday, 26 Aug 2022
04:22 Joseph Mingrone (jrm) search for other commits by this committer
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
commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 commit hash: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 5aec6e4
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Friday, 22 Nov 2019
15:32 jrm search for other commits by this committer
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.
Original commitRevision:518150 
Wednesday, 6 Nov 2019
12:48 antoine search for other commits by this committer
Mark a few ports BROKEN, unfetchable
Original commitRevision:516880 
Tuesday, 26 Feb 2019
15:12 jrm search for other commits by this committer
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.

- codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7
(FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This
option uses the observed codon or amino acid frequencies for the
mutation-selection models of codon usage. Instead the program estimates the
frequencies using maximum likeihood, which is what the option estFreq = 1
does. Look at the README file in the examples/mtCDNAape/ folder.

- codeml clade model D: The bounds for the w (dN/dS) ratios in the first
site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in
versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model
D in 4.9b. The motivation for the bounds is that site class 0 represents
strong purifying selection with a small w0, while site class 1 should
include sites under weak purifying selection with a larger w1. However the
bounds are arbitrary. In some datasets, the MLEs are found to be at the
bounds, making the interpretation awkward. I have changed the bounds to the
following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user
should swap the estimates of w0 and w2 if w0 > w1.
Original commitRevision:493971 
Thursday, 26 Apr 2018
15:36 jrm search for other commits by this committer
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
Original commitRevision:468355 
Wednesday, 25 Apr 2018
20:36 jrm search for other commits by this committer
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:

prior = 0: gamma-Dirichlet (dos Reis 2014).  This is the default.
prior = 1: conditional i.i.d. prior (Zhu et al. 2015).

I believe these two are similar especially if the number of loci
(partitions) is large, but no serious comparisons between the two
priors have been published.

Thanks to Adnan Moussalli for pointing out the errors.

(*) codeml.  It was discovered that the mechanistic amino acid
substitution model implemented in Yang et al. (1998; see table 3),
specified by seqtype = 2 model = 6, has been broken for a long time,
since version 3.0 (2000) at least.  Version 2.0 (1999) seems to be
correct.  This means that the model become broken soon since it was
published.  I have now fixed this.

This model of amino acid substitution starts from a Markov chain for
codons and then aggregate the states and merge the synonymous codons
into one state (the coded amino acid).  This is an approximate
formulation since the process after state aggregation is not Markovian
anymore.

I have now added another codon-based amino acid substitution model
that treats amino acids as ambiguities codons.  The model is specified
by seqtype = 2 model = 5.  This is an exact formulation.

(*) codeml.  The number of categories in the BEB calculation under M2
and M8 is unintentionally set to 4 rather than 10.  I have changed
this back to 10.  The details of this calculation are in Yang et
al. 2005 MBE.

Version 4.9g, December 2017

(*) codeml.  A bug caused the BEB calculation under the site model M8
(NSsites = 8) to be incorrect, with the program printing out warming
messages like "strange: f[ 5] = -0.0587063 very small."  This bug was
introduced in version 4.9b and affects versions 4.9b-f.  A different
bug was introduced in version 4.9f that causes the log likelihood
function under the site model M8 (NSsites = 8) to be calculated
incorrectly.  These are now fixed.

Version 4.9f, October 2017

(*) baseml, nonhomogeneous models (nhomo & fix_kappa).  Those models
allow different branches on the tree to have different Q matrices.
Roughly nhomo controls the base frequency parameters while gix_kappa
controls kappa or the exchangeability parameters (a b c d e in
GTR/REV, for example).  I added the option (nhomo = 5, fix_kappa = 2),
which lets the user to define branch types, so that branches of the
same type have the same exchangeability parameters (a b c d e for GTR)
and base composition parameters, while branches of different types
have different parameters.  Branch types are labeled (using # and $),
0, 1, 2, ....  The labels should be consecutive positive integers.
The old options nhomo = 3 or 4 work for some models like GTR, but not
some other models which also have base composition parameters.  In
this update, I think those options should work with all those models.
I have also edited the documentation (look for option variable nhomo
for baseml).

(*) baseml & codeml.  i added an option fix_blength = 3
(proportional), which means that branch lengths will be proporational
to those given in the tree file, and the proportionality factor is
estimated by ML.

(*) codeml.  The program does not count the parameters correctly for
model M0 when fix_kappa = 1.  The bug was introduced in version 4.9c
and affects versions 4.9c-e.  This is now fixed.

(*) codeml (seqtype = 2 model = 2).  If you are analyzing multiple
protein data sets (ndata > 1) under the empirical models such as wag,
jtt, dayhoff.  The results for the first data set are correct, but all
later data sets are analyzed incorrectly under the corresponding +F
models, that is, wag+F, jtt+F, dayhoff+F, etc.  A bug in the program
means that for the second and later data sets, the equilibrium amino
acid frequencies are taken from the real data and not correctly set to
those specified by the empirical models.  I note that this bug was
recorded in the update Version 3.14b, April 2005, but it was somehow
not fixed, even in that version.  This is now fixed.  Thanks to Nick
Goldman for reporting this again.

(*) evolver (options 5, 6, 7 for simulating nucleotide, codon and
amino acid alignments).  If you choose the option of printing out the
site pattern counts instead of the sequences (specified at the
beginning of the control file such as MCbase.dat), and if you are
simulating two or more alignments, the program crashes after finishing
the first alignment.  This is now fixed.

(*) mcmctree.  The program crashes if you have a mixture of
morphological loci and molecular loci, if not all the morphological
loci are before the molecular loci.  I have now fixed this.
I think this was never described anyway.

Version 4.9e, March 2017

(*) Edited the readme files to change the license to GPL.

(*) mcmctree.  A bug was introduced in version 4.9b which causes the
program to read the fossil calibration information in the tree file
incorrectly, if joint (minimum and maximum) bounds are specified using
the symbol '<' and '>'.  If you use the notation "B()", "L()", and
'U()', the information is read correctly.  This bug was introduced in
version 4.9b and exists in 4.9c and 4.9d.  Versions 4.9a and earlier
were correct.

Version 4.9d, February 2017

(*) mcmctree.  Changed the default prior for rates for loci to
gamma-Dirichlet (dos Reis 2014), and updated the documentation as
well.  It was set to the conditional i.i.d. prior (Zhu et al. 2015).

(*) mcmctree.  Added Bayes factor calculation.  A program called
BFdriver is included in the release, as well as a pdf document in the
folder examples/DatingSoftBound/BFdriverDOC.pdf.  We suggest that you
use the exact likelihood calculation when you use this option, since the
normal approximation is unreliable when the power posterior is close to
the prior (when beta is small).
Original commitRevision:468297 
Wednesday, 2 Nov 2016
22:45 mat search for other commits by this committer
Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Original commitRevision:425174 
Thursday, 29 Sep 2016
21:12 jrm search for other commits by this committer
Update PORTREVISION and dinstinfo due to upstream tarball change

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8083
Original commitRevision:422950 
Wednesday, 28 Sep 2016
02:30 jrm search for other commits by this committer
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
Original commitRevision:422846 
Friday, 23 Sep 2016
21:42 jrm search for other commits by this committer
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
Original commitRevision:422697 
Monday, 16 May 2016
16:10 amdmi3 search for other commits by this committer
- Update to 4.9a
- While here, simplify WRKSRC and use options helpers

PR:		209535
Submitted by:	jrm@ftfl.ca (maintainer)
Original commitRevision:415338 
Friday, 10 Apr 2015
15:39 brd search for other commits by this committer
Update biology/paml to 4.8a and unbreak.

PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)
Original commitRevision:383736 
Sunday, 5 Apr 2015
17:55 bapt search for other commits by this committer
Mark as broken unfetchable ports
Original commitRevision:383309 
Monday, 19 Jan 2015
12:11 wen search for other commits by this committer
- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>
Original commitRevision:377397 
Tuesday, 29 Jul 2014
19:11 adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
Original commitRevision:363374 
Saturday, 5 Apr 2014
10:56 wen search for other commits by this committer
- Update to 4.8
- Reset maintainer to ports@
Original commitRevision:350214 
Friday, 14 Mar 2014
12:59 ehaupt search for other commits by this committer
Support staging
Original commitRevision:348221 
Thursday, 13 Mar 2014
07:41 miwi search for other commits by this committer
- Convert USE_GMAKE to USES
Original commitRevision:348042 
Friday, 21 Feb 2014
13:35 ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
Original commitRevision:345397 
Monday, 10 Feb 2014
13:54 ehaupt search for other commits by this committer
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)
Original commitRevision:343634 
Friday, 3 Jan 2014
15:46 adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
Original commitRevision:338550 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Saturday, 1 Jun 2013
14:22 wen search for other commits by this committer
- Trim Makefile headers
Original commitRevision:319570 
Wednesday, 8 Sep 2010
00:16 wen search for other commits by this committer
- Update to 4.4c
Original commit
Tuesday, 20 Apr 2010
08:42 wen search for other commits by this committer
- Update to 4.4a
- Update my mail address to FreeBSD
Original commit
Thursday, 13 Aug 2009
17:00 miwi search for other commits by this committer
- Update to 4.3

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

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

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

PR:             127683
Submitted by:   Wen heping <wenheping@gmail.com>
Original commit
Sunday, 11 Mar 2007
03:21 linimon search for other commits by this committer
Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:            portmgr
Original commit
Saturday, 20 May 2006
18:52 sem search for other commits by this committer
- Update to 3.15

PR:             ports/96941
Submitted by:   Paul Schmehl <pauls@utdallas.edu>
Approved by:    maintainer timeout
Original commit
Thursday, 10 Nov 2005
01:21 mnag search for other commits by this committer
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
Original commit
Saturday, 6 Nov 2004
03:55 kevlo search for other commits by this committer
Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>
Original commit
Friday, 14 Feb 2003
23:21 naddy search for other commits by this committer
* Update to 3.13.

PR:             48255
Submitted by:   David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
Original commit
Wednesday, 29 Aug 2001
13:00 wjv search for other commits by this committer
- Update to version 3.1    
Original commit
Tuesday, 3 Jul 2001
09:17 wjv search for other commits by this committer
Update to version 3.04    
Original commit
Monday, 2 Apr 2001
06:16 mharo search for other commits by this committer
update to 3.03    
Original commit
Monday, 10 Jul 2000
04:21 steve search for other commits by this committer
Add paml version 3.01.   A set of utilities for performing Phylogenetic Analysis
by Maximum   Likelihood (PAML).    
Original commit

Number of commits found: 43