biology/paml4.10.10

biology/paml: Update to 4.10.10

Release notes:	https://github.com/abacus-gene/paml/releases/tag/v4.10.10
Sponsored by:	The FreeBSD Foundation

biology/paml: Update to 4.10.9

Also patch out upstream's newly introduced hardcoded values for CC and
CFLAGS.

Release notes:	https://github.com/abacus-gene/paml/releases/tag/v4.10.8
		https://github.com/abacus-gene/paml/releases/tag/v4.10.9
Sponsored by:	The FreeBSD Foundation

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

biology/paml: Update to 4.10.6

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

Sponsored by:	The FreeBSD Foundation

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

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)

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

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

Remove # $FreeBSD$ from Makefiles.

biology/paml: fix the build with LLVM 11

LLVM 11 switched from -fcommon to -fno-common by default. This revealed a
slight misposition of names in paml.h, which caused one symbol per enum
that's not used anywhere.

The fix just moves the names back so that the enums are named that, rather
than creating new unused symbols.

Reviewed by:	zeising
Approved by:	jrm (maintainer)
MFH:		2020Q3

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.

Mark a few ports BROKEN, unfetchable

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.

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

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).

Cleanup no longer needed CHMOD usage after r424898.

PR:		213743
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight

Update PORTREVISION and dinstinfo due to upstream tarball change

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8083

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

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

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

- Update to 4.9a - While here, simplify WRKSRC and use options helpers

PR:		209535
Submitted by:	jrm@ftfl.ca (maintainer)

Update biology/paml to 4.8a and unbreak.

PR:		199264
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	bdrewery (mentor)

Mark as broken unfetchable ports

- Pass maintainership to submitter

PR:		196859
Submitted by:	Joseph Mingrone<jrm@ftfl.ca>

Cleanup plist

Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)

- Update to 4.8 - Reset maintainer to ports@

Support staging

- Convert USE_GMAKE to USES

Remove trailing whitespaces from category biology

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)

Fix properties on pkg-plist

Convert biology to MDOCS and MEXAMPLES

Add NO_STAGE all over the place in preparation for the staging support (cat: biology)

- Trim Makefile headers

- Get Rid MD5 support

- Update to 4.4c

- Update to 4.4a - Update my mail address to FreeBSD

- Update to 4.3

PR:		137625
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)

- Update to 4.2b

PR:		132249
Submitted by:	Wen Heping <wenheping@gmail.com>

- Update to 4.2

PR:		129895
Submitted by:	Wen Heping <wenheping@gmail.com> (maintainer)

- Update to 4.1 - Pass maintainership to submitter

PR:		127683
Submitted by:	Wen heping <wenheping@gmail.com>

Reset dbader@eece.unm.edu due to maintainer-timeouts.

Hat:		portmgr

- Update to 3.15

PR:		ports/96941
Submitted by:	Paul Schmehl <pauls@utdallas.edu>
Approved by:	maintainer timeout

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

Update to 3.14

PR: ports/72422
Submitted by: Choe, Cheng-Dae <whitekid@gmail.com>

SIZEify (maintainer timeout)

Cosmetic fix: use %%DOCSDIR%% macro. No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
A part of PR:	57992

* Update to 3.13.

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

* Also honor CC/CFLAGS.

- Update to version 3.1

PR:		30176
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)