svn commit: r518150 - head/biology/paml

[Joseph Mingrone]

Author: jrm
Date: Fri Nov 22 15:32:40 2019
New Revision: 518150
URL: https://svnweb.freebsd.org/changeset/ports/518150

Log:
  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.

Modified:
  head/biology/paml/Makefile   (contents, props changed)
  head/biology/paml/distinfo   (contents, props changed)

Modified: head/biology/paml/Makefile
==============================================================================
--- head/biology/paml/Makefile	Fri Nov 22 15:28:20 2019	(r518149)
+++ head/biology/paml/Makefile	Fri Nov 22 15:32:40 2019	(r518150)
@@ -2,15 +2,13 @@
 # $FreeBSD$
 
 PORTNAME=	paml
-PORTVERSION=	4.9i
+PORTVERSION=	4.9j
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
 DISTNAME=	${PORTNAME}${DISTVERSION}
 
 MAINTAINER=	jrm at FreeBSD.org
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
-
-BROKEN=		unfetchable
 
 LICENSE=	GPLv3
 

Modified: head/biology/paml/distinfo
==============================================================================
--- head/biology/paml/distinfo	Fri Nov 22 15:28:20 2019	(r518149)
+++ head/biology/paml/distinfo	Fri Nov 22 15:32:40 2019	(r518150)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1551192920
-SHA256 (paml4.9i.tgz) = bc11af500b88d977a8765161f6c014f178273cbd887657eebd6330a3a967b4cc
-SIZE (paml4.9i.tgz) = 6556407
+TIMESTAMP = 1574435935
+SHA256 (paml4.9j.tgz) = 97aac6cb8f23844202545e9ba4e42020231c2a30051b36f4e4d2f423e270d461
+SIZE (paml4.9j.tgz) = 6562281