academic/PhyML: Updated for version 20131112.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

5 files changed, 117 insertions, 18 deletions

diff --git a/academic/PhyML/20130219.patch b/academic/PhyML/20131112.patch
index 59250c71dbe6e..e7eb2670b6f56 100644
--- a/academic/PhyML/20130219.patch
+++ b/academic/PhyML/20131112.patch
@@ -1,5 +1,4 @@
-Common subdirectories: ./phyml-20120412/src/.deps and ./phyml-20120412-new-bak/src/.deps
-diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c
+unchanged:
 --- ./phyml-20120412/src/help.c	2011-09-22 14:51:57.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/help.c	2013-02-18 21:51:51.448662440 +1300
 @@ -96,7 +96,7 @@
@@ -11,7 +10,7 @@ diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c
    PhyML_Printf("%s\t\tChanges interleaved format (default) to sequential format.\n",FLAT);
    PhyML_Printf("\n");
  
-diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c
+unchanged:
 --- ./phyml-20120412/src/lk.c	2012-04-05 14:47:37.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/lk.c	2013-02-19 10:22:22.665284529 +1300
 @@ -472,7 +472,7 @@
@@ -217,7 +216,7 @@ diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c
  		  
  		  if(p_lk[site*NsNg+catg*Ns+i] < smallest_p_lk) smallest_p_lk = p_lk[site*NsNg+catg*Ns+i] ;
  		}
-diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile
+unchanged:
 --- ./phyml-20120412/src/Makefile	1970-01-01 12:00:00.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/Makefile	2013-02-18 21:54:46.957806553 +1300
 @@ -0,0 +1,1082 @@
@@ -1303,7 +1302,7 @@ diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile
 +# Tell versions [3.59,3.63) of GNU make to not export all variables.
 +# Otherwise a system limit (for SysV at least) may be exceeded.
 +.NOEXPORT:
-diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c
+unchanged:
 --- ./phyml-20120412/src/mcmc.c	2012-03-20 14:10:49.000000000 +1300
 +++ ./phyml-20120412-new-bak/src/mcmc.c	2013-02-18 21:51:51.459662430 +1300
 @@ -1977,7 +1977,7 @@
@@ -1315,7 +1314,7 @@ diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c
  	  else
  	    {
  	      For(i,tree->mod->n_catg) PhyML_Fprintf(fp,"%G\t",tree->mod->gamma_r_proba->v[i]);
-diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c
+unchanged:
 --- ./phyml-20120412/src/optimiz.c	2012-03-13 19:04:03.000000000 +1300
 +++ ./phyml-20120412-new-bak/src/optimiz.c	2013-02-18 21:51:51.462662427 +1300
 @@ -979,29 +979,18 @@
@@ -1355,13 +1354,13 @@ diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c
  
        tree->mod->gamma_r_proba_unscaled->v[tree->mod->n_catg-1] = 100.;
        For(i,tree->mod->n_catg-1)
-diff -uN ./phyml-20120412/src/tree ./phyml-20120412-new-bak/src/tree
+unchanged:
 --- ./phyml-20120412/src/tree	1970-01-01 12:00:00.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/tree	2013-02-19 10:09:36.962892889 +1300
 @@ -0,0 +1 @@
 +((((((tax6:0.01,(tax5:0.01,tax1:0.026):0.008):0.003,(tax7:0.003,tax3:0.003):0.01271127):0.01,tax2:0.01):0.01,tax10:0.01):0.01,tax9:0.01):0.01,tax8:0.01,tax4:0.1);
 \ No newline at end of file
-diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities.c
+unchanged:
 --- ./phyml-20120412/src/utilities.c	2012-04-11 11:48:30.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/utilities.c	2013-02-19 10:16:57.770281203 +1300
 @@ -1668,6 +1668,7 @@
@@ -1505,7 +1504,7 @@ diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities
    list = (t_node ***)mCalloc(node_list_size,sizeof(t_node **));
    For(i,node_list_size) list[i] = (t_node **)mCalloc(2*tree->n_otu-1,sizeof(t_node *));
    size = (int *)mCalloc(node_list_size,sizeof(int));
-diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities.h
+unchanged:
 --- ./phyml-20120412/src/utilities.h	2012-04-11 11:39:02.000000000 +1200
 +++ ./phyml-20120412-new-bak/src/utilities.h	2013-02-18 21:51:51.452662435 +1300
 @@ -272,6 +272,8 @@
@@ -1517,3 +1516,76 @@ diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities
  
  
  /*!********************************************************/
+unchanged:
+--- utilities.c	2013-10-31 08:57:09.622430940 +1300
++++ utilities.new.c	2013-10-31 08:55:49.522433717 +1300
+@@ -4769,8 +4769,6 @@
+   t_node *n_e, *n_f;
+ 
+   n_otu                   = t_full->n_otu;
+-  t_empt->n_root          = t_full->n_root;
+-  t_empt->e_root          = t_full->e_root;
+   t_empt->c_lnL_sorted    = t_full->c_lnL_sorted;
+   t_empt->log_site_lk_cat = t_full->log_site_lk_cat;
+   t_empt->cur_site_lk     = t_full->cur_site_lk;
+@@ -6993,6 +6991,7 @@
+ 	  boot_tree->mat = boot_mat;
+ 	}
+ 
++
+       boot_tree->mod                = boot_mod;
+       boot_tree->io                 = tree->io;
+       boot_tree->data               = boot_data;
+@@ -7002,6 +7001,7 @@
+       boot_tree->io->print_site_lnl = 0;
+       boot_tree->io->print_trace    = 0;
+ 
++
+       if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE)) Random_Tree(boot_tree);
+       Order_Tree_CSeq(boot_tree,boot_data);
+       Share_Lk_Struct(tree,boot_tree);
+@@ -7010,6 +7010,7 @@
+       Fill_Dir_Table(boot_tree);
+       Update_Dirs(boot_tree);
+ 
++
+       if(tree->mod->s_opt->greedy) Init_P_Lk_Tips_Double(boot_tree);
+       else                         Init_P_Lk_Tips_Int(boot_tree);
+       Init_Ui_Tips(boot_tree);
+@@ -13307,11 +13308,15 @@
+       Warn_And_Exit("");
+     }
+ 
++  has_outgrp = NO;
++
++  /* 'Root' node is t_nodes[0] */ 
+   if(strstr(tree->t_nodes[0]->name,"*"))
+     {
+       /* PhyML_Printf("\n. Found outgroup taxon: %s",tree->t_nodes[0]->name); */
+       tree->t_nodes[0]->s_ingrp[0]  = 0;
+       tree->t_nodes[0]->s_outgrp[0] = 1;
++      has_outgrp = YES;
+     }
+   else
+     {
+@@ -13319,7 +13324,6 @@
+       tree->t_nodes[0]->s_outgrp[0] = 0;
+     }
+ 
+-  has_outgrp = NO;
+   Get_Best_Root_Position_Post(tree->t_nodes[0],tree->t_nodes[0]->v[0],&has_outgrp,tree);  
+   Get_Best_Root_Position_Pre(tree->t_nodes[0],tree->t_nodes[0]->v[0],tree);  
+ 
+only in patch2:
+unchanged:
+--- src/utilities.c	2012-04-11 11:48:30.000000000 +1200
++++ src.new/utilities.c	2013-11-12 14:19:11.600689913 +1300
+@@ -13995,7 +13995,7 @@ int Check_Topo_Constraints(t_tree *big_t
+   For(i,2*big_tree_cpy->n_otu-3) big_tree_cpy->t_edges[i]->bip_score = 0;
+   For(i,2*small_tree->n_otu-3) small_tree->t_edges[i]->bip_score = 0;
+ 
+-  diffs = Compare_Bip(small_tree,big_tree_cpy,YES);
++  diffs = Compare_Bip(small_tree,big_tree_cpy,NO);
+ 
+   /* printf("\n"); */
+   /* printf("\n. %s",Write_Tree(big_tree_cpy,NO)); */
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 9946b20954c90..3578b7288c51e 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for PhyML
 
-# Copyright 2011-2013  Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2011-2013  Petar Petrov, petar.petrov@student.oulu.fi
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,7 +25,7 @@
 # Thanks to Niels Horn for some handy modifications and corrections.
 
 PRGNAM=PhyML
-VERSION=${VERSION:-20130219}
+VERSION=${VERSION:-20131112}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -69,16 +69,17 @@ tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
 cd $SRCNAM-$SRCVER
 chown -R root:root .
 find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-# Apply patch 20130219
+# Apply version patch
 cd src
   patch -i $CWD/$VERSION.patch
 cd ..
 
+# This is PhyML
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
@@ -97,6 +98,26 @@ CXXFLAGS="$SLKCFLAGS" \
 make
 make install DESTDIR=$PKG
 
+# And this is PhyTime
+./configure \
+  --prefix=/usr \
+  --libdir=/usr/lib${LIBDIRSUFFIX} \
+  --sysconfdir=/etc \
+  --localstatedir=/var \
+  --enable-phytime \
+  --mandir=/usr/man \
+  --docdir=/usr/doc/$PRGNAM-$VERSION \
+  --build=$ARCH-slackware-linux
+
+# Use our CFLAGS
+sed -i "/^CFLAGS/s/=/+=/" src/Makefile
+sed -i "/^CFLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make
+make install DESTDIR=$PKG
+
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index 52478c9962787..e37d35be73e39 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,5 +1,5 @@
 PRGNAM="PhyML"
-VERSION="20130219"
+VERSION="20131112"
 HOMEPAGE="http://code.google.com/p/phyml/"
 DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz"
 MD5SUM="d2207a3d6caf633c43239a01ce70f244"
@@ -7,4 +7,4 @@ DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
 MAINTAINER="Petar Petrov"
-EMAIL="ppetrov@paju.oulu.fi"
+EMAIL="petar.petrov@student.oulu.fi"
diff --git a/academic/PhyML/README b/academic/PhyML/README
index b52080e622359..60178833a84ce 100644
--- a/academic/PhyML/README
+++ b/academic/PhyML/README
@@ -9,6 +9,8 @@ It also implements two methods to evaluate branch supports in a sound
 statistical framework (the non-parametric bootstrap and the
 approximate likelihood ratio test).
 
+The script also builds the additional program PhyTime.
+
 For details and citation
 New Algorithms and Methods to Estimate Maximum-Likelihood
 Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S.,
diff --git a/academic/PhyML/References b/academic/PhyML/References
index 17fd35add28ff..41f1be6bb2787 100644
--- a/academic/PhyML/References
+++ b/academic/PhyML/References
@@ -2,3 +2,7 @@ New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
 Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F.,
 Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,
 59(3):307-21, 2010.
+
+Bayesian estimation of divergence times from large sequence alignments.
+Mol Biol Evol. 2010 Aug;27(8):1768-81. doi: 10.1093/molbev/msq060.
+Epub 2010 Mar 1.