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Date:      Sat, 29 Aug 2020 08:34:28 +0000 (UTC)
From:      "Tobias C. Berner" <tcberner@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r546884 - head/biology/phyml/files
Message-ID:  <202008290834.07T8YS60061683@repo.freebsd.org>

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Author: tcberner
Date: Sat Aug 29 08:34:27 2020
New Revision: 546884
URL: https://svnweb.freebsd.org/changeset/ports/546884

Log:
  biology/phyml: fix build on recent current
  
  mostly backport of:
  	https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a
  
  Obtained from:	https://github.com/stephaneguindon/phyml/commit/3574fb82d54438518d50d5ba8f74423d5395a96a

Added:
  head/biology/phyml/files/
  head/biology/phyml/files/patch-src_io.c   (contents, props changed)
  head/biology/phyml/files/patch-src_phyrex.c   (contents, props changed)
  head/biology/phyml/files/patch-src_utilities.c   (contents, props changed)
  head/biology/phyml/files/patch-src_utilities.h   (contents, props changed)

Added: head/biology/phyml/files/patch-src_io.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/phyml/files/patch-src_io.c	Sat Aug 29 08:34:27 2020	(r546884)
@@ -0,0 +1,20 @@
+--- src/io.c.orig	2020-07-09 11:49:16 UTC
++++ src/io.c
+@@ -39,8 +39,6 @@ t_tree *Read_Tree(char **s_tree)
+       if((*s_tree)[i] == ',') n_otu++;
+     }
+   n_otu+=1;
+-
+-
+   
+   tree = Make_Tree_From_Scratch(n_otu,NULL);
+   subs = Sub_Trees((*s_tree),&degree);
+@@ -2312,7 +2310,7 @@ void Print_Fp_Out(FILE *fp_out, time_t t_beg, time_t t
+   div_t hour,min;
+   int i, j;
+   
+-  if (precision > 0) snprintf (format, 8, "%%.%df", precision);
++  if (precision > 0) snprintf(format,8,"%%.%huf",(unsigned short)precision);
+   
+   if(n_data_set == 1)
+     {

Added: head/biology/phyml/files/patch-src_phyrex.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/phyml/files/patch-src_phyrex.c	Sat Aug 29 08:34:27 2020	(r546884)
@@ -0,0 +1,11 @@
+--- src/phyrex.c.orig	2020-07-09 11:49:16 UTC
++++ src/phyrex.c
+@@ -958,7 +958,7 @@ phydbl *PHYREX_MCMC(t_tree *tree)
+           PHYREX_Label_Nodes_With_Locations(tree);
+           PHYREX_Label_Edges(tree);
+           char *s = Write_Tree(tree);
+-          PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->sample_num,tree->c_lnL,s);
++          PhyML_Fprintf(fp_tree,"\ntree %d [&lnP=%f,precision={1.e-1,1e-02,1e-01}] = [&R] %s",tree->mcmc->run,tree->c_lnL,s);
+           PhyML_Fprintf(fp_tree,"\nend;");
+           fseek(fp_tree,-5,SEEK_END);
+           tree->write_tax_names = YES;

Added: head/biology/phyml/files/patch-src_utilities.c
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/phyml/files/patch-src_utilities.c	Sat Aug 29 08:34:27 2020	(r546884)
@@ -0,0 +1,30 @@
+--- src/utilities.c.orig	2020-07-09 11:49:16 UTC
++++ src/utilities.c
+@@ -17,6 +17,9 @@ the GNU public licence. See http://www.opensource.org 
+ #include "beagle_utils.h"
+ #endif
+ 
++int CALL;
++int TIME;
++
+ //////////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////////
+ 
+@@ -3066,7 +3069,7 @@ int Assign_State_With_Ambiguity(char *c, int datatype,
+       if(Is_Ambigu(c,GENERIC,stepsize)) state[0] = T_MAX_ALPHABET-1;
+       else
+         {
+-          char format[6];
++          char format[20];
+           sprintf(format,"%%%dd",stepsize);
+           if(!sscanf(c,format,state))
+             {
+@@ -4891,7 +4894,7 @@ int Are_Compatible(char *statea, char *stateb, int ste
+       else
+         {
+           int a,b;
+-          char format[6];
++          char format[20];
+           
+           sprintf(format,"%%%dd",stepsize);
+           

Added: head/biology/phyml/files/patch-src_utilities.h
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/phyml/files/patch-src_utilities.h	Sat Aug 29 08:34:27 2020	(r546884)
@@ -0,0 +1,13 @@
+--- src/utilities.h.orig	2020-08-29 08:31:23 UTC
++++ src/utilities.h
+@@ -94,8 +94,8 @@ static inline int isinf_ld (long double x) { return is
+ #endif
+ 
+ 
+-int CALL;
+-int TIME;
++extern int CALL;
++extern int TIME;
+ 
+ #define SLFV_GAUSSIAN 0 /* Spatial Lambda-Fleming-Viot model (Gaussian) */
+ #define SLFV_UNIFORM 1 /* Spatial Lambda-Fleming-Viot model (Uniform) */



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