4 files changed, 74 insertions, 0 deletions

diff --git a/biology/phyml/files/patch-src_io.c b/biology/phyml/files/patch-src_io.c
new file mode 100644
index 000000000000..00fdcf48030f
--- /dev/null
+++ b/biology/phyml/files/patch-src_io.c
@@ -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)
+     {
diff --git a/biology/phyml/files/patch-src_phyrex.c b/biology/phyml/files/patch-src_phyrex.c
new file mode 100644
index 000000000000..661ee785dd32
--- /dev/null
+++ b/biology/phyml/files/patch-src_phyrex.c
@@ -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;
diff --git a/biology/phyml/files/patch-src_utilities.c b/biology/phyml/files/patch-src_utilities.c
new file mode 100644
index 000000000000..99740e857571
--- /dev/null
+++ b/biology/phyml/files/patch-src_utilities.c
@@ -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);
+           
diff --git a/biology/phyml/files/patch-src_utilities.h b/biology/phyml/files/patch-src_utilities.h
new file mode 100644
index 000000000000..14b65b1fff53
--- /dev/null
+++ b/biology/phyml/files/patch-src_utilities.h
@@ -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) */