2 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch
new file mode 100644
index 000000000000..66eeb8a56b86
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.9j-fno-common.patch
@@ -0,0 +1,14 @@
+--- a/src/paml.h
++++ b/src/paml.h
+@@ -372,9 +372,9 @@
+ void printSptree(void);
+ 
+ 
+-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
++typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
+ 
+-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
++typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
+ 
+ 
+ /* use mean (0; default) for discrete gamma instead of median (1) */
diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch
new file mode 100644
index 000000000000..611b80444c89
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.9j-makefile.patch
@@ -0,0 +1,42 @@
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,27 +1,18 @@
+-PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 
+-CC = cc # cc, gcc, cl
++PRGS =  baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2
+ 
+-CFLAGS = -O3
++CFLAGS += -Wno-unused-result
+ #CFLAGS = -fast
+ 
+-LIBS = -lm # -lM
++LDLIBS = -lm
+ 
+ all : $(PRGS)
+ 
+-baseml : baseml.c tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
+-basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+-codeml : codeml.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
+-evolver : evolver.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
+-pamp : pamp.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
+-mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
+-yn00: yn00.c tools.c paml.h
+-	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+-chi2 : chi2.c
+-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++baseml: tools.o paml.h 
++basemlg: tools.o paml.h 
++codeml: tools.o paml.h 
++evolver: tools.o paml.h 
++pamp: tools.o paml.h 
++mcmctree: tools.o paml.h 
++infinitesites: tools.o paml.h 
++	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)
++yn00: tools.o paml.h