gentoo auto-resync : 09:05:2024 - 00:01:03

1 files changed, 60 insertions, 0 deletions

diff --git a/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
new file mode 100644
index 000000000000..492396a0fd83
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
@@ -0,0 +1,60 @@
+https://github.com/abacus-gene/paml/pull/46
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -9,39 +9,39 @@ LIBS = -lm # -lM
+ all : $(PRGS)
+ 
+ baseml : baseml.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ baseml.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.o tools.o $(LIBS)
+ basemlg : basemlg.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ basemlg.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.o tools.o $(LIBS)
+ codeml : codeml.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ codeml.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.o tools.o $(LIBS)
+ evolver : evolver.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ evolver.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.o tools.o $(LIBS)
+ pamp : pamp.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ pamp.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.o tools.o $(LIBS)
+ mcmctree : mcmctree.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
+-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
+ yn00: yn00.o tools.o paml.h
+-	$(CC) $(CFLAGS) -o $@ yn00.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.o tools.o $(LIBS)
+ chi2 : chi2.o
+-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
+ 
+ tools.o : paml.h tools.c
+-	$(CC) $(CFLAGS) -c tools.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c tools.c
+ baseml.o : paml.h baseml.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c baseml.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c baseml.c
+ basemlg.o : paml.h basemlg.c treesub.c
+-	$(CC) $(CFLAGS) -c basemlg.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c basemlg.c
+ codeml.o : paml.h codeml.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c codeml.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c codeml.c
+ evolver.o: evolver.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c evolver.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c evolver.c
+ mcmctree.o : paml.h mcmctree.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c mcmctree.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c mcmctree.c
+ pamp.o : paml.h pamp.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c pamp.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c pamp.c
+ yn00.o : paml.h yn00.c
+-	$(CC) $(CFLAGS) -c yn00.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c yn00.c
+ 
+ clean :
+ 	-rm *.o $(PRGS)