2 files changed, 74 insertions, 10 deletions
diff --git a/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
new file mode 100644
index 000000000000..9b1d9e03ca14
--- /dev/null
+++ b/sci-biology/phyml/files/phyml-2.4.5-fix-build-system.patch
@@ -0,0 +1,67 @@
+Fix build system to honour user flags.
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,10 +1,4 @@
+-hello !!!
+-
+-CC = gcc #cc
+-CFLAGS = -O4 -fomit-frame-pointer -Wall -static
+-# CFLAGS = -Wall
+-# CFLAGS = -g -Wall
+-# CFLAGS = -pg -Wall -fprofile-arcs -static
++CC ?= gcc
+ LIBS = -lm
+ 
+ PROG = PHYML
+@@ -23,39 +17,39 @@
+ 
+ 
+ $(EXEC) : $(OBJS)
+-	$(CC) -o $(EXEC) $(OBJS) $(LIBS) $(CFLAGS)
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $(EXEC) $(OBJS) $(LIBS)
+ 
+ clean :
+ 	@rm *.o
+ ######################################################################################################
+ 
+ eigen.o : eigen.c eigen.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c eigen.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c eigen.c
+ 
+ simu.o : simu.c simu.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c simu.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c simu.c
+ 
+ lk.o : lk.c lk.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c lk.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c lk.c
+ 
+ utilities.o : utilities.c utilities.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c utilities.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c utilities.c
+ 
+ optimiz.o : optimiz.c optimiz.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c optimiz.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c optimiz.c
+ 
+ bionj.o : bionj.c bionj.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c bionj.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c bionj.c
+ 
+ main.o : main.c
+-	$(CC) $(CFLAGS) $(DFLAG) -c main.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c main.c
+ 
+ models.o : models.c models.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c models.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c models.c
+ 
+ free.o : free.c free.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c free.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c free.c
+ 
+ options.o : options.c options.h
+-	$(CC) $(CFLAGS) $(DFLAG) -c options.c
++	$(CC) $(CFLAGS) $(DFLAG) $(CPPFLAGS) -c options.c
+ 
diff --git a/sci-biology/phyml/phyml-2.4.5-r2.ebuild b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
index 7d9815baa78b..37f7aa478ebd 100644
--- a/sci-biology/phyml/phyml-2.4.5-r2.ebuild
+++ b/sci-biology/phyml/phyml-2.4.5-r3.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=2
+EAPI=6
 
 inherit toolchain-funcs
 
@@ -19,16 +19,13 @@ IUSE=""
 
 S=${WORKDIR}/${MY_P}
 
-src_prepare() {
-	sed -e 's/^hello !!!//' \
-		-e 's/$(CC) -o/$(CC) $(LDFLAGS) -o/' \
-		-i Makefile || die
-}
+PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch )
 
-src_compile() {
-	emake -e CC="$(tc-getCC)" || die
+src_prepare() {
+	default
+	tc-export CC
 }
 
 src_install() {
-	dobin phyml || die
+	dobin phyml
 }