From 26ed15e9e7d3fea5414e009936290fbb52e0c0a9 Mon Sep 17 00:00:00 2001
From: Sam James <sam@gentoo.org>
Date: Wed, 8 May 2024 17:55:15 +0100
Subject: sci-biology/paml: respect CC, CPPFLAGS, LDFLAGS

Signed-off-by: Sam James <sam@gentoo.org>
---
 sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch | 60 ++++++++++++++++++++++++
 sci-biology/paml/paml-4.10.7.ebuild              |  8 ++--
 2 files changed, 64 insertions(+), 4 deletions(-)
 create mode 100644 sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch

(limited to 'sci-biology')

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)
diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
index 53a41c38fd11..598c844c5ce1 100644
--- a/sci-biology/paml/paml-4.10.7.ebuild
+++ b/sci-biology/paml/paml-4.10.7.ebuild
@@ -13,12 +13,12 @@ LICENSE="free-noncomm"
 SLOT="0"
 KEYWORDS="~amd64"
 
-src_configure() {
-	tc-export CC
-}
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch
+)
 
 src_compile() {
-	emake -C src
+	emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
-- 
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