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authorSam James <sam@gentoo.org>2024-05-08 17:55:15 +0100
committerSam James <sam@gentoo.org>2024-05-08 17:56:05 +0100
commit26ed15e9e7d3fea5414e009936290fbb52e0c0a9 (patch)
tree413a45eaf239f5b8d8b1e3cdd3d31c0e14297c7b /sci-biology
parentsci-biology/paml: add 4.10.7 (diff)
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sci-biology/paml: respect CC, CPPFLAGS, LDFLAGS
Signed-off-by: Sam James <sam@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch60
-rw-r--r--sci-biology/paml/paml-4.10.7.ebuild8
2 files changed, 64 insertions, 4 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 $(PRGS)
diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
index 53a41c38fd11..598c844c5ce1 100644
--- a/sci-biology/paml/paml-4.10.7.ebuild
+++ b/sci-biology/paml/paml-4.10.7.ebuild
@@ -13,12 +13,12 @@ LICENSE="free-noncomm"
SLOT="0"
KEYWORDS="~amd64"
-src_configure() {
- tc-export CC
-}
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch
+)
src_compile() {
- emake -C src
+ emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
}
src_install() {