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sci-biology/paml: respect CC, CPPFLAGS, LDFLAGS

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Signed-off-by: Sam James <sam@gentoo.org>
This commit is contained in:
Sam James
2024-05-08 17:55:15 +01:00
parent 8a73a8d755
commit 26ed15e9e7
2 changed files with 64 additions and 4 deletions
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60
sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch Normal file
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@@ -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)

8
sci-biology/paml/paml-4.10.7.ebuild
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@@ -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() {