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| author |   David Seifert <soap@gentoo.org> | 2020-11-01 19:35:53 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2020-11-01 19:35:53 +0100 |
| commit | 9d4c4862d17a28af87e503a3f30b866efd544aad (patch) | |
| tree | a2d31a9e63ab05ec4e239d74a7985b85ca93d6fd /sci-biology/paml/files | |
| parent | sci-biology/dialign-tx: Fix -fno-common (diff) | |
| download | gentoo-9d4c4862d17a28af87e503a3f30b866efd544aad.tar.gz gentoo-9d4c4862d17a28af87e503a3f30b866efd544aad.tar.bz2 gentoo-9d4c4862d17a28af87e503a3f30b866efd544aad.zip | |
sci-biology/paml: Version bump to 4.9j
Bug: https://bugs.gentoo.org/706708
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology/paml/files')
| -rw-r--r-- | sci-biology/paml/files/paml-4.9j-fno-common.patch | 14 | ||||
| -rw-r--r-- | sci-biology/paml/files/paml-4.9j-makefile.patch | 42 |
2 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch new file mode 100644 index 000000000000..66eeb8a56b86 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-fno-common.patch @@ -0,0 +1,14 @@ +--- a/src/paml.h ++++ b/src/paml.h +@@ -372,9 +372,9 @@ + void printSptree(void); + + +-enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; ++typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; + +-enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; ++typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; + + + /* use mean (0; default) for discrete gamma instead of median (1) */ diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch new file mode 100644 index 000000000000..611b80444c89 --- /dev/null +++ b/sci-biology/paml/files/paml-4.9j-makefile.patch @@ -0,0 +1,42 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -1,27 +1,18 @@ +-PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2
+-CC = cc # cc, gcc, cl
++PRGS = baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2
+
+-CFLAGS = -O3
++CFLAGS += -Wno-unused-result
+ #CFLAGS = -fast
+
+-LIBS = -lm # -lM
++LDLIBS = -lm
+
+ all : $(PRGS)
+
+-baseml : baseml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
+-basemlg : basemlg.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+-codeml : codeml.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
+-evolver : evolver.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
+-pamp : pamp.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
+-mcmctree : mcmctree.c tools.c treesub.c treespace.c paml.h
+- $(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+- $(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)
+-yn00: yn00.c tools.c paml.h
+- $(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
+-chi2 : chi2.c
+- $(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++baseml: tools.o paml.h
++basemlg: tools.o paml.h
++codeml: tools.o paml.h
++evolver: tools.o paml.h
++pamp: tools.o paml.h
++mcmctree: tools.o paml.h
++infinitesites: tools.o paml.h
++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)
++yn00: tools.o paml.h
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