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>

4 files changed, 100 insertions, 0 deletions

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index ca4a6f9a9d8b..e0bf2de61716 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1 +1,2 @@
 DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a
+DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758
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

diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild
new file mode 100644
index 000000000000..e8a5d07ee40c
--- /dev/null
+++ b/sci-biology/paml/paml-4.9j.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+S="${WORKDIR}/${P/-/}"
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.9j-makefile.patch
+	"${FILESDIR}"/${PN}-4.9j-fno-common.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.txt doc/.
+
+	insinto /usr/share/${PN}/control
+	doins *.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r stewart* *.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}