gentoo resync : 25.11.2020

5 files changed, 103 insertions, 49 deletions

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 02b763e3dba9..e0f9ddd35a94 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,3 +1,5 @@
-DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a
-EBUILD paml-4.4c-r1.ebuild 983 BLAKE2B 4c4da7c1bdfdb0f479b65b27c39463d3797384e69e11929e446e867a741a8d49102842aad00a3187abd119885fa23879f4c13128577d64de23b6011455271352 SHA512 a7d590056e148c08607c6c15e872f6fc4ea87166336f19eeef497efb4852481b782b83f8e40b6f50005dffaa45b1fb6d028cd101fd54efa643e3678e60836b04
+AUX paml-4.9j-fno-common.patch 521 BLAKE2B 93dda51495e65cde9b3e92379e43756c5efe77953b114ceb88c8dc9ae6453d5b2742e250cf9a2d6feec3e86ff430417a4ecd8fd06b199a899b14d0aeac5199e2 SHA512 c24431264c7a69077f9ea9f511e93d45ac8adc4a5cc41446ca96de4e270b918543fb1a424b9119bc1723b2a9574434321a55a5af88712e0f3d51ef5c964575fb
+AUX paml-4.9j-makefile.patch 1540 BLAKE2B 9ffa0f8fab089d26e325688596975944a10e9e62ba1554b532b3f31c7f508b5b1001f5481ad9b8ae7fa97ffd8bcdffda3c285935c8efa3442175f4686e0a44ad SHA512 51b05e865ff68d58cf0f8cc2bc23e8e90e5d12ac8daceb96ac9cc64fdf75c704b5b16b6b8248a0e3cd03c1b18e5bbb61727c281ad46b4988a197f695b464c80d
+DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758
+EBUILD paml-4.9j.ebuild 843 BLAKE2B 8f92ab034a78571de1bccecc21d04fc9eef7414d98c5a3f4a6d4a96f59ddcd32e0c0c1c82928ed3949f7c64a493fbf5c3962016425ab8bcef6b3718cf50e49ba SHA512 74100d6e6a0913c0c1a56039468b5a78c86fc13fab054a0dc6fe307ba975f84865c999f5472c1e18a5bf28c7f0fe37359f3c557965b251968eba692bec49e607
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
deleted file mode 100644
index 27fe5ed4c769..000000000000
--- a/sci-biology/paml/paml-4.4c-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs versionator
-
-MY_P=$(version_format_string '${PN}$1$2')
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	# Notice send by mail to prof. Ziheng Yang
-	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
-}
-
-src_compile() {
-	emake -C src \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dodoc README.txt doc/*
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins stewart* *.dat dat/*
-
-	insinto /usr/share/${PN}
-	doins -r examples/
-
-	cd src || die
-	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
-}
diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild
new file mode 100644
index 000000000000..e8a5d07ee40c
--- /dev/null
+++ b/sci-biology/paml/paml-4.9j.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="http://abacus.gene.ucl.ac.uk/software/${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
+}