commit: 9d4c4862d17a28af87e503a3f30b866efd544aad Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun Nov 1 18:35:53 2020 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun Nov 1 18:35:53 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9d4c4862
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 <AT> gentoo.org> sci-biology/paml/Manifest | 1 + sci-biology/paml/files/paml-4.9j-fno-common.patch | 14 ++++++++ sci-biology/paml/files/paml-4.9j-makefile.patch | 42 ++++++++++++++++++++++ sci-biology/paml/paml-4.9j.ebuild | 43 +++++++++++++++++++++++ 4 files changed, 100 insertions(+) diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest index ca4a6f9a9d8..e0bf2de6171 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 00000000000..66eeb8a56b8 --- /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 00000000000..611b80444c8 --- /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 $(LDLIBS) ++yn00: tools.o paml.h diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild new file mode 100644 index 00000000000..e8a5d07ee40 --- /dev/null +++ b/sci-biology/paml/paml-4.9j.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit toolchain-funcs + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"; +SRC_URI="http://abacus.gene.ucl.ac.uk/software/${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 +}
