From d934827bf44b7cfcf6711964418148fa60877668 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 25 Nov 2020 22:39:15 +0000 Subject: gentoo resync : 25.11.2020 --- sci-biology/paml/Manifest | 6 ++- 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-4.4c-r1.ebuild | 47 ----------------------- sci-biology/paml/paml-4.9j.ebuild | 43 +++++++++++++++++++++ 5 files changed, 103 insertions(+), 49 deletions(-) create mode 100644 sci-biology/paml/files/paml-4.9j-fno-common.patch create mode 100644 sci-biology/paml/files/paml-4.9j-makefile.patch delete mode 100644 sci-biology/paml/paml-4.4c-r1.ebuild create mode 100644 sci-biology/paml/paml-4.9j.ebuild (limited to 'sci-biology/paml') 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 +} -- cgit v1.2.3