commit: 18d0de11ad388be416dc787a8dea264325be4e46 Author: NHOrus <jy6x2b32pie9 <AT> yahoo <DOT> com> AuthorDate: Tue Feb 10 17:05:09 2026 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Wed Feb 11 03:42:08 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18d0de11
sci-biology/paml: add 4.10.10, drop 4.9j Changed license in new one to actual one used. Closes: https://bugs.gentoo.org/968714 Bug: https://bugs.gentoo.org/944917 Signed-off-by: NHOrus <jy6x2b32pie9 <AT> yahoo.com> Part-of: https://github.com/gentoo/gentoo/pull/45731 Closes: https://github.com/gentoo/gentoo/pull/45731 Signed-off-by: Sam James <sam <AT> gentoo.org> sci-biology/paml/Manifest | 2 +- 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-4.10.10.ebuild | 33 +++++++++++++++++ sci-biology/paml/paml-4.9j.ebuild | 43 ----------------------- 5 files changed, 34 insertions(+), 100 deletions(-) diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest index 4e828eff1360..afb22bd8917b 100644 --- a/sci-biology/paml/Manifest +++ b/sci-biology/paml/Manifest @@ -1,2 +1,2 @@ +DIST paml-4.10.10.tar.gz 3835148 BLAKE2B 170915e094bd7f4c95895b4cb56e31d4e11f7b70c0f4b8c5c9104a88c68af62c635e18b36a7f56c96170e7eb490966d9ece0ab0e73aa42142def867a1bdce0bc SHA512 e3a3a0f2300213823f4126914073f538fc9859a2378a8494303c3b5fedf935e42c44311e9a89dac4eebc97fdd5653aa95c4d20e1b3ec62866f3bffffcbc9689c DIST paml-4.10.7.tar.gz 5250841 BLAKE2B 4d2a7fdc8eb93abe200165f7805520a02f4251dc651f26c4e1bf6fb11eee3d0721fd9d6f3c96979bae0f51b77f168e8d8a12f3dd3cbbfec7e8210a70b7c4bb9e SHA512 e450c0a28ecef946279fd92834eb5ddfb50805167655364cc959ef21839a75280a37d79209918373e80dacb0fc35decaccdb1477e53a81fd99fb140a0ce839fe -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 deleted file mode 100644 index 66eeb8a56b86..000000000000 --- a/sci-biology/paml/files/paml-4.9j-fno-common.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- 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 deleted file mode 100644 index 611b80444c89..000000000000 --- a/sci-biology/paml/files/paml-4.9j-makefile.patch +++ /dev/null @@ -1,42 +0,0 @@ ---- 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 $(LDLIBS) -+yn00: tools.o paml.h diff --git a/sci-biology/paml/paml-4.10.10.ebuild b/sci-biology/paml/paml-4.10.10.ebuild new file mode 100644 index 000000000000..068e46ee72dd --- /dev/null +++ b/sci-biology/paml/paml-4.10.10.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2026 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" +HOMEPAGE="https://github.com/abacus-gene/paml/wiki"; +SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_compile() { + emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" +} + +src_install() { + dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2} + + dodoc -r README.md doc/. + + insinto /usr/share/${PN}/control + doins examples/*.ctl + + insinto /usr/share/${PN}/dat + doins -r examples/stewart* examples/*.dat dat/. + + insinto /usr/share/${PN} + doins -r examples +} diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild deleted file mode 100644 index e8a5d07ee40c..000000000000 --- a/sci-biology/paml/paml-4.9j.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood" -HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"; -SRC_URI="http://abacus.gene.ucl.ac.uk/software/${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 -}
