From bdd44d58a0c4eba140c1a24ca420f32f53e7490d Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 29 Apr 2013 10:05:59 +0000 Subject: sci-biology/mafft: Version Bump (Portage version: 2.2.0_alpha173/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) --- sci-biology/mafft/ChangeLog | 10 +- sci-biology/mafft/files/mafft-7.037-respect.patch | 217 ++++++++++++++++++++++ sci-biology/mafft/mafft-7.037.ebuild | 45 +++++ sci-biology/mafft/metadata.xml | 2 +- 4 files changed, 271 insertions(+), 3 deletions(-) create mode 100644 sci-biology/mafft/files/mafft-7.037-respect.patch create mode 100644 sci-biology/mafft/mafft-7.037.ebuild (limited to 'sci-biology/mafft') diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog index 2449852694fc..9c0792768c95 100644 --- a/sci-biology/mafft/ChangeLog +++ b/sci-biology/mafft/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/mafft -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.9 2011/11/21 15:30:19 jlec Exp $ +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.10 2013/04/29 10:05:58 jlec Exp $ + +*mafft-7.037 (29 Apr 2013) + + 29 Apr 2013; Justin Lecher +mafft-7.037.ebuild, + +files/mafft-7.037-respect.patch, metadata.xml: + Version Bump 21 Nov 2011; Justin Lecher mafft-6.811.ebuild: keyworded for ~x86-macos ~x64-macos, tested by Johan Hattne #390123 diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch new file mode 100644 index 000000000000..6fba7153622d --- /dev/null +++ b/sci-biology/mafft/files/mafft-7.037-respect.patch @@ -0,0 +1,217 @@ + core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- + 1 file changed, 50 insertions(+), 50 deletions(-) + +diff --git a/core/Makefile b/core/Makefile +index 9acebb3..3838a45 100644 +--- a/core/Makefile ++++ b/core/Makefile +@@ -145,151 +145,151 @@ mltaln.h : functions.h + touch mltaln.h + + version : version.c mltaln.h +- $(CC) -o $@ version.c $(MYCFLAGS) ++ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) + + addsingle : $(OBJADDSINGLE) +- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c +@@ -525,7 +525,7 @@ install : all + chmod 755 $(SCRIPTS) + $(INSTALL) $(SCRIPTS) $(BINDIR) + chmod 755 $(PROGS) +- $(INSTALL) -s $(PROGS) $(LIBDIR) ++ $(INSTALL) $(PROGS) $(LIBDIR) + $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) + + ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.037.ebuild b/sci-biology/mafft/mafft-7.037.ebuild new file mode 100644 index 000000000000..00cf1a80f4e9 --- /dev/null +++ b/sci-biology/mafft/mafft-7.037.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.037.ebuild,v 1.1 2013/04/29 10:05:58 jlec Exp $ + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { + epatch "${FILESDIR}"/${P}-respect.patch + use threads && append-flags -Denablemultithread + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" +} + +src_compile() { + pushd core + emake \ + ENABLE_MULTITHREAD=1 \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" \ + || die "make failed" + popd +} + +src_install() { + pushd core + emake PREFIX="${ED}usr" install || die "install failed" + popd + dodoc readme || die +} diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml index 34294c65ca04..f17a827e3101 100644 --- a/sci-biology/mafft/metadata.xml +++ b/sci-biology/mafft/metadata.xml @@ -1,5 +1,5 @@ -sci-biology + sci-biology -- cgit v1.2.3-65-gdbad