From cf8848d5138c458f814b893dcfd9fe0603653e93 Mon Sep 17 00:00:00 2001 From: David Seifert Date: Wed, 22 Apr 2020 11:29:43 +0200 Subject: sci-biology/mafft: Remove old Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: David Seifert --- sci-biology/mafft/Manifest | 2 - sci-biology/mafft/files/mafft-7.037-respect.patch | 217 ---------------------- sci-biology/mafft/mafft-7.050.ebuild | 60 ------ sci-biology/mafft/mafft-7.215.ebuild | 64 ------- 4 files changed, 343 deletions(-) delete mode 100644 sci-biology/mafft/files/mafft-7.037-respect.patch delete mode 100644 sci-biology/mafft/mafft-7.050.ebuild delete mode 100644 sci-biology/mafft/mafft-7.215.ebuild (limited to 'sci-biology') diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest index 0cf407adadf0..cc67db0ab402 100644 --- a/sci-biology/mafft/Manifest +++ b/sci-biology/mafft/Manifest @@ -1,3 +1 @@ -DIST mafft-7.050-without-extensions-src.tgz 380375 BLAKE2B 86b5813c3cc9897a4f52e4dd3d7317d96b78e5f39530d1d5a34c3493965ba12f80e95fbecbc61a58738913132541a2b7265cd928327019dfdbeafcb10c060351 SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e -DIST mafft-7.215-without-extensions-src.tgz 393239 BLAKE2B a8aad83a004d468c5723a15c20b30745f6edb47157d545622b0cb1904d8663d1ce64a1a4d067ce96a150e58bfacb90db933967ad4dda61f14f29b68bc1c4d4a4 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch deleted file mode 100644 index 6fba7153622d..000000000000 --- a/sci-biology/mafft/files/mafft-7.037-respect.patch +++ /dev/null @@ -1,217 +0,0 @@ - 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 $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild deleted file mode 100644 index 5da5d12d1b31..000000000000 --- a/sci-biology/mafft/mafft-7.050.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread - sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" -} - -src_compile() { - pushd core > /dev/null || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS}" - popd > /dev/null || die -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - pushd core - emake PREFIX="${ED}usr" install - popd - dodoc readme -} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild deleted file mode 100644 index 05c3d8d52399..000000000000 --- a/sci-biology/mafft/mafft-7.215.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils flag-o-matic multilib toolchain-funcs - -EXTENSIONS="-without-extensions" - -DESCRIPTION="Multiple sequence alignments using a variety of algorithms" -HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html" -SRC_URI="https://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="threads" - -S="${WORKDIR}"/${P}${EXTENSIONS} - -src_prepare() { -# epatch "${FILESDIR}"/${PN}-7.037-respect.patch - use threads && append-cppflags -Denablemultithread -# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die - sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" - sed \ - -e 's:$(LDFLAGS)::g' \ - -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ - -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ - -e '/INSTALL/s: -s : :g' \ - -i core/Makefile || die -} - -src_compile() { - cd core || die - emake \ - $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ - PREFIX="${EPREFIX}"/usr \ - CC="$(tc-getCC)" \ - CFLAGS="${CFLAGS} -Wno-unused-result" -} - -src_test() { - export MAFFT_BINARIES="${S}"/core - cd test || die - bash ../core/mafft sample > test.fftns2 || die - bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die - bash ../core/mafft --globalpair sample > test.gins1 || die - bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die - bash ../core/mafft --localpair sample > test.lins1 || die - bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die - - diff test.fftns2 sample.fftns2 || die - diff test.fftnsi sample.fftnsi || die - diff test.gins1 sample.gins1 || die - diff test.ginsi sample.ginsi || die - diff test.lins1 sample.lins1 || die -} - -src_install() { - dodoc readme - cd core || die - emake PREFIX="${ED}usr" install -} -- cgit v1.2.3-65-gdbad