summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorDavid Seifert <soap@gentoo.org>2020-04-22 11:29:43 +0200
committerDavid Seifert <soap@gentoo.org>2020-04-22 11:29:43 +0200
commitcf8848d5138c458f814b893dcfd9fe0603653e93 (patch)
tree7ad9cc340d4bff20be1e6208d984fe161edc3351 /sci-biology
parentsci-biology/mafft: Fix -fno-common / GCC 10 (diff)
downloadgentoo-cf8848d5138c458f814b893dcfd9fe0603653e93.tar.gz
gentoo-cf8848d5138c458f814b893dcfd9fe0603653e93.tar.bz2
gentoo-cf8848d5138c458f814b893dcfd9fe0603653e93.zip
sci-biology/mafft: Remove old
Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/mafft/Manifest2
-rw-r--r--sci-biology/mafft/files/mafft-7.037-respect.patch217
-rw-r--r--sci-biology/mafft/mafft-7.050.ebuild60
-rw-r--r--sci-biology/mafft/mafft-7.215.ebuild64
4 files changed, 0 insertions, 343 deletions
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 0cf407adadf..cc67db0ab40 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 6fba7153622..00000000000
--- 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 $(BINDIR); \
diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
deleted file mode 100644
index 5da5d12d1b3..00000000000
--- a/sci-biology/mafft/mafft-7.050.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="https://mafft.cbrc.jp/alignment/software/${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 05c3d8d5239..00000000000
--- 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
-}