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-rw-r--r--sci-biology/mafft/Manifest8
-rw-r--r--sci-biology/mafft/files/mafft-7.037-respect.patch217
-rw-r--r--sci-biology/mafft/files/mafft-7.305-fno-common.patch8
-rw-r--r--sci-biology/mafft/mafft-7.050.ebuild60
-rw-r--r--sci-biology/mafft/mafft-7.215.ebuild64
-rw-r--r--sci-biology/mafft/mafft-7.305.ebuild3
6 files changed, 12 insertions, 348 deletions
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index b5bb9dcd4893..974e08b0ca57 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,8 +1,4 @@
-AUX mafft-7.037-respect.patch 7463 BLAKE2B a7218e21a08452aab65ea544cfff91a0a88f3400e667cbe945848cba7507b678e9c1d1f03bdb4b4b3b1d7b43df2a3f2097090f588274c04f6ecfe53436149245 SHA512 ba706bc83b1c249c08fa7e39d6b80df42be058ea2e68baf1028125dcad289764ead3a6269e557bffc62da87a7ac2ff9856a602e20ca5eae052060d44b431994b
-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
+AUX mafft-7.305-fno-common.patch 185 BLAKE2B 1230b838fa93b560fe0b0d9dd124cec2daf92d1dbcd75e371af92cc070bf62cea23c7c9ee3d87798de70911e4c316e444c875e79b3cf93f757b7a6fdfe2e279b SHA512 fe9de41eaea3bf799065fac88b336ec45af3c5b4d7d5272a477d99165b88c27f7e7765908e7955eaa0a74bb59df10a0ab77b822fd29bebca601d124938f3489d
DIST mafft-7.305-without-extensions-src.tgz 458448 BLAKE2B 5d5fa86e6faa472182c5c48f42056d81bbf545db56426969ff44a24146d4189a7650e85ea6e9fa8b40bb613392bf53bc5dea26012a86eb873c18bee91e6fdc41 SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9
-EBUILD mafft-7.050.ebuild 1796 BLAKE2B 7377a5d75e2c0d61e9502e16c8a61d5031f12adcbfb53ba58e1ec0ef7a7eab730aa0bbfbc1c7f6da77b185e5eb429300bd8c997e31dea9927738fc2b31c764cd SHA512 2c5e8078a76c44ccc8151b6493f74038ed2e7bdff336fdebe4171d87c34a3664d2b794030198f798606231c13d3b4b0dabc101c429b438c3675f3909d93a1c1e
-EBUILD mafft-7.215.ebuild 1976 BLAKE2B e490252063bc448db647d0de765c49c468bc2b395b06c2fa26b6368d8d5e26eceb99204f879f0d3104930881393e3f99ecfc9a915b936f299863750cfceb656d SHA512 f297da061416bdbbb3d7ebcaa4efe62b88cb7ca8eedcf0eeaf61fcfb8af42f7dd8b1cbec270ae247efd7a4c7c95ee04a44903d26116e4b73e87ea9fe349d38fa
-EBUILD mafft-7.305.ebuild 2015 BLAKE2B baae93bd674fc22dcbdc14c728c1bd30216f6d94aaceef3b0889ced8fb5b9f55114d03f9a84679f8dfcb54db630a4ff70df538af46b33da2251345b657bdab89 SHA512 c5102f225b1bbe7b89d497e14a78c742f05e873c73a9947669c125bda951d59806da697a29134b639043fef49375a1bb73aeb935445a1e698124fdb78ddb6004
+EBUILD mafft-7.305.ebuild 2067 BLAKE2B 679f6b2270aa60b51416b4f1cf3322a217db912d98a84397134064035b21151b9a20c5ab387f0d671365f8c8abecee924cade70ade9a5174c1e24f8e3d08a7c1 SHA512 d3781c854315146303f8702b4f80ce0ce1de9e543a8e85fb267be27b422a8eeba716f21353853d4e618ae89635bb993f12f446c625a7e6b5e79807b967202b01
MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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 $(BINDIR); \
diff --git a/sci-biology/mafft/files/mafft-7.305-fno-common.patch b/sci-biology/mafft/files/mafft-7.305-fno-common.patch
new file mode 100644
index 000000000000..0287b6367f8b
--- /dev/null
+++ b/sci-biology/mafft/files/mafft-7.305-fno-common.patch
@@ -0,0 +1,8 @@
+--- a/core/mltaln.h
++++ b/core/mltaln.h
+@@ -336,4 +336,4 @@
+
+ extern double sueff_global;
+ extern double lenfaca, lenfacb, lenfacc, lenfacd;
+-int maxl, tsize;
++extern int maxl, tsize;
diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild
deleted file mode 100644
index 5da5d12d1b31..000000000000
--- a/sci-biology/mafft/mafft-7.050.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-EXTENSIONS="-without-extensions"
-
-DESCRIPTION="Multiple sequence alignments using a variety of algorithms"
-HOMEPAGE="https://mafft.cbrc.jp/alignment/software/index.html"
-SRC_URI="https://mafft.cbrc.jp/alignment/software/${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
-}
diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild
index 9f9f631416b2..f4863892571a 100644
--- a/sci-biology/mafft/mafft-7.305.ebuild
+++ b/sci-biology/mafft/mafft-7.305.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -17,6 +17,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
IUSE="threads"
S="${WORKDIR}/${P}${EXTENSIONS}"
+PATCHES=( "${FILESDIR}"/${PN}-7.305-fno-common.patch )
src_prepare() {
default
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 21:04:11 +0000