Version BUmp, keyworded for prefix, repecting multilib and LDFLAGS

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 251 insertions, 7 deletions

diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog
index a0d2b6397d68..a07155e73edb 100644
--- a/sci-biology/mafft/ChangeLog
+++ b/sci-biology/mafft/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/mafft
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.6 2009/07/27 05:53:45 dberkholz Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.7 2010/06/15 13:17:02 jlec Exp $
+
+*mafft-6.811 (15 Jun 2010)
+
+  15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/6.811-respect.patch,
+  +mafft-6.811.ebuild:
+  Version BUmp, keyworded for prefix, repecting multilib and LDFLAGS
 
 *mafft-6.707 (27 Jul 2009)
 
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 095d25930c8d..465b8b15fd48 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,17 +1,20 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
+AUX 6.811-respect.patch 6327 RMD160 03c7abe1a03a161698cfdad2f271cbf8d5308bc0 SHA1 be7eea3fcdb65b3bccd4d900cf53b8a41610482f SHA256 3d527220ce3fb90e4fa2dd2f41bca1f2684bb03f0de94313d7aea432b955e37c
 AUX mafft-6.240-mktemp.patch 6497 RMD160 ffa5d5889315614fd065e72425b1db3e8272f7b2 SHA1 5584719991e7b5c7d014c8cb1b59391f71f24668 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533
 DIST mafft-6.240-src.tgz 657197 RMD160 1cb77af7a5a6b9ab818560d9626e746fb7a3b839 SHA1 8fc05350d9dcf8a9f56bdeed20790a4e1f21ceba SHA256 d0183ab1d6a5e0d1132b95cb917fedb3b6dc16c38d3fde35d7140ecdca555e8f
 DIST mafft-6.707-without-extensions-src.tgz 455884 RMD160 6676133b9f50c2037f13f50ea86e9543022028ce SHA1 1dd955255e5572b8c4a0b23c65cea832383b6a97 SHA256 08789aa9351128e32b0003cb524668c3f2e35aec7ea9f834047f0780851989a0
+DIST mafft-6.811-without-extensions-src.tgz 500063 RMD160 1b26aeb742df3bf8ed3849907ca966b1ebd41ebc SHA1 09bc404c1d39609373989faffe9e04b043c2355e SHA256 a99b57444787b2e910b0b56a5cc8c69949dc987b7ff12995650a1dd0be065c43
 EBUILD mafft-6.240-r1.ebuild 910 RMD160 c09e76a79148cd64c8c931e33a9dbf4fdee086b7 SHA1 3de8b46a86dd83496ae1520893a576179b77ddf0 SHA256 45ebb273c1f05c1012a16b79305916792a8dedb42020d1ada18244ea5ea2d6aa
 EBUILD mafft-6.707.ebuild 873 RMD160 5551f700c2d01ea25d1b0074273db8292d22157f SHA1 6d1d10296e13df14ed3db9ae9ded77adbad10ed4 SHA256 fd2c6d4be6a8eb56fed19bfd0fecba8ad41beff499189bd0e0f982eaebe173eb
-MISC ChangeLog 1514 RMD160 6f172ceb02ccf3feedc704091c8e714a87721aeb SHA1 4b96fdce6c2bea0513c8a225154b05426872fb21 SHA256 8ec35ebab8941b0556090eb5eae3d22179dbeb8c14269f786cd8145a5c2372c2
+EBUILD mafft-6.811.ebuild 1045 RMD160 491da2411ecd105d3b576a2ff87f78d79fd18e89 SHA1 902b6030b177b42491775f283a3a48d65c1f84e3 SHA256 6c603b6fd89a3e05419089c52676b6f4f87bf74871338a5762ec084a62392937
+MISC ChangeLog 1705 RMD160 3aec29961e6d241bc2981887f81c492ad59d4b00 SHA1 4d0e7f4d9f894f9ed2b8a9c87f054812aab62163 SHA256 4a949fdd1d7104e1f3fd200fb361af55312adf1ef3e3aa57abdebb494c1b3c83
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkptQO4ACgkQXVaO67S1rtu95ACeNshhryiG4aQEsQel8uuBMgPJ
-25IAoJnpxQ3/MrTlK/qjYrzAsWiwJvSE
-=2HX7
+iEYEARECAAYFAkwXfVQACgkQgAnW8HDreRYqtgCgio15P2ZtblpM3MudSoGPimoH
+0s4Ani2O54CA4qBpfDWS3s01jeW/sID2
+=G0+h
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/mafft/files/6.811-respect.patch b/sci-biology/mafft/files/6.811-respect.patch
new file mode 100644
index 000000000000..ebfb2c7be7b8
--- /dev/null
+++ b/sci-biology/mafft/files/6.811-respect.patch
@@ -0,0 +1,192 @@
+diff --git a/core/Makefile b/core/Makefile
+index 8bb8baf..cf28559 100644
+--- a/core/Makefile
++++ b/core/Makefile
+@@ -1,5 +1,5 @@
+ PREFIX = /usr/local
+-LIBDIR = $(PREFIX)/lib/mafft
++LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
+ BINDIR = $(PREFIX)/bin
+ MANDIR = $(PREFIX)/man/man1
+ 
+@@ -127,136 +127,136 @@ mltaln.h : functions.h
+ 	touch mltaln.h
+ 
+ ord : $(OBJORD)
+-	$(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
+ 
+ tbfast : $(OBJTBFAST)
+-	$(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
+ 
+ tbfast2 : $(OBJTBFAST2)
+-	$(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ disttbfast : $(OBJDISTTBFAST)
+-	$(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splittbfast : $(OBJSPLITTBFAST)
+-	$(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splitfromaln : $(OBJSPLITFROMALN)
+-	$(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
+ 
+ splittbfast2 : $(OBJSPLITTBFAST2)
+-	$(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ dummy : $(OBJDUMMY)
+-	$(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
+ 
+ setcore : $(OBJSETCORE)
+-	$(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
+ 
+ countlen : $(OBJCOUNTLEN)
+-	$(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
+ 
+ seq2regtable : $(OBJSEQ2REGTABLE)
+-	$(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
+ 
+ regtable2seq : $(OBJREGTABLE2SEQ)
+-	$(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
+ 
+ f2cl : $(OBJF2CL)
+-	$(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
+ 
+ mccaskillwrap : $(OBJMCCASKILLWRAP)
+-	$(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
+ 
+ contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+-	$(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
+ 
+ pairlocalalign : $(OBJPAIRLOCALALIGN)
+-	$(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
+ 
+ pairash : $(OBJPAIRASH)
+-	$(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
+ 
+ rnatest : $(OBJRNATEST)
+-	$(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
+ 
+ pair2hat3s : $(OBJPAIR2HAT3S)
+-	$(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ multi2hat3s : $(OBJMULTI2HAT3S)
+-	$(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ getlag : $(OBJGETLAG)
+-	$(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
+ 
+ tditr : $(OBJTDITR)
+-	$(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
+ 
+ dvtditr : $(OBJDVTDITR)
+-	$(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
+ 
+ mafft-profile : $(OBJGALN)
+-	$(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
+ 
+ gapfill : $(OBJGAPFILL)
+-	$(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
+ 
+ dndfast4 : $(OBJDNDFAST4)
+-	$(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
+ 
+ dndfast5 : $(OBJDNDFAST5)
+-	$(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
+ 
+ dndfast6 : $(OBJDNDFAST6)
+-	$(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
+ 
+ dndfast7 : $(OBJDNDFAST7)
+-	$(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
+ 
+ dndblast : $(OBJDNDBLAST)
+-	$(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
+ 
+ dndfast3 : $(OBJDNDFAST3)
+-	$(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
+ 
+ triplet : $(OBJTRIPLET)
+-	$(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
+ 
+ triplet3 : $(OBJTRIPLET3)
+-	$(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
+ 
+ sextet3 : $(OBJSEXTET3)
+-	$(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
+ 
+ sextet4 : $(OBJSEXTET4)
+-	$(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
+ 
+ sextet5 : $(OBJSEXTET5)
+-	$(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
+ 
+ mafft-distance : $(OBJDISTANCE)
+-	$(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
+ 
+ triplet5 : $(OBJTRIPLET5)
+-	$(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
+ 
+ triplet6 : $(OBJTRIPLET6)
+-	$(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
+ 
+ octet4 : $(OBJOCTET4)
+-	$(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
+ 
+ dndpre : $(OBJDNDPRE)
+-	$(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
+ 
+ dndpre2 : $(OBJDNDPRESCORE)
+-	$(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
+ 
+ score : $(OBJSCORE)
+-	$(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
+ 
+ genMtx : $(OBJGENMTX)
+-	$(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
+ 
+ gapfill.o : gapfill.c $(HEADER)
+ 	$(CC) $(CFLAGS) -c gapfill.c
diff --git a/sci-biology/mafft/mafft-6.811.ebuild b/sci-biology/mafft/mafft-6.811.ebuild
new file mode 100644
index 000000000000..6b4aa944516b
--- /dev/null
+++ b/sci-biology/mafft/mafft-6.811.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-6.811.ebuild,v 1.1 2010/06/15 13:17:02 jlec Exp $
+
+EAPI="3"
+
+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="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PV}-respect.patch
+	use threads && append-flags -Denablemultithread
+	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile
+}
+
+src_compile() {
+	pushd core
+	emake \
+		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
+}