Merge branch 'master' of git+ssh://git@git.overlays.gentoo.org/proj/sci

6 files changed, 130 insertions, 110 deletions

diff --git a/sci-biology/fasta/ChangeLog b/sci-biology/fasta/ChangeLog
index e1143c67b..4fb40ad41 100644
--- a/sci-biology/fasta/ChangeLog
+++ b/sci-biology/fasta/ChangeLog
@@ -1,7 +1,16 @@
 # ChangeLog for sci-biology/fasta
-# Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*fasta-35.4.9 (11 Nov 2009)
+
+  11 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/35.4.9-ldflags.patch, -fasta-35.3.6.ebuild, -fasta-35.4.8.ebuild,
+  +fasta-35.4.9.ebuild:
+  Version bump
+  Fix of the ebuild
+  src_test is broken
+
   06 Jul 2008; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
   Initial import, thanks to Jose Maria Fernandez Gonzalez.
 
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 261337882..006c5c2a1 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,6 +1,15 @@
-DIST fasta-35.3.6.tar.gz 614606 RMD160 f0d8a5514a430d592a030afd69348413d1ac8c63 SHA1 335f2f3732f9b03ba0d6102fd94674f5ac616297 SHA256 4525232e2a1a42388921760d75c5ece6e058d9ce2c35cba074ce544d6e56df15
-DIST fasta-35.4.8.tar.gz 630387 RMD160 9504f8924594cfa2fc8c7d21dd7da2e80ff678f4 SHA1 f076dde53c4f59887828bf919e3060831912aea9 SHA256 2347ca3af2c9f3ee43148852cd31dc7a89a2cb5d130280d0ec0d3287cb833d33
-EBUILD fasta-35.3.6.ebuild 1171 RMD160 058a268f6e8f9d2dcf4f4479303d6b328d5f1a05 SHA1 446781c0ce28898309b77c1311f83580f16a5537 SHA256 2456a736004083126ac3041773810bc612b66e3af0f77fd3bed85467000fcc3c
-EBUILD fasta-35.4.8.ebuild 1185 RMD160 1beb885b72ccf998bce824ade6e6677f7730369e SHA1 9b194bcac3617962802a0f412d7f6ddf11403dc8 SHA256 e030d3e8c7b2d4b686cfda5896a71f899c3c9ab1599d343444f3092ac219f4cb
-MISC ChangeLog 237 RMD160 a2ce23a123f5d353398a267d84bc81663f034abc SHA1 103e50d0f241a7e4d467f627cf98983056e640b8 SHA256 002d044f54613ed80b5b8e261d91f0d56f90cb42745a044560090dc1d3749b80
-MISC metadata.xml 307 RMD160 0993f9568f191dc314f2f742417cca45456af8ff SHA1 94fe99112096a2e23c199fbf22aa8ad8be475b7e SHA256 e998d3ee356e25351b86abf709647bde3856ccceafce876ff17dbd8ea0a8d41b
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 35.4.9-ldflags.patch 1036 RMD160 49cfa8e067824012b46086e6878699dcadf2938e SHA1 1013030756dfadf0ef9d04305e4500701c9a3561 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe
+DIST fasta-35.4.9.tar.gz 631440 RMD160 753d18142932e88b0f2e3d82e460063331be7fce SHA1 bd3d0c5c8419159f4fd80ea1a4557e4a36cd49d1 SHA256 49d18880e20c6ee717844884746415916ca4c29b368c1e7458f6782795543966
+EBUILD fasta-35.4.9.ebuild 1486 RMD160 180a8defedde7717d5eb50235c33c040b406e5ce SHA1 31a0286083c507b09b75baefbd444b76d6586a4f SHA256 c41c71ca8a230a4a7ce97db15aa260b77556e350226aa5030e5d729cbaf09be6
+MISC ChangeLog 479 RMD160 5b17cd6f9bd7672043bd273a7ecc0ef8b88beaaf SHA1 02c07c282c0a6765c92936b262deab5d67c57472 SHA256 4e97be28c22a28f0b9a18236e14b124399f9106ffdf09a10fd2baf521577faf5
+MISC metadata.xml 382 RMD160 75d40acc3b5a8fb8ea656817aa204cc524ef7059 SHA1 7c7a5b42930a24b3fb2609716b7238ba3193e18d SHA256 2d9cc9ccec1bcd41294ff75ff29b4b449868a1dc2cd763ac28ee946a90611185
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkr7OFAACgkQgAnW8HDreRbVBwCfe5Y3N++g1NsYPolLntfFIJ+/
+uwAAn3WjHRZTa1D+NvAhT1R749Vcuk30
+=KYb6
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/fasta/fasta-35.3.6.ebuild b/sci-biology/fasta/fasta-35.3.6.ebuild
deleted file mode 100644
index 39c6c5247..000000000
--- a/sci-biology/fasta/fasta-35.3.6.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="debug icc sse2"
-
-DEPEND="icc? ( dev-lang/icc )"
-RDEPEND=""
-
-CC_ALT=
-CFLAGS_ALT=
-ALT=
-
-if use debug ; then
-	CFLAGS_ALT=-g -DDEBUG
-fi
-
-if use icc ; then
-	CC_ALT=icc
-	ALT="${ALT}_icc"
-else
-	CC_ALT=gcc
-fi
-
-if use sse2 ; then
-	ALT="${ALT}_sse2"
-	CFLAGS_ALT="${CFLAGS_ALT} -msse2"
-	if ! use icc ; then
-		CFLAGS_ALT="${CFLAGS_ALT} -ffast-math"
-	fi
-fi
-
-src_compile() {
-	einfo "Using $CC_ALT compiler"
-	make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" all
-}
-
-src_install() {
-	dodir /usr/bin
-	make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" XDIR="${D}/usr/bin" install
-	doman fasta3.1  fasta35.1  fastf3.1  fasts3.1  map_db.1  prss3.1  ps_lav.1 pvcomp.1
-	dodoc COPYRIGHT FASTA_LIST README README.versions fasta20.doc
-	dohtml changes_v34.html changes_v35.html search.html
-}
diff --git a/sci-biology/fasta/fasta-35.4.8.ebuild b/sci-biology/fasta/fasta-35.4.8.ebuild
deleted file mode 100644
index 403d84073..000000000
--- a/sci-biology/fasta/fasta-35.4.8.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
-HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
-
-LICENSE="fasta"
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-IUSE="debug icc sse2"
-
-DEPEND="icc? ( dev-lang/icc )"
-RDEPEND=""
-
-CC_ALT=
-CFLAGS_ALT=
-ALT=
-
-if use debug ; then
-	CFLAGS_ALT=-g -DDEBUG
-fi
-
-if use icc ; then
-	CC_ALT=icc
-	ALT="${ALT}_icc"
-else
-	CC_ALT=gcc
-fi
-
-if use sse2 ; then
-	ALT="${ALT}_sse2"
-	CFLAGS_ALT="${CFLAGS_ALT} -msse2"
-	if ! use icc ; then
-		CFLAGS_ALT="${CFLAGS_ALT} -ffast-math"
-	fi
-fi
-
-src_compile() {
-	einfo "Using $CC_ALT compiler"
-#	cd src
-	make -f make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" all
-}
-
-src_install() {
-	dodir /usr/bin
-	make -f Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" XDIR="${D}/usr/bin" install
-	doman fasta3.1  fasta35.1  fastf3.1  fasts3.1  map_db.1  prss3.1  ps_lav.1 pvcomp.1
-	dodoc COPYRIGHT FASTA_LIST README README.versions fasta20.doc
-	dohtml changes_v34.html changes_v35.html search.html
-}
diff --git a/sci-biology/fasta/fasta-35.4.9.ebuild b/sci-biology/fasta/fasta-35.4.9.ebuild
new file mode 100644
index 000000000..c57529f9c
--- /dev/null
+++ b/sci-biology/fasta/fasta-35.4.9.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit eutils
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="debug icc sse2 test"
+
+DEPEND="
+	icc? ( dev-lang/icc )
+	test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	if use debug ; then
+		CFLAGS_ALT="-g -DDEBUG"
+	fi
+
+	if use icc ; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT=gcc
+
+		case $(uname -m) in
+
+			i*86		)
+				ALT="32";;
+
+			x86_64	)
+				ALT="64";;
+
+		esac
+	fi
+
+	if use sse2 ; then
+		ALT="${ALT}_sse2"
+		CFLAGS_ALT="${CFLAGS_ALT} -msse2"
+		if ! use icc ; then
+			CFLAGS_ALT="${CFLAGS_ALT} -ffast-math"
+		fi
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export CFLAGS_ALT="${CFLAGS_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+	einfo "Using $CC_ALT compiler"
+	cd src
+	make -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS} ${CFLAGS_ALT}" HFLAGS="${LDFLAGS} -o" all || die
+}
+
+src_test() {
+	cd test
+	PATH="${S}/bin:${PATH}" csh test.sh
+}
+
+src_install() {
+	dobin bin/* || die
+	doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
+}
diff --git a/sci-biology/fasta/files/35.4.9-ldflags.patch b/sci-biology/fasta/files/35.4.9-ldflags.patch
new file mode 100644
index 000000000..c3b7a9b56
--- /dev/null
+++ b/sci-biology/fasta/files/35.4.9-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index a808667..405be95 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+ 
+ res_stats : res_stats.o scale_se.o
+-	$(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm