Fixup for amd64. Looks like repoman is going to mangle my patches again :(

Package-Manager: portage-2.1.3.9

4 files changed, 119 insertions, 13 deletions

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index 28e5a6febb17..086d6e8d4c57 100644
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/meme
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.3 2007/09/17 06:00:16 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.4 2007/09/17 14:11:13 je_fro Exp $
+
+*meme-3.5.4-r1 (17 Sep 2007)
+
+  17 Sep 2007; <jeff@gentoo.org> files/meme-3.5.4-patch1.patch,
+  files/meme-3.5.4-patch2.patch, +meme-3.5.4-r1.ebuild:
+  Once again, remove parallel install for amd64 boxes, and add upstream patches.
 
   17 Sep 2007; <jeff@gentoo.org> -meme-3.5.4-r1.ebuild:
   Whoa...this version worked in my overlay. Pulling until I figure out what
diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 68d1c1b9e698..bbff97cd1874 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -2,23 +2,27 @@ AUX meme-3.5.4-Makefile.am.patch 377 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93
 MD5 1340a30b4b010637181605a11e78a950 files/meme-3.5.4-Makefile.am.patch 377
 RMD160 a8d4551bcb53b66044ded24421cd2a17bf93b3ad files/meme-3.5.4-Makefile.am.patch 377
 SHA256 ef3f0d8ccca728325d9f9b4f485e8cd4db2ced50fc975f8b66f3b76fcf17b5e8 files/meme-3.5.4-Makefile.am.patch 377
-AUX meme-3.5.4-patch1.patch 8019 RMD160 c443da2f16552c488b77e897bdae543839a0738d SHA1 d37473061f4294d342521570729d65421ead0d99 SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6
-MD5 491211c1a3d87abd057280406f95220c files/meme-3.5.4-patch1.patch 8019
-RMD160 c443da2f16552c488b77e897bdae543839a0738d files/meme-3.5.4-patch1.patch 8019
-SHA256 7f42f3de330e19630ab5eb335043749afd94652b8d2b1564ce8cd6856acf81e6 files/meme-3.5.4-patch1.patch 8019
-AUX meme-3.5.4-patch2.patch 2496 RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 SHA1 cbc691788e2d30cde438f15d94a97f637fdce4a5 SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21
-MD5 7b0765e479af87218368f29ae7041fb8 files/meme-3.5.4-patch2.patch 2496
-RMD160 1d492e01a9e06aa0564e2c15235eb49f28f4d2b7 files/meme-3.5.4-patch2.patch 2496
-SHA256 2571bff727505cddfe59aefa931f2b2436ed2a2daf1e35b5a1d6c6014a753a21 files/meme-3.5.4-patch2.patch 2496
+AUX meme-3.5.4-patch1.patch 8064 RMD160 28a81c1013ec6b064f597265ef78c7d29e95cbf5 SHA1 724f8baaa1f7183437116f5a5a0eae05ea869997 SHA256 a15d1283805fd1ce414f47aa7cb2095f2f6ac4f9b375bc0e3a63f9eed7c58a01
+MD5 763f02a29abf3835c8005f8c5432ad9e files/meme-3.5.4-patch1.patch 8064
+RMD160 28a81c1013ec6b064f597265ef78c7d29e95cbf5 files/meme-3.5.4-patch1.patch 8064
+SHA256 a15d1283805fd1ce414f47aa7cb2095f2f6ac4f9b375bc0e3a63f9eed7c58a01 files/meme-3.5.4-patch1.patch 8064
+AUX meme-3.5.4-patch2.patch 2526 RMD160 1fed3c07b38b1b0244c09e50f6c0c103d69a8268 SHA1 540bc56122e974ae9f1d2cf3ee28241786fc8b8f SHA256 c3eb7c56d769c13a62843d51da0b7c980089353ab97b789fce0bc8d34cc30ff7
+MD5 c0e790d6a390da2798d6effe809249d1 files/meme-3.5.4-patch2.patch 2526
+RMD160 1fed3c07b38b1b0244c09e50f6c0c103d69a8268 files/meme-3.5.4-patch2.patch 2526
+SHA256 c3eb7c56d769c13a62843d51da0b7c980089353ab97b789fce0bc8d34cc30ff7 files/meme-3.5.4-patch2.patch 2526
 DIST meme_3.5.4.tar.gz 1045501 RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 SHA1 d780dba0b900f840a599cf69cfeba4eefd4856b4 SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86
+EBUILD meme-3.5.4-r1.ebuild 2828 RMD160 53c0031f0f8f02d92bb40e5014a4fdab42ad645a SHA1 2a1d3707b20e03980020662ae826789ab05524aa SHA256 dc252b0cf3cd0e450f5bcda22a6ccb620fa4f4084fad84d93343fbf7d4403a0a
+MD5 8dfda51f16c86842a4e7a2743a38afea meme-3.5.4-r1.ebuild 2828
+RMD160 53c0031f0f8f02d92bb40e5014a4fdab42ad645a meme-3.5.4-r1.ebuild 2828
+SHA256 dc252b0cf3cd0e450f5bcda22a6ccb620fa4f4084fad84d93343fbf7d4403a0a meme-3.5.4-r1.ebuild 2828
 EBUILD meme-3.5.4.ebuild 2522 RMD160 91306d472533051cbe7ccb08594a0c527be86d5d SHA1 ca5cc1df4a8fadd2456423231cba5e2168a4eef3 SHA256 1a2e88d01b7183d530d1796b144fc0e4de6f3f0b0faa138e5552ba9a65f9c188
 MD5 f2a6ac226bbcea335120135f8a490df8 meme-3.5.4.ebuild 2522
 RMD160 91306d472533051cbe7ccb08594a0c527be86d5d meme-3.5.4.ebuild 2522
 SHA256 1a2e88d01b7183d530d1796b144fc0e4de6f3f0b0faa138e5552ba9a65f9c188 meme-3.5.4.ebuild 2522
-MISC ChangeLog 713 RMD160 bf5b78869b6c9f4da082482075db25b10387b00b SHA1 20c2c4dde29b952b7a06787e5d8f291c6958a590 SHA256 986e970eb962a95df3fcc1b2c34d7a7a9808477962b5473707fa1ffdf8c6ad3b
-MD5 de2cfd75223564ceb4ffb9888d2fa1a6 ChangeLog 713
-RMD160 bf5b78869b6c9f4da082482075db25b10387b00b ChangeLog 713
-SHA256 986e970eb962a95df3fcc1b2c34d7a7a9808477962b5473707fa1ffdf8c6ad3b ChangeLog 713
+MISC ChangeLog 945 RMD160 3e33164438e93a10b6b48a9ceb12db79b8c1109b SHA1 434af03eac11b1fc23881119bac378cec0741e69 SHA256 1f79b29f2747b0dcc6bae8b7048f8a29d7a61cde794505cacdd7fb384dc33425
+MD5 ad7e086bd3ccb54eff94f19527a9495d ChangeLog 945
+RMD160 3e33164438e93a10b6b48a9ceb12db79b8c1109b ChangeLog 945
+SHA256 1f79b29f2747b0dcc6bae8b7048f8a29d7a61cde794505cacdd7fb384dc33425 ChangeLog 945
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
 MD5 aec0225cc3c4bc9490275e897849b449 metadata.xml 165
 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 metadata.xml 165
@@ -26,3 +30,6 @@ SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132 metadata
 MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4 235
 RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4 235
 SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4 235
+MD5 1eaad7de1310f43b70c0414c120687f6 files/digest-meme-3.5.4-r1 235
+RMD160 ed97244306a01084ca6973c50c49726724212632 files/digest-meme-3.5.4-r1 235
+SHA256 98b3e51f5544aa86ee4cfed70da0b3d9068cd677c3744e750b4f0bee2be5be8b files/digest-meme-3.5.4-r1 235
diff --git a/sci-biology/meme/files/digest-meme-3.5.4-r1 b/sci-biology/meme/files/digest-meme-3.5.4-r1
new file mode 100644
index 000000000000..01fad3060d81
--- /dev/null
+++ b/sci-biology/meme/files/digest-meme-3.5.4-r1
@@ -0,0 +1,3 @@
+MD5 9a8b3d21c6094616cc7b9b424352c697 meme_3.5.4.tar.gz 1045501
+RMD160 063a804c18f07349e95f4aba2a3c97cb025ed2a8 meme_3.5.4.tar.gz 1045501
+SHA256 b753ee276bc5eafeab8ff310e6d938977da11f466d26cfd3ae9c0f0a7a91de86 meme_3.5.4.tar.gz 1045501
diff --git a/sci-biology/meme/meme-3.5.4-r1.ebuild b/sci-biology/meme/meme-3.5.4-r1.ebuild
new file mode 100644
index 000000000000..fe197fe6aba4
--- /dev/null
+++ b/sci-biology/meme/meme-3.5.4-r1.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-3.5.4-r1.ebuild,v 1.3 2007/09/17 14:11:13 je_fro Exp $
+
+inherit autotools eutils toolchain-funcs
+
+DESCRIPTION="The MEME/MAST system - Motif discovery and search"
+HOMEPAGE="http://meme.sdsc.edu/meme"
+SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
+LICENSE="meme"
+
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+# Other possible USE flags include "debug", "client", "server", "web",
+# "queue". Other variables must be set at compile time, but only when
+# the Web server is built. Right now, Web server and client are disabled.
+IUSE="mpi"
+
+# Works only with LAM-MPI.
+DEPEND=">=dev-lang/perl-5.6.1
+	mpi? ( sys-cluster/lam-mpi )"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_unpack() {
+	unpack ${A}
+
+	cd "${S}"
+	epatch "${FILESDIR}/${P}-Makefile.am.patch"
+	epatch "${FILESDIR}/${P}-patch1.patch"
+	epatch "${FILESDIR}/${P}-patch2.patch"
+	einfo "Regenerating autotools files..."
+	eautoreconf
+}
+
+src_compile() {
+	local EXTRA_CONF
+	# Build system is too bugy to make the programs use standard locations.
+	# Put everything in "/opt" instead.
+	EXTRA_CONF="${EXTRA_CONF} --prefix=/opt/${PN}"
+	EXTRA_CONF="${EXTRA_CONF} --with-logs=/var/log/${PN}"
+	# Connect hyperlinks to official Web site.
+	EXTRA_CONF="${EXTRA_CONF} --with-url=http://meme.nbcr.net/meme"
+	# Disable Web server, client and Web site.
+	EXTRA_CONF="${EXTRA_CONF} --disable-server --disable-client --disable-web"
+	# Parallel implementation
+	if ! use mpi; then
+		EXTRA_CONF="${EXTRA_CONF} --enable-serial"
+	fi
+
+	./configure ${EXTRA_CONF} || die "Configure failed."
+	CC="$(tc-getCC)" ac_cc_opt="${CFLAGS}"  make -e || die "Make failed."
+
+# Install parallel files only on x86, otherwise the install fails with the error:
+# i386 architecture of input file `mp.o' is incompatible with i386:x86-64 output
+	if [[ "${ARCH}" == "x86" ]] ; then
+		if use mpi; then
+			cd src/parallel
+			make || die "Parallel make failed."
+		fi
+	fi
+}
+
+src_install() {
+	make install DESTDIR="${D}" || die "Failed to install program files."
+	exeinto "/opt/${PN}/bin"
+	if [[ "${ARCH}" == "x86" ]] ; then
+		if use mpi; then
+		doexe "${S}/src/parallel/${PN}_p" || \
+			die "Failed to install parallel MEME implementation."
+		fi
+	fi
+	keepdir "/var/log/${PN}"
+	fperms 777 "/var/log/${PN}"
+}
+
+pkg_postinst() {
+	echo
+	einfo 'Prior to using MEME/MAST, you should source "/opt/meme/etc/meme.sh"'
+	einfo '(or "/opt/meme/etc/meme.csh" if you use a csh-style shell). To do'
+	einfo 'this automatically with bash, add the following statement to your'
+	einfo '"~/.bashrc" file (without the quotes): "source /opt/meme/etc/meme.sh".'
+	echo
+	einfo 'Log files are produced in the "/var/log/meme" directory.'
+	echo
+}
+
+src_test() {
+	make test || die "Regression tests failed."
+}