sci-biology/meme: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1

3 files changed, 0 insertions, 220 deletions

diff --git a/sci-biology/meme/Manifest b/sci-biology/meme/Manifest
index 4496d777cb23..54d47df7b6ea 100644
--- a/sci-biology/meme/Manifest
+++ b/sci-biology/meme/Manifest
@@ -1,2 +1 @@
 DIST meme_4.11.2.tar.gz 18004930 SHA256 6e3ff843366588ea13fa8060306be9e2c144521912dfb268f03638003bcdd581 SHA512 c97c3815e71e2fb5491548152f00688cdfbf4365f6027657e0ffc68e5d96cdd10a4708e0882ab7a5a61d78d93113c925cf5bb300fbe93fa4b2961becef497894 WHIRLPOOL 6b77d7832342658d5cf546af0b005b59664c811d25a0412df765a15a8c80a75d9618a1f9966c9a2824750eced6605b534d41199382a6f2641e7430540ba19fcf
-DIST meme_4.8.1.tar.gz 8703632 SHA256 c3ad3ca26bc2a7130c5eceb64e1745275c317a5469e98fc8759a9e56babccb8c SHA512 31833169ffa9bd82387d1872be40b0fc4312f4a05bb7abb84daf372244ce3f2a68c89c96722c0453f7bcd9eb4fc84fd3d66e1278af55d556715b94b0df5f87ba WHIRLPOOL 4b5e8968e6964479081d1fe036ff3aa7a50dc56bafc0031890d2e47dbdc8e0273e62ffe01800d8908b2fa9824a4766254bb0fd94003d9ca14784073d5357793e
diff --git a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch b/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
deleted file mode 100644
index e84006295735..000000000000
--- a/sci-biology/meme/files/meme-4.8.1-Makefile.am.patch
+++ /dev/null
@@ -1,134 +0,0 @@
- Makefile.am                                        |  6 +++---
- doc/Makefile.am                                    |  2 +-
- doc/examples/Makefile.am                           | 24 +++++++++++-----------
- .../Makefile.am                                    |  2 +-
- doc/examples/sample_opal_scripts/Makefile.am       |  2 +-
- doc/images/Makefile.am                             |  2 +-
- scripts/Makefile.am                                |  2 +-
- 7 files changed, 20 insertions(+), 20 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 4a69e34..842e33f 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -18,11 +18,11 @@ ARCHIVE_REVISION:
- install-data-hook: dbdir
- 
- dbdir:
--	mkdir -p $(MEME_DB)
-+	mkdir -p $(DESTDIR)$(MEME_DB)
- 
- install-data-local:
--	mkdir -p $(MEME_LOGS)
--	chmod a+w $(MEME_LOGS)
-+	mkdir -p $(DESTDIR)$(MEME_LOGS)
-+	chmod a+w $(DESTDIR)$(MEME_LOGS)
- 
- distdir = $(PACKAGE)_$(VERSION)
- 
-diff --git a/doc/Makefile.am b/doc/Makefile.am
-index e0d6af9..e7bcb4f 100644
---- a/doc/Makefile.am
-+++ b/doc/Makefile.am
-@@ -202,7 +202,7 @@ COMMON_DOC = \
- if WEBSITE
- MEME_DOC_DIR = $(WEBDIR)/doc
- else
--MEME_DOC_DIR = $(prefix)/doc
-+MEME_DOC_DIR = $(docdir)/html
- endif
- 
- memedocdir = $(MEME_DOC_DIR)
-diff --git a/doc/examples/Makefile.am b/doc/examples/Makefile.am
-index 12970b5..633492c 100644
---- a/doc/examples/Makefile.am
-+++ b/doc/examples/Makefile.am
-@@ -51,24 +51,24 @@ if WEBSITE
- exdir = $(WEBDIR)/examples
- other_exdir = $(WEBDIR)/doc/examples
- else
--exdir = $(prefix)/doc/examples
-+exdir = $(prefix)/share/meme/examples
- other_exdir = $(exdir)
- endif
- 
- ex_DATA = $(EXAMPLES)
- 
- install-data-hook:
--	tar xzvf centrimo_example_output_files.tgz -C $(other_exdir)
--	tar xzvf dreme_example_output_files.tgz -C $(other_exdir)
--	tar xzvf fimo_example_output_files.tgz -C $(other_exdir)
--	tar xzvf glam2_example_output_files.tgz -C $(other_exdir)
--	tar xzvf glam2scan_example_output_files.tgz -C $(other_exdir)
--	tar xzvf mast_example_output_files.tgz -C $(other_exdir)
--	tar xzvf mcast_example_output_files.tgz -C $(other_exdir)
--	tar xzvf meme_example_output_files.tgz -C $(other_exdir)
--	tar xzvf memechip_example_output_files.tgz -C $(other_exdir)
--	tar xzvf spamo_example_output_files.tgz -C $(other_exdir)
--	tar xzvf tomtom_example_output_files.tgz -C $(other_exdir)
-+	tar xzvf centrimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf dreme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf fimo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf glam2_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf glam2scan_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf mast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf mcast_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf meme_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf memechip_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf spamo_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
-+	tar xzvf tomtom_example_output_files.tgz -C $(DESTDIR)/$(other_exdir)
- 
- # If .svnignore file doesn't exist
- # create an empty one
-diff --git a/doc/examples/compute_prior_dist_example_output_files/Makefile.am b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-index 747028d..a358f58 100644
---- a/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-+++ b/doc/examples/compute_prior_dist_example_output_files/Makefile.am
-@@ -22,7 +22,7 @@ EXAMPLES = \
- if WEBSITE
- exdir = $(WEBDIR)/doc/examples/compute_prior_dist_example_output_files
- else
--exdir = $(prefix)/doc/examples/compute_prior_dist_example_output_files
-+exdir = $(prefix)/share/meme/examples/compute_prior_dist_example_output_files
- endif
- 
- ex_DATA = $(EXAMPLES)
-diff --git a/doc/examples/sample_opal_scripts/Makefile.am b/doc/examples/sample_opal_scripts/Makefile.am
-index 3a638b3..30925bb 100644
---- a/doc/examples/sample_opal_scripts/Makefile.am
-+++ b/doc/examples/sample_opal_scripts/Makefile.am
-@@ -18,7 +18,7 @@ EXAMPLES = \
- if WEBSITE
- exdir = $(WEBDIR)/doc/examples/sample_opal_scripts
- else
--exdir = $(prefix)/doc/examples/sample_opal_scripts
-+exdir = $(prefix)/share/meme/examples/sample_opal_scripts
- endif
- 
- ex_DATA = $(EXAMPLES)
-diff --git a/doc/images/Makefile.am b/doc/images/Makefile.am
-index c879621..a4696cd 100644
---- a/doc/images/Makefile.am
-+++ b/doc/images/Makefile.am
-@@ -28,7 +28,7 @@ MEME_IMAGES = \
- if WEBSITE
- memeimgdir = $(WEBDIR)/doc/images
- else
--memeimgdir = $(prefix)/doc/images
-+memeimgdir = $(docdir)/html/images
- endif
- 
- memeimg_DATA = $(MEME_IMAGES)
-diff --git a/scripts/Makefile.am b/scripts/Makefile.am
-index 4143e46..8a5c021 100644
---- a/scripts/Makefile.am
-+++ b/scripts/Makefile.am
-@@ -8,7 +8,7 @@
- if WEBSITE
- MEME_DOC_DIR = $(WEBDIR)/doc
- else
--MEME_DOC_DIR = $(prefix)/doc
-+MEME_DOC_DIR = $(docdir)
- endif
- 
- ARCHIVE_REVISION = $(shell cat ../ARCHIVE_REVISION)
diff --git a/sci-biology/meme/meme-4.8.1-r2.ebuild b/sci-biology/meme/meme-4.8.1-r2.ebuild
deleted file mode 100644
index 8a1482c0b32d..000000000000
--- a/sci-biology/meme/meme-4.8.1-r2.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=4
-
-PYTHON_DEPEND="2"
-
-inherit autotools eutils python
-
-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="amd64 x86"
-IUSE="debug examples mpi"
-
-DEPEND="
-	app-shells/tcsh
-	dev-libs/libxml2:2
-	dev-libs/libxslt
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}_${PV}"
-
-#pkg_setup() {
-	# generate meme group to restrict logging to /var/log/meme
-#	enewgroup meme
-#	python_pkg_setup
-#	python_set_active_version 2
-#}
-
-src_prepare() {
-	use examples || sed -e '/SUBDIRS/s:examples::g' -i doc/Makefile.am
-	sed \
-		-e '/flags/s:-O3::g' \
-		-e '/opt/s:-O::g' \
-		-e '/debug/s:-ggdb::' \
-		-e '/debug/s:-g::' \
-		-e 's:CFLAGS=:CFLAGS+=:g' \
-		-i configure.ac || die
-	epatch \
-		"${FILESDIR}"/${P}-Makefile.am.patch
-	eautoreconf
-}
-
-src_configure() {
-	MY_PREFIX="${ROOT}opt/meme"
-	USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi
-	econf \
-		--sysconfdir="${EPREFIX}/etc/meme" \
-		--with-logs="${ROOT}var/log/meme" \
-		$(use_enable debug) \
-		$USE_DISABLE_MPI
-}
-
-src_test() {
-	# bug #297070
-	emake -j1 test
-}
-
-src_install() {
-	local i
-	default
-
-	for i in "${ED}"/usr/bin/*; do
-		mv "${ED}"/usr/bin/{,meme-}$(basename ${i}) || die
-	done
-
-	echo "PATH=/opt/${PN}/bin" > 99${PN}
-	doenvd 99${PN}
-
-	# allow logging only for members of meme group
-	# diropts -m 0770 -g meme -o root
-	diropts -m ugo+rwxt -o root
-	keepdir /var/log/meme
-}
-
-#pkg_postinst() {
-#	einfo 'Log files are produced in the "/var/log/meme" directory. Users'
-#	einfo 'need to be part of the meme group to use this facility.'
-#}