InCvs

13 files changed, 0 insertions, 462 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
deleted file mode 100644
index fcfbff20b..000000000
--- a/sci-chemistry/apbs/ChangeLog
+++ /dev/null
@@ -1,55 +0,0 @@
-# ChangeLog for sci-chemistry/apbs
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*apbs-1.2 (28 Oct 2009)
-
-  28 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +apbs-1.2.ebuild,
-  +files/apbs-1.2-LDFLAGS.patch, +files/apbs-1.2-contrib.patch,
-  +files/apbs-1.2-install-fix.patch, +files/apbs-1.2-vgrid-maloc.patch:
-  version bump
-  openmp support added
-
-  27 Apr 2009; Alexey Shvetsov <alexxy@gentoo.org> apbs-1.1.0-r1.ebuild:
-  fix epatch
-
-*apbs-1.1.0-r1 (27 Apr 2009)
-
-  27 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +apbs-1.1.0-r1.ebuild, -apbs-1.1.0.ebuild:
-  needed version bump because of collosion with ZSI
-
-  24 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> apbs-1.1.0.ebuild:
-  removed bundled opal and ZSI
-
-  22 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> apbs-1.1.0.ebuild:
-  adopted things to changed upstream tarball
-
-  20 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/apbs-1.1.0-automagic.patch, apbs-1.1.0.ebuild:
-  Ugly automagic removed
-
-  19 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  files/apbs-1.1.0-install-fix.patch, metadata.xml, apbs-1.1.0.ebuild:
-  fix of doc installation dir
-
-*apbs-1.1.0 (18 Mar 2009)
-
-  18 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
-  +files/apbs-1.1.0-LDFLAGS.patch, +files/apbs-1.1.0-install-fix.patch,
-  +files/apbs-1.1.0-vgrid-maloc.patch, +metadata.xml, +apbs-1.1.0.ebuild:
-  version bump to 1.1.0
-  New USE flags:
-	fetk support for Fetk
-	arpack support for arpack
-  fixed some mpi things	
-
-  27 Jan 2009; justin Lecher (jlec) <jlec@j-schmitz.net>
-  apbs-1.0.0-r2.ebuild:
-  URI fixed
-
-  11 Oct 2008; Justin Lecher <justin@j-schmitz.net>
-  +files/apbs-1.0.0-LDFLAGS.patch, metadata.xml, -apbs-0.5.1-r1.ebuild,
-  -apbs-1.0.0.ebuild, +apbs-1.0.0-r2.ebuild:
-  revision bump from portage
-
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
deleted file mode 100644
index 66ec51503..000000000
--- a/sci-chemistry/apbs/Manifest
+++ /dev/null
@@ -1,24 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-AUX apbs-1.1.0-LDFLAGS.patch 1186 RMD160 0c45d0dfde403a5b2755a51ae3ccbf4297da4f86 SHA1 5a91fe04f20ca62fb00a00bcc97cb8aa30146295 SHA256 268ce48a04995027dc71448ecc454ea843c0bf07ea8270ff5ad7316fd83e654a
-AUX apbs-1.1.0-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457 SHA1 653295c9ff7ac075613dd82ce332b41b0e2ea37e SHA256 0b2a1c518c66de6010954f101c1622cfd570bbfcc4774d98607174e57e67f1b3
-AUX apbs-1.1.0-install-fix.patch 1384 RMD160 6d2b8bb6ceb92d4b9aa54e8aa3fde1c95087692e SHA1 3d94968961bf91814fce8044b530129630a9c3b1 SHA256 e2dd5c492231d66d4b21494a6d8aec2fab6a3f290abec03d137af606eb07c31e
-AUX apbs-1.1.0-vgrid-maloc.patch 1306 RMD160 f6932bd7bb16d5bca69840bd7356ef08507a5f00 SHA1 4a7db2cd90084cd68fcef88d4e32ea0d6ce74074 SHA256 241ca937f2ac63bcd13c4b546da7e1f0b1f1ac69c83c6f0cbe1c9740729f0457
-AUX apbs-1.2-LDFLAGS.patch 1186 RMD160 0c45d0dfde403a5b2755a51ae3ccbf4297da4f86 SHA1 5a91fe04f20ca62fb00a00bcc97cb8aa30146295 SHA256 268ce48a04995027dc71448ecc454ea843c0bf07ea8270ff5ad7316fd83e654a
-AUX apbs-1.2-contrib.patch 382 RMD160 4c0c75e57fb6a0c298606d87785a5b9daa8db457 SHA1 653295c9ff7ac075613dd82ce332b41b0e2ea37e SHA256 0b2a1c518c66de6010954f101c1622cfd570bbfcc4774d98607174e57e67f1b3
-AUX apbs-1.2-install-fix.patch 1384 RMD160 6d2b8bb6ceb92d4b9aa54e8aa3fde1c95087692e SHA1 3d94968961bf91814fce8044b530129630a9c3b1 SHA256 e2dd5c492231d66d4b21494a6d8aec2fab6a3f290abec03d137af606eb07c31e
-AUX apbs-1.2-vgrid-maloc.patch 1306 RMD160 f6932bd7bb16d5bca69840bd7356ef08507a5f00 SHA1 4a7db2cd90084cd68fcef88d4e32ea0d6ce74074 SHA256 241ca937f2ac63bcd13c4b546da7e1f0b1f1ac69c83c6f0cbe1c9740729f0457
-DIST apbs-1.1.0-source.tar.gz 10582742 RMD160 f03c5617067cc33cb43e425acc74a5df3374744f SHA1 7274a3a896da551f2bb689bb32ea5c852cbd32bb SHA256 8c561920a22e314070baf9e200fa324912ad49de4595c0b54c7608ea3a759b45
-DIST apbs-1.2-source.tar.gz 10593537 RMD160 62cb82da9ca5276c3d7127a4d1f9737747dac315 SHA1 43e766a8c6166288c25229e0615a72dca5e8a3b5 SHA256 b8b74d80f8b4e553cd2e51727efc79436152cd4f5e02be076e7cdf994aa5424e
-EBUILD apbs-1.1.0-r1.ebuild 2506 RMD160 a4a8f96162a9fe5850c7bc68d8eb34d73e6a187c SHA1 92ee51345408623b631031c47cd139ba6579c414 SHA256 50724722d38be418b978e66d0e570c98624d405bc5631eb2ea7f399258d642b7
-EBUILD apbs-1.2.ebuild 2703 RMD160 df64c9e5edb83ad490e9cc1c2f98323b093158eb SHA1 ee5b997ad58f6229263fe22d654b74df769a791d SHA256 67fe8d8c8a02e73f501b6caa0ecf2858efd9f73ab0f4bb468981ebd8bf502a4d
-MISC ChangeLog 1834 RMD160 c0310433728dea204fab3ba55c068c41958d6f0f SHA1 6084f8ac058dcafcd4174be2f363de85a3066fc6 SHA256 ecc04d74cf80f400dabf3e6749f650f0845dbfe19266fb6657549d26c1aa608a
-MISC metadata.xml 458 RMD160 3f41064ca200d7f85d3f790de6711aada270ac43 SHA1 69d50a5bfb0ed66870727f24f50f828dbc4abedb SHA256 c49607c06b8f41e5b3268d27258ad33b7784e29564f49585f3996d8f03568e17
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.11 (GNU/Linux)
-
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-gGkAn3STnOrMCEE5Z/YhxGh2kbD/3pR5
-=UH3b
------END PGP SIGNATURE-----
diff --git a/sci-chemistry/apbs/apbs-1.1.0-r1.ebuild b/sci-chemistry/apbs/apbs-1.1.0-r1.ebuild
deleted file mode 100644
index 47d01c94b..000000000
--- a/sci-chemistry/apbs/apbs-1.1.0-r1.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit eutils fortran autotools python
-
-MY_P="${P}-source"
-S="${WORKDIR}"/"${MY_P}"
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-LICENSE="BSD"
-HOMEPAGE="http://apbs.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-IUSE="arpack blas doc fetk mpi python tinker"
-KEYWORDS="~x86 ~amd64"
-
-DEPEND="dev-libs/maloc[mpi=]
-	blas? ( virtual/blas )
-	python? ( dev-lang/python )
-	sys-libs/readline
-	arpack? ( sci-libs/arpack )
-	mpi? ( virtual/mpi )
-	fetk? ( dev-libs/punc )
-	tinker? ( sci-chemistry/tinker )
-	dev-python/zsi
-	dev-python/opal-client"
-RDEPEND="${DEPEND}"
-
-FORTRAN="g77 gfortran ifc"
-
-src_prepare() {
-	python_version
-
-	epatch "${FILESDIR}"/${P}-install-fix.patch
-	epatch "${FILESDIR}"/${P}-contrib.patch
-	epatch "${FILESDIR}"/${P}-LDFLAGS.patch
-	epatch "${FILESDIR}"/${P}-vgrid-maloc.patch
-	sed "s:GENTOO_PKG_NAME:${P}:g" \
-	-i Makefile.am || die "Cannot correct package name"
-	eautoreconf
-
-	find "${S}" -type f -name "*.py" \
-		-exec sed -e "s|/usr/bin/env python|${python}|g" -i '{}' \;
-}
-
-src_configure() {
-	local myconf="--docdir=/usr/share/doc/${PF}"
-	use blas && myconf="${myconf} --with-blas=-lblas"
-	use arpack && myconf="${myconf} --with-arpack=/usr/$(get_libdir)"
-	use fetk && myconf="${myconf} $(use_enable fetk) --with-fetk-include=/usr/include --with-fetk-library=/usr/$(get_libdir)"
-
-	# check which mpi version is installed and tell configure
-	if use mpi; then
-		export CC="/usr/bin/mpicc"
-		export F77="/usr/bin/mpif77"
-
-		if has_version sys-cluster/mpich; then
-	 		myconf="${myconf} --with-mpich=/usr"
-		elif has_version sys-cluster/mpich2; then
-			myconf="${myconf} --with-mpich2=/usr"
-		elif has_version sys-cluster/lam-mpi; then
-			myconf="${myconf} --with-lam=/usr"
-		elif has_version sys-cluster/openmpi; then
-			myconf="${myconf} --with-openmpi=/usr"
-		fi
-	fi || die "Failed to select proper mpi implementation"
-
-	econf $(use_enable python) \
-		$(use_enable tinker) \
-		--disable-maloc-rebuild \
-		${myconf} || die "configure failed"
-}
-
-src_compile() {
-	emake -j1 || die "make failed"
-}
-
-src_test() {
-	cd examples && make test \
-		|| die "Tests failed"
-}
-
-src_install() {
-	emake -j1 DESTDIR="${D}" install || die "make install failed"
-	dodoc AUTHORS INSTALL README NEWS ChangeLog \
-		|| die "Failed to install docs"
-	use doc || rm -rf "${D}"/usr/share/${P}/doc
-}
diff --git a/sci-chemistry/apbs/apbs-1.2.ebuild b/sci-chemistry/apbs/apbs-1.2.ebuild
deleted file mode 100644
index 60ca56d8c..000000000
--- a/sci-chemistry/apbs/apbs-1.2.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils fortran flag-o-matic python
-
-MY_P="${P}-source"
-FORTRAN="g77 gfortran ifc"
-
-DESCRIPTION=" Software for evaluating the electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="http://apbs.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz"
-
-SLOT="0"
-KEYWORDS="~x86 ~amd64"
-LICENSE="BSD"
-IUSE="arpack blas doc fetk mpi openmp python tinker"
-
-DEPEND="
-	dev-libs/maloc[mpi=]
-	dev-python/zsi
-	dev-python/opal-client
-	sys-libs/readline
-	arpack? ( sci-libs/arpack )
-	blas? ( virtual/blas )
-	fetk? ( dev-libs/punc )
-	mpi? ( virtual/mpi )
-	python? ( dev-lang/python )
-	tinker? ( sci-chemistry/tinker )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${MY_P}"
-
-src_prepare() {
-	python_version
-	epatch \
-		"${FILESDIR}"/${P}-install-fix.patch \
-		"${FILESDIR}"/${P}-contrib.patch \
-		"${FILESDIR}"/${P}-LDFLAGS.patch \
-		"${FILESDIR}"/${P}-vgrid-maloc.patch
-
-	sed \
-		-e "s:GENTOO_PKG_NAME:${P}:g" \
-		-i Makefile.am || die "Cannot correct package name"
-
-	eautoreconf
-
-	find "${S}" -type f -name "*.py" \
-		-exec sed -e "s|/usr/bin/env python|${python}|g" -i '{}' \;
-}
-
-src_configure() {
-	local myconf="--docdir=/usr/share/doc/${PF}"
-	use arpack && myconf="${myconf} --with-arpack=/usr/$(get_libdir)"
-	use blas && myconf="${myconf} --with-blas=-lblas"
-	use fetk && myconf="${myconf} $(use_enable fetk) --with-fetk-include=/usr/include --with-fetk-library=/usr/$(get_libdir)"
-
-	# The configure is somehow borked, but does the same as the following lines
-	if use openmp; then
-		append-flags -fopenmp
-	else
-		myconf="${myconf} --disable-openmp"
-	fi
-
-	# check which mpi version is installed and tell configure
-	if use mpi; then
-		export CC="/usr/bin/mpicc"
-		export F77="/usr/bin/mpif77"
-
-		if has_version sys-cluster/mpich; then
-	 		myconf="${myconf} --with-mpich=/usr"
-		elif has_version sys-cluster/mpich2; then
-			myconf="${myconf} --with-mpich2=/usr"
-		elif has_version sys-cluster/lam-mpi; then
-			myconf="${myconf} --with-lam=/usr"
-		elif has_version sys-cluster/openmpi; then
-			myconf="${myconf} --with-openmpi=/usr"
-		fi
-	fi || die "Failed to select proper mpi implementation"
-	econf \
-		$(use_enable python) \
-		$(use_enable tinker) \
-		--disable-maloc-rebuild \
-		${myconf} || die "configure failed"
-}
-
-src_compile() {
-	emake -j1 || die "make failed"
-}
-
-src_test() {
-	cd examples && make test \
-		|| die "Tests failed"
-}
-
-src_install() {
-	emake -j1 DESTDIR="${D}" install || die "make install failed"
-	dodoc AUTHORS INSTALL README NEWS ChangeLog \
-		|| die "Failed to install docs"
-	use doc || rm -rf "${D}"/usr/share/${P}/doc
-}
diff --git a/sci-chemistry/apbs/files/apbs-1.1.0-LDFLAGS.patch b/sci-chemistry/apbs/files/apbs-1.1.0-LDFLAGS.patch
deleted file mode 100644
index 4fd03d93c..000000000
--- a/sci-chemistry/apbs/files/apbs-1.1.0-LDFLAGS.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- tools/python/Makefile.am	2009-03-17 16:46:16.000000000 +0100
-+++ tools/python/Makefile.am.new	2009-03-17 16:46:08.000000000 +0100
-@@ -15,5 +15,5 @@
- 
- noinst_PROGRAMS       = _apbslib.so
- _apbslib_so_SOURCES   = apbslib.c
--_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
- _apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
---- tools/python/vgrid/Makefile.am	2009-03-17 16:46:00.000000000 +0100
-+++ tools/python/vgrid/Makefile.am.new	2009-03-17 16:45:52.000000000 +0100
-@@ -15,6 +15,6 @@
- if PY_PRESENT
-    noinst_PROGRAMS     = _vgrid.so
-    _vgrid_so_SOURCES   = vgridlib.c
--   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-    _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
- endif
diff --git a/sci-chemistry/apbs/files/apbs-1.1.0-contrib.patch b/sci-chemistry/apbs/files/apbs-1.1.0-contrib.patch
deleted file mode 100644
index 6bfc9ffaa..000000000
--- a/sci-chemistry/apbs/files/apbs-1.1.0-contrib.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- contrib/Makefile.am	2009-03-05 21:30:09.000000000 +0100
-+++ contrib/Makefile.am.new	2009-04-24 19:08:39.000000000 +0200
-@@ -9,6 +9,6 @@
- AUTOMAKE_OPTIONS = no-dependencies
- SUFFIXES = .H .h .C .c .f .o
- 
--always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal
-+always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua
- 
- SUBDIRS = $(always_built_SUBDIRS) .
diff --git a/sci-chemistry/apbs/files/apbs-1.1.0-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.1.0-install-fix.patch
deleted file mode 100644
index 855c20748..000000000
--- a/sci-chemistry/apbs/files/apbs-1.1.0-install-fix.patch
+++ /dev/null
@@ -1,40 +0,0 @@
---- Makefile.am	2009-03-05 21:30:56.000000000 +0100
-+++ Makefile.am.new	2009-03-17 16:43:38.000000000 +0100
-@@ -28,10 +28,20 @@
- 	-rm -f ./bin/apbs
- 
- install-data-local:
--	mkdir -p ${prefix}/share
--	-cp -rf examples ${prefix}/share 
--	-cp -rf doc ${prefix}/share 
--	-cp -rf tools ${prefix}/share
-+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
-+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
-+	-rm -f doc/LICENSE.txt
-+	-rm -f tools/manip/*.pyc
-+	-rm -f tools/**/*.o
-+	-rm -f tools/**/Makefile*
-+	-rm -f tools/**/**/*.o
-+	-rm -f tools/**/**/Makefile*
-+	-rm -f tools/Makefile*
-+	-rm -f examples/Makefile*
-+	-rm -f examples/**/Makefile*
-+	-cp -rf doc $(DESTDIR)${prefix}/share/doc/GENTOO_PKG_NAME/html
-+	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
-+	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
- 
- test:
- 	cd examples; make test
---- bin/Makefile.am	2009-03-05 21:30:49.000000000 +0100
-+++ bin/Makefile.am.new	2009-03-18 13:04:00.000000000 +0100
-@@ -30,6 +30,6 @@
- include_HEADERS = routines.h
- 
- install-data-local:
--	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
--	-chmod 755 ${prefix}/bin/ApbsClient.py
--	-rm -f ${prefix}/bin/wsdl2py 
-\ No newline at end of file
-+	-cp -p ${top_apbsdir}/bin/ApbsClient.py $(DESTDIR)${prefix}/bin
-+	-chmod 755 $(DESTDIR)${prefix}/bin/ApbsClient.py
-+	-rm -f $(DESTDIR)${prefix}/bin/wsdl2py 
diff --git a/sci-chemistry/apbs/files/apbs-1.1.0-vgrid-maloc.patch b/sci-chemistry/apbs/files/apbs-1.1.0-vgrid-maloc.patch
deleted file mode 100644
index 722cf3665..000000000
--- a/sci-chemistry/apbs/files/apbs-1.1.0-vgrid-maloc.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- tools/python/vgrid/Makefile.am	2009-03-18 10:00:14.000000000 +0100
-+++ tools/python/vgrid/Makefile.am.new	2009-03-18 10:06:14.000000000 +0100
-@@ -16,5 +16,5 @@
-    noinst_PROGRAMS     = _vgrid.so
-    _vgrid_so_SOURCES   = vgridlib.c
-    _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
--   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
-+   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) @lib_list@
- endif
-
---- tools/python/Makefile.am	2009-03-18 10:51:15.000000000 +0100
-+++ tools/python/Makefile.am.new	2009-03-18 10:53:33.000000000 +0100
-@@ -16,4 +16,4 @@
- noinst_PROGRAMS       = _apbslib.so
- _apbslib_so_SOURCES   = apbslib.c
- _apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
--_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
-+_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS)
-
diff --git a/sci-chemistry/apbs/files/apbs-1.2-LDFLAGS.patch b/sci-chemistry/apbs/files/apbs-1.2-LDFLAGS.patch
deleted file mode 100644
index 4fd03d93c..000000000
--- a/sci-chemistry/apbs/files/apbs-1.2-LDFLAGS.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- tools/python/Makefile.am	2009-03-17 16:46:16.000000000 +0100
-+++ tools/python/Makefile.am.new	2009-03-17 16:46:08.000000000 +0100
-@@ -15,5 +15,5 @@
- 
- noinst_PROGRAMS       = _apbslib.so
- _apbslib_so_SOURCES   = apbslib.c
--_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+_apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
- _apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
---- tools/python/vgrid/Makefile.am	2009-03-17 16:46:00.000000000 +0100
-+++ tools/python/vgrid/Makefile.am.new	2009-03-17 16:45:52.000000000 +0100
-@@ -15,6 +15,6 @@
- if PY_PRESENT
-    noinst_PROGRAMS     = _vgrid.so
-    _vgrid_so_SOURCES   = vgridlib.c
--   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-+   _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
-    _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
- endif
diff --git a/sci-chemistry/apbs/files/apbs-1.2-contrib.patch b/sci-chemistry/apbs/files/apbs-1.2-contrib.patch
deleted file mode 100644
index 6bfc9ffaa..000000000
--- a/sci-chemistry/apbs/files/apbs-1.2-contrib.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- contrib/Makefile.am	2009-03-05 21:30:09.000000000 +0100
-+++ contrib/Makefile.am.new	2009-04-24 19:08:39.000000000 +0200
-@@ -9,6 +9,6 @@
- AUTOMAKE_OPTIONS = no-dependencies
- SUFFIXES = .H .h .C .c .f .o
- 
--always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua opal
-+always_built_SUBDIRS = @apbs_do_blas@ @apbs_do_maloc@ pmgZ aqua
- 
- SUBDIRS = $(always_built_SUBDIRS) .
diff --git a/sci-chemistry/apbs/files/apbs-1.2-install-fix.patch b/sci-chemistry/apbs/files/apbs-1.2-install-fix.patch
deleted file mode 100644
index 855c20748..000000000
--- a/sci-chemistry/apbs/files/apbs-1.2-install-fix.patch
+++ /dev/null
@@ -1,40 +0,0 @@
---- Makefile.am	2009-03-05 21:30:56.000000000 +0100
-+++ Makefile.am.new	2009-03-17 16:43:38.000000000 +0100
-@@ -28,10 +28,20 @@
- 	-rm -f ./bin/apbs
- 
- install-data-local:
--	mkdir -p ${prefix}/share
--	-cp -rf examples ${prefix}/share 
--	-cp -rf doc ${prefix}/share 
--	-cp -rf tools ${prefix}/share
-+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/examples 
-+	mkdir -p $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/tools
-+	-rm -f doc/LICENSE.txt
-+	-rm -f tools/manip/*.pyc
-+	-rm -f tools/**/*.o
-+	-rm -f tools/**/Makefile*
-+	-rm -f tools/**/**/*.o
-+	-rm -f tools/**/**/Makefile*
-+	-rm -f tools/Makefile*
-+	-rm -f examples/Makefile*
-+	-rm -f examples/**/Makefile*
-+	-cp -rf doc $(DESTDIR)${prefix}/share/doc/GENTOO_PKG_NAME/html
-+	-cp -rf examples $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
-+	-cp -rf tools $(DESTDIR)${prefix}/share/GENTOO_PKG_NAME/
- 
- test:
- 	cd examples; make test
---- bin/Makefile.am	2009-03-05 21:30:49.000000000 +0100
-+++ bin/Makefile.am.new	2009-03-18 13:04:00.000000000 +0100
-@@ -30,6 +30,6 @@
- include_HEADERS = routines.h
- 
- install-data-local:
--	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
--	-chmod 755 ${prefix}/bin/ApbsClient.py
--	-rm -f ${prefix}/bin/wsdl2py 
-\ No newline at end of file
-+	-cp -p ${top_apbsdir}/bin/ApbsClient.py $(DESTDIR)${prefix}/bin
-+	-chmod 755 $(DESTDIR)${prefix}/bin/ApbsClient.py
-+	-rm -f $(DESTDIR)${prefix}/bin/wsdl2py 
diff --git a/sci-chemistry/apbs/files/apbs-1.2-vgrid-maloc.patch b/sci-chemistry/apbs/files/apbs-1.2-vgrid-maloc.patch
deleted file mode 100644
index 722cf3665..000000000
--- a/sci-chemistry/apbs/files/apbs-1.2-vgrid-maloc.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- tools/python/vgrid/Makefile.am	2009-03-18 10:00:14.000000000 +0100
-+++ tools/python/vgrid/Makefile.am.new	2009-03-18 10:06:14.000000000 +0100
-@@ -16,5 +16,5 @@
-    noinst_PROGRAMS     = _vgrid.so
-    _vgrid_so_SOURCES   = vgridlib.c
-    _vgrid_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
--   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) ${top_builddir}/contrib/lib/libmaloc.a @lib_list@
-+   _vgrid_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS) @lib_list@
- endif
-
---- tools/python/Makefile.am	2009-03-18 10:51:15.000000000 +0100
-+++ tools/python/Makefile.am.new	2009-03-18 10:53:33.000000000 +0100
-@@ -16,4 +16,4 @@
- noinst_PROGRAMS       = _apbslib.so
- _apbslib_so_SOURCES   = apbslib.c
- _apbslib_so_LINK      = $(PY_CC) $(PY_LINKFLAGS) $(LDFLAGS) -o $@ $(PY_SHARED)
--_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a ${top_builddir}/contrib/lib/libmaloc.a ${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS)
-+_apbslib_so_LDADD     = ${top_builddir}/bin/.libs/libapbsmainroutines.a ${top_builddir}/src/aaa_lib/.libs/libapbs.a $(PY_LDFLAGS)
-
diff --git a/sci-chemistry/apbs/metadata.xml b/sci-chemistry/apbs/metadata.xml
deleted file mode 100644
index db53a6231..000000000
--- a/sci-chemistry/apbs/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<pkgmetadata>
-<herd>no-herd</herd>
-<maintainer>
-  <email>jlec@j-schmitz.net</email>
-</maintainer>
-<use>
-  <flag name='fetk'>Include support for Finite Element ToolKit</flag>
-  <flag name='arpack'>Include support for arpack libs</flag>
-  <flag name='tinker'>Include support for  TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems</flag>
-</use>
-</pkgmetadata>