sci-chemistry/apbs: Drop old

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 20 insertions, 310 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 13ceeb972cbe..dd3e75012ba4 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.71 2015/01/04 19:08:24 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.72 2015/01/22 09:05:05 jlec Exp $
+
+  22 Jan 2015; Justin Lecher <jlec@gentoo.org> -apbs-1.3-r3.ebuild,
+  -apbs-1.4.1-r1.ebuild:
+  Drop old
 
   04 Jan 2015; Justin Lecher <jlec@gentoo.org> apbs-1.4.1-r2.ebuild:
   Make test use newly build libs
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 394a1f1dc67c..ae6483db81d5 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -37,30 +37,27 @@ AUX apbs-1.4.1-manip.patch 1522 SHA256 155c6fcd777c1c00e313bbdae60b6ccf373af0d50
 AUX apbs-1.4.1-multilib.patch 3301 SHA256 21c1934eb5694737d6049eb8da868ee81f15ff86dacc09f89f0024c263929ddc SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0 WHIRLPOOL 07ae32ecd14c21d3cce59bb904533faa1b9de532d6411176d5ee2d52ed91ef6da88b52cec0ef7b989dab253300a9d89182ddc25323347a48eb8d3355c16cb3a4
 AUX apbs-1.4.1-python.patch 4109 SHA256 793257f3581c768951c27742ecf299f462fbc7fc78635e2d7c8dd0ade69c9738 SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092 WHIRLPOOL 39d2445e7d3ed1974dffeaad4c0772238cf6e508f4e002636c833921f124fe7d7d9732d23a7ffc5341815152d4ddc6cd0565bebc46988caf7f742bb2f3031033
 DIST apbs-1.2.1b-source.tar.gz 40647966 SHA256 7d088def1ed7689127eb64014ea44069b9d7bfc995941fe5800ff753d48c87be
-DIST apbs-1.3-source.tar.gz 48625351 SHA256 5fa5b597f7d5a3d9bb55429ec4fefc69e7d0f918d568c3c4a288088c0fde9ef2 SHA512 3db8f5b5d4418d353b42381a6da7451fecbc26141a166905afabab94d1f14f856b6d79cffa2c783011834be9d813d7155472f92b441b4a075d6cbf68fe630b2e WHIRLPOOL 5fe2be11039adb5b162725f9dd15d085000e8c701086948e7d88d2eaf282f72e9af5b63e882aebc03f7e4446b4cdc7ce6b4915cf5aebcc15ff8e8e4d7a1b2c0b
 DIST apbs-1.4.1.zip 37999283 SHA256 1156c44fb65bb7c884801f3111ca1cdb1dfba6f5308226587db112aac4969027 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a WHIRLPOOL 6729571f13c953ec0bcf90da73ef0c39cf769f1498a767d3280de3ffbeea18eda718373efca0468436c4b18357fe450865f661daba79eeb66778c572c43ff39a
 EBUILD apbs-1.2.1b-r4.ebuild 3611 SHA256 0c38e680838e539110402eec44dda6569d12ac70a9f6ae3d4f40c5f4723ce568 SHA512 447a1c810b5b4393fe3e95cea47d2c13d7ff296cdebd0d599b830700bc7ace89f731b6554aba66959687b5b33182193cec10cd5cbbadcb45e932021182a85259 WHIRLPOOL 4bcb114704e4fcba1966680dd882993204a8890777342e2a7130523b52df2d51237c0001b5b652d589e74f5933cfe473342fd09eff5e67da641f9690e5d0594a
-EBUILD apbs-1.3-r3.ebuild 4281 SHA256 9786340ad9fed6e51e16c9dde4c2e3dc35137069a569c3d9687e0e74507a6e8b SHA512 b20a75745a42a0ce3b8af9cecd50fd7cf31d05a4759057c7eb28bc8d72a4784eb34bb6a897a0aad9beb4769009a33667fd7bc965115ded3a61493c377287fe07 WHIRLPOOL 127c0a1a8e9244a538808c887b1d972a62fe744ab0973d91ac2abeb66fda21c4196a1f1e86240bfd901c4c6328160bb3b602ee30695d84b794ae3182e43ef6c8
-EBUILD apbs-1.4.1-r1.ebuild 3086 SHA256 50b5e1bcafe663ee580b982fffa7f67926d0677c36e54aaa7852db03a88ef682 SHA512 3f889ee44eae080dfc426171aa9ce0cb1a2b258427ddddd702b68b71536da303967f25289a332ebd4c661f1e55c39eddc5a8e52a1d438ec3db093b9b66aef4b8 WHIRLPOOL e4794d70a65b80fdff2072d508b63df2f70da061af28e218f45b6df86fb2c7735e92b463e31fe40f71fc5d115919fdb8bdf882ad584e1e4fa260b61dbe4f9a39
 EBUILD apbs-1.4.1-r2.ebuild 3185 SHA256 35c16764be780e7b0ffb1f889e495fca769ec56a39dd502335f008114ee70fd5 SHA512 7f54341d5c5be89bf550c919488541ec6fc984d75dc526624cd33ea090a6e06304a6f38447d2b83f936067343a31603a16d0d2365349d204081a13e10cbfac59 WHIRLPOOL 443ad60e373c8da4aed645300a23292464f8f24f09cb2dbdafbb1dd68e465bc574bca7f509e3bc339fc00c4c5f2b6af708ad2641255b804568da659ffd481368
-MISC ChangeLog 12374 SHA256 e0373f439f6e90e798f7e45f6dc0466d637b37e6bf0c3a5ef0e5dbe7f71cf5b6 SHA512 20722e79e354fcb13f7e3dac0478b7a4b69aee98533acbaf327c8aa7f3d0b8f984af5d634efbb36d5f179609d82a1cc7380d1964583677df1fe02cd38e92640b WHIRLPOOL be81716478b6b5c035b23d693e97fabe5da951e3f4c42f8095a87eddc8d4dde8fd5f99d764359e9009a2ddb29acda38314c357cbc637275bc9e38a9e9407d614
+MISC ChangeLog 12479 SHA256 ceba18df48387679ba1d069d7bc3c03ee3fa06fc3b5ee511efbc3753aa9703b5 SHA512 3b132472d9f853605af2e02df1f335d02f6cf3cb9d10b1fccb887f919629dd811aa0ec2b3cc61c544db6f9c0c2510f0a42355207c0066e18d3db21256ba89cc0 WHIRLPOOL 2bb271be0c81982f9afbc7d36bbed77958d67cc10d14bea9f25518072cb52df393eb14984eac88a49031b9f567d79d67e308287d5be132633434ba1820413d47
 MISC metadata.xml 948 SHA256 ed8d35d9a0f77c758a6699bc5b5baa7e1e59603677dc9d13da6b9d445204f1e9 SHA512 ff99fbdf53cff0078f32fd95fafbd482dc064885dc4e4bc621a654fad3e134d7f6d4087770523ce6220011b33ecfb83dad8d8f749f20f329aba55f9d1c10f59b WHIRLPOOL 4f88e33d5b391fec5b1bdb09f5848be8dc8be0d14644c529d8cc82a04f556821a16bd1fc60838b98a67778405b10600d4409e70cd796432bdf08c77ce4c4ce94
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diff --git a/sci-chemistry/apbs/apbs-1.3-r3.ebuild b/sci-chemistry/apbs/apbs-1.3-r3.ebuild
deleted file mode 100644
index 154132c2fce1..000000000000
--- a/sci-chemistry/apbs/apbs-1.3-r3.ebuild
+++ /dev/null
@@ -1,166 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.3-r3.ebuild,v 1.5 2013/05/02 15:16:35 jlec Exp $
-
-EAPI=4
-
-PYTHON_DEPEND="python? 2"
-
-inherit autotools-utils eutils fortran-2 python toolchain-funcs versionator
-
-MY_PV=$(get_version_component_range 1-3)
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
-SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="arpack doc examples fetk mpi openmp python static-libs tools"
-REQUIRED_USE="mpi? ( !python )"
-
-RDEPEND="
-	dev-libs/maloc[mpi=]
-	virtual/blas
-	sys-libs/readline
-	arpack? ( sci-libs/arpack )
-	fetk? (
-		sci-libs/fetk
-		sci-libs/amd
-		sci-libs/umfpack
-		sci-libs/superlu )
-	mpi? ( virtual/mpi )"
-DEPEND="${DEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}"/"${MY_P}-source"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-MAKEOPTS+=" -j1"
-
-pkg_setup() {
-	fortran-2_pkg_setup
-	use python && python_set_active_version 2 && python_pkg_setup
-	if [[ -z ${MAXMEM} ]]; then
-		einfo "You can specify the max amount of RAM used"
-		einfo "by setting MAXMEM=\"your size in MB\""
-	else
-		einfo "Settings max memory usage to ${MAXMEM} MB"
-	fi
-}
-
-# git clone ssh://woodpecker/home/jlec/apbs.git
-PATCHES=( "${FILESDIR}"/${P}/00{01..16}* )
-
-src_prepare() {
-	rm -rf contrib/{blas,maloc,opal,zlib} || die
-	find -name "._*" -delete || die
-
-	EPATCH_OPTS="-p1" \
-		autotools-utils_src_prepare
-
-	sed \
-		-e "s:GENTOO_PKG_NAME:${PN}:g" \
-		-i Makefile.am || die "Cannot correct package name"
-	sed \
-		-e 's:libmaloc.a:libmaloc.so:g' \
-		-e 's:-lblas::g' \
-		-i configure.ac || die
-	sed -e 's:opal::g' -i contrib/Makefile.am || die
-	sed \
-		-e 's:noinst_PROGRAMS:bin_PROGRAMS:g' \
-		-i tools/*/Makefile.am || die
-
-	sed \
-		-e "s:AM_CONFIG_HEADER:AC_CONFIG_HEADERS:g" \
-		-e "s:AM_PROG_CC_STDC:AC_PROG_CC:g" \
-		-i configure.ac || die
-
-	AT_NOELIBTOOLIZE=yes eautoreconf
-}
-
-src_configure() {
-	local myeconfargs=( --docdir="${EPREFIX}/usr/share/doc/${PF}" )
-	use arpack && myeconfargs+=( --with-arpack="${EPREFIX}/usr/$(get_libdir)" )
-
-	# check which mpi version is installed and tell configure
-	if use mpi; then
-		export CC="${EPREFIX}/usr/bin/mpicc"
-		export F77="${EPREFIX}/usr/bin/mpif77"
-
-		if has_version sys-cluster/mpich; then
-	 		myeconfargs+=( --with-mpich="${EPREFIX}/usr" )
-		elif has_version sys-cluster/mpich2; then
-			myeconfargs+=( --with-mpich2="${EPREFIX}/usr" )
-		elif has_version sys-cluster/openmpi; then
-			myeconfargs+=( --with-openmpi="${EPREFIX}/usr" )
-		fi
-	fi || die "Failed to select proper mpi implementation"
-
-	if use fetk; then
-		myeconfargs+=( --with-fetk-include="${EPREFIX}/usr/include" --with-fetk-library="${EPREFIX}/usr/$(get_libdir)" )
-	else
-		myeconfargs+=( --disable-fetk )
-	fi
-
-	[[ -n ${MAXMEM} ]] && myeconfargs+=( --with-maxmem=${MAXMEM} )
-
-	if use python; then
-		myeconfargs+=( --enable-tools  )
-	else
-		myeconfargs+=( $(use_enable tools) )
-	fi
-
-	myeconfargs+=(
-		--disable-maloc-rebuild
-		--enable-shared
-		$(use_enable openmp)
-		$(use_enable python)
-		)
-	autotools-utils_src_configure
-}
-
-src_test() {
-	export LC_NUMERIC=C
-	cd examples && make test \
-		|| die "Tests failed"
-	grep -q 'FAILED' "${S}"/examples/TESTRESULTS.log && die "Tests failed"
-}
-
-src_install() {
-	autotools-utils_src_install
-
-	use doc && dohtml -r doc/*
-	use examples && insinto /usr/share/${PN} && doins -r examples
-	use tools && emake DESTDIR="${D}" install-tools
-
-	if use python && ! use mpi; then
-		insinto $(python_get_sitedir)/${PN}
-		doins tools/manip/*.py
-		doins tools/python/{*.py,*.pqr}
-		doins tools/python/*/{*.py,*.so}
-		python_clean_installation_image
-	fi
-
-	if use python || use tools; then
-		mv "${ED}"/usr/bin/analysis{,_apbs} || die
-		mv "${ED}"/usr/bin/smooth{,_apbs} || die
-	fi
-}
-
-pkg_postinst() {
-	use python && python_mod_optimize ${PN}
-	if use python || use tools; then
-		echo
-		elog "Following apps have been renamed"
-		elog "${EPREFIX}/usr/bin/analysis -> ${EPREFIX}/usr/bin/analysis_apbs"
-		elog "${EPREFIX}/usr/bin/smooth -> ${EPREFIX}/usr/bin/smooth_apbs"
-		echo
-	fi
-}
-
-pkg_postrm() {
-	use python && python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild
deleted file mode 100644
index f005123c55bd..000000000000
--- a/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild,v 1.2 2014/10/30 07:30:54 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
-
-GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
-
-DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
-#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
-
-SLOT="0"
-LICENSE="BSD"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="debug doc examples fast +fetk mpi openmp python tools"
-
-REQUIRED_USE="
-	mpi? ( !python )
-	python? ( tools fetk ${PYTHON_REQUIRED_USE} )"
-
-RDEPEND="
-	dev-cpp/eigen:3
-	dev-libs/maloc[mpi=]
-	virtual/blas
-	sys-libs/readline
-	fetk? (
-		sci-libs/fetk
-		sci-libs/amd
-		sci-libs/umfpack
-		sci-libs/superlu
-	)
-	mpi? ( virtual/mpi )
-	python? ( ${PYTHON_DEPS} )
-"
-DEPEND="${DEPEND}
-	virtual/pkgconfig
-	doc? ( app-doc/doxygen )
-"
-
-S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
-
-PATCHES=(
-	"${FILESDIR}"/${P}-multilib.patch
-	"${FILESDIR}"/${P}-manip.patch
-	"${FILESDIR}"/${P}-python.patch
-)
-
-src_prepare() {
-	cmake-utils_src_prepare
-	append-cppflags $($(tc-getPKG_CONFIG) --cflags eigen3)
-
-	sed \
-		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
-		-e "/TOOLS_PATH/d" \
-		-i CMakeLists.txt || die
-	use doc && MAKEOPTS+=" -j1"
-	if use python; then
-		unset PATCHES || die
-		cd tools/python && distutils-r1_src_prepare
-	fi
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_SKIP_RPATH=ON
-		-DTOOLS_PATH="${ED}"/usr
-		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
-		-DLIBRARY_INSTALL_PATH=$(get_libdir)
-		-DFETK_PATH="${EPREFIX}"/usr/
-		-DBUILD_SHARED_LIBS=ON
-		-DENABLE_QUIT=OFF
-		$(cmake-utils_use_build doc DOC)
-		$(cmake-utils_use_build tools TOOLS)
-		-DENABLE_BEM=OFF
-# ENABLE_BEM: Boundary element method using TABIPB
-		$(cmake-utils_use_enable debug DEBUG)
-		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
-		$(cmake-utils_use_enable fast FAST)
-		$(cmake-utils_use_enable fetk FETK)
-		$(cmake-utils_use_enable mpi MPI)
-		$(cmake-utils_use_enable python PYTHON)
-# ENABLE_TINKER: Enable TINKER support
-# ENABLE_iAPBS: Enable iAPBS
-		-DENABLE_iAPBS=ON
-# MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
-	)
-	cmake-utils_src_configure
-	if use python; then
-		cd tools/python && distutils-r1_src_configure
-	fi
-}
-
-src_compile(){
-	cmake-utils_src_compile
-	if use python; then
-		append-ldflags -L"${S}"/lib
-		cd tools/python && distutils-r1_src_compile
-	fi
-}
-
-src_test() {
-	cd tests || die
-	"${PYTHON}" apbs_tester.py -l log || die
-	grep -q 'FAILED' log && die "Tests failed"
-}
-
-src_install() {
-	dodir /usr/bin
-	cmake-utils_src_install
-	local i
-	for i in "${ED}"/usr/bin/*; do
-		if [[ ! "${i}" =~ .*apbs$ ]]; then
-			mv "${i}" "${i}-apbs" || die
-		fi
-	done
-	if use python; then
-		cd tools/python && distutils-r1_src_install
-	fi
-}