Dropp old

(Portage version: 2.2.0_alpha4/cvs/Linux x86_64)

6 files changed, 6 insertions, 881 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index 683ffcb43d09..4f2c8f0008ec 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.28 2010/11/18 17:05:04 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.29 2010/11/19 08:57:24 jlec Exp $
+
+  19 Nov 2010; Justin Lecher <jlec@gentoo.org> -cns-1.2.ebuild,
+  -cns-1.2-r1.ebuild, -cns-1.2.1-r1.ebuild, -cns-1.2.1-r3.ebuild,
+  -cns-1.2.1-r4.ebuild:
+  Dropp old
 
   18 Nov 2010; Justin Lecher <jlec@gentoo.org> -cns-1.2.1-r2.ebuild,
   cns-1.2.1-r3.ebuild, cns-1.2.1-r4.ebuild, cns-1.2.1-r5.ebuild,
diff --git a/sci-chemistry/cns/cns-1.2-r1.ebuild b/sci-chemistry/cns/cns-1.2-r1.ebuild
deleted file mode 100644
index dbec50254253..000000000000
--- a/sci-chemistry/cns/cns-1.2-r1.ebuild
+++ /dev/null
@@ -1,149 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2-r1.ebuild,v 1.4 2010/02/06 21:49:39 jlec Exp $
-
-inherit eutils fortran toolchain-funcs
-
-MY_PN="${PN}_solve"
-MY_P="${MY_PN}_${PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="${MY_P}_all.tar.gz"
-RESTRICT="fetch"
-LICENSE="cns"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND="app-shells/tcsh
-	!app-text/dos2unix"
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${MY_P}"
-
-FORTRAN="g77 gfortran"
-
-pkg_nofetch() {
-	einfo "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	einfo "and place these files:"
-	einfo ${A}
-	einfo "in ${DISTDIR}."
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	# The length of time must be at least 10, not 9
-	# http://gcc.gnu.org/ml/fortran/2006-02/msg00198.html
-	epatch "${FILESDIR}"/1.1-time-length-10.patch
-
-	epatch "${FILESDIR}"/1.2-allow-unknown-architectures.patch
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${S}"/.cns_solve_env_sh
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN=
-	if [[ ${FORTRANC} = g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# make install really means build, since it's expected to be used in-place
-	emake \
-		CC="$(tc-getCC)" \
-		F77="${FORTRANC}" \
-		LD="${FORTRANC}" \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		g77install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source .cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:\$CNS_LIB:\$CNS_DATA:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/bin/cns_info:g" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/data:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:\$CNS_LIB:\$CNS_DATA:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/bin/cns_info:g" \
-		"${S}"/.cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${S}"/.cns_solve_env_sh
-
-	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*_g77/utils/Makefile
-
-	dobin "${S}"/*_g77/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
-	doins "${S}"/bin/cns_info
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh
-	newins "${S}"/.cns_solve_env_sh cns_solve_env.sh
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/*
-}
diff --git a/sci-chemistry/cns/cns-1.2.1-r1.ebuild b/sci-chemistry/cns/cns-1.2.1-r1.ebuild
deleted file mode 100644
index 8d722bed9e09..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r1.ebuild
+++ /dev/null
@@ -1,187 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r1.ebuild,v 1.4 2010/11/17 13:14:53 jlec Exp $
-
-EAPI="2"
-
-inherit eutils fortran toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="${MY_P}_all-mp.tar.gz"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-S="${WORKDIR}/${MY_P}"
-
-FORTRAN="g77 gfortran"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-pkg_setup() {
-	fortran_pkg_setup
-	tc-has-openmp
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-
-	use openmp && append-fflags -fopenmp
-
-	# the code uses Intel-compiler-specific directives
-	epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-
-	use openmp && OMPLIB="-lgomp"
-
-	use amd64 && \
-		append-cflags "-DINTEGER='long long int'" && \
-		append-fflags -fdefault-integer-8
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${T}"/cns_solve_env_sh
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ ${FORTRANC} = g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FORTRANC} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	emake \
-		CC="$(tc-getCC)" \
-		F77="${FORTRANC}" \
-		LD="${FORTRANC}" \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		g77install \
-		|| die "emake failed"
-
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT /usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${T}"/cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${T}"/cns_solve_env_sh
-
-	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*_g77/utils/Makefile
-
-	dobin "${S}"/*_g77/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
-	doins "${S}"/bin/cns_info
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/cns-1.2.1-r3.ebuild b/sci-chemistry/cns/cns-1.2.1-r3.ebuild
deleted file mode 100644
index d556cf1d4ec1..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r3.ebuild
+++ /dev/null
@@ -1,204 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r3.ebuild,v 1.4 2010/11/18 17:05:04 jlec Exp $
-
-EAPI="3"
-
-inherit eutils fortran toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="${MY_P}_all-mp.tar.gz
-	aria? ( aria2.3.1.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-S="${WORKDIR}/${MY_P}"
-
-FORTRAN="g77 gfortran"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-pkg_setup() {
-	fortran_pkg_setup
-	tc-has-openmp
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	epatch "${FILESDIR}"/${PV}-parallel.patch
-
-	pushd "${WORKDIR}"/aria* >& /dev/null
-	if use aria; then
-		# Update the cns sources in aria for version 1.2.1
-		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-		# Update the code with aria specific things
-		cp -rf cns/src/* "${S}"/source/
-	fi
-	popd >& /dev/null
-
-	use openmp && append-fflags -fopenmp
-
-	# the code uses Intel-compiler-specific directives
-	epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-
-	use openmp && OMPLIB="-lgomp"
-
-	use amd64 && \
-		append-cflags "-DINTEGER='long long int'" && \
-		append-fflags -fdefault-integer-8
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${T}"/cns_solve_env_sh
-
-	einfo "Fixing shebangs..."
-	find "${S}" -type f \
-		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ ${FORTRANC} = g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FORTRANC} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		F77="${FORTRANC}" \
-		LD="${FORTRANC}" \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		g77install \
-		|| die "emake failed"
-
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${T}"/cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${T}"/cns_solve_env_sh
-
-	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*_g77/utils/Makefile
-
-	dobin "${S}"/*_g77/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web || die
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
-	doins "${S}"/bin/cns_info || die
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh || die
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/cns-1.2.1-r4.ebuild b/sci-chemistry/cns/cns-1.2.1-r4.ebuild
deleted file mode 100644
index 581854446537..000000000000
--- a/sci-chemistry/cns/cns-1.2.1-r4.ebuild
+++ /dev/null
@@ -1,215 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r4.ebuild,v 1.4 2010/11/18 17:05:04 jlec Exp $
-
-EAPI="3"
-
-inherit eutils fortran toolchain-funcs versionator flag-o-matic
-
-MY_PN="${PN}_solve"
-MY_PV="$(delete_version_separator 2)"
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="${MY_P}_all-mp.tar.gz
-	aria? ( aria2.3.1.tar.gz )"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="aria openmp"
-
-RDEPEND="app-shells/tcsh"
-DEPEND="${RDEPEND}"
-
-RESTRICT="fetch"
-S="${WORKDIR}/${MY_P}"
-
-FORTRAN="gfortran ifc"
-
-pkg_nofetch() {
-	elog "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	use aria && elog "and http://aria.pasteur.fr/"
-	elog "and place these files:"
-	elog ${A}
-	elog "in ${DISTDIR}."
-}
-
-pkg_setup() {
-	fortran_pkg_setup
-	tc-has-openmp
-}
-
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-gentoo.patch
-	epatch "${FILESDIR}"/${PV}-parallel.patch
-
-	if use aria; then
-	pushd "${WORKDIR}"/aria* >& /dev/null
-		# Update the cns sources in aria for version 1.2.1
-		epatch "${FILESDIR}"/1.2.1-aria2.3.patch
-
-		# Update the code with aria specific things
-		cp -rf cns/src/* "${S}"/source/
-	popd >& /dev/null
-	fi
-
-	# the code uses Intel-compiler-specific directives
-	if [[ ${FORTRANC} == gfortran ]]; then
-		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
-		use openmp && \
-			OMPLIB="-lgomp" && append-flags -fopenmp
-		COMP="gfortran"
-		use amd64 && \
-			append-fflags -fdefault-integer-8
-	else
-		epatch "${FILESDIR}"/${PV}-ifort.patch
-		use openmp && OMPLIB="-lgomp" && \
-			append-flags -openmp && append-ldflags -openmp
-		COMP="ifort"
-		use amd64 && append-fflags -i8
-		append-fflags -Vaxlib
-		append-ldflags -Vaxlib
-	fi
-
-	use amd64 && \
-		append-cflags "-DINTEGER='long long int'"
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-		"${T}"/cns_solve_env_sh
-
-	einfo "Fixing shebangs..."
-	find "${S}" -type f \
-		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die
-}
-
-src_compile() {
-	local GLOBALS
-	local MALIGN
-	if [[ ${FORTRANC} = g77 ]]; then
-		GLOBALS="-fno-globals"
-		MALIGN='\$(CNS_MALIGN_I86)'
-	fi
-
-	# Set up the compiler to use
-	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
-	ln -s Makefile.header Makefile.header.${FORTRANC} || die
-	popd 2>/dev/null
-
-	# make install really means build, since it's expected to be used in-place
-	# -j1 doesn't mean we do no respect MAKEOPTS!
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		F77="${FORTRANC}" \
-		LD="${FORTRANC}" \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		LDFLAGS="${LDFLAGS}" \
-		F77OPT="${FFLAGS:- -O2} ${MALIGN}" \
-		F77STD="${GLOBALS}" \
-		OMPLIB="${OMPLIB}" \
-		compiler="${COMP}" \
-		install \
-		|| die "emake failed"
-
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	sh -c \
-		"export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${S}"/cns_solve_env
-	# I don't entirely understand why the sh version requires a leading /
-	# for CNS_SOLVE and CNS_ROOT, but it does
-	sed -i \
-		-e "s:${S}:/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \
-		-e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-		"${T}"/cns_solve_env_sh
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-	sed -i \
-		-e "84,$ d" \
-		-e "39,50 d" \
-		"${T}"/cns_solve_env_sh
-
-	newbin "${S}"/*linux*/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*linux*/utils/Makefile
-
-	dobin "${S}"/*linux*/utils/* || die "install utils failed"
-
-	sed -i \
-		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-		"${S}"/bin/cns_web || die
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die
-	doins "${S}"/bin/cns_info || die
-
-	insinto /etc/profile.d
-	newins "${S}"/cns_solve_env cns_solve_env.csh || die
-	newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/* || die
-	# Conflits with app-text/dos2unix
-	rm -f "${D}"/usr/bin/dos2unix
-}
-
-pkg_info() {
-	if use openmp; then
-		elog "Set OMP_NUM_THREADS to the number of threads you want."
-		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
-		elog "variable if using gcc (16384 should be good)."
-	fi
-}
-
-pkg_postinst() {
-	pkg_info
-}
diff --git a/sci-chemistry/cns/cns-1.2.ebuild b/sci-chemistry/cns/cns-1.2.ebuild
deleted file mode 100644
index c33d0c0b3b85..000000000000
--- a/sci-chemistry/cns/cns-1.2.ebuild
+++ /dev/null
@@ -1,125 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.ebuild,v 1.3 2010/02/06 21:49:39 jlec Exp $
-
-inherit eutils fortran toolchain-funcs
-
-MY_PN="${PN}_solve"
-MY_P="${MY_PN}_${PV}"
-
-DESCRIPTION="Crystallography and NMR System"
-HOMEPAGE="http://cns.csb.yale.edu/"
-SRC_URI="${MY_P}_all.tar.gz"
-RESTRICT="fetch"
-LICENSE="cns"
-SLOT="0"
-KEYWORDS="~ppc ~x86"
-IUSE=""
-RDEPEND="app-shells/tcsh
-	!app-text/dos2unix"
-DEPEND="${RDEPEND}"
-S="${WORKDIR}/${MY_P}"
-
-FORTRAN="g77 gfortran"
-
-pkg_nofetch() {
-	einfo "Fill out the form at http://cns.csb.yale.edu/cns_request/"
-	einfo "and place these files:"
-	einfo ${A}
-	einfo "in ${DISTDIR}."
-}
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-
-	# The length of time must be at least 10, not 9
-	# http://gcc.gnu.org/ml/fortran/2006-02/msg00198.html
-	epatch "${FILESDIR}"/1.1-time-length-10.patch
-
-	# Set up location for the build directory
-	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
-	sed -i \
-		-e "s:_CNSsolve_location_:${S}:g" \
-		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-		"${S}"/cns_solve_env
-}
-
-src_compile() {
-	local GLOBALS
-	if [[ ${FORTRANC} = g77 ]]; then
-		GLOBALS="-fno-globals"
-	fi
-
-	# make install really means build, since it's expected to be used in-place
-	emake \
-		CC="$(tc-getCC)" \
-		F77="${FORTRANC}" \
-		LD="${FORTRANC}" \
-		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
-		F77OPT="${FFLAGS:- -O2} \$(CNS_MALIGN_I86)" \
-		F77STD="${GLOBALS}" \
-		LDFLAGS="${LDFLAGS}" \
-		g77install \
-		|| die "emake failed"
-}
-
-src_test() {
-	# We need to force on g77 manually, because we can't get aliases working
-	# when we source in a -c
-	einfo "Running tests ..."
-	csh -c \
-		"setenv CNS_G77; source cns_solve_env; make run_tests" \
-		|| die "tests failed"
-	einfo "Displaying test results ..."
-	cat "${S}"/*_g77/test/*.diff-test
-}
-
-src_install() {
-	# Install to locations resembling FHS
-	sed -i \
-		-e "s:${S}:usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT usr:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/data:g" \
-		-e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \
-		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-		-e "s:\$CNS_LIB:\$CNS_DATA:g" \
-		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/bin/cns_info:g" \
-		"${S}"/cns_solve_env
-
-	# Get rid of setup stuff we don't need in the installed script
-	sed -i \
-		-e "83,$ d" \
-		-e "37,46 d" \
-		"${S}"/cns_solve_env
-
-	newbin "${S}"/*_g77/bin/cns_solve* cns_solve \
-		|| die "install cns_solve failed"
-
-	# Can be run by either cns_solve or cns
-	dosym cns_solve /usr/bin/cns
-
-	# Don't want to install this
-	rm -f "${S}"/*_g77/utils/Makefile
-
-	dobin "${S}"/*_g77/utils/* || die "install utils failed"
-
-	dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed"
-
-	insinto /usr/share/cns
-	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
-	doins "${S}"/bin/cns_info
-	doins "${S}"/cns_solve_env
-
-	dohtml \
-		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-		-f all_cns_info_template,omac,def \
-		-r doc/html/*
-}
-
-pkg_postinst() {
-	ewarn "You must source ${ROOT}usr/share/cns/cns_solve_env"
-	ewarn "before running CNS. It's a C-shell script,"
-	ewarn "so you also must be using csh or tcsh."
-}