proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

13 files changed, 1265 insertions, 0 deletions

diff --git a/sci-chemistry/cns/Manifest b/sci-chemistry/cns/Manifest
new file mode 100644
index 000000000000..d0d2b7b0dc55
--- /dev/null
+++ b/sci-chemistry/cns/Manifest
@@ -0,0 +1,4 @@
+DIST aria2.3.1.tar.gz 1833973 SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc SHA512 79a2cd89e2120acecb04f286a153dbf52c16500e8956c9dad49b1e1ed94a7b2449c7b044bae6f87e0d2b452a1467a2c02de74f0fa85b0eae66042386e2f5e2d5 WHIRLPOOL 2ff003322601b42bec0d2431e2f1f85819b3982f8da612ff778bb404e51f0fcbca3faa6998e9c0635f9e73899609bb1e273420cac182952aa744364c20299723
+DIST aria2.3.2.tar.gz 1836270 SHA256 30727ea8bdc2e3b44e5970545008fcfa07fa59aa28b76824956a2aa71daa9615 SHA512 009a1d0079f5cc162dc732749ddd2b33297268f0d988b2f37bda4ed50c7764ceef7ae5b56b322c7ac79427a4a2a92d1239199891445cb5e2b3d0908ed670e2aa WHIRLPOOL f18af5b751e79c92e04f4dc12b6b806a1c505b269559a2342bdd6280b790f9f0df9bb4afe366af03beaf09af0128c6b68c39bc66603d51ad24914c78b2579cf3
+DIST cns_solve_1.21_all-mp.tar.gz 32748040 SHA256 7ab464e20932eb024ba6378738da77a4a03642d63b0ca9772b612a7cf27baec1 SHA512 383324d771570b501e388fba9bf20789f483a3a4044eb3334c7a7e7835e0c345b784e0d344b22d20a10fe1c33ed21c9013adb1af5912808af480b96abe275857 WHIRLPOOL fecd0b2dfba43e5525a9fcc8543a55867602b376744848ddafd4c132bcdfc32225780f543742fa225b5e0f0ce658c1029a9ca8b80d5ee3f2491b6d63e8ad91b0
+DIST cns_solve_1.3_all.tar.gz 64167735 SHA256 2ee368022c5ecabf66ce7d32059d93cd7d885ad2d684a094b87c64f6b3dfea0d SHA512 4fe73820e96999bb33a59ff6da979794628552f49bc03cdebcb9439b57e6042b92190e04bb7e4079157adf06a6facc5c16b8ae91621bd24a4b35ee382e53ae37 WHIRLPOOL b3cd14ab7a8a29a44f6e6c3cbc22ee2c665eb8c8565969337b24deffb2a1fd007fae11c5eb73ac38ddf9a38e850948e3b2df2548931722a2a383d5e8c72607a1
diff --git a/sci-chemistry/cns/cns-1.2.1-r8.ebuild b/sci-chemistry/cns/cns-1.2.1-r8.ebuild
new file mode 100644
index 000000000000..d9cc723f98b3
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r8.ebuild
@@ -0,0 +1,233 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 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="
+	${MY_P}_all-mp.tar.gz
+	aria? ( aria2.3.2.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+FORTRAN_NEED_OPENMP=1
+
+S="${WORKDIR}/${MY_P}"
+
+RESTRICT="fetch test"
+
+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}."
+}
+
+get_fcomp() {
+	case $(tc-getFC) in
+		*gfortran* )
+			FCOMP="gfortran" ;;
+		ifort )
+			FCOMP="ifc" ;;
+		* )
+			FCOMP=$(tc-getFC) ;;
+	esac
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	get_fcomp
+}
+
+get_bitness() {
+	echo > "${T}"/test.c
+	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
+	case $(file "${T}"/test.o) in
+		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
+		*32-bit*|*ppc*|*i386*) export _bitness="32";;
+		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
+	esac
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${PV}-parallel.patch
+
+	get_bitness
+
+	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/ || die
+		popd >& /dev/null
+	fi
+
+	# the code uses Intel-compiler-specific directives
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
+		use openmp && \
+			append-flags -fopenmp && append-ldflags -fopenmp
+		COMP="gfortran"
+		[[ ${_bitness} == 64 ]] && \
+			append-fflags -fdefault-integer-8
+	elif [[ $(tc-getFC) == if* ]]; then
+		epatch "${FILESDIR}"/${PV}-ifort.patch
+		use openmp && \
+			append-flags -openmp && append-ldflags -openmp
+		COMP="ifort"
+		[[ ${_bitness} == 64 ]] && append-fflags -i8
+	fi
+
+	[[ ${_bitness} == 64 ]] && \
+		append-cflags "-DINTEGER='long long int'"
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die
+	sed \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		-i "${S}"/cns_solve_env || die
+	sed \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
+		-i "${T}"/cns_solve_env_sh || die
+
+	einfo "Fixing shebangs..."
+	find "${S}" -type f \
+		-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die
+}
+
+src_compile() {
+	local GLOBALS
+	local MALIGN
+	if [[ $(tc-getFC) =~ g77 ]]; then
+		GLOBALS="-fno-globals"
+		MALIGN='\$(CNS_MALIGN_I86)'
+	fi
+
+	# Set up the compiler to use
+	ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die
+
+	# 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="$(tc-getCC)" \
+		F77=$(tc-getFC) \
+		LD=$(tc-getFC) \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FCFLAGS} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		compiler="${COMP}" \
+		install
+}
+
+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 \
+		"export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \
+		|| die "tests failed"
+	einfo "Displaying test results ..."
+	cat "${S}"/*_g77/test/*.diff-test
+}
+
+src_install() {
+	# Install to locations resembling FHS
+	sed \
+		-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/${PF}:g" \
+		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		-e "/^g77on/d" \
+		-i "${S}"/cns_solve_env || die
+	# I don't entirely understand why the sh version requires a leading /
+	# for CNS_SOLVE and CNS_ROOT, but it does
+	sed \
+		-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/${PF}:g" \
+		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		-e "/^g77on/d" \
+		-e "/^g77off/d" \
+		-i "${T}"/cns_solve_env_sh || die
+
+	# Get rid of setup stuff we don't need in the installed script
+	sed \
+		-e "83,$ d" \
+		-e "37,46 d" \
+		-i "${S}"/cns_solve_env || die
+	sed \
+		-e "84,$ d" \
+		-e "39,50 d" \
+		-i "${T}"/cns_solve_env_sh || die
+
+	newbin "${S}"/*linux*/bin/cns_solve* cns_solve
+
+	# Can be run by either cns_solve or cns
+	dosym cns_solve /usr/bin/cns
+
+	# Don't want to install this
+	rm -f "${S}"/*linux*/utils/Makefile || die
+
+	dobin "${S}"/*linux*/utils/*
+
+	sed \
+		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+		-i "${S}"/bin/cns_web || die
+
+	dobin "${S}"/bin/cns_{edit,header,transfer,web}
+
+	insinto /usr/share/cns
+	doins -r "${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 "${T}"/cns_solve_env_sh cns_solve_env.sh
+
+	dohtml \
+		-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
+		-f all_cns_info_template,omac,def \
+		-r doc/html/*
+	# Conflits with app-text/dos2unix
+	rm -f "${D}"/usr/bin/dos2unix || die
+}
+
+pkg_postinst() {
+	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
+}
diff --git a/sci-chemistry/cns/cns-1.3_p7-r1.ebuild b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild
new file mode 100644
index 000000000000..724c62f7e98c
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.3_p7-r1.ebuild
@@ -0,0 +1,216 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils fortran-2 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="
+	${MY_P/p7}_all.tar.gz
+	aria? ( aria2.3.1.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+FORTRAN_NEED_OPENMP=1
+
+S="${WORKDIR}/${MY_P/p7}"
+
+RESTRICT="fetch"
+
+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}."
+}
+
+get_fcomp() {
+	case $(tc-getFC) in
+		*gfortran* )
+			FCOMP="gfortran" ;;
+		ifort )
+			FCOMP="ifc" ;;
+		* )
+			FCOMP=$(tc-getFC) ;;
+	esac
+}
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	get_fcomp
+}
+
+get_bitness() {
+	echo > "${T}"/test.c
+	$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
+	case $(file "${T}"/test.o) in
+		*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
+		*32-bit*|*ppc*|*i386*) export _bitness="32";;
+		*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
+	esac
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-gentoo.patch \
+		"${FILESDIR}"/${PV}-delete.patch
+
+	get_bitness
+
+	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/ || die
+		popd >& /dev/null
+	fi
+
+	# the code uses Intel-compiler-specific directives
+	if [[ $(tc-getFC) =~ gfortran ]]; then
+		use openmp && \
+			append-flags -fopenmp && append-ldflags -fopenmp
+		COMP="gfortran"
+		[[ ${_bitness} == 64 ]] && \
+			append-fflags -fdefault-integer-8
+	elif [[ $(tc-getFC) == if* ]]; then
+		use openmp && \
+			append-flags -openmp && append-ldflags -openmp
+		COMP="ifort"
+		[[ ${_bitness} == 64 ]] && append-fflags -i8
+	fi
+
+	[[ ${_bitness} == 64 ]] && \
+		append-cflags "-DINTEGER='long long int'"
+
+	# Set up location for the build directory
+	# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
+	cp "${FILESDIR}"/cns_solve_env_sh-${PV} "${T}"/cns_solve_env_sh || die
+	sed \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
+		-i "${S}"/cns_solve_env || die
+	sed \
+		-e "s:_CNSsolve_location_:${S}:g" \
+		-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
+		-e "s:setenv OMP_STACKSIZE 256m:export OMP_STACKSIZE=256m:g" \
+		-e "s:^limit:^ulimit:g" \
+		-i "${T}"/cns_solve_env_sh || die
+
+	ebegin "Fixing shebangs..."
+		find "${S}" -type f \
+			-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die
+		find . -name "Makefile*" \
+			-exec \
+				sed \
+					-e "s:^SHELL=/bin/sh:SHELL=${EPREFIX}/bin/sh:g" \
+					-e "s:/bin/ls:ls:g" \
+					-e "s:/bin/rm:rm:g" \
+					-i '{}' + || die
+	eend
+}
+
+src_compile() {
+	local GLOBALS
+	local MALIGN
+
+	# Set up the compiler to use
+	ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die
+
+	# make install really means build, since it's expected to be used in-place
+	# -j1 doesn't mean we do no respect MAKEOPTS!
+	emake -j1 \
+		CC="$(tc-getCC)" \
+		CXX="$(tc-getCXX)" \
+		F77=$(tc-getFC) \
+		LD=$(tc-getFC) \
+		CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		CXXFLAGS="${CXXFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
+		LDFLAGS="${LDFLAGS}" \
+		F77OPT="${FCFLAGS} ${MALIGN}" \
+		F77STD="${GLOBALS}" \
+		OMPLIB="${OMPLIB}" \
+		compiler="${COMP}" \
+		install
+}
+
+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() {
+	cat >> "${T}"/66cns <<- EOF
+	CNS_SOLVE="${EPREFIX}/usr"
+	CNS_ROOT="${EPREFIX}/usr"
+	CNS_DATA="${EPREFIX}/usr/share/cns"
+	CNS_DOC="${EPREFIX}/usr/share/doc/cns-1.3"
+	CNS_LIB="${EPREFIX}/usr/share/cns/libraries"
+	CNS_MODULE="${EPREFIX}/usr/share/cns/modules"
+	CNS_TOPPAR="${EPREFIX}/usr/share/cns/libraries/toppar"
+	CNS_CONFDB="${EPREFIX}/usr/share/cns/libraries/confdb"
+	CNS_XTALLIB="${EPREFIX}/usr/share/cns/libraries/xtal"
+	CNS_NMRLIB="${EPREFIX}/usr/share/cns/libraries/nmr"
+	CNS_XRAYLIB="${EPREFIX}/usr/share/cns/libraries/xray"
+	CNS_XTALMODULE="${EPREFIX}/usr/share/cns/modules/xtal"
+	CNS_NMRMODULE="${EPREFIX}/usr/share/cns/modules/nmr"
+	CNS_HELPLIB="${EPREFIX}/usr/share/cns/helplib"
+	EOF
+
+	doenvd "${T}"/66cns || die
+
+	# Don't want to install this
+	rm -f "${S}"/*linux*/utils/Makefile || die
+
+	sed \
+		-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
+		-i "${S}"/bin/cns_web || die
+
+	newbin "${S}"/*linux*/bin/cns_solve* cns_solve
+
+	# Can be run by either cns_solve or cns
+	dosym cns_solve /usr/bin/cns
+
+	dobin \
+		"${S}"/*linux*/utils/* \
+		"${S}"/bin/cns_{edit,header,import_cif,transfer,web}
+
+	insinto /usr/share/cns
+	doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib "${S}"/bin/cns_info
+
+	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/*
+	# Conflits with app-text/dos2unix
+	rm -f "${D}"/usr/bin/dos2unix || die
+}
+
+pkg_postinst() {
+	if use openmp; then
+		elog "Set OMP_NUM_THREADS to the number of threads you want."
+		elog "If you get segfaults on large structures, set the GOMP_STACKSIZE"
+		elog "variable if using gcc (16384 should be good)."
+	fi
+}
diff --git a/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch
new file mode 100644
index 000000000000..42b9b0572231
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-allow-gcc-openmp.patch
@@ -0,0 +1,20 @@
+--- source/xfft.f.orig	2008-08-03 00:36:52.000000000 -0700
++++ source/xfft.f	2008-08-03 00:37:06.000000000 -0700
+@@ -514,7 +514,7 @@
+       LOGICAL QHERM
+       DOUBLE PRECISION XRCELL(9), MAPR
+ C local
+-!$    integer omp_get_max_threads, kmp_get_stacksize
++!$    integer omp_get_max_threads
+       LOGICAL DONE
+       DOUBLE PRECISION ZERO
+       PARAMETER (ZERO=0.0D0)
+@@ -537,7 +537,7 @@
+       NBPP=1
+ ! The following command is only relevant for the ifort compiler (if -openmp option is used).
+ ! If your compiler is not ifort, and gives an error, just comment the next line out:
+-!$      if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
++!       if (kmp_get_stacksize().lt.2**23) call kmp_set_stacksize(2**23)
+ ! Explanation: the default KMP_STACKSIZE of ifort is 2**21 bytes (2Mb) for 32bit, 
+ ! and 2**22 bytes (4Mb) for 64bit.
+ ! This may be low for big structures, which leads to segmentation faults!
diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch
new file mode 100644
index 000000000000..8c6939d8eb92
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch
@@ -0,0 +1,22 @@
+diff --git a/cns/src/cns.f b/cns/src/cns.f
+index a3c2cbe..51a34f8 100644
+--- a/cns/src/cns.f
++++ b/cns/src/cns.f
+@@ -470,6 +470,7 @@ C local
+       INTEGER      HNLEN, TMP, PTRSZ, STLEN
+       CHARACTER*(1) CNSPTMP
+       CHARACTER*(4) ST
++!$    integer omp_get_max_threads
+ C
+ C write header
+       WRITE(6,'(10X,A)')
+@@ -526,6 +527,9 @@ C
+       WRITE(6,'(10X,7A)')
+      & ' Running on machine: ',HOSTNM(1:HNLEN),
+      & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)'
++!$    write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(),
++!$   &  ' threads'
++!$C (to change use setenv OMP_NUM_THREADS x)
+ C
+       CALL GETNAM(USERNM,12,TMP)
+       WRITE(6,'(10X,2A)')
diff --git a/sci-chemistry/cns/files/1.2.1-gentoo.patch b/sci-chemistry/cns/files/1.2.1-gentoo.patch
new file mode 100644
index 000000000000..2b47bfcc7d86
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-gentoo.patch
@@ -0,0 +1,63 @@
+--- cns_solve_1.21/instlib/source/Makefile.proto	2000-09-07 20:35:33.000000000 +0200
++++ cns_solve_1.21/instlib/source/Makefile.proto.new	2009-07-14 09:18:37.000000000 +0200
+@@ -11,6 +11,8 @@
+ 
+ SHELL=/bin/sh
+ 
++cns_string=`date "+%y%m%d%H%M"`
++
+ # commands
+ RM = /bin/rm
+ 
+@@ -25,26 +27,20 @@
+ 
+ # rule for the fortran routines
+ $(OBJS): 
+-	@ echo "compiling: $(@:.o=.f)"; \
+-	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
++	$(F77) -c $(F77FLAGS) $(@:.o=.f)
+ 
+ # rule for the dynamic memory allocation C routines
+ dmemory.o: dmemory.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the machine specific C routines
+ machine_c.o: machine_c.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the executable itself
+ ../bin/cns_solve: $(DEPENDS) 
+-	@ echo ; echo "linking: cns_solve"; echo
+-	@ cns_string=`date "+%y%m%d%H%M"`; \
+-	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
+-	                                      $(LDFLAGS) \
+-	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
++	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
++	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
+ 	  if [ -x cns_solve-$$cns_string.exe ]; \
+ 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
+ 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
+--- cns_solve_1.21/instlib/utils/Makefile	2004-08-30 00:40:35.000000000 +0200
++++ cns_solve_1.21/instlib/utils/Makefile.new	2009-07-14 09:50:27.000000000 +0200
+@@ -22,14 +22,14 @@
+ 	make clean
+ 
+ .f:
+-	$(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
++	$(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
+ 
+ .c:
+-	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
++	$(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
+ 
+ .l:
+ 	lex $(@).l
+-	$(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
++	$(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
+ 
+ relink:
+ 	@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`
diff --git a/sci-chemistry/cns/files/1.2.1-ifort.patch b/sci-chemistry/cns/files/1.2.1-ifort.patch
new file mode 100644
index 000000000000..ba44bebd1b68
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-ifort.patch
@@ -0,0 +1,126 @@
+diff --git a/source/angledb.f b/source/angledb.f
+index 28ad657..eaa847d 100644
+--- a/source/angledb.f
++++ b/source/angledb.f
+@@ -1416,10 +1416,10 @@ C include files
+ C local variables
+       INTEGER COUNT, SPTR, OLDCLASS, OLDMAXANGLEDBS
+       INTEGER THETYPE, CURPSIS, CURPHIS
+-      INTEGER CLASSINDEX
++      INTEGER CLASINDEX
+       DOUBLE PRECISION K1, CUTOFF
+       CHARACTER*4 THENAME
+-      CHARACTER*20 CLASSNAME
++      CHARACTER*20 CLASNAME
+ C begin
+ C
+       IF (ANGLEDBFLAG) THEN
+@@ -1450,10 +1450,10 @@ C
+            ELSE IF (WD(1:4).EQ.'CLAS') THEN
+                 OLDCLASS = CURANGLEDBCLASS
+                 CALL NEXTWD('class name =')
+-                CLASSNAME = WD(1:20)
++                CLASNAME = WD(1:20)
+                 ANGLEDBMODE = NEW
+                 DO COUNT = 1, NANGLEDBCLASSES
+-                     IF (ANGDBCLASSNAMES(COUNT).EQ.CLASSNAME) THEN
++                     IF (ANGDBCLASSNAMES(COUNT).EQ.CLASNAME) THEN
+                           ANGLEDBMODE = UPDATE
+                           CURANGLEDBCLASS = COUNT
+                      END IF
+@@ -1472,7 +1472,7 @@ C
+                      END IF
+                      NANGLEDBCLASSES = NANGLEDBCLASSES + 1
+                      CURANGLEDBCLASS = NANGLEDBCLASSES
+-                     ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASSNAME
++                     ANGDBCLASSNAMES(CURANGLEDBCLASS) = CLASNAME
+                      ANGLEDBASSNDX(CURANGLEDBCLASS) = NANGLEDBS
+                 END IF
+ C
+@@ -1733,16 +1733,16 @@ C
+      &                         HEAP(ANGLEDBTPTR))
+                      ELSE IF (WD(1:4).EQ.'CLAS') THEN
+                           CALL NEXTWD('Class name>')
+-                          CLASSNAME = WD(1:20)
+-                          CLASSINDEX = 0
++                          CLASNAME = WD(1:20)
++                          CLASINDEX = 0
+                           DO COUNT = 1, NANGLEDBCLASSES
+                                IF (ANGDBCLASSNAMES(COUNT).EQ.
+-     &                              CLASSNAME) THEN
++     &                              CLASNAME) THEN
+                                     PRINTTHISCLASS(COUNT) = .TRUE.
+-                                    CLASSINDEX = COUNT
++                                    CLASINDEX = COUNT
+                                END IF
+                           END DO
+-                          IF (CLASSINDEX.EQ.0) THEN
++                          IF (CLASINDEX.EQ.0) THEN
+                                CALL DSPERR('ANGLEDB',
+      &                              'unknown class. Using first.')
+                                PRINTTHISCLASS(1) = .TRUE.
+diff --git a/source/rama.f b/source/rama.f
+index c5d14f2..3063e7b 100644
+--- a/source/rama.f
++++ b/source/rama.f
+@@ -1468,11 +1468,11 @@ C include files
+ C local variables
+       INTEGER COUNT, SPTR, OLDCLASS, OLDMAXRAMAS,
+      &     THETYPE, CURPSIS, CURPHIS,
+-     &     CURCHIS, CURTHTS, CLASSINDEX
++     &     CURCHIS, CURTHTS, CLASINDEX
+       INTEGER CLEN
+       DOUBLE PRECISION K1, CUTOFF
+       CHARACTER*4 THENAME
+-      CHARACTER*50 CLASSNAME
++      CHARACTER*50 CLASNAME
+ C begin
+ C
+ C this is used by READRAMA2 to hold the selection
+@@ -1503,10 +1503,10 @@ C
+            ELSE IF (WD(1:4).EQ.'CLAS') THEN
+                 OLDCLASS = CURRAMACLASS
+                 CALL NEXTWD('class name =')
+-                CLASSNAME = WD(1:50)
++                CLASNAME = WD(1:50)
+                 RAMAMODE = NEW
+                 DO COUNT = 1, NRAMACLASSES
+-                     IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME) THEN
++                     IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME) THEN
+                           RAMAMODE = UPDATE
+                           CURRAMACLASS = COUNT
+                      END IF
+@@ -1525,7 +1525,7 @@ C
+                      END IF
+                      NRAMACLASSES = NRAMACLASSES + 1
+                      CURRAMACLASS = NRAMACLASSES
+-                     RAMACLASSNAMES(CURRAMACLASS) = CLASSNAME
++                     RAMACLASSNAMES(CURRAMACLASS) = CLASNAME
+                 END IF
+ C
+ C set force constant for current class,
+@@ -1954,18 +1954,18 @@ C
+      &                         HEAP(RAMAATOMPTR), 0)
+                      ELSE IF (WD(1:4).EQ.'CLAS') THEN
+                           CALL NEXTWD('Class name>')
+-                          CLASSINDEX = 0
++                          CLASINDEX = 0
+                           DO COUNT = 1, NRAMACLASSES
+-                               IF (RAMACLASSNAMES(COUNT).EQ.CLASSNAME)
+-     &                              CLASSINDEX = COUNT
++                               IF (RAMACLASSNAMES(COUNT).EQ.CLASNAME)
++     &                              CLASINDEX = COUNT
+                           END DO
+-                          IF (CLASSINDEX.EQ.0) THEN
++                          IF (CLASINDEX.EQ.0) THEN
+                                CALL DSPERR('RAMA',
+      &                              'unknown class. Using first.')
+-                               CLASSINDEX = 1
++                               CLASINDEX = 1
+                           END IF
+                           CALL PRINTRAMAS(CUTOFF, HEAP(CALCRAMAPTR),
+-     &                         HEAP(RAMAATOMPTR), CLASSINDEX)
++     &                         HEAP(RAMAATOMPTR), CLASINDEX)
+                      ELSE
+                           CALL DSPERR('RAMA',
+      &                         'Expected ALL or CLASs.')
diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch
new file mode 100644
index 000000000000..dfaa40021d66
--- /dev/null
+++ b/sci-chemistry/cns/files/1.2.1-parallel.patch
@@ -0,0 +1,17 @@
+diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
+index 0d0dd3e..ae9e422 100644
+--- a/instlib/source/Makefile.proto
++++ b/instlib/source/Makefile.proto
+@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
+ 
+ # the default is to make the cns executable
+ cns_solve:
+-	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k exepurge
++	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make exepurge
+ 
+ # rule for the fortran routines
+ $(OBJS): 
diff --git a/sci-chemistry/cns/files/1.3_p7-delete.patch b/sci-chemistry/cns/files/1.3_p7-delete.patch
new file mode 100644
index 000000000000..cbddf4289158
--- /dev/null
+++ b/sci-chemistry/cns/files/1.3_p7-delete.patch
@@ -0,0 +1,13 @@
+diff --git a/utils/cluster_struc.cpp b/utils/cluster_struc.cpp
+index b64467a..5f727db 100644
+--- a/utils/cluster_struc.cpp
++++ b/utils/cluster_struc.cpp
+@@ -173,7 +173,7 @@ int main(int argc, char *argv[]) {
+         for (int i = 0; i < nrstruc; i++) {
+           delete[] neighbor[i];
+         }
+-        delete[] neighbor, neighborcount;
++        delete[] neighbor, delete[] neighborcount;
+         return 5;
+       }
+       if (rmsd < cutoff) {
diff --git a/sci-chemistry/cns/files/1.3_p7-gentoo.patch b/sci-chemistry/cns/files/1.3_p7-gentoo.patch
new file mode 100644
index 000000000000..7942c55abfb9
--- /dev/null
+++ b/sci-chemistry/cns/files/1.3_p7-gentoo.patch
@@ -0,0 +1,80 @@
+diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto
+index 0d0dd3e..dd4b680 100644
+--- a/instlib/source/Makefile.proto
++++ b/instlib/source/Makefile.proto
+@@ -11,6 +11,8 @@
+ 
+ SHELL=/bin/sh
+ 
++cns_string=`date "+%y%m%d%H%M"`
++
+ # commands
+ RM = /bin/rm
+ 
+@@ -19,32 +21,26 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o
+ 
+ # the default is to make the cns executable
+ cns_solve:
+-	@ make -k printflags       F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
+-	@ make -k exepurge
++	@ make printflags       F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)"
++	@ make exepurge
+ 
+ # rule for the fortran routines
+ $(OBJS): 
+-	@ echo "compiling: $(@:.o=.f)"; \
+-	  $(F77) -c $(F77FLAGS) $(@:.o=.f)
++	$(F77) -c $(F77FLAGS) $(@:.o=.f)
+ 
+ # rule for the dynamic memory allocation C routines
+ dmemory.o: dmemory.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the machine specific C routines
+ machine_c.o: machine_c.c
+-	@ echo ; echo "compiling: $?"
+-	@ $(CC) -c $(CCFLAGS) $?
++	$(CC) -c $(CCFLAGS) $?
+ 
+ # rule for the executable itself
+ ../bin/cns_solve: $(DEPENDS) 
+-	@ echo ; echo "linking: cns_solve"; echo
+-	@ cns_string=`date "+%y%m%d%H%M"`; \
+-	  $(LD) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
+-	                                      $(LDFLAGS) \
+-	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
++	$(LD) $(LDFLAGS) -o cns_solve-$$cns_string.exe $(OBJS) dmemory.o machine_c.o \
++	                                      $(CNS_FFTDIR) $(CNS_FFTLIB); \
+ 	  if [ -x cns_solve-$$cns_string.exe ]; \
+ 	    then echo "created executable file cns_solve-$$cns_string.exe"; \
+ 	         echo ""; cd ../bin; $(RM) -f cns_solve; $(RM) -f cns; \
+diff --git a/instlib/utils/Makefile b/instlib/utils/Makefile
+index 98de84f..4f32b34 100644
+--- a/instlib/utils/Makefile
++++ b/instlib/utils/Makefile
+@@ -22,17 +22,17 @@ utils:
+ 	make clean
+ 
+ .f:
+-	$(F77) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
++	$(F77) $(LDFLAGS) -o $@ $(F77FLAGS) $(@).f $(F77LINK)
+ 
+ .c:
+-	$(CC) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
++	$(CC) $(LDFLAGS) -o $@ $(CCFLAGS) $(@).c $(CCLINK)
+ 
+ .cpp:
+-	$(CPP) -o $@ $(CCFLAGS) $(@).cpp $(CCLINK)
++	$(CXX) $(LDFLAGS) -o $@ $(CXXFLAGS) $(@).cpp $(CCLINK)
+ 
+ .l:
+ 	lex $(@).l
+-	$(CC) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
++	$(CC) $(LDFLAGS) $(CCFLAGS) -o $@ lex.yy.c $(CCLINK) -l$(LEXLIB)
+ 
+ relink:
+ 	@ cd $(CNS_INST)/utils; touch x; rm -f x `ls * | grep -v Makefile`
diff --git a/sci-chemistry/cns/files/cns_solve_env_sh b/sci-chemistry/cns/files/cns_solve_env_sh
new file mode 100644
index 000000000000..34e1a2b635cf
--- /dev/null
+++ b/sci-chemistry/cns/files/cns_solve_env_sh
@@ -0,0 +1,221 @@
+#!/bin/sh
+#
+# This file sets up the appropriate environmental variables and paths
+# for CNSsolve. In the case of the same machines with different versions
+# of the OS, backward compatibility is assumed - ie. a later version will
+# be setup for a previous version of the OS if nothing else is available.
+#
+#   written by: Paul Adams
+#
+#   copyright Yale University
+#
+# ==========================================================================
+#
+# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
+#
+# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
+
+	CNS_SOLVE=_CNSsolve_location_
+
+#
+# ==========================================================================
+#
+# full expansion of the CNS_SOLVE variable prior to use.
+#
+export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
+#
+# ==========================================================================
+#
+# set the number of threads for SGI multiprocessors
+# if this causes a problem on other systems it can be commented out
+#
+export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1
+#
+# ==========================================================================
+#
+# get the machine architecture
+#
+if [ -d $CNS_SOLVE ]; then
+  if [ ! "$CNS_ARCH" ]; then
+    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
+  fi
+else
+  export CNS_ARCH; CNS_ARCH='unknown'
+fi
+#
+# system variables (this is needed for openmp)
+#
+ulimit -s unlimited
+# ==========================================================================
+#
+# general environmental variables
+#
+export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
+export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
+export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
+export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
+export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
+export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
+export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
+export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
+export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
+export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
+#
+# general user aliases
+#
+cns_web () { $CNS_SOLVE/bin/cns_web; }
+cns_header () { $CNS_SOLVE/bin/cns_header; }
+cns_info () { cat $CNS_SOLVE/bin/cns_info; }
+cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
+if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
+  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
+else
+  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
+fi
+run_tutorial () { "csh -f tutorial.csh"; }
+#
+# g77 compilation and use
+#
+g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
+g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
+#
+# developer aliases
+#
+run_tests () { $CNS_SOLVE/bin/run_tests; }
+run_diffs () { $CNS_SOLVE/bin/run_diffs; }
+maketar () { $CNS_SOLVE/bin/maketar; }
+create_patch () { $CNS_SOLVE/bin/create_patch; }
+#
+#
+# ==========================================================================
+#
+# to do expansions - unset noglob just in case user has it otherwise
+#
+set +f
+#
+# try to set up appropriate path
+#
+# first strip off any trailing information (eg. _g77)
+#
+CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
+#
+cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
+cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
+cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
+cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
+cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
+#
+# if we are looking for a specific type of setup then limit search
+#
+cns_dirs=""
+if [ ! "$CNS_G77" ]; then
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+else
+  CNS_ARCH="${CNS_ARCH}_g77"
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+fi
+#
+# first look for an exact match (with os version)
+#
+#
+cns_found=0
+if [ -n "$cns_dirs" ]; then
+  for cns_dir in $cns_dirs ; do
+    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
+    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
+           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
+        cns_archenv=$cns_dir
+        cns_found=1
+      fi
+    fi
+  done
+#
+#
+# now look for an exact match (without os version)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
+             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
+          cns_archenv=$cns_dir
+          cns_found=1
+        fi
+      fi
+    done
+  fi
+#
+# now look for a backwards compatible match (with os version major/minor)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
+	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
+            if [ $osv_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+#
+# now look for a wildcard match on cpu
+#
+  if [ $cns_found -eq 0 ]; then
+    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
+    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
+        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
+               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
+  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
+            if [ $cpu_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+fi
+#
+# if found set environment
+#
+if [ $cns_found -eq 1 ]; then
+  #
+  # set installation and source directory
+  #
+  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
+  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
+  #
+  # path for CNSsolve utility programs
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
+  fi
+  #
+  # path for CNSsolve executable if installed
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
+  fi
+fi
+#
+unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
+unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
+unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
+#
diff --git a/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7 b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7
new file mode 100644
index 000000000000..12368f87b596
--- /dev/null
+++ b/sci-chemistry/cns/files/cns_solve_env_sh-1.3_p7
@@ -0,0 +1,229 @@
+#!/bin/sh
+#
+# This file sets up the appropriate environmental variables and paths
+# for CNSsolve. In the case of the same machines with different versions
+# of the OS, backward compatibility is assumed - ie. a later version will
+# be setup for a previous version of the OS if nothing else is available.
+#
+#   written by: Paul Adams
+#
+#   copyright Yale University
+#
+# ==========================================================================
+#
+# >>>>>> Important: define the location of the CNSsolve directory <<<<<<
+#
+# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
+
+	CNS_SOLVE=_CNSsolve_location_
+
+#
+# ==========================================================================
+#
+# full expansion of the CNS_SOLVE variable prior to use.
+#
+export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
+#
+# ==========================================================================
+#
+# get the machine architecture
+#
+if [ -d $CNS_SOLVE ]; then
+  if [ ! "$CNS_ARCH" ]; then
+    export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
+  fi
+else
+  export CNS_ARCH; CNS_ARCH='unknown'
+fi
+#
+# ==========================================================================
+#
+# system variables for OpenMP
+#
+# The default stack sizes are usually insufficient, especially when
+# CNS is compiled using OpenMP. If the stack sizes are too
+# small segfaults may occur. Recommended setting for "stacksize":
+limit stacksize unlimited
+#
+# KMP_STACKSIZE is specific for Intel ifort, icc:
+##setenv KMP_STACKSIZE 256m
+#
+# OMP_STACKSIZE is used by all compilers:
+setenv OMP_STACKSIZE 256m
+#
+# Uncomment the following line and change as appropriate to set the number 
+# of processors (threads) to use. 
+###setenv OMP_NUM_THREADS 4
+#
+# ==========================================================================
+#
+# general environmental variables
+#
+export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
+export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
+export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
+export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
+export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
+export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
+export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
+export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
+export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
+export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
+#
+# general user aliases
+#
+cns_web () { $CNS_SOLVE/bin/cns_web; }
+cns_header () { $CNS_SOLVE/bin/cns_header; }
+cns_info () { cat $CNS_SOLVE/bin/cns_info; }
+cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
+if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
+  cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
+else
+  cns_edit () { $CNS_SOLVE/bin/cns_edit; }
+fi
+#
+# g77 compilation and use
+#
+g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
+g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
+#
+# developer aliases
+#
+run_tests () { $CNS_SOLVE/bin/run_tests; }
+run_diffs () { $CNS_SOLVE/bin/run_diffs; }
+maketar () { $CNS_SOLVE/bin/maketar; }
+create_patch () { $CNS_SOLVE/bin/create_patch; }
+#
+#
+# ==========================================================================
+#
+# to do expansions - unset noglob just in case user has it otherwise
+#
+set +f
+#
+# try to set up appropriate path
+#
+# first strip off any trailing information (eg. _g77)
+#
+CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
+#
+cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
+cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
+cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
+cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
+cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
+#
+# if we are looking for a specific type of setup then limit search
+#
+cns_dirs=""
+if [ ! "$CNS_G77" ]; then
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+else
+  CNS_ARCH="${CNS_ARCH}_g77"
+  if /bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 >/dev/null 2>&1 ; then
+    cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-*_g77 2>&1 | awk 'BEGIN{FS="/"}{print $NF}' | sort -t\- -n -r -k 3 -k 4`"
+  fi
+fi
+#
+# first look for an exact match (with os version)
+#
+#
+cns_found=0
+if [ -n "$cns_dirs" ]; then
+  for cns_dir in $cns_dirs ; do
+    cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}'`
+    if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+      if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major} -o \
+           $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-${cns_major}_g77 ]; then
+        cns_archenv=$cns_dir
+        cns_found=1
+      fi
+    fi
+  done
+#
+#
+# now look for an exact match (without os version)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+        if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os} -o \
+             $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}_g77 ]; then
+          cns_archenv=$cns_dir
+          cns_found=1
+        fi
+      fi
+    done
+  fi
+#
+# now look for a backwards compatible match (with os version major/minor)
+#
+  if [ $cns_found -eq 0 ]; then
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_major=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $4}' | sed 's/_g77//g'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cns_cpu}-${cns_os}-* ]; then
+	    osv_test=`echo $cns_major $cns_tmp_major | awk '{if ($1 > $2) print 1}'`
+            if [ $osv_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+#
+# now look for a wildcard match on cpu
+#
+  if [ $cns_found -eq 0 ]; then
+    cpu_cpu=`echo $cns_cpu | sed 's/[0-9]*\.*[0-9]*$//'`
+    cpu_ver=`echo $cns_cpu | sed 's/[A-Za-z]*//'`
+    for cns_dir in $cns_dirs ; do
+      if [ $cns_found -eq 0 ]; then
+        cns_tmp_cpu=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[0-9]*\.*[0-9]*$//'`
+        cns_tmp_ver=`echo $cns_dir | awk 'BEGIN{FS="-"}{print $2}' | sed 's/[A-Za-z]*//'`
+        if [ -f $CNS_SOLVE/$cns_dir/bin/cns_solve ]; then
+          if [ $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major} -o \
+               $cns_dir = ${cns_vendor}-${cpu_cpu}*-${cns_os}-${cns_major}_g77 ]; then
+  	    cpu_test=`echo $cpu_ver $cns_tmp_ver | awk '{if ($1 > $2) print 1}'`
+            if [ $cpu_test -eq 1 ]; then
+              cns_archenv=$cns_dir
+	      cns_found=1
+            fi
+          fi
+        fi
+      fi
+    done
+  fi
+fi
+#
+# if found set environment
+#
+if [ $cns_found -eq 1 ]; then
+  #
+  # set installation and source directory
+  #
+  export CNS_INST; CNS_INST=$CNS_SOLVE/$cns_archenv
+  export CNS_SOURCE; CNS_SOURCE=$CNS_INST/source
+  #
+  # path for CNSsolve utility programs
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/utils ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/utils`
+  fi
+  #
+  # path for CNSsolve executable if installed
+  #
+  if [ -d $CNS_SOLVE/$cns_archenv/bin ]; then
+    export PATH; PATH=`$CNS_SOLVE/bin/modify_path -sh $CNS_SOLVE/$cns_archenv/bin`
+  fi
+fi
+#
+unset cns_vendor cns_cpu cns_os cns_major cns_minor cns_tmp_major cns_tmp_minor
+unset cns_dir cns_dirs cns_found cns_archenv cns_diff cns_count cns_same
+unset cpu_cpu cpu_ver cns_tmp_cpu cns_tmp_ver cpu_test osv_test
+#
diff --git a/sci-chemistry/cns/metadata.xml b/sci-chemistry/cns/metadata.xml
new file mode 100644
index 000000000000..a9cb92ec3f79
--- /dev/null
+++ b/sci-chemistry/cns/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
+  <use>
+    <flag name="aria"> Support patch for sci-chemistry/aria</flag>
+  </use>
+  <longdescription>
+Crystallography and NMR System (CNS) is the result of an international
+collaborative effort among several research groups. The program has 
+been designed to provide a flexible multi-level hierachical approach for the
+most commonly used algorithms in macromolecular structure determination. 
+Highlights include heavy atom searching, experimental phasing (including 
+MAD and MIR), density modification, crystallographic refinement with maximum
+likelihood targets, and NMR structure calculation using NOEs, J-coupling, 
+chemical shift, and dipolar coupling data.
+</longdescription>
+</pkgmetadata>