Bump patches to aria-2.3.2

(Portage version: 2.2.0_alpha51/cvs/Linux x86_64)

3 files changed, 257 insertions, 8 deletions

diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog
index a0236a7f6a9f..1bd239e64d35 100644
--- a/sci-chemistry/cns/ChangeLog
+++ b/sci-chemistry/cns/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/cns
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.41 2011/06/21 16:05:16 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.42 2011/08/30 13:48:39 jlec Exp $
+
+*cns-1.2.1-r7 (30 Aug 2011)
+
+  30 Aug 2011; Justin Lecher <jlec@gentoo.org> +cns-1.2.1-r7.ebuild,
+  metadata.xml:
+  Bump patches to aria-2.3.2
 
   21 Jun 2011; Justin Lecher <jlec@gentoo.org> cns-1.1.ebuild,
   cns-1.2.1.ebuild, cns-1.2.1-r5.ebuild, cns-1.2.1-r6.ebuild,
diff --git a/sci-chemistry/cns/cns-1.2.1-r7.ebuild b/sci-chemistry/cns/cns-1.2.1-r7.ebuild
new file mode 100644
index 000000000000..64faf0bedc57
--- /dev/null
+++ b/sci-chemistry/cns/cns-1.2.1-r7.ebuild
@@ -0,0 +1,243 @@
+# Copyright 1999-2011 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-r7.ebuild,v 1.1 2011/08/30 13:48:39 jlec Exp $
+
+EAPI=3
+
+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="
+	${MY_P}_all-mp.tar.gz
+	aria? ( aria2.3.2.tar.gz )"
+
+SLOT="0"
+LICENSE="cns"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="aria openmp"
+
+RDEPEND="
+	virtual/fortran
+	app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+FORTRAN_NEED_OPENMP=1
+
+S="${WORKDIR}/${MY_P}"
+
+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}-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/
+	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 "${T}"/
+	sed -i \
+		-e "s:_CNSsolve_location_:${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 [[ $(tc-getFC) =~ g77 ]]; then
+		GLOBALS="-fno-globals"
+		MALIGN='\$(CNS_MALIGN_I86)'
+	fi
+
+	# Set up the compiler to use
+	pushd instlib/machine/unsupported/g77-unix 2>/dev/null
+	ln -s Makefile.header Makefile.header.${FCOMP} || 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="$(tc-getCC)" \
+		F77=$(tc-getFC) \
+		LD=$(tc-getFC) \
+		CCFLAGS="${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/${PF}:g" \
+		-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		-e "/^g77on/d" \
+		"${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/${PF}:g" \
+		-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
+		-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
+		-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
+		-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
+		-e "/^g77on/d" \
+		-e "/^g77off/d" \
+		"${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/metadata.xml b/sci-chemistry/cns/metadata.xml
index 9d53ac3f3a11..3fbfefd30233 100644
--- a/sci-chemistry/cns/metadata.xml
+++ b/sci-chemistry/cns/metadata.xml
@@ -1,11 +1,11 @@
 <?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>
+	<herd>sci-chemistry</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
+	<use>
+		<flag name="aria"> Support patch for sci-chemistry/aria</flag>
+	</use>
 </pkgmetadata>