sci-chemistry/ccp4-apps: Add fix for tcl-8.6

(Portage version: 2.2.0_alpha149/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

1 files changed, 394 insertions, 0 deletions

diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild
new file mode 100644
index 000000000000..e9ddb76c4103
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild
@@ -0,0 +1,394 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r12.ebuild,v 1.1 2013/01/10 17:29:47 jlec Exp $
+
+EAPI=3
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils fortran-2 flag-o-matic gnuconfig python toolchain-funcs
+
+MY_P="${PN/-apps}-${PV}"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+PATCH_TOT="0"
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+SRC_URI="
+	${SRC}/${PV}/${MY_P}-core-src.tar.gz
+	http://dev.gentooexperimental.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2"
+# patch tarball from upstream
+	[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
+# patches created by us
+	[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
+
+for i in $(seq $PATCH_TOT); do
+	NAME="PATCH${i}[1]"
+	SRC_URI="${SRC_URI}
+		${SRC}/${PV}/patches/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples X"
+
+X11DEPS="
+	x11-libs/libX11
+	x11-libs/libXaw
+	x11-libs/libXt
+	x11-libs/libxdl_view"
+
+TKDEPS="
+	>=dev-lang/tk-8.3
+	>=dev-tcltk/blt-2.4
+	dev-tcltk/iwidgets
+	dev-tcltk/itcl
+	dev-tcltk/itk
+	>=dev-tcltk/tdom-0.8
+	dev-tcltk/tktreectrl"
+
+SCILIBS="
+	~sci-libs/ccp4-libs-${PV}
+	>=sci-libs/ccp4-libs-${PV}-r7
+	sci-libs/clipper
+	sci-libs/fftw:2.1
+	sci-libs/mmdb
+	sci-libs/ssm
+	virtual/blas
+	virtual/lapack"
+
+SCIAPPS="
+	sci-chemistry/pdb-extract
+	sci-chemistry/pymol
+	sci-chemistry/rasmol
+	>=sci-chemistry/oasis-4.0-r1"
+
+RDEPEND="
+	${TKDEPS}
+	${SCILIBS}
+	app-shells/tcsh
+	dev-python/pyxml
+	dev-libs/libxml2:2
+	dev-libs/libjwc_c
+	dev-libs/libjwc_f
+	dev-libs/boehm-gc
+	!app-office/sc
+	!<sci-chemistry/ccp4-6.1.3
+	X? ( ${X11DEPS} )"
+DEPEND="${RDEPEND}
+	X? (
+		x11-misc/imake
+		x11-proto/inputproto
+		x11-proto/xextproto
+	)"
+PDEPEND="${SCIAPPS}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	fortran-2_pkg_setup
+	python_set_active_version 2
+}
+
+src_prepare() {
+	einfo "Applying upstream patches ..."
+	for patch in $(seq $PATCH_TOT); do
+		base="PATCH${patch}"
+		dir=$(eval echo \${${base}[0]})
+		p=$(eval echo \${${base}[1]})
+		pushd "${dir}" >& /dev/null
+		ccp_patch "${DISTDIR}/${p}"
+		popd >& /dev/null
+	done
+	einfo "Done."
+	echo
+
+	[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
+
+	einfo "Applying Gentoo patches ..."
+
+	# it tries to create libdir, bindir etc on live system in configure
+	ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
+
+	# We already have sci-chemistry/rasmol
+	# Also remember to create the bindir.
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch
+
+	# libraries come from sci-libs/ccp4-libs
+	ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch
+
+	# We have seperate ebuilds for those
+	for bin in molref xia scala imosflm balbes; do
+		ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch
+	done
+
+	# don't configure what is not build
+	ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-pisa.patch
+
+	# Set python paths correctly
+	ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch
+
+	# Fix upstreams code
+	ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch
+
+	# Not renaming, but unbundling libs
+	ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch
+
+	# Use pkg-config to detect BLAS/LAPCK
+	ccp_patch "${FILESDIR}"/${PV}-lapack.patch
+
+	# unbundle libs
+	ccp_patch "${FILESDIR}"/${PV}-unbundle.patch
+
+	# tcl-8.6
+	ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch
+
+	# Update things for oasis 4 usage
+	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
+	sed 's: oasis : :g' -i src/Makefile.in || die
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete
+
+	sed \
+		-e "s:/usr:${EPREFIX}/usr:g" \
+		-e 's:-Wl,-rpath,$CLIB::g' \
+		-e 's: -rpath $CLIB::g' \
+		-e 's: -I${srcdir}/include/cpp_c_headers::g' \
+		-e 's:sleep 1:sleep .2:g' \
+		-e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \
+		-e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \
+		-e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \
+		-e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \
+		-i configure || die
+
+	sed \
+		-e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \
+		-i src/Makefile* || die
+
+	find "${S}" -name "Makefile.*" \
+		-exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \;
+
+	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
+	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die
+
+	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
+	pushd src/rapper 2>/dev/null
+		eautoreconf
+	popd 2>/dev/null
+
+	gnuconfig_update
+
+	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
+}
+
+src_configure() {
+	# Build system is broken if we set LDFLAGS
+	export GENTOOLDFLAGS="${LDFLAGS}"
+	unset LDFLAGS
+
+	# These are broken with ./src/procheck/ps.f
+	filter-flags "-floop-*"
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "$(tc-getFC)" = "ifort" ]]; then
+		if use ia64; then
+			GENTOO_OSNAME="ia64_linux_intel"
+		else
+			# Should be valid for x86, maybe amd64
+			GENTOO_OSNAME="linux_intel_compilers"
+		fi
+	else
+		# Should be valid for x86 and amd64, at least
+		GENTOO_OSNAME="linux"
+	fi
+
+	# Sets up env
+	ln -s \
+		ccp4.setup-bash \
+		"${S}"/include/ccp4.setup
+
+	# We agree to the license by emerging this, set in LICENSE
+	sed -i \
+		-e "s~^\(^agreed=\).*~\1yes~g" \
+		"${S}"/configure || die
+
+	# Fix up variables -- need to reset CCP4_MASTER at install-time
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \
+		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup* || die
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=$(tc-getFC)
+	export FOPTIM=${FFLAGS:- -O2}
+	export BINSORT_SCR="${T}"
+	export CCP4_MASTER="${WORKDIR}"
+	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
+	export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}"
+
+	# Can't use econf, configure rejects unknown options like --prefix
+	./configure \
+		$(use_enable X x) \
+		--with-shared-libs \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-warnings \
+		--disable-pdb_extract \
+		--disable-cctbx \
+		--disable-phaser \
+		--disable-diffractionImg \
+		--disable-clipper \
+		--disable-ssm \
+		--disable-mosflm \
+		--disable-mrbump \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "configure failed"
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+	econf \
+		--prefix="${S}" \
+		--bindir="${ED}"/usr/libexec/ccp4/bin \
+		--with-ccp4="${S}" \
+		--with-clipper="${EPREFIX}/usr" \
+		--with-fftw="${EPREFIX}/usr" \
+		--with-mmdb="${EPREFIX}/usr" \
+		CXX=$(tc-getCXX)
+	popd 2>/dev/null
+}
+
+src_compile() {
+	# fsplit is required for the programs
+	pushd lib/src 2>/dev/null
+		emake fsplit -j1 || die
+	popd 2>/dev/null
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+		emake || die
+	popd 2>/dev/null
+
+	emake -j1 || die "emake failed"
+}
+
+src_install() {
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	# if we don't make this, a ton of programs fail to install
+	mkdir "${S}"/bin || die
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd "${S}"/src/clipper_progs 2>/dev/null
+		emake install || die
+	popd 2>/dev/null
+
+	einstall || die "install failed"
+
+	# Collision with sci-chemistry/mrbump
+	rm -f "${S}"/bin/{mrbump,pydbviewer} || die
+
+	# Bins
+	exeinto /usr/libexec/ccp4/bin/
+	doexe "${S}"/bin/* || die
+
+	# Libs
+	for file in "${S}"/lib/*; do
+		if [[ -d ${file} ]]; then
+			continue
+		elif [[ -x ${file} ]]; then
+			dolib.so ${file} || die
+		else
+			insinto /usr/$(get_libdir)
+			doins ${file} || die
+		fi
+	done
+
+	rm -f "${S}"/include/ccp4.setup*
+
+	# smartie -- log parsing
+	insinto /usr/share/ccp4
+	doins -r "${S}"/share/smartie || die
+
+	# Install docs and examples
+	local _man
+	pushd "${S}"/man/cat1 > /dev/null
+	for _man in *; do
+		newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2}
+	done
+	popd > /dev/null
+
+	mv "${S}"/manual/README "${S}"/manual/README-manual
+	dodoc manual/* README CHANGES doc/* examples/README || die
+
+	rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.*
+	rm "${ED}"/usr/share/doc/${PF}/COPYING.*
+
+	dohtml -r "${S}"/html/*
+
+	if use examples; then
+		for i in data rnase toxd; do
+			docinto examples/${i}
+			dodoc "${S}"/examples/${i}/*
+		done
+
+		docinto examples/tutorial
+		dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css
+		for i in data results; do
+			docinto examples/tutorial/${i}
+			dodoc "${S}"/examples/tutorial/${i}/*
+		done
+
+		for i in non-runnable runnable; do
+			docinto examples/unix/${i}
+			dodoc "${S}"/examples/unix/${i}/*
+		done
+	fi
+	# Needed for ccp4i docs to work
+	dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die
+	dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die
+
+	cat >> "${T}"/baubles <<- EOF
+	#!${EPREFIX}/bin/bash
+	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
+	EOF
+
+	exeinto /usr/libexec/ccp4/bin/
+	doexe "${T}"/baubles || die
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}