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

Package-Manager: portage-2.2.0_alpha149/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

5 files changed, 540 insertions, 9 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index 4ba560a0906e..286ea0168ac6 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/ccp4-apps
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.39 2012/10/19 09:41:15 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.40 2013/01/10 17:29:47 jlec Exp $
+
+*ccp4-apps-6.1.3-r12 (10 Jan 2013)
+
+  10 Jan 2013; Justin Lecher <jlec@gentoo.org> +ccp4-apps-6.1.3-r12.ebuild,
+  +files/ccp4-apps-6.1.3-tcl8.6.patch, metadata.xml:
+  Add fix for tcl-8.6
 
   19 Oct 2012; Justin Lecher <jlec@gentoo.org> ccp4-apps-6.1.3-r11.ebuild:
   Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest
index 3ed5edacfcaf..9e0e758dc9e5 100644
--- a/sci-chemistry/ccp4-apps/Manifest
+++ b/sci-chemistry/ccp4-apps/Manifest
@@ -17,16 +17,17 @@ AUX 6.1.3-pisa.patch 714 SHA256 42a581d2a9747239c1b129dbeffc76a2532de320629dd581
 AUX 6.1.3-pythonpath.patch 2716 SHA256 41ca8ed3fc1701caa18b30f44af7475d49fc0042ee058bae3d8c8617a6d9bcc2 SHA512 e6d9560976a07f4beb8f0e8de4d151ac0c3434cc7c30b4c14bcebeaae0fd411c25023684978c67f3680ade87351c751d61e55f75ec742bd3b4442647b2227246 WHIRLPOOL 18525a440fb7456b44e58185d701d86638c58f7d5e5ec327a50d8fa6c831fc802157bc54385f9165d6ca05ce2c434260de2e1cc84a18e4cdce146f1d722c8e36
 AUX 6.1.3-rename-rapper-ng.patch 2241 SHA256 7a476133860463b91b39189aa5628607f0404224cae1273b4da1c500a845dfdb SHA512 93dd483454d5b7f9423f20e29d09d8c067fd07b40db94bc92836ea4b51b3cbf37d7bbed86290ec95cd6174a7dddc74c575965360f922f77ed835ac934dab6bba WHIRLPOOL 9015d7ac00d1a50fa73a06a86c98b61f69510a856fecaa043604db6a180a296bedba91372b89e0051e7603ba7f92bb6c5cb406674d8d68f0aa511c2eeaacf498
 AUX 6.1.3-unbundle.patch 5736 SHA256 1d50917bdd3733d099cf64df651c8743ab40ce1ea19416bfacf806e324b2bea2 SHA512 1953ac8d566f606cdd3bba002bc75cbad1c94845f6ac6fe1ea0e0d1a2838f536cbe9f0e5e58f631d6a452c4eb79e1d20e438611f3eef967229faffc2f2fc1486 WHIRLPOOL e2aeae28f23ce6d75879882ce490832aba975e4bd32a98c1c0c49499d50d732083f33c8c4b35c01109fc95b18b1ea592d9d57760acebbe666bfaebef4952fdb8
+AUX ccp4-apps-6.1.3-tcl8.6.patch 6027 SHA256 665d21a30b78e55480c8eddd83ef2c7e77573b0bffe3cef7e48c065d2601b8b6 SHA512 6bab6305bd3f902309ef0427e510a8000883fb115e5ca302dcad110d3687b71778cd0da31f619b50b477d83a330aba7db608556ccda2efd6087ee99d7dea1648 WHIRLPOOL 865b870abc4d53697d41ce30057cd6716eb032ca38c786c11e6e28bfaf25ecd70cb05ac401bed66faeded62a433b919005da3e9012f1c9dc7d1459b68b78f505
 DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820
 DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c
 EBUILD ccp4-apps-6.1.3-r11.ebuild 9982 SHA256 188340e65b4b3db2196543fc7f8cc7e3de899e4ec85cb2ffa72a1991628fe638 SHA512 2e917437b5ac5f3cb56310b63767bf58ab77dc3eeba280c4470b1f591984baadd4fb76b63f25f07ff4fb1df22bfb073adf43758bf02db5e9bf05e7557e19d6c5 WHIRLPOOL 6d861fbd1d35c42d5d3ed28128641f3cd4500b310a9347b24cf55cd7c04c708e2e681d526663afd11526e2ff73aef13487d249c826c6e7124ea1965a16b09467
-MISC ChangeLog 7222 SHA256 149554f7f1f4879aae0e3dc93eb950f24b9a657858d671eb4cb43721bffa7dff SHA512 3d2ee530bc2c00d68028d65c4d0715b46b6d4e98f8cc79fbabecaf06ed993fd6cbcf524f8b4d91effe75cec77499bffdd77bdf8eace5d7e9787cf3dd4adc1c0c WHIRLPOOL cafe56ab3627b9296f644568ea983f5aeeed175eafa4fe698af0526937eefb20d560bb64c6fe658cfd3aae3b9c93e1772ae157e7e6c1433fdcc9e04c5ad042a0
-MISC metadata.xml 167 SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 SHA512 0f65f650c91edb15011884892b3e2447ec2342f207b6b71541ec25939fed33cd219b1fcd85dd06008b56a50622973febeb63c9c6158f62435c63c4fbd3ab93bd WHIRLPOOL 0823fd1d22e4aea50bcf78c359303d804128475e21e39514505ee6528c9c46376ceafc1f13bb1cc4e1143d434397fb4ef65dc028e924fdc831521947534fd93f
+EBUILD ccp4-apps-6.1.3-r12.ebuild 10039 SHA256 fbd956878149377797dce43758494a5e7b25346576c50bb258d8579f8e05118c SHA512 50a80b7732a7e4b646e60d6cdc53683ab39099f6b908aa30891c8aede7f77b8f8397af1924c5dde570007b88a88dff658766151aa88052f9d20289ea05072e1b WHIRLPOOL afb00f618a745d46bc330a45d515191c3b72cda1299d898812da647bd9a7fb378a5aa493925db120db1e6fb27f8f15ea415390fc5471422f245bdac5eb9284ac
+MISC ChangeLog 7410 SHA256 ded879e9add83f62f0da0626ff77e6a20158e4d76ee24932d2455e940f87446d SHA512 0465c0b3e9cc8b369bbab2c0745aa6cb4370c8238147c722a4923ba48a13ffb1e25d3ff6b528985dfcd127238c071ea9fcb6dd27e684f60acb5f20a13cd8f7aa WHIRLPOOL 6d09ee15c05704a05741625de31ccf6e3c191db7cc595cc84a43c824237f2e1e3b3d433dae51423365aa3585fbb06c415567ea5064f73388cc125ce14cc93160
+MISC metadata.xml 168 SHA256 705462092174cd3e2e3ec1557a28108a746b7351f803d8ca6d1b925b3111c3ff SHA512 f0073fb277e20adb7781aa6ea7f8237bc2d350f0aa43f0f0cca33e02cf52b8fc117bd984c11721ac519a2637ea145976148ac1aba7335dc74c42f7b9531cbed3 WHIRLPOOL 07dd7a302e695440f5033889e5b20cada57beedf17ad33f95d45fb5c39da98bf206eaff13334c20c1c08140a9c5e6041341d29c58efc5ca59b112b60e1662318
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.19 (GNU/Linux)
-Comment: GPGTools - http://gpgtools.org
 
-iEYEAREIAAYFAlCBIDwACgkQgAnW8HDreRYmvgCZAfTLDeknh25oaKGOD+/plYns
-QY0AniF961DmcJ8GKfMf7qKZvjBf3P4k
-=evpK
+iEYEAREIAAYFAlDu+owACgkQgAnW8HDreRbVeACfRYryJ/kaJY8M3jQQq8etE7gK
+xI8An0ShSSrRKiPmSjh6c4PSI9GWhTJ6
+=i0Rs
 -----END PGP SIGNATURE-----
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}
+}
diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
new file mode 100644
index 000000000000..4b98545eec83
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
@@ -0,0 +1,130 @@
+ src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++---------------
+ 1 file changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
+index 2c9f02f..98d814a 100755
+--- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
++++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
+@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags,
+     puts("canvas_draw_line: about to evaluate the command...");
+   }
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result);
++    printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
+     return 0;
+   }
+   if (CCP4MAPWISH_CANVAS_DIAG)
+@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y,
+     puts("canvas_draw_rectangle: about to evaluate the command...");
+   }
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result);
++    printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
+     printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units);
+     return 0;
+   }
+@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y,
+   /* Execute the command which draws the label */
+   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command);
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale)
+   /* Execute the command which scales the canvas */
+   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command);
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas)
+   /* Execute the command which resizes the canvas */
+   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty)
+   /* Execute the command which resizes the canvas */
+   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag)
+   /* Execute the command which deletes the tagged items */
+   if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command);
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+@@ -892,15 +892,15 @@ int canvas_exists(char *canvas)
+ 
+   sprintf(tmpstr,"winfo exists %s",canvas);
+   if (Tcl_Eval(interp,tmpstr) != TCL_OK) {
+-    printf("canvas_exists: error from Tcl_Eval: %s",interp->result);
++    printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
+     return 0;
+   }
+   /* Extract a long int using strtol
+      If no conversion takes place then "endptr" will be equal
+      to "result" */
+-  istatus = (int) strtol(interp->result,&endptr,10);
+-  if (strcmp(interp->result,endptr) == 0) {
+-    printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result);
++  istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10);
++  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
++    printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+   if (!istatus) {
+@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units)
+ 
+   /* Execute the tk scaling command */
+   if (Tcl_Eval(interp,"tk scaling") != TCL_OK) {
+-    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result);
++    printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
+     return (float) 0.0;
+   }
+ 
+   /* Extract a float from the result */
+-  tkscale = ((float) strtod(interp->result,&endptr));
+-  if (strcmp(interp->result,endptr) == 0) {
++  tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr));
++  if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
+     printf("canvas_get_tk_scaling: couldn't extract scale factor\n");
+     return (float) 0.0;
+   }
+@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4])
+ 
+   /* Evaluate the command */
+   if (Tcl_Eval(interp,command) != TCL_OK) {
+-    printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result);
++    printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
+     return 0;
+   }
+ 
+   /* Process the result - it should consist of 4 integers */
+   /* Use strtok which can split the string based on tokens
+      set by the programmer - in this case a space */
+-  if (!interp->result) {
++  if (!Tcl_GetStringResult(interp)) {
+     puts("canvas_get_limits: failed to fetch canvas limits");
+     return TCL_ERROR;
+   }
+   i = 0;
+-  p = strtok(interp->result," ");
++  p = strtok(Tcl_GetStringResult(interp)," ");
+   if (p == NULL) {
+     return 0;
+   }
diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml
index e42d0af60f42..51fdedab1b38 100644
--- a/sci-chemistry/ccp4-apps/metadata.xml
+++ b/sci-chemistry/ccp4-apps/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci-chemistry</herd>
+  <herd>sci-chemistry</herd>
 </pkgmetadata>