Collision fix with raptor, #342005; Implicit declaration fixes

(Portage version: 2.2.0_alpha1/cvs/Linux x86_64)

3 files changed, 494 insertions, 1 deletions

diff --git a/sci-chemistry/ccp4-apps/ChangeLog b/sci-chemistry/ccp4-apps/ChangeLog
index 56005843b8ed..ae6677abc71c 100644
--- a/sci-chemistry/ccp4-apps/ChangeLog
+++ b/sci-chemistry/ccp4-apps/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/ccp4-apps
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.14 2010/06/24 18:04:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/ChangeLog,v 1.15 2010/10/26 18:59:33 jlec Exp $
+
+*ccp4-apps-6.1.3-r5 (26 Oct 2010)
+
+  26 Oct 2010; Justin Lecher <jlec@gentoo.org> +files/6.1.3-impl-dec.patch,
+  +ccp4-apps-6.1.3-r5.ebuild:
+  Collision fix with raptor, #342005; Implicit declaration fixes
 
   24 Jun 2010; Justin Lecher <jlec@gentoo.org> ccp4-apps-6.1.3-r4.ebuild:
   Added missing EPREFIX, thanks to Johan Hattne
diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild
new file mode 100644
index 000000000000..c8e91bd0b81c
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r5.ebuild
@@ -0,0 +1,451 @@
+# Copyright 1999-2010 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-r5.ebuild,v 1.1 2010/10/26 18:59:33 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools eutils flag-o-matic fortran gnuconfig python toolchain-funcs
+
+FORTRAN="g77 gfortran ifc"
+
+MY_P="${PN/-apps}-${PV}"
+
+SRC="ftp://ftp.ccp4.ac.uk/ccp4"
+
+#UPDATE="04_03_09"
+#PATCHDATE="090511"
+
+PATCH_TOT="0"
+# Here's a little scriptlet to generate this list from the provided
+# index.patches file
+#
+# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
+# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
+# index.patches
+#PATCH1=( src/topp_
+#topp.f-r1.16.2.5-r1.16.2.6.diff )
+#PATCH2=( .
+#configure-r1.372.2.18-r1.372.2.19.diff )
+
+DESCRIPTION="Protein X-ray crystallography toolkit"
+HOMEPAGE="http://www.ccp4.ac.uk/"
+RESTRICT="mirror"
+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/${!NAME}"
+done
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples X"
+
+X11DEPS="
+	x11-libs/libX11
+	x11-libs/libXaw
+	x11-libs/libXt
+	x11-libs/libxdl_view"
+
+TKDEPS="
+	>=dev-lang/tk-8.3
+	>=dev-tcltk/blt-2.4
+	dev-tcltk/iwidgets
+	dev-tcltk/itcl
+	dev-tcltk/itk
+	>=dev-tcltk/tdom-0.8
+	dev-tcltk/tkimg
+	dev-tcltk/tktreectrl"
+
+SCILIBS="
+	~sci-libs/ccp4-libs-${PV}
+	>=sci-libs/ccp4-libs-${PV}-r2
+	sci-libs/clipper
+	=sci-libs/fftw-2*
+	sci-libs/mmdb
+	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
+	dev-libs/libjwc_c
+	dev-libs/libjwc_f
+	dev-libs/boehm-gc
+	!app-office/sc
+	!<sci-chemistry/ccp4-6.1.2
+	X? ( ${X11DEPS} )"
+DEPEND="${RDEPEND}
+	=sys-devel/automake-1.6*
+	X? (
+		x11-misc/imake
+		x11-proto/inputproto
+		x11-proto/xextproto
+	)"
+PDEPEND="${SCIAPPS}"
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	python_set_active_version 2
+	fortran_pkg_setup
+}
+
+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
+
+	# coreutils installs a binary called truncate
+#	ccp_patch "${FILESDIR}"/${PV}-rename-truncate.patch
+#	mv ./doc/truncate.doc ./doc/ftruncate.doc || die
+#	mv ./html/truncate.html ./html/ftruncate.html || die
+
+	# conflicts with media-libs/raptor
+#	ccp_patch "${FILESDIR}"/${PV}-rename-rapper.patch
+#	mv ./doc/rapper.doc ./doc/rappermc.doc || die
+#	mv ./html/rapper.html ./html/rappermc.html || die
+
+	# 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}"/${PV}-impl-dec.patch
+
+	# Update things for oasis 4 usage
+	epatch "${WORKDIR}"/${PV}-oasis4.0.patch
+	sed 's: oasis : :g' -i src/Makefile.in || die
+
+	einfo "Done." # done applying Gentoo patches
+	echo
+
+	# Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version
+	sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure
+
+	# Rapper bundles libxml2 and boehm-gc. Don't build, use or install those.
+	pushd src/rapper 2>/dev/null
+	sed -i \
+		-e '/^AC_CONFIG_SUBDIRS(\[gc7.0 libxml2\])/d' \
+		configure.ac
+	sed -i \
+		-e '/^SUBDIRS/s:libxml2 gc7.0::g' \
+		Makefile.am
+	sed -i \
+		-e '/^rapper_LDADD/s:../gc7.0/libgc.la ../libxml2/libxml2.la:-lgc -lxml2:g' \
+		LOOP/Makefile.am
+	sed -i \
+		-e "/^INCLUDES/s:-I../gc7.0/include -I../libxml2/include:-I${EPREFIX}/usr/include/gc -I${EPREFIX}/usr/include/libxml2:g" \
+		LOOP/Makefile.am
+	eautoreconf
+	popd 2>/dev/null
+
+	gnuconfig_update
+
+	python_convert_shebangs $(python_get_version) src/ccp4_pipeline_simple.py ./share/smartie/*.py
+}
+
+src_configure() {
+	# Build system is broken if we set LDFLAGS
+	unset LDFLAGS
+
+	# These are broken with ./src/procheck/ps.f
+	filter-flags "-floop-*"
+
+	# GENTOO_OSNAME can be one of:
+	# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
+	# linux_compaq_compilers linux_intel_compilers generic Darwin
+	# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
+	if [[ "${FORTRANC}" = "ifc" ]]; 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
+
+	# 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" \
+		-e "s~^\(export CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
+		"${S}"/include/ccp4.setup*
+
+	# Set up variables for build
+	source "${S}"/include/ccp4.setup-sh
+
+	export CC=$(tc-getCC)
+	export CXX=$(tc-getCXX)
+	export COPTIM=${CFLAGS}
+	export CXXOPTIM=${CXXFLAGS}
+	# Default to -O2 if FFLAGS is unset
+	export FC=${FORTRANC}
+	export FOPTIM=${FFLAGS:- -O2}
+	export BINSORT_SCR="${T}"
+	export CCP4_MASTER="${WORKDIR}"
+	export CCP4I_TCLTK="${EPREFIX}/usr/bin"
+
+	# 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-mosflm \
+		--disable-mrbump \
+		--tmpdir="${TMPDIR}" \
+		${GENTOO_OSNAME} || die "econf failed"
+
+	# We do this manually, since disabling the clipper libraries also
+	# disables the clipper programs
+	pushd src/clipper_progs 2>/dev/null
+	econf \
+		--prefix="${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) \
+		|| die
+	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 "${S}"/include/ccp4.setup-sh
+
+#	make install || die "install failed"
+
+	# if we don't make this, a ton of programs fail to install
+	mkdir "${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"
+
+	# Fix env
+#		-e "s~^\(.*setenv PYTHONPATH .*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
+#		-e "s~^\(.*export PYTHONPATH.*\)\${CCP4}.*~\1\${CCP4}/share/ccp4/python~g" \
+	sed -i \
+		-e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
+		-e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \
+		-e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+		-e "s~^\(setenv DBCCP4I_TOP\).*~\1 \$CCP4/share/ccp4/dbccp4i~g" \
+		-e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
+		-e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \
+		-e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*setenv CLIB .*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
+		-e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "s~^\(export CCP4_MASTER.*\)${WORKDIR}~\1${EPREFIX}/usr~g" \
+		-e "s~^\(export CCP4.*\$CCP4_MASTER\).*~\1~g" \
+		-e "s~^\(export CCP4I_TOP\).*~\1=\$CCP4/$(get_libdir)/ccp4/ccp4i~g" \
+		-e "s~^\(export DBCCP4I_TOP\).*~\1=\$CCP4/share/ccp4/dbccp4i~g" \
+		-e "s~^\(.*export CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \
+		-e "s~^\(.*export CLIBD.*\$CCP4\).*~\1/share/ccp4/data~g" \
+		-e "s~^\(.*export CLIBD_MON.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*export MOLREPLIB.*\)\$CCP4.*~\1\$CCP4/share/ccp4/data/monomers/~g" \
+		-e "s~^\(.*export CLIB=.*\)\$CCP4.*~\1\$CCP4/$(get_libdir)~g" \
+		-e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \
+		-e "/IMOSFLM_VERSION/d" \
+		"${S}"/include/ccp4.setup* || die
+
+#		-e "s~\$CCP4/share/XIAROOT/setup.sh~\$CCP4/share/ccp4/XIAROOT/setup.sh~g" \
+
+	# Don't check for updates on every sourcing of /etc/profile
+	sed -i \
+		-e "s:\(eval python.*\):#\1:g"
+		"${S}"/include/ccp4.setup* || die
+
+	# Collision with sci-chemistry/mrbump
+	rm -f "${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 ${file} || die
+		fi
+	done
+
+	sed \
+		-e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \
+		-i "${S}"/include/ccp4.setup-sh || die
+
+	# Setup scripts
+	insinto /etc/profile.d
+#	newins "${S}"/include/ccp4.setup-bash ccp4.setup.bash || die
+	newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh || die
+#	newins "${S}"/include/ccp4.setup-zsh ccp4.setup.zsh || die
+	newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh || die
+	rm -f "${S}"/include/ccp4.setup*
+
+	# Environment files, setup scripts, etc.
+	insinto /usr/share/ccp4/include
+	doins "${S}"/include/* || die
+
+	# smartie -- log parsing
+	insinto /usr/share/ccp4
+	doins -r "${S}"/share/smartie || die
+
+	# Install docs and examples
+	doman "${S}"/man/cat1/*
+
+	mv "${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
+
+	# Fix overlaps with other packages
+	rm -f "${ED}"/usr/share/man/man1/rasmol.1* "${ED}"/usr/lib/font84.dat || die
+	mv "${ED}"/usr/share/man/man1/truncate{,-ccp4}.1 || die
+	mv "${ED}"/usr/share/man/man1/rapper{,-ccp4}.1 || die
+	mv "${ED}"/usr/share/man/man1/sc{,-ccp4}.1 || die
+
+	cat >> "${T}"/baubles <<- EOF
+	#!${EPREFIX}/bin/bash
+	exec $(PYTHON) \${CCP4}/share/ccp4/smartie/baubles.py
+	EOF
+
+	exeinto /usr/libexec/ccp4/bin/
+	doexe "${T}"/baubles || die
+}
+
+pkg_postinst() {
+	einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"
+	einfo "in ${EPREFIX}/etc/profile.d/ccp4.setup* to modify this."
+}
+
+# Epatch wrapper for bulk patching
+ccp_patch() {
+	EPATCH_SINGLE_MSG="  ${1##*/} ..." epatch ${1}
+}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
new file mode 100644
index 000000000000..7529ea5de593
--- /dev/null
+++ b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
@@ -0,0 +1,36 @@
+diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
+index ee8af24..c6fb3cd 100755
+--- a/lib/src/fsplit.c
++++ b/lib/src/fsplit.c
+@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c	5.5 (Berkeley) 3/12/91";
+ #include <string.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
++#include <unistd.h>
+ 
+ /*
+  *	usage:		fsplit [-e efile] ... [file]
+diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
+index ea52e96..30dbd56 100755
+--- a/src/clipper_progs/src/pirate/compress42.c
++++ b/src/clipper_progs/src/pirate/compress42.c
+@@ -142,6 +142,7 @@
+ #include	<sys/types.h>
+ #include	<sys/stat.h>
+ #include	<errno.h>
++#include	<unistd.h>
+ 
+ #ifdef DIRENT
+ #	include	<dirent.h>
+diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
+index e224430..c7b82f4 100755
+--- a/src/mtz2cif_/mtz2cif.c
++++ b/src/mtz2cif_/mtz2cif.c
+@@ -28,6 +28,7 @@
+ #include "cmtzlib.h"
+ #include "ccp4_parser.h"
+ #include "ccp4_general.h"
++#include "ccp4_program.h"
+ #include "csymlib.h"
+ #include "mtz2cif_lib.h"
+