Fix changes in gcc-4.6

(Portage version: 2.2.0_alpha29/cvs/Linux x86_64)

3 files changed, 229 insertions, 1 deletions

diff --git a/sci-libs/cctbx/ChangeLog b/sci-libs/cctbx/ChangeLog
index 87e6cfa408ca..fd6cfb73ef30 100644
--- a/sci-libs/cctbx/ChangeLog
+++ b/sci-libs/cctbx/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/cctbx
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.16 2011/01/24 15:53:27 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/ChangeLog,v 1.17 2011/04/10 14:51:51 jlec Exp $
+
+*cctbx-2010.03.29.2334-r4 (10 Apr 2011)
+
+  10 Apr 2011; Justin Lecher <jlec@gentoo.org>
+  +files/2010.03.29.2334-gcc-4.6.patch, +cctbx-2010.03.29.2334-r4.ebuild:
+  Fix changes in gcc-4.6
 
   24 Jan 2011; Justin Lecher <jlec@gentoo.org>
   -cctbx-2010.03.29.2334-r1.ebuild:
diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r4.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r4.ebuild
new file mode 100644
index 000000000000..dd29d25bda0a
--- /dev/null
+++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r4.ebuild
@@ -0,0 +1,193 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/cctbx/cctbx-2010.03.29.2334-r4.ebuild,v 1.1 2011/04/10 14:51:51 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils prefix python toolchain-funcs
+
+MY_PV="${PV//./_}"
+
+DESCRIPTION="Computational Crystallography Toolbox"
+HOMEPAGE="http://cctbx.sourceforge.net/"
+SRC_URI="http://cci.lbl.gov/cctbx_build/results/${MY_PV}/${PN}_bundle.tar.gz -> ${P}.tar.gz"
+
+LICENSE="cctbx-2.0"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="+minimal openmp threads"
+
+RDEPEND="
+	>dev-libs/boost-1.39
+	sci-libs/clipper
+	sci-libs/fftw
+	!minimal? (
+		sci-chemistry/cns
+		sci-chemistry/shelx )"
+DEPEND="${RDEPEND}
+	>=dev-util/scons-1.2"
+
+S="${WORKDIR}"
+MY_S="${WORKDIR}"/cctbx_sources
+MY_B="${WORKDIR}"/cctbx_build
+
+pkg_setup() {
+	if use openmp && ! tc-has-openmp; then
+		ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 and icc"
+		ewarn "If you want to build ${PN} with OpenMP, abort now,"
+		ewarn "and switch CC to an OpenMP capable compiler"
+	fi
+	python_set_active_version 2
+}
+
+src_prepare() {
+	local opts
+	local optsld
+
+	epatch \
+		"${FILESDIR}"/${PV}-tst_server.py.patch \
+		"${FILESDIR}"/${PV}-boost.patch \
+		"${FILESDIR}"/${PV}-clipper.patch \
+		"${FILESDIR}"/${PV}-flags.patch \
+		"${FILESDIR}"/${PV}-soname.patch \
+		"${FILESDIR}"/${PV}-gcc-4.6.patch
+
+	eprefixify "${MY_S}"/scitbx/libtbx_refresh.py
+
+	rm -rf "${MY_S}/scons" "${MY_S}/boost" "${MY_S}/PyCifRW" || die
+	find "${MY_S}/clipper" -name "*.h" -delete || die
+
+	echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py
+}
+
+src_configure() {
+	local compiler
+	local myconf
+
+	myconf="${MY_S}/libtbx/configure.py"
+
+	compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)')
+	myconf="${myconf} --compiler=${compiler}"
+
+	# Additional USE flag usage
+	check_use openmp
+	myconf="${myconf} --enable-openmp-if-possible=${USE_openmp}"
+
+	use threads && USEthreads="--enable-boost-threads" && \
+		ewarn "If using boost threads openmp support is disabled"
+
+	myconf="${myconf} ${USE_threads} --scan-boost --use_environment_flags"
+
+	mkdir "${MY_B}" && myconf="${myconf} --current_working_directory=${MY_B}"
+	cd "${MY_B}"
+
+	myconf="${myconf} --build=release fftw3tbx rstbx smtbx mmtbx clipper_adaptbx fable"
+	einfo "configuring with ${python} ${myconf}"
+
+	$(PYTHON) ${myconf} || die "configure failed"
+}
+
+src_compile() {
+	local makeopts_exp
+
+	cd "${MY_B}"
+
+	makeopts_exp=${MAKEOPTS/j/j }
+	makeopts_exp=${makeopts_exp%-l[0-9]*}
+
+	source setpaths_all.sh
+
+	einfo "compiling with libtbx.scons ${makeopts_exp}"
+	libtbx.scons ${makeopts_exp} .|| die "make failed"
+}
+
+src_test(){
+	source "${MY_B}"/setpaths_all.sh
+	libtbx.python $(libtbx.show_dist_paths boost_adaptbx)/tests/tst_rational.py && \
+	libtbx.python ${SCITBX_DIST}/run_tests.py ${MAKEOPTS_EXP} && \
+	libtbx.python ${CCTBX_DIST}/run_tests.py  ${MAKEOPTS_EXP} \
+	|| die "test failed"
+}
+
+src_install(){
+#	find cctbx_build/ -type f \( -name "*.py" -o -name "*sh" \) -exec \
+#	sed -e "s:${MY_S}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_sources:g" \
+#	    -e "s:${MY_B}:${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build:g"  \
+#	    -i '{}' \; || die "Fail to correct path"
+
+	sed \
+		-e "s:${MY_B}:${EPREFIX}/usr:g" \
+		-e "s:${MY_S}:${EPREFIX}/$(python_get_sitedir):g" \
+		-i "${MY_B}/libtbx_env" || die
+
+	insinto /usr/share/cctbx
+	doins "${MY_B}/libtbx_env" || die
+
+	ebegin "removing unnessary files"
+		rm -r "${S}"/cctbx_sources/{clipper,ccp4io,ucs-fonts,TAG} || die "failed to remove uneeded scons"
+		find "${S}" -type f -name "*conftest*" -delete || die "failed to remove uneeded *.o"
+		find "${S}" -type f -name "*.o" -delete || die "failed to remove uneeded *.o"
+		find "${S}" -type f -name "*.c" -delete || die "failed to remove uneeded *.c"
+		find "${S}" -type f -name "*.f" -delete || die "failed to remove uneeded *.c"
+		find "${S}" -type f -name "*.cpp" -delete || die "failed to remove uneeded *.cpp"
+		find "${S}" -type f -name "*.pyc" -delete || die "failed to remove uneeded *.pyc"
+		find "${S}" -type f -name "SCons*" -delete || die "failed to remove uneeded *.pyc"
+		find "${S}" -type f -name "Makefile" -delete || die "failed to remove uneeded *.pyc"
+		find "${S}" -type f -name "config.log" -delete || die "failed to remove uneeded *.pyc"
+		find "${S}" -type d -empty -delete || die
+		find "${MY_B}" -maxdepth 1 -type f -delete || die
+	eend
+
+	dobin "${MY_B}"/bin/* || die
+	rm -rf "${MY_B}/bin"
+	dolib.so "${MY_B}"/lib/lib* || die
+	rm -f "${MY_B}"/lib/lib*
+
+	insinto /usr/include
+	doins -r "${MY_B}"/include/* || die
+	rm -rf "${MY_B}/include"
+
+	insinto /usr/libexec/${PN}
+	doins -r "${MY_B}"/* || die
+	find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \;
+
+	cd "${MY_S}"
+	insinto $(python_get_sitedir)
+	doins -r * || die
+	exeinto $(python_get_sitedir)
+	doexe "${MY_B}"/lib/* || die
+	rm -rvf "${MY_B}/lib"
+
+	sed \
+		-e "/PYTHONPATH/s:${MY_S}:$(python_get_sitedir):g" \
+		-e "/PYTHONPATH/s:${MY_B}:$(python_get_sitedir):g" \
+		-e "/LD_LIBRARY_PATH/s:${MY_B}/lib:${EPREFIX}/usr/$(get_libdir):g" \
+		-e "/PATH/s:${MY_B}/bin:${EPREFIX}/usr/bin:g" \
+		-e "/PATH/s:${MY_B}/exe:${EPREFIX}/usr/bin:g" \
+		-e "/exec/s:${MY_S}:$(python_get_sitedir):g" \
+		-e "/LIBTBX_BUILD/s:${MY_B}:${EPREFIX}/usr/share/cctbx:g" \
+		-e "s:${MY_B}/exe_dev/:${EPREFIX}/usr/libexec/${PN}/exe_dev/:g" \
+		-i "${ED}"/usr/bin/* || die
+
+}
+
+pkg_postinst () {
+	python_mod_optimize boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
+}
+
+pkg_postrm () {
+	python_mod_cleanup boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx chiltbx clipper_adaptbx crys3d fable fftw3tbx gltbx iotbx libtbx mmtbx omptbx rstbx scitbx smtbx spotfinder tntbx
+}
+
+check_use() {
+	for var in $@; do
+		if use ${var}; then
+			printf -v "USE_$var" True
+		else
+			printf -v "USE_$var" False
+		fi
+	shift
+	done
+}
diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch
new file mode 100644
index 000000000000..e54cfa16838b
--- /dev/null
+++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch
@@ -0,0 +1,29 @@
+ cctbx_sources/scitbx/array_family/detail/misc.h    |    1 +
+ .../scitbx/fortran_io/details/istream_scanner.h    |    2 +-
+ 2 files changed, 2 insertions(+), 1 deletions(-)
+
+diff --git a/cctbx_sources/scitbx/array_family/detail/misc.h b/cctbx_sources/scitbx/array_family/detail/misc.h
+index 6ed881e..d7f7f52 100644
+--- a/cctbx_sources/scitbx/array_family/detail/misc.h
++++ b/cctbx_sources/scitbx/array_family/detail/misc.h
+@@ -2,6 +2,7 @@
+ #define SCITBX_ARRAY_FAMILY_MISC_H
+ 
+ #include <scitbx/array_family/type_traits.h>
++#include <memory>
+ 
+ namespace scitbx { namespace af {
+ 
+diff --git a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
+index 8a0ac25..03a0e20 100644
+--- a/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
++++ b/cctbx_sources/scitbx/fortran_io/details/istream_scanner.h
+@@ -32,7 +32,7 @@ class istream_scanner
+     }
+ 
+   private:
+-    mutable std::basic_istream<CharType> &input;
++    std::basic_istream<CharType> &input;
+     mutable value_t current;
+ };
+