Fix changes in gcc-4.6

Package-Manager: portage-2.2.0_alpha29/cvs/Linux x86_64

4 files changed, 236 insertions, 6 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/Manifest b/sci-libs/cctbx/Manifest
index 2b58aaa08b71..c4c468af7c32 100644
--- a/sci-libs/cctbx/Manifest
+++ b/sci-libs/cctbx/Manifest
@@ -4,16 +4,18 @@ Hash: SHA1
 AUX 2010.03.29.2334-boost.patch 18175 RMD160 cf972e6d792d98d152eb18453f0349c87efbbb97 SHA1 f9dac88aea0e898259537a343650cbcd53b6f01f SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7
 AUX 2010.03.29.2334-clipper.patch 2209 RMD160 1bfc13f0834e837a55f0e41554649acd1e45b80c SHA1 a81ee2cc94805b6ef1e609c2ea402a1c9f429d62 SHA256 e7c8bf813bedd3b67de5ce727d5f75e9635568769373f237e7b624ed143351b1
 AUX 2010.03.29.2334-flags.patch 3336 RMD160 fdbb0b71499e00c666629e1ff04b5bdcbe376b13 SHA1 ef97099dbd93727bd356015f22e82480a48e1a0c SHA256 769edb3e5dcb608b54ab4d33c5933b523f73ff62c6cb627c4eb4b1a2086e40b1
+AUX 2010.03.29.2334-gcc-4.6.patch 1059 RMD160 c999a541a0164438c13d5b9da5e00476fd37df03 SHA1 e4a5c60493d74a9c102aea4cc9d5607fc10fc526 SHA256 dad06be10e1ba3fefee9f9aa79a897635cb8362f5719c5c8c5e5c25d1bea6236
 AUX 2010.03.29.2334-soname.patch 5177 RMD160 c6cad498c4edb7046696428008408b126efa954c SHA1 7c5d78110c4270c9ca113ae5ea77c7c2451e2b21 SHA256 dd4ea6dbf34c1b2d9572adec5a33fe6a73b1a99e8c4364123e69382bb161ce74
 AUX 2010.03.29.2334-tst_server.py.patch 774 RMD160 12e1115b2ccc0b6b01b365925bf311d29ef08c7a SHA1 09549cc6103f502777acced13a3ed483d713dfc0 SHA256 df058d16d2dc5beaac9f1a1fbf2e640994c7e881d449eb01ac338dadbfb15ac3
 DIST cctbx-2010.03.29.2334.tar.gz 15570372 RMD160 e543578dbe6568f5f8f80b3ce7a20b10e01193bc SHA1 1442dbd5d1ef3b91e718dce039a24fc1637104d3 SHA256 e1fae804caaf8593c7a3f32e4544046f4c00293063d9099721578cc8fbd17213
 EBUILD cctbx-2010.03.29.2334-r3.ebuild 5939 RMD160 688044529f86e8324342ed918b3e660f77695d78 SHA1 51fef6efbf8e49f02aa49fa5ae2b45de377afada SHA256 5d20f7149b72b3672b038ced1ee119aaac1a00b30fad7a09a8d66987a7e27e1e
-MISC ChangeLog 3224 RMD160 4aaf3695bc6cccb6672b4375973cd609c611661c SHA1 301b8c09438845d404889ef78d552d122bc6ad06 SHA256 3425d37287977db5c55231c1247cb5e7c65f2ad52ea67b6baf819c417ef255d7
+EBUILD cctbx-2010.03.29.2334-r4.ebuild 5978 RMD160 868242df69fdc595c1dc3850016a4ac2de70e1f7 SHA1 9964fbb6a029bb3adfd30c0108c299c94bbf59a1 SHA256 abaff7cf14da7f1c18f41fe3a64bac0325fa276e257db5382c22d655045d3e5a
+MISC ChangeLog 3412 RMD160 e1c7641e4eddc954294bc1a23346ebeb3403c6c0 SHA1 0cdc7cf082895f8cd9eeccce91080367a4438354 SHA256 40db145c13e584e6347a02a663703c58e7eec5b55ca5f3f1d9ee153af4764fd7
 MISC metadata.xml 767 RMD160 c2fc3bcc534e407e6066ee98beb6878d78a0f6e9 SHA1 a653677e160cf0726e1747b06b5d0cd95e51ac5f SHA256 ef36fc1a1d5d657ba67f88b303f08eef5a1a814d22a2091c07616dc16928e3fa
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.16 (GNU/Linux)
+Version: GnuPG v2.0.17 (GNU/Linux)
 
-iEYEARECAAYFAk09oIEACgkQgAnW8HDreRbhWwCfUEOU33zKbbSLriFvh+35tqY0
-UgQAn2eO18aJBk31cNYOKYpsP6AHKc6g
-=GbzC
+iEYEARECAAYFAk2hxAwACgkQgAnW8HDreRaXRwCfc3vEyMiGZYHDCYvstmuBLHpj
+2fEAn3+IAkGan1m7DlE6nTZvEpG0fYYa
+=1YTc
 -----END PGP SIGNATURE-----
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;
+ };
+