From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-libs/cctbx/Manifest | 13 + sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild | 189 ++++++++ sci-libs/cctbx/files/2010.03.29.2334-boost.patch | 516 +++++++++++++++++++++ sci-libs/cctbx/files/2010.03.29.2334-clipper.patch | 77 +++ sci-libs/cctbx/files/2010.03.29.2334-flags.patch | 94 ++++ .../files/2010.03.29.2334-format-security.patch | 117 +++++ sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch | 29 ++ sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch | 154 ++++++ sci-libs/cctbx/files/2010.03.29.2334-soname.patch | 123 +++++ .../files/2010.03.29.2334-tst_server.py.patch | 15 + sci-libs/cctbx/metadata.xml | 20 + 11 files changed, 1347 insertions(+) create mode 100644 sci-libs/cctbx/Manifest create mode 100644 sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-boost.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-clipper.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-flags.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-format-security.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-soname.patch create mode 100644 sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch create mode 100644 sci-libs/cctbx/metadata.xml (limited to 'sci-libs/cctbx') diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest new file mode 100644 index 000000000000..a7323ca2432a --- /dev/null +++ b/sci-libs/cctbx/Manifest @@ -0,0 +1,13 @@ +AUX 2010.03.29.2334-boost.patch 18175 SHA256 f6a8a246dfd42e7981687802a0e00d933759d3c749c0344bfbfbfde12814f4d7 SHA512 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72a2193f9df4c8bac19018122f5746ac055f81ca7498d5f75c2a136095df99fadb5705d4378065b87b698cf090a1e52e1048136d43df3e93cd27c2f5a1087a1b diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild new file mode 100644 index 000000000000..5ac1e461f684 --- /dev/null +++ b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild @@ -0,0 +1,189 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils fortran-2 multilib prefix python-single-r1 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" + +REQUIRED_USE=" + ${PYTHON_REQUIRED_USE} + ?? ( openmp threads )" + +RDEPEND=" + ${PYTHON_DEPS} + >=dev-libs/boost-1.48[python,${PYTHON_USEDEP}] + sci-libs/clipper + sci-libs/fftw:3.0= + !minimal? ( + sci-chemistry/cns + sci-chemistry/shelx )" +DEPEND="${RDEPEND} + !prefix? ( >=dev-util/scons-1.2[${PYTHON_USEDEP}] )" + +S="${WORKDIR}" +MY_S="${WORKDIR}"/cctbx_sources +MY_B="${WORKDIR}"/cctbx_build + +pkg_setup() { + use openmp && FORTRAN_NEED_OPENMP="1" + 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 ${PN} with OpenMP, abort now," + ewarn "and switch CC to an OpenMP capable compiler" + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + python-single-r1_pkg_setup +} + +src_prepare() { + local opts + local optsld + + epatch \ + "${FILESDIR}"/${PV}-tst_server.py.patch \ + "${FILESDIR}"/${PV}-boost.patch \ + "${FILESDIR}"/${PV}-clipper.patch \ + "${FILESDIR}"/${PV}-flags.patch \ + "${FILESDIR}"/${PV}-soname.patch \ + "${FILESDIR}"/${PV}-gcc-4.6.patch \ + "${FILESDIR}"/${PV}-gcc-4.7.patch \ + "${FILESDIR}"/${PV}-format-security.patch + + eprefixify "${MY_S}"/scitbx/libtbx_refresh.py + + rm -rvf "${MY_S}/boost" "${MY_S}/PyCifRW" >> "${T}"/clean.log || die + if ! use prefix; then + rm -rvf "${MY_S}/scons" >> "${T}"/clean.log || die + echo "import os, sys; os.execvp('scons', sys.argv)" > "${MY_S}"/libtbx/command_line/scons.py || die + fi + + find "${MY_S}/clipper" -name "*.h" -print -delete >> "${T}"/clean.log || die + + sed \ + -e "/LIBS/s:boost_python:boost_python-$(echo ${EPYTHON} | sed 's/python//'):g" \ + -i "${MY_S}"/boost_adaptbx/SConscript "${MY_S}"/scitbx/boost_python/SConscript || die +} + +src_configure() { + local compiler + local myconf + + myconf="${MY_S}/libtbx/configure.py" + + compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') + myconf="${myconf} --compiler=${compiler}" + + # Additional USE flag usage + myconf="${myconf} --enable-openmp-if-possible=$(usex openmp true false)" + + use threads && USEthreads="--enable-boost-threads" + + 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}" + + ${EPYTHON} ${myconf} || die "configure failed" +} + +src_compile() { + local makeopts_exp + + cd "${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(){ + local lib baselib +# 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 -O3 "${S}" -type f \ + \( -name "*conftest*" -o -name "*.o" -o -name "*.c" -o -name "*.f" -o -name "*.cpp" -o \ + -name "*.pyc" -o -name "SCons*" -o -name "Makefile" -o -name "config.log" \) -delete \ + -print >> "${T}"/clean.log || die + find "${S}" -type d -empty -delete -print >> "${T}"/clean.log || die + find "${MY_B}" -maxdepth 1 -type f -delete -print >> "${T}"/clean.log || die + eend + + dobin "${MY_B}"/bin/* + rm -vrf "${MY_B}/bin" >> "${T}"/clean.log || die + dolib.so "${MY_B}"/lib/lib* + mv "${ED}"/usr/$(get_libdir)/libscitbx_min{,i}pack.so || die + rm -vf "${MY_B}"/lib/lib* >> "${T}"/clean.log || die + + for lib in "${ED}"/usr/$(get_libdir)/*.so; do + baselib=$(basename ${lib}) + mv ${lib}{,.0.0} || die + dosym ${baselib}.0.0 /usr/$(get_libdir)/${baselib} + done + + insinto /usr/include + doins -r "${MY_B}"/include/* || die + rm -rvf "${MY_B}/include" >> "${T}"/clean.log || die + + insinto /usr/libexec/${PN} + doins -r "${MY_B}"/* || die + find "${ED}"/usr/libexec/${PN} -type f -exec chmod 755 '{}' \; + + cd "${MY_S}" + python_domodule * "${MY_B}"/lib/* + rm -rvf "${MY_B}/lib" >> "${T}"/clean.log || die + + 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 + + python_optimize +} diff --git a/sci-libs/cctbx/files/2010.03.29.2334-boost.patch b/sci-libs/cctbx/files/2010.03.29.2334-boost.patch new file mode 100644 index 000000000000..5b4439ee6780 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-boost.patch @@ -0,0 +1,516 @@ +From 7e77ff8694b87e95efe56ed961fbc8dd30d8c238 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +Date: Sun, 4 Jul 2010 12:21:10 +0200 +Subject: [PATCH] Unbundle boost. + +--- + work/cctbx_sources/boost_adaptbx/SConscript | 260 ------------------------- + work/cctbx_sources/cbflib_adaptbx/SConscript | 1 - + work/cctbx_sources/cctbx/SConscript | 1 - + work/cctbx_sources/clipper_adaptbx/SConscript | 1 - + work/cctbx_sources/fable/SConscript | 1 - + work/cctbx_sources/fable/libtbx_config | 2 +- + work/cctbx_sources/fftw3tbx/SConscript | 1 - + work/cctbx_sources/gltbx/SConscript | 1 - + work/cctbx_sources/iotbx/SConscript | 2 - + work/cctbx_sources/mmtbx/SConscript | 1 - + work/cctbx_sources/omptbx/libtbx_config | 2 +- + work/cctbx_sources/rstbx/SConscript | 1 - + work/cctbx_sources/scitbx/SConscript | 1 - + work/cctbx_sources/scitbx/libtbx_config | 2 +- + work/cctbx_sources/scitbx/libtbx_refresh.py | 3 +- + work/cctbx_sources/smtbx/SConscript | 1 - + work/cctbx_sources/spotfinder/SConscript | 1 - + work/cctbx_sources/tntbx/SConscript | 1 - + 18 files changed, 4 insertions(+), 279 deletions(-) + +diff --git a/work/cctbx_sources/boost_adaptbx/SConscript b/work/cctbx_sources/boost_adaptbx/SConscript +index 0701816..9f8cbf9 100644 +--- a/work/cctbx_sources/boost_adaptbx/SConscript ++++ b/work/cctbx_sources/boost_adaptbx/SConscript +@@ -8,39 +8,9 @@ import string + import sys, os + op = os.path + Import("env_base", "env_etc") +-env_etc.boost_dist = libtbx.env.dist_path("boost") +-env_etc.boost_include = env_etc.boost_dist + env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx") + env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist) + +-def build_boost_thread(): +- if (not libtbx.env.build_options.enable_boost_threads): +- return +- if (sys.platform == "win32"): s = "win32" +- else: s = "pthread" +- join = os.path.join +- src = join("libs", "thread", "src", s) +- prefix = "#" + join(os.path.basename(env_etc.boost_dist), src) +- source = [] +- for node in sorted(os.listdir(join(env_etc.boost_dist, src))): +- if (not node.lower().endswith(".cpp")): continue +- source.append(join(prefix, node)) +- env = env_base.Clone( +- SHLINKFLAGS=env_etc.shlinkflags) +- env.Append(SHCXXFLAGS=["-DBOOST_THREAD_BUILD_DLL"]) +- env_etc.include_registry.append( +- env=env, +- paths=[env_etc.boost_include]) +- darwin_shlinkcom(env_etc, env, +- lo="boost/libs/thread/src/libboost_thread.lo", +- dylib="lib/libboost_thread.dylib") +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- env.SharedLibrary( +- target='#lib/boost_thread', +- source=source) +- +-build_boost_thread() +- + if (not env_etc.no_boost_python): + env_etc.cxxflags_bpl_defines_base = [ + "-DBOOST_PYTHON_MAX_BASES=2"] +@@ -64,12 +34,10 @@ if (not env_etc.no_boost_python): + ' /manifest ${TARGET}.manifest']) + Export("env_no_includes_boost_python_ext") + env_pure_boost_python_ext = env_no_includes_boost_python_ext.Clone() +- env_etc.include_registry.set_boost_dir_name(env_etc.boost_dist) + env_etc.include_registry.append( + env=env_pure_boost_python_ext, + paths=[ + "#include", +- env_etc.boost_include, + env_etc.python_include]) + env_boost_python_ext = env_pure_boost_python_ext.Clone() + env_etc.include_registry.prepend( +@@ -113,234 +81,6 @@ if (not env_etc.no_boost_python): + target="tests/tst_optional_copy", + source="tests/tst_optional_copy.cpp") + +- import os, os.path +- env = env_base.Clone(LIBS=env_etc.libs_python) +- env.Append(LIBPATH=env_etc.libpath_python) +- env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base) +- env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_SOURCE"]) +- if (libtbx.env.build_options.boost_python_bool_int_strict): +- env.Append(SHCXXFLAGS=["-DBOOST_PYTHON_BOOL_INT_STRICT"]) +- env.Replace(SHLINKFLAGS=env_etc.shlinkflags) +- env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base) +- env.Append(CXXFLAGS="-DBOOST_PYTHON_SOURCE") +- env.Replace(LINKFLAGS=env_etc.shlinkflags) +- env_etc.include_registry.append( +- env=env, +- paths=[env_etc.boost_include, env_etc.python_include]) +- +- darwin_shlinkcom(env_etc, env, +- lo="boost/libs/python/src/libboost_python.lo", +- dylib="lib/libboost_python.dylib") +- +- # fixed list of file names introduced 2009-09-29, due to major changes in +- # boost/libs/python/build/Jamfile.v2 svn rev. 56305 (new Python 3 support) +- bpl_dll_sources = """\ +-numeric.cpp +-list.cpp +-long.cpp +-dict.cpp +-tuple.cpp +-str.cpp +-slice.cpp +-converter/from_python.cpp +-converter/registry.cpp +-converter/type_id.cpp +-object/enum.cpp +-object/class.cpp +-object/function.cpp +-object/inheritance.cpp +-object/life_support.cpp +-object/pickle_support.cpp +-errors.cpp +-module.cpp +-converter/builtin_converters.cpp +-converter/arg_to_python_base.cpp +-object/iterator.cpp +-object/stl_iterator.cpp +-object_protocol.cpp +-object_operators.cpp +-wrapper.cpp +-import.cpp +-exec.cpp +-object/function_doc_signature.cpp +-""".splitlines() +- prefix = "#"+os.path.join( +- os.path.basename(env_etc.boost_dist), "libs", "python", "src") +- bpl_dll_sources = [os.path.join(prefix, path) for path in bpl_dll_sources] +- # +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- if (env_etc.static_bpl): +- env.StaticLibrary(target="#lib/boost_python", source=bpl_dll_sources) +- else: +- env.SharedLibrary(target="#lib/boost_python", source=bpl_dll_sources) +- if (int(ARGUMENTS.get("boost_python_tests", 0))): +- warn_if_unexpected_md5_hexdigest( +- path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"), +- expected_md5_hexdigests=[ +- "c7a3dd81bf730635146f5c908ac982eb", # svn revision 39065M +- "d40aac0029bcd28f6e205ae3b30a1284", # svn revision 40216 +- "b79f016d3ec10cf1625a9e006e605428", # svn revision 40714 +- "f948983d970fd47e83a3a785bb54520a", # svn revision 41550 +- "c3d84006331d534840c42ab956fdfa05", # svn revision 50367M +- "cedfd061d767a27413ef4a75ee0e446f", # svn revision 56310 +- "e5507482a1937825e4c9f3ffe555fc59", # svn revision 59331 +- ]) +- bpl_tests = Split(""" +-staticmethod +-shared_ptr +-enable_shared_from_this +-andreas_beyer +-polymorphism +-polymorphism2 +-auto_ptr +-minimal +-args +-numpy +-enum +-exception_translator +-test_pointer_adoption +-operators +-callbacks +-defaults +-object +-list +-long +-dict +-tuple +-str +-virtual_functions +-back_reference +-implicit +-data_members +-ben_scott1 +-bienstman1 +-bienstman2 +-bienstman3 +-multi_arg_constructor +-extract +-opaque +-pickle1 +-pickle2 +-pickle3 +-pickle4 +-nested +-docstring +-pytype_function +-bienstman4 +-bienstman5 +-test_builtin_converters,builtin_converters_ext,test_builtin_converters +-cltree,cltree,test_cltree +-m1,m1,newtest +-m2,m2,newtest +-iterator,iterator_ext,iterator +-input_iterator,input_iterator,iterator +-crossmod_exception_a,crossmod_exception_a,crossmod_exception +-crossmod_exception_b,crossmod_exception_b,crossmod_exception +-vector_indexing_suite +-return_arg +-keywords,keywords,keywords_test +-properties +-map_indexing_suite;int_map_indexing_suite;a_map_indexing_suite,map_indexing_suite_ext,map_indexing_suite +-injected +-slice +-const_argument +-raw_ctor +-pointer_vector +-wrapper_held_type +-polymorphism2_auto_ptr +-stl_iterator +-voidptr +-crossmod_opaque_a,crossmod_opaque_a,crossmod_opaque +-crossmod_opaque_b,crossmod_opaque_b,crossmod_opaque +-""") +-# non-portable tests are not included above: +-# calling_conventions +-# calling_conventions_mf +-# +- Import("env_boost_python_ext") +- test_dir = libtbx.env.under_dist("boost", "libs/python/test") +- prefix = "#"+os.path.join( +- os.path.basename(env_etc.boost_dist), "libs", "python", "test") +- all_tst = [] +- for bpl_test in bpl_tests: +- flds = bpl_test.split(",") +- assert len(flds) in (1,3) +- if (len(flds) == 1): +- src = bpl_test +- pyd = bpl_test + "_ext" +- tst = bpl_test +- else: +- src = flds[0] +- pyd = flds[1] +- tst = flds[2] +- env = env_pure_boost_python_ext.Clone() +- env.Repository(os.path.dirname(env_etc.boost_dist)) +- ok = True +- source = [] +- for s in src.split(";"): +- cpp = "%s.cpp" % s +- file_name = os.path.join(test_dir, cpp) +- if (not os.path.isfile(file_name)): +- print "Warning: source file not available:", show_string(file_name) +- ok = False +- else: +- source.append(os.path.join(prefix, cpp)) +- if (ok): +- if (not tst in all_tst): +- all_tst.append(tst) +- env.SharedLibrary(target="#lib/%s" % pyd, source=source) +- all_tst = [os.path.join(test_dir, tst+".py") for tst in all_tst] +- # +- if (sys.platform == "linux2"): +- base_lib = libtbx.env.under_build(path="base/lib") +- if (os.path.isdir(base_lib)): +- env_prog = env.Clone() +- env_prog.Append(LIBPATH=[base_lib]) +- env_prog.Append(LIBS=[ +- "-lpython%d.%d" % sys.version_info[:2], +- "-lpthread", +- "-lutil", +- "-ldl"]) +- exe = env_prog.Program( +- target="boost/libs/python/test/exec_dynamic", +- source=[os.path.join(prefix, "exec.cpp")]) +- libtbx.env.write_dispatcher_in_bin( +- source_file=exe[0].get_abspath(), +- target_file="boost_libs_python_test_exec_dynamic") +- all_tst.append("$ boost_libs_python_test_exec_dynamic %s" +- % show_string(os.path.join(test_dir, "exec.py"))) +- # +- if (os.name != "nt"): +- env.SharedLibrary( +- target="#lib/boost_adaptbx_char_array_ext", +- source=["char_array_ext.cpp"]) +- all_tst.append( +- libtbx.env.under_dist("boost_adaptbx", "tests/tst_char_array.py")) +- # +- if (os.name == "nt"): +- boost_python_run_tests = \ +- "%s\\boost_python_run_tests.bat" % libtbx.env.build_path +- f = open(boost_python_run_tests, "w") +- for tst in all_tst: +- if (tst.startswith("$ ")): +- print >> f, 'call %s' % tst[2:] +- else: +- print >> f, 'call libtbx.python %s' % show_string(tst) +- f.close() +- else: +- boost_python_run_tests = \ +- "%s/boost_python_run_tests.csh" % libtbx.env.build_path +- f = open(boost_python_run_tests, "w") +- print >> f, "#! /bin/csh -f" +- print >> f, "set verbose" +- for tst in all_tst: +- if (tst.startswith("$ ")): +- print >> f, tst[2:] +- else: +- print >> f, 'libtbx.python "%s"' % show_string(tst) +- f.close() +- os.chmod(boost_python_run_tests, 0755) +- + def write_type_id_eq_h(): + unsigned_types = [ + "unsigned short", +diff --git a/work/cctbx_sources/cbflib_adaptbx/SConscript b/work/cctbx_sources/cbflib_adaptbx/SConscript +index 78c1297..dffc247 100644 +--- a/work/cctbx_sources/cbflib_adaptbx/SConscript ++++ b/work/cctbx_sources/cbflib_adaptbx/SConscript +@@ -14,7 +14,6 @@ env_etc.cbflib_common_includes = [ + env_etc.libtbx_include, + env_etc.scitbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.cbflib_dist, # for the adaptor cpp files + env_etc.cbflib_include[0], # for the cbflib c-files + env_etc.cbflib_include[1], # for the cbflib c-files +diff --git a/work/cctbx_sources/cctbx/SConscript b/work/cctbx_sources/cctbx/SConscript +index 6ec7c93..2dfb442 100644 +--- a/work/cctbx_sources/cctbx/SConscript ++++ b/work/cctbx_sources/cctbx/SConscript +@@ -10,7 +10,6 @@ env_etc.cctbx_common_includes = [ + env_etc.scitbx_include, + env_etc.chiltbx_include, + env_etc.omptbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone( +diff --git a/work/cctbx_sources/fable/SConscript b/work/cctbx_sources/fable/SConscript +index bf8e198..b6acccf 100644 +--- a/work/cctbx_sources/fable/SConscript ++++ b/work/cctbx_sources/fable/SConscript +@@ -13,7 +13,6 @@ if (not env_etc.no_boost_python): + env_etc.libtbx_include, + env_etc.fable_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.python_include]) + env.SharedLibrary( + target="#lib/fable_ext", +diff --git a/work/cctbx_sources/fable/libtbx_config b/work/cctbx_sources/fable/libtbx_config +index d456588..f00ae86 100644 +--- a/work/cctbx_sources/fable/libtbx_config ++++ b/work/cctbx_sources/fable/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx"], + } +diff --git a/work/cctbx_sources/fftw3tbx/SConscript b/work/cctbx_sources/fftw3tbx/SConscript +index ecc3a03..4fc1ec1 100755 +--- a/work/cctbx_sources/fftw3tbx/SConscript ++++ b/work/cctbx_sources/fftw3tbx/SConscript +@@ -8,7 +8,6 @@ env_etc.fftw3tbx_dist = libtbx.env.dist_path("fftw3tbx") + env_etc.fftw3tbx_common_includes = [ + env_etc.libtbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + base_include = libtbx.env.under_build("base/include") +diff --git a/work/cctbx_sources/gltbx/SConscript b/work/cctbx_sources/gltbx/SConscript +index 56a7115..f6214a4 100644 +--- a/work/cctbx_sources/gltbx/SConscript ++++ b/work/cctbx_sources/gltbx/SConscript +@@ -7,7 +7,6 @@ env_etc.gltbx_common_includes = [ + env_etc.libtbx_include, + env_etc.gltbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + if (not env_etc.no_boost_python): +diff --git a/work/cctbx_sources/iotbx/SConscript b/work/cctbx_sources/iotbx/SConscript +index df17856..c5cf7da 100644 +--- a/work/cctbx_sources/iotbx/SConscript ++++ b/work/cctbx_sources/iotbx/SConscript +@@ -10,7 +10,6 @@ env_etc.iotbx_common_includes = [ + env_etc.iotbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + env_etc.boost_adaptbx_include, + ] + +@@ -37,7 +36,6 @@ if (not env_etc.no_boost_python): + env_etc.include_registry.append( + env=env, + paths=[env_etc.libtbx_include, +- env_etc.boost_include, + env_etc.python_include]) + env.SharedLibrary( + target="#lib/iotbx_wildcard_ext", +diff --git a/work/cctbx_sources/mmtbx/SConscript b/work/cctbx_sources/mmtbx/SConscript +index 0532878..9bcaeb2 100755 +--- a/work/cctbx_sources/mmtbx/SConscript ++++ b/work/cctbx_sources/mmtbx/SConscript +@@ -10,7 +10,6 @@ env_etc.mmtbx_common_includes = [ + env_etc.mmtbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + if (not env_etc.no_boost_python): +diff --git a/work/cctbx_sources/omptbx/libtbx_config b/work/cctbx_sources/omptbx/libtbx_config +index d456588..f00ae86 100644 +--- a/work/cctbx_sources/omptbx/libtbx_config ++++ b/work/cctbx_sources/omptbx/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx"], + } +diff --git a/work/cctbx_sources/rstbx/SConscript b/work/cctbx_sources/rstbx/SConscript +index 2213c2f..232b5d7 100644 +--- a/work/cctbx_sources/rstbx/SConscript ++++ b/work/cctbx_sources/rstbx/SConscript +@@ -11,7 +11,6 @@ env_etc.rstbx_common_includes = [ + env_etc.scitbx_include, + env_etc.chiltbx_include, + env_etc.omptbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags) +diff --git a/work/cctbx_sources/scitbx/SConscript b/work/cctbx_sources/scitbx/SConscript +index f30b9db..10e0967 100644 +--- a/work/cctbx_sources/scitbx/SConscript ++++ b/work/cctbx_sources/scitbx/SConscript +@@ -9,7 +9,6 @@ env_etc.scitbx_common_includes = [ + env_etc.scitbx_include, + env_etc.omptbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + ] + + SConscript("error/SConscript") +diff --git a/work/cctbx_sources/scitbx/libtbx_config b/work/cctbx_sources/scitbx/libtbx_config +index 87cc3c7..d147819 100644 +--- a/work/cctbx_sources/scitbx/libtbx_config ++++ b/work/cctbx_sources/scitbx/libtbx_config +@@ -1,4 +1,4 @@ + { +- "modules_required_for_build": ["boost"], ++ "modules_required_for_build": [], + "modules_required_for_use": ["boost_adaptbx", "omptbx"], + } +diff --git a/work/cctbx_sources/scitbx/libtbx_refresh.py b/work/cctbx_sources/scitbx/libtbx_refresh.py +index 10d4ee0..c8374b2 100644 +--- a/work/cctbx_sources/scitbx/libtbx_refresh.py ++++ b/work/cctbx_sources/scitbx/libtbx_refresh.py +@@ -13,8 +13,7 @@ if (self.env.is_ready_for_build()): + generate_all.refresh(array_family=os.path.dirname(target_dir)) + # + warn_if_unexpected_md5_hexdigest( +- path=self.env.under_dist( +- module_name="boost", path="boost/random/mersenne_twister.hpp"), ++ path="@GENTOO_PORTAGE_EPREFIX@/usr/include/boost/random/mersenne_twister.hpp", + expected_md5_hexdigests=[ + "a2533c79a21f0f773f2e0d29a37371b0", # CVS revision 1.21 + "378432b5b280c9c0c894f7c80f0dad92", # CVS revision 1.20 +diff --git a/work/cctbx_sources/smtbx/SConscript b/work/cctbx_sources/smtbx/SConscript +index f5031ee..02f81a4 100644 +--- a/work/cctbx_sources/smtbx/SConscript ++++ b/work/cctbx_sources/smtbx/SConscript +@@ -7,7 +7,6 @@ env_etc.smtbx_common_includes = [ + env_etc.cctbx_include, + env_etc.scitbx_include, + env_etc.chiltbx_include, +- env_etc.boost_include, + ] + + env = env_base.Clone( +diff --git a/work/cctbx_sources/spotfinder/SConscript b/work/cctbx_sources/spotfinder/SConscript +index 1d280d4..9dc9195 100644 +--- a/work/cctbx_sources/spotfinder/SConscript ++++ b/work/cctbx_sources/spotfinder/SConscript +@@ -13,7 +13,6 @@ env_etc.spotfinder_common_includes = [ + env_etc.iotbx_include, + os.path.dirname(env_etc.spotfinder_dist), + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.annlib_dist, + env_etc.annlib_include[0], + env_etc.annlib_include[1], +diff --git a/work/cctbx_sources/tntbx/SConscript b/work/cctbx_sources/tntbx/SConscript +index e773186..ee29f10 100755 +--- a/work/cctbx_sources/tntbx/SConscript ++++ b/work/cctbx_sources/tntbx/SConscript +@@ -10,7 +10,6 @@ env_etc.tntbx_common_includes = [ + env_etc.tntbx_include, + env_etc.tntbx_tnt_include, + env_etc.scitbx_include, +- env_etc.boost_include, + ] + + Import("env_base", "env_etc") +-- +1.7.1.1 diff --git a/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch b/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch new file mode 100644 index 000000000000..8830dd8a054e --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch @@ -0,0 +1,77 @@ +diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript +index 9cce49e..1046ed0 100644 +--- a/cctbx_sources/clipper_adaptbx/SConscript ++++ b/cctbx_sources/clipper_adaptbx/SConscript +@@ -1,56 +1,13 @@ + import libtbx.load_env + Import("env_base", "env_etc") + +-env_etc.clipper_dist = libtbx.env.dist_path("clipper") +-env_etc.clipper_include = env_etc.clipper_dist +- + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags, + LIBS=env_etc.libm) +-env.Prepend(CPPPATH=[env_etc.clipper_include]) +- +-if (env_etc.static_libraries): builder = env.StaticLibrary +-else: builder = env.SharedLibrary +-builder(target='#lib/clipper', +- source = ["../clipper/clipper/core/"+file_name for file_name in """ +- atomsf.cpp +- cell.cpp +- clipper_memory.cpp +- clipper_message.cpp +- clipper_stats.cpp +- clipper_types.cpp +- clipper_util.cpp +- container.cpp +- container_hkl.cpp +- container_map.cpp +- container_types.cpp +- coords.cpp +- derivs.cpp +- hkl_compute.cpp +- hkl_data.cpp +- hkl_datatypes.cpp +- hkl_info.cpp +- hkl_lookup.cpp +- hkl_operators.cpp +- map_interp.cpp +- map_utils.cpp +- nxmap.cpp +- nxmap_operator.cpp +- ramachandran.cpp +- resol_basisfn.cpp +- resol_fn.cpp +- resol_targetfn.cpp +- rotation.cpp +- spacegroup.cpp +- spacegroup_data.cpp +- symop.cpp +- xmap.cpp +-""".split()]) +-# fftmap_sparse.cpp +-# fftmap.cpp + + env_exe = env.Clone() +-env_exe.Prepend(LIBS=["clipper"]) ++env_exe.Prepend(LIBS=["clipper-minimol","clipper-mmdb","clipper-cns","clipper-cif","clipper-contrib","clipper-ccp4","clipper-phs","clipper-core"]) ++env_exe.Prepend(SHLINKFLAGS=["-Wl,--as-needed"]) + + exe = env_exe.Program( + target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest' +@@ -76,12 +33,10 @@ if (hasattr(env_etc, "cctbx_include")): + env_etc.include_registry.append( + env=env_clipper_boost_python_ext, + paths=[ +- env_etc.clipper_include, + env_etc.libtbx_include, + env_etc.cctbx_include, + env_etc.scitbx_include, + env_etc.boost_adaptbx_include, +- env_etc.boost_include, + env_etc.python_include]) + Export("env_clipper_boost_python_ext") +- SConscript("clipper/SConscript") ++ diff --git a/sci-libs/cctbx/files/2010.03.29.2334-flags.patch b/sci-libs/cctbx/files/2010.03.29.2334-flags.patch new file mode 100644 index 000000000000..8a8033234713 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-flags.patch @@ -0,0 +1,94 @@ +diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript +index 16d22b6..f85b664 100644 +--- a/cctbx_sources/libtbx/SConscript ++++ b/cctbx_sources/libtbx/SConscript +@@ -5,6 +5,7 @@ from libtbx.str_utils import show_string + from libtbx.path import norm_join, full_command_path + import platform + import sys, os ++import SCons.Util + + if (hasattr(Environment, "Clone")): + Environment.Copy = Environment.Clone # XXX backward compatibility 2008_03_30 +@@ -132,9 +133,7 @@ if (env_etc.compiler == "unix_icpc"): + static_exe = libtbx.env.build_options.static_exe + + def gcc_common_warn_options(): +- result = ["-Wall", "-Wno-sign-compare", "-Wno-unknown-pragmas"] +- if (env_etc.gcc_version >= 40000): +- result.append("-Winit-self") ++ result = [""] + return result + + def enable_more_warnings(env): +@@ -355,16 +354,22 @@ else: + cc = env_etc.compiler.replace("unix_", "") + cxx = cc.replace("gcc", "g++") + env_etc.gcc_version = libtbx.env_config.get_gcc_version(command_name=cc) ++# linkerflags = os.environ.get("LDFLAGS") ++# link_flags=env_etc.ldflags ++ link_flags=os.environ.get("LDFLAGS") ++ linker_options=SCons.Util.CLVar(os.environ['LDFLAGS']) + env_base.Replace( + CC=cc, + SHCC=cc, + CXX=cxx, + LINK=cxx, ++ LINKFLAGS=linker_options, + SHCXX=cxx, + SHLINK=cxx, + SHLIBSUFFIX=env_etc.shlibsuffix, + ) +- env_etc.c_link = cc ++# linkerflags = env_etc.ldflags ++# env_etc.c_link = cc + " " + linkerflags + env_etc.ccflags_base = [ + "-fPIC", + "-fno-strict-aliasing"] +@@ -380,7 +385,7 @@ else: + warn_options = gcc_common_warn_options() + ["-Werror"] + env_etc.ccflags_base.extend(warn_options) + if (libtbx.env.build_options.optimization): +- opts = ["-DNDEBUG", "-O3", "-ffast-math"] ++ opts = ["-DNDEBUG"] + if (env_etc.gcc_version >= 40300): + opts.append("-fno-associative-math") + opts.append("-ftrapping-math") +@@ -401,6 +406,7 @@ else: + env_base.Prepend(LINKFLAGS=["-static"]) + static_exe = None + env_etc.shlinkflags = ["-shared"] ++ env_etc.shlinkflags.append(linker_options) + env_etc.shlinkflags_bpl = env_etc.shlinkflags + if (libtbx.env.build_options.mode == "profile"): + env_base.Prepend(LINKFLAGS=["-pg"]) +diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py +index ca510b9..68c58ea 100644 +--- a/cctbx_sources/libtbx/env_config.py ++++ b/cctbx_sources/libtbx/env_config.py +@@ -1608,6 +1608,7 @@ class build_options: + self.env_cxxflags = "" + self.env_cflags = "" + self.env_cppflags = "" ++ self.env_ldflags = "" + flg = os.environ.get("CXXFLAGS") + if flg is not None: + self.env_cxxflags = flg +@@ -1617,6 +1618,9 @@ class build_options: + flg = os.environ.get("CPPFLAGS") + if flg is not None: + self.env_cppflags = flg ++ flg = os.environ.get("LDFLAGS") ++ if flg is not None: ++ self.env_ldflags = flg + + def report(self, f=None): + if (f is None): f = sys.stdout +@@ -1640,6 +1644,7 @@ class build_options: + print >>f, " CXXFLAGS = ", self.env_cxxflags + print >>f, " CFLAGS = ", self.env_cflags + print >>f, " CPPFLAGS = ", self.env_cppflags ++ print >>f, " LDFLAGS = ", self.env_ldflags + + class include_registry: + diff --git a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch new file mode 100644 index 000000000000..057c135f9953 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch @@ -0,0 +1,117 @@ + cctbx_sources/scitbx/lbfgsb/raw.h | 54 +++++++++++++++++++-------------------- + 1 file changed, 27 insertions(+), 27 deletions(-) + +diff --git a/cctbx_sources/scitbx/lbfgsb/raw.h b/cctbx_sources/scitbx/lbfgsb/raw.h +index 21afed7..5b15055 100644 +--- a/cctbx_sources/scitbx/lbfgsb/raw.h ++++ b/cctbx_sources/scitbx/lbfgsb/raw.h +@@ -853,7 +853,7 @@ namespace raw { + if (iprint >= 99) { + printf(" LINE SEARCH%12d times; norm of step = %.15G\n", + iback, xstep); +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + if (iprint > 100) { + write_ref1(" X =", x); + write_ref1(" G =", g); +@@ -862,7 +862,7 @@ namespace raw { + else if (iprint > 0) { + int imod = iter % iprint; + if (imod == 0) { +- printf(fmt_2001, iter,f,sbgnrm); ++ printf("%s %i %f %f", fmt_2001, iter,f,sbgnrm); + } + } + if (iprint >= 1) { +@@ -967,9 +967,9 @@ namespace raw { + " 2 rounding error dominate computation.\n"; + if (task.substr(0,5) == "ERROR") goto lbl_999; + if (iprint >= 0) { +- printf(fmt_3003); +- printf(fmt_3004); +- printf(fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); ++ printf("%s", fmt_3003); ++ printf("%s", fmt_3004); ++ printf("%s %i %i %i %i %i %i %f %f", fmt_3005, n,iter,nfgv,nintol,nskip,nact,sbgnrm,f); + if (iprint >= 100) { + write_ref1(" X =", x); + } +@@ -977,40 +977,40 @@ namespace raw { + } + lbl_999: + if (iprint >= 0) { +- printf(fmt_3009, task.c_str()); ++ printf("%s %s", fmt_3009, task.c_str()); + if (info != 0) { +- if (info == -1) printf(fmt_9011); +- if (info == -2) printf(fmt_9012); +- if (info == -3) printf(fmt_9013); +- if (info == -4) printf(fmt_9014); +- if (info == -5) printf(fmt_9015); ++ if (info == -1) printf("%s", fmt_9011); ++ if (info == -2) printf("%s", fmt_9012); ++ if (info == -3) printf("%s", fmt_9013); ++ if (info == -4) printf("%s", fmt_9014); ++ if (info == -5) printf("%s", fmt_9015); + if (info == -6) { + printf(" Input nbd(%12d) is invalid.\n", k); + } + if (info == -7) { + printf(" l(%12d) > u(%12d). No feasible solution.\n", k, k); + } +- if (info == -8) printf(fmt_9018); +- if (info == -9) printf(fmt_9019); ++ if (info == -8) printf("%s", fmt_9018); ++ if (info == -9) printf("%s", fmt_9019); + } +- if (iprint >= 1) printf(fmt_3007, cachyt,sbtime,lnscht); +- printf(fmt_3008, time); ++ if (iprint >= 1) printf("%s %f %f %f", fmt_3007, cachyt,sbtime,lnscht); ++ printf("%s %f", fmt_3008, time); + if (iprint >= 1) { + if (info == -4 || info == -9) { +- printf(fmt_3002, ++ printf("%s %i %i %i %i %s %i %f %f", fmt_3002, + iter,nfgv,nint,nact,word.c_str(),iback,stp,xstep); // itfile + } +- printf(fmt_3009, task.c_str()); // itfile ++ printf("%s %s", fmt_3009, task.c_str()); // itfile + if (info != 0) { +- if (info == -1) printf(fmt_9011); // itfile +- if (info == -2) printf(fmt_9012); // itfile +- if (info == -3) printf(fmt_9013); // itfile +- if (info == -4) printf(fmt_9014); // itfile +- if (info == -5) printf(fmt_9015); // itfile +- if (info == -8) printf(fmt_9018); // itfile +- if (info == -9) printf(fmt_9019); // itfile ++ if (info == -1) printf("%s", fmt_9011); // itfile ++ if (info == -2) printf("%s", fmt_9012); // itfile ++ if (info == -3) printf("%s", fmt_9013); // itfile ++ if (info == -4) printf("%s", fmt_9014); // itfile ++ if (info == -5) printf("%s", fmt_9015); // itfile ++ if (info == -8) printf("%s", fmt_9018); // itfile ++ if (info == -9) printf("%s", fmt_9019); // itfile + } +- printf(fmt_3008, time); // itfile ++ printf("%s %f", fmt_3008, time); // itfile + } + } + } +@@ -3902,7 +3902,7 @@ namespace raw { + " refresh the lbfgs memory and restart the iteration.\n"; + if (info != 0) { + // singular triangular system detected; refresh the lbfgs memory. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; +@@ -3968,7 +3968,7 @@ namespace raw { + if (info != 0) { + // singular triangular system detected; + // refresh the lbfgs memory and restart the iteration. +- if(iprint >= 1) printf(fmt_1005); ++ if(iprint >= 1) printf("%s", fmt_1005); + info = 0; + col = 0; + head = 1; 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 ++#include + + 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 &input; ++ std::basic_istream &input; + mutable value_t current; + }; + diff --git a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch new file mode 100644 index 000000000000..96cb21531bbf --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch @@ -0,0 +1,154 @@ + .../scitbx/math/boost_python/distributions.cpp | 60 +++++++++++++------ + cctbx_sources/scitbx/rigid_body/spatial_lib.h | 1 + + cctbx_sources/scitbx/rigid_body/tardy.h | 4 +- + .../refinement/boost_python/weighting_schemes.cpp | 4 +- + .../smtbx/structure_factors/direct/standard_xray.h | 4 +- + 5 files changed, 48 insertions(+), 25 deletions(-) + +diff --git a/cctbx_sources/scitbx/math/boost_python/distributions.cpp b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +index a676798..68818e7 100644 +--- a/cctbx_sources/scitbx/math/boost_python/distributions.cpp ++++ b/cctbx_sources/scitbx/math/boost_python/distributions.cpp +@@ -59,29 +59,51 @@ namespace { + { + typedef Distribution wt; + ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self) { \ ++ return boost::math::name(self); \ ++ } ++ ++ NEW_MEMBER(mean); ++ NEW_MEMBER(median); ++ NEW_MEMBER(mode); ++ NEW_MEMBER(variance); ++ NEW_MEMBER(standard_deviation); ++ NEW_MEMBER(skewness); ++ NEW_MEMBER(kurtosis); ++ ++ #undef NEW_MEMBER ++ ++ #define NEW_MEMBER(name) \ ++ static FloatType name(wt const &self, FloatType arg) { \ ++ return boost::math::name(self, arg); \ ++ } ++ ++ NEW_MEMBER(pdf); ++ NEW_MEMBER(cdf); ++ NEW_MEMBER(quantile); ++ ++ #undef NEW_MEMBER ++ ++ static scitbx::af::shared quantiles(wt const &self, std::size_t n) { ++ return scitbx::math::quantiles(self, n); ++ } ++ + static void + wrap() + { + using namespace boost::python; +- def("mean", (FloatType(*)(wt const&)) boost::math::mean); +- def("median", (FloatType(*)(wt const&)) boost::math::median); +- def("mode", (FloatType(*)(wt const&)) boost::math::mode); +- def("variance", (FloatType(*)(wt const&)) boost::math::variance); +- def("standard_deviation", +- (FloatType(*)(wt const&)) boost::math::standard_deviation); +- def("skewness", (FloatType(*)(wt const&)) boost::math::skewness); +- def("kurtosis", (FloatType(*)(wt const&)) boost::math::kurtosis); +- def("pdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::pdf); +- def("cdf", (FloatType(*)(wt const&, FloatType const&)) boost::math::cdf); +- def("quantile", (FloatType(*)(wt const&, FloatType const&)) +- boost::math::quantile); +- def("quantiles", +-#if BOOST_WORKAROUND(__EDG_VERSION__, BOOST_TESTED_AT(306)) +- (scitbx::af::shared(*)(wt const&, std::size_t)) quantiles +-#else +- quantiles +-#endif +- ); ++ def("mean" , mean); ++ def("median" , median); ++ def("mode" , mode); ++ def("variance" , variance); ++ def("standard_deviation", standard_deviation); ++ def("skewness" , skewness); ++ def("kurtosis" , kurtosis); ++ def("pdf" , pdf); ++ def("cdf" , cdf); ++ def("quantile" , quantile); ++ def("quantiles" , quantiles); + } + }; + +diff --git a/cctbx_sources/scitbx/rigid_body/spatial_lib.h b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +index a084f0f..e377292 100755 +--- a/cctbx_sources/scitbx/rigid_body/spatial_lib.h ++++ b/cctbx_sources/scitbx/rigid_body/spatial_lib.h +@@ -2,6 +2,7 @@ + #define SCITBX_RIGID_BODY_SPATIAL_LIB_H + + #include ++#include + #include + + namespace scitbx { namespace rigid_body { +diff --git a/cctbx_sources/scitbx/rigid_body/tardy.h b/cctbx_sources/scitbx/rigid_body/tardy.h +index 104f16b..a8f76cc 100755 +--- a/cctbx_sources/scitbx/rigid_body/tardy.h ++++ b/cctbx_sources/scitbx/rigid_body/tardy.h +@@ -346,7 +346,7 @@ namespace tardy { + unsigned nb = this->bodies_size(); + af::shared > result((af::reserve(nb))); + af::shared > +- tau_array = f_ext_as_tau(f_ext_array().const_ref()); ++ tau_array = this->f_ext_as_tau(f_ext_array().const_ref()); + for(unsigned ib=0;ibbodies[ib]->joint->tau_as_d_e_pot_d_q(tau_array[ib])); +@@ -379,7 +379,7 @@ namespace tardy { + qdd_array() + { + if (!qdd_array_) { +- qdd_array_ = forward_dynamics_ab( ++ qdd_array_ = this->forward_dynamics_ab( + /*tau_array*/ af::const_ref >(0, 0), + f_ext_array().const_ref(), + /*grav_accn*/ af::const_ref(0, 0)); +diff --git a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +index ce0c27b..904e8d7 100644 +--- a/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp ++++ b/cctbx_sources/smtbx/refinement/boost_python/weighting_schemes.cpp +@@ -25,9 +25,9 @@ namespace smtbx { namespace refinement { namespace least_squares { + : base_t(name, boost::python::no_init) + { + using namespace boost::python; +- def("__call__", &wt::operator(), ++ this->def("__call__", &wt::operator(), + (arg("fo_sq"), arg("sigma"), arg("fc_sq"))); +- def("__call__", weights, ++ this->def("__call__", weights, + (arg("fo_sq"), arg("sigmas"), arg("fc_sq"))); + } + }; +diff --git a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +index 5e2df76..911bfde 100644 +--- a/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h ++++ b/cctbx_sources/smtbx/structure_factors/direct/standard_xray.h +@@ -161,7 +161,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); + f *= dw; +@@ -336,7 +336,7 @@ namespace smtbx { namespace structure_factors { namespace direct { + for (int k=0; k < hr_ht.groups.size(); ++k) { + hr_ht_group const &g = hr_ht.groups[k]; + float_type hrx = g.hr * scatterer.site; +- complex_type f = exp_i_2pi(hrx + g.ht); ++ complex_type f = this->exp_i_2pi(hrx + g.ht); + float_type fa = f.real(), fb = f.imag(); + if (scatterer.flags.use_u_aniso()) { + float_type dw = debye_waller_factor_u_star(g.hr, scatterer.u_star); diff --git a/sci-libs/cctbx/files/2010.03.29.2334-soname.patch b/sci-libs/cctbx/files/2010.03.29.2334-soname.patch new file mode 100644 index 000000000000..2c0efcabeb13 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-soname.patch @@ -0,0 +1,123 @@ +diff --git a/cctbx_sources/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript +index 4ff2232..2ee3991 100644 +--- a/cctbx_sources/ccp4io_adaptbx/SConscript ++++ b/cctbx_sources/ccp4io_adaptbx/SConscript +@@ -40,6 +40,7 @@ def replace_printf(file_name): + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libccp4io.so.0.0"]) + env.Append(CCFLAGS=env_etc.ccp4io_defines) + env.Append(SHCCFLAGS=env_etc.ccp4io_defines) + env_etc.include_registry.append( +diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript +index 6ec7c93..7f2e788 100644 +--- a/cctbx_sources/cctbx/SConscript ++++ b/cctbx_sources/cctbx/SConscript +@@ -15,6 +15,7 @@ env_etc.cctbx_common_includes = [ + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libcctbx.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=env_etc.cctbx_common_includes) +diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript +index c0a4bb0..d3c1e45 100644 +--- a/cctbx_sources/iotbx/mtz/SConscript ++++ b/cctbx_sources/iotbx/mtz/SConscript +@@ -6,6 +6,7 @@ ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz") + env.Prepend(LIBS=["cctbx", ccp4io_lib]+env_etc.libm) + env.Append(CXXFLAGS=env_etc.ccp4io_defines) + env.Append(SHCXXFLAGS=env_etc.ccp4io_defines) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_mtz.so.0.0"]) + env_etc.enable_more_warnings(env=env) + if (env_etc.static_libraries): builder = env.StaticLibrary + else: builder = env.SharedLibrary +diff --git a/cctbx_sources/iotbx/pdb/SConscript b/cctbx_sources/iotbx/pdb/SConscript +index c1415c8..9e1af8d 100644 +--- a/cctbx_sources/iotbx/pdb/SConscript ++++ b/cctbx_sources/iotbx/pdb/SConscript +@@ -2,6 +2,7 @@ Import("env_base", "env_etc") + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libiotbx_pdb.so.0.0"]) + env_etc.enable_more_warnings(env=env) + env_etc.include_registry.append( + env=env, +diff --git a/cctbx_sources/mmtbx/masks/SConscript b/cctbx_sources/mmtbx/masks/SConscript +index e70ab3c..cf2f530 100755 +--- a/cctbx_sources/mmtbx/masks/SConscript ++++ b/cctbx_sources/mmtbx/masks/SConscript +@@ -17,7 +17,9 @@ builder( + target="#lib/mmtbx_masks", + source=lib_sources) + +-env = env.Clone() ++env = env.Clone( ++ SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libmmtbx_masks.so.0.0"]) + env.Prepend(LIBS=["mmtbx_masks", "iotbx_pdb", "cctbx_sgtbx_asu"]) + env.Program( target = "tst_mask", source="tst_mask.cpp") + +diff --git a/cctbx_sources/omptbx/SConscript b/cctbx_sources/omptbx/SConscript +index 43aac91..ce4b4f3 100644 +--- a/cctbx_sources/omptbx/SConscript ++++ b/cctbx_sources/omptbx/SConscript +@@ -7,6 +7,7 @@ env_etc.omptbx_include = os.path.dirname(env_etc.omptbx_dist) + + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libomptbx.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=[env_etc.omptbx_include]) +diff --git a/cctbx_sources/rstbx/SConscript b/cctbx_sources/rstbx/SConscript +index 2213c2f..cae7542 100644 +--- a/cctbx_sources/rstbx/SConscript ++++ b/cctbx_sources/rstbx/SConscript +@@ -15,6 +15,7 @@ env_etc.rstbx_common_includes = [ + ] + + env = env_base.Clone(SHLINKFLAGS=env_etc.shlinkflags) ++env.Append(SHLINKFLAGS=["-Wl,-soname,librstbx.so.0.0"]) + env.Append(LIBS=["cctbx"] + env_etc.libm) + env_etc.include_registry.append( + env=env, +diff --git a/cctbx_sources/scitbx/boost_python/SConscript b/cctbx_sources/scitbx/boost_python/SConscript +index 6f221d0..c4698d8 100644 +--- a/cctbx_sources/scitbx/boost_python/SConscript ++++ b/cctbx_sources/scitbx/boost_python/SConscript +@@ -4,6 +4,7 @@ Import("env_scitbx_boost_python_ext") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_boost_python.so.0.0"]) + env.Append(CXXFLAGS=env_etc.cxxflags_bpl_defines_base) + env.Append(SHCXXFLAGS=env_etc.cxxflags_bpl_defines_base) + env.Append(LIBS=["boost_python"]) +diff --git a/cctbx_sources/scitbx/minpack/SConscript b/cctbx_sources/scitbx/minpack/SConscript +index 7c325cb..cc23a04 100644 +--- a/cctbx_sources/scitbx/minpack/SConscript ++++ b/cctbx_sources/scitbx/minpack/SConscript +@@ -3,6 +3,7 @@ Import("env_base", "env_etc") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_minipack.so.0.0"]) + env_etc.include_registry.append( + env=env, + paths=env_etc.scitbx_common_includes) +diff --git a/cctbx_sources/scitbx/slatec/SConscript b/cctbx_sources/scitbx/slatec/SConscript +index ca9b6da..9c79d47 100644 +--- a/cctbx_sources/scitbx/slatec/SConscript ++++ b/cctbx_sources/scitbx/slatec/SConscript +@@ -3,6 +3,7 @@ Import("env_base", "env_etc") + env = env_base.Clone( + SHLINKFLAGS=env_etc.shlinkflags) + env_etc.enable_more_warnings(env=env) ++env.Append(SHLINKFLAGS=["-Wl,-soname,libscitbx_slatec.so.0.0"]) + env.Append(LIBS=env_etc.libm) + if (env_etc.static_libraries): builder = env.StaticLibrary + else: builder = env.SharedLibrary diff --git a/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch b/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch new file mode 100644 index 000000000000..f6509260d313 --- /dev/null +++ b/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch @@ -0,0 +1,15 @@ +diff --git a/mmtbx/monomer_library/tst_server.py b/mmtbx/monomer_library/tst_server.py +index 519d203..91ba783 100644 +--- cctbx_sources/mmtbx/monomer_library/tst_server.py ++++ cctbx_sources/mmtbx/monomer_library/tst_server.py +@@ -86,8 +86,8 @@ def exercise(): + for base_code in ["A", "C", "G"]: + rna_atoms = srv.get_comp_comp_id_direct(base_code+"r").atom_dict() + dna_atoms = srv.get_comp_comp_id_direct(base_code+"d").atom_dict() +- for as,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]: +- for a in as.keys(): ++ for as_,bs,c in [(rna_atoms,dna_atoms,"d"), (dna_atoms,rna_atoms,"r")]: ++ for a in as_.keys(): + b = bs.get(a, None) + if (b is None): + print "Not in %s: %s" % (base_code+c, a) diff --git a/sci-libs/cctbx/metadata.xml b/sci-libs/cctbx/metadata.xml new file mode 100644 index 000000000000..3288d4956c5a --- /dev/null +++ b/sci-libs/cctbx/metadata.xml @@ -0,0 +1,20 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + + The Computational Crystallography Toolbox (cctbx) is being developed + as the open source component of the PHENIX system. The goal of + the PHENIX project is to advance automation of macromolecular structure + determination. PHENIX depends on the cctbx, but not vice versa. This + hierarchical approach enforces a clean design as a reusable library. + The cctbx is therefore also useful for small-molecule crystallography + and even general scientific applications. + + + cctbx + + -- cgit v1.2.3