commit: a57dee12f49e88bf428e6a5e5bd68ce2b6398b13 Author: Matt Turner <mattst88 <AT> gentoo <DOT> org> AuthorDate: Sat Aug 10 04:03:36 2019 +0000 Commit: Matt Turner <mattst88 <AT> gentoo <DOT> org> CommitDate: Sat Aug 10 04:05:37 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a57dee12
sci-libs/cctbx: Remove Closes: https://bugs.gentoo.org/639760 Signed-off-by: Matt Turner <mattst88 <AT> gentoo.org> sci-libs/cctbx/Manifest | 1 - 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, 1335 deletions(-) diff --git a/sci-libs/cctbx/Manifest b/sci-libs/cctbx/Manifest deleted file mode 100644 index ddab059a5f1..00000000000 --- a/sci-libs/cctbx/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST cctbx-2010.03.29.2334.tar.gz 15570372 BLAKE2B ad0b98fa27b8b13af7a1f41ee3764ce558afc4d53b8e7605c169ed86a9b0dd0e86ad58a72eec6dc570bdbf6574dcee25ca357633d727a36ed36f00186c9cc503 SHA512 7aafd647db49925fc1df16a9ccb4f8caf040b4d73e9601731eb3da3051467c3005fb2cc95b498501c899cd1bd378e6a6135cffe734cb4f93eccacbc13575b2c8 diff --git a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild b/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild deleted file mode 100644 index 5ac1e461f68..00000000000 --- a/sci-libs/cctbx/cctbx-2010.03.29.2334-r7.ebuild +++ /dev/null @@ -1,189 +0,0 @@ -# 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 deleted file mode 100644 index 5b4439ee678..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-boost.patch +++ /dev/null @@ -1,516 +0,0 @@ -From 7e77ff8694b87e95efe56ed961fbc8dd30d8c238 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <[email protected]> -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 deleted file mode 100644 index 8830dd8a054..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-clipper.patch +++ /dev/null @@ -1,77 +0,0 @@ -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 deleted file mode 100644 index 8a803323471..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-flags.patch +++ /dev/null @@ -1,94 +0,0 @@ -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 deleted file mode 100644 index 057c135f995..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-format-security.patch +++ /dev/null @@ -1,117 +0,0 @@ - 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 deleted file mode 100644 index e54cfa16838..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.6.patch +++ /dev/null @@ -1,29 +0,0 @@ - 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; - }; - 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 deleted file mode 100644 index 96cb21531bb..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-gcc-4.7.patch +++ /dev/null @@ -1,154 +0,0 @@ - .../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<FloatType> quantiles(wt const &self, std::size_t n) { -+ return scitbx::math::quantiles<FloatType>(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<FloatType>(*)(wt const&, std::size_t)) quantiles --#else -- quantiles<FloatType, wt> --#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 <scitbx/rotr3.h> -+#include <scitbx/rigid_body/matrix_helpers.h> - #include <scitbx/array_family/versa_matrix.h> - - 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<af::small<ft, 7> > result((af::reserve(nb))); - af::shared<af::small<ft, 6> > -- 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;ib<nb;ib++) { - result.push_back( - this->bodies[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<af::small<ft, 6> >(0, 0), - f_ext_array().const_ref(), - /*grav_accn*/ af::const_ref<ft>(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<float_type> 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<float_type> 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 deleted file mode 100644 index 2c0efcabeb1..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-soname.patch +++ /dev/null @@ -1,123 +0,0 @@ -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 deleted file mode 100644 index f6509260d31..00000000000 --- a/sci-libs/cctbx/files/2010.03.29.2334-tst_server.py.patch +++ /dev/null @@ -1,15 +0,0 @@ -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 deleted file mode 100644 index d9a96052956..00000000000 --- a/sci-libs/cctbx/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> - 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. - </longdescription> - <upstream> - <remote-id type="sourceforge">cctbx</remote-id> - </upstream> -</pkgmetadata>
