[gentoo-commits] repo/gentoo:master commit in: sci-libs/cctbx/, sci-libs/cctbx/files/

[Matt Turner]

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?= <gentoo@××××××××××.pl>
-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>sci-chemistry@g.o</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>