[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-17-g4e91db3
Radostan Riedel
raybuntu at googlemail.com
Sat Jul 14 19:50:20 UTC 2012
The following commit has been merged in the master branch:
commit 4e91db309af3fdd47101e798fadb475246877b1a
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Sat Jul 14 16:48:16 2012 +0200
Add upstream fix to use system libraries
diff --git a/debian/control b/debian/control
index 0c467e6..6d70bac 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Maintainer: Radostan Riedel <raybuntu at googlemail.com>
X-Python-Version: >= 2.6
Build-Depends: debhelper (>= 7), python-all-dev (>= 2.6.6-3),
libfftw3-dev, libcbf-dev, libann-dev, libclipper-dev,
- libboost-python-dev, scons, libboost-thread-dev,
+ libboost-python-dev(>= 1.49), scons, libboost-thread-dev,
python-setuptools (>= 0.6b3-1~), libgl1-mesa-dev,
libglu1-mesa-dev, libtool, coreutils
Standards-Version: 3.9.3
diff --git a/debian/patches/0008-upstream-fix-to-use-system-libraries.patch b/debian/patches/0008-upstream-fix-to-use-system-libraries.patch
new file mode 100644
index 0000000..6065085
--- /dev/null
+++ b/debian/patches/0008-upstream-fix-to-use-system-libraries.patch
@@ -0,0 +1,234 @@
+From: Radostan Riedel <raybuntu at googlemail.com>
+Date: Fri, 13 Jul 2012 15:11:27 +0200
+Subject: upstream fix to use system libraries
+
+---
+ cctbx_sources/boost_adaptbx/SConscript | 21 +++---
+ cctbx_sources/clipper_adaptbx/SConscript | 84 ++++++++++++----------
+ cctbx_sources/clipper_adaptbx/clipper/SConscript | 2 +-
+ cctbx_sources/libtbx/SConscript | 4 ++
+ cctbx_sources/libtbx/env_config.py | 7 ++
+ 5 files changed, 70 insertions(+), 48 deletions(-)
+
+diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
+index 0d95318..86dbc94 100644
+--- a/cctbx_sources/boost_adaptbx/SConscript
++++ b/cctbx_sources/boost_adaptbx/SConscript
+@@ -9,7 +9,10 @@ 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
++if not env_etc.use_system_libs:
++ env_etc.boost_include = env_etc.boost_dist
++else:
++ env_etc.boost_include = '/usr/include'
+ env_etc.boost_adaptbx_dist = libtbx.env.dist_path("boost_adaptbx")
+ env_etc.boost_adaptbx_include = os.path.dirname(env_etc.boost_adaptbx_dist)
+
+@@ -35,9 +38,10 @@ def build_boost_thread():
+ 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)
++ if not env_etc.use_system_libs:
++ env.SharedLibrary(
++ target='#lib/boost_thread',
++ source=source)
+
+ build_boost_thread()
+
+@@ -238,10 +242,11 @@ object/function_doc_signature.cpp
+ 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 not env_etc.use_system_libs:
++ 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 (bool(int(ARGUMENTS.get("boost_python_tests", "0")))):
+ warn_if_unexpected_md5_hexdigest(
+ path=libtbx.env.under_dist("boost", "libs/python/test/Jamfile.v2"),
+diff --git a/cctbx_sources/clipper_adaptbx/SConscript b/cctbx_sources/clipper_adaptbx/SConscript
+index 9cce49e..a522057 100644
+--- a/cctbx_sources/clipper_adaptbx/SConscript
++++ b/cctbx_sources/clipper_adaptbx/SConscript
+@@ -3,54 +3,59 @@ Import("env_base", "env_etc")
+
+ env_etc.clipper_dist = libtbx.env.dist_path("clipper")
+ env_etc.clipper_include = env_etc.clipper_dist
++env_etc.clipper_sysinclude = '/usr/include'
+
+ env = env_base.Clone(
+ SHLINKFLAGS=env_etc.shlinkflags,
+ LIBS=env_etc.libm)
+-env.Prepend(CPPPATH=[env_etc.clipper_include])
++if not env_etc.use_system_libs:
++ env.Prepend(CPPPATH=[env_etc.clipper_include])
++else:
++ env.Prepend(CPPPATH=[env_etc.clipper_sysinclude])
+
+ 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
++if not env_etc.use_system_libs:
++ builder(target='#lib/clipper-core',
++ 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-core"])
+
+ exe = env_exe.Program(
+ target='#exe_dev/'+env["PROGPREFIX"]+'clipper.symtest'
+@@ -77,6 +82,7 @@ if (hasattr(env_etc, "cctbx_include")):
+ env=env_clipper_boost_python_ext,
+ paths=[
+ env_etc.clipper_include,
++ env_etc.clipper_sysinclude,
+ env_etc.libtbx_include,
+ env_etc.cctbx_include,
+ env_etc.scitbx_include,
+diff --git a/cctbx_sources/clipper_adaptbx/clipper/SConscript b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+index 9f79f83..37280af 100644
+--- a/cctbx_sources/clipper_adaptbx/clipper/SConscript
++++ b/cctbx_sources/clipper_adaptbx/clipper/SConscript
+@@ -1,6 +1,6 @@
+ Import("env_clipper_boost_python_ext")
+ env = env_clipper_boost_python_ext.Clone()
+-env.Prepend(LIBS=["clipper", "cctbx"])
++env.Prepend(LIBS=["clipper-core", "cctbx"])
+ env.SharedLibrary(
+ target="#lib/clipper_ext",
+ source=[
+diff --git a/cctbx_sources/libtbx/SConscript b/cctbx_sources/libtbx/SConscript
+index 1443e6c..beae6b8 100644
+--- a/cctbx_sources/libtbx/SConscript
++++ b/cctbx_sources/libtbx/SConscript
+@@ -1082,4 +1082,8 @@ if (libtbx.env.build_options.libtoolize):
+ env_etc.shlinkflags.extend(rpath_link)
+ env_etc.set_libtool(env_base, env_etc.rpath)
+
++env_etc.use_system_libs = False
++if (libtbx.env.build_options.use_system_libs):
++ env_etc.use_system_libs = True
++
+ Export("env_base", "env_etc")
+diff --git a/cctbx_sources/libtbx/env_config.py b/cctbx_sources/libtbx/env_config.py
+index 2285c9d..d992c2c 100644
+--- a/cctbx_sources/libtbx/env_config.py
++++ b/cctbx_sources/libtbx/env_config.py
+@@ -703,6 +703,7 @@ Wait for the command to finish, then try again.""" % vars())
+ static_exe=command_line.options.static_exe,
+ libtoolize=command_line.options.libtoolize,
+ rpath=command_line.options.rpath,
++ use_system_libs=command_line.options.use_system_libs,
+ scan_boost=command_line.options.scan_boost,
+ write_full_flex_fwd_h=command_line.options.write_full_flex_fwd_h,
+ boost_python_no_py_signatures
+@@ -1762,6 +1763,7 @@ class build_options:
+ static_libraries,
+ static_exe,
+ libtoolize,
++ use_system_libs,
+ rpath,
+ scan_boost,
+ write_full_flex_fwd_h=default_write_full_flex_fwd_h,
+@@ -1833,6 +1835,7 @@ class build_options:
+ print >> f, "Enable OpenMP if possible:", self.enable_openmp_if_possible
+ print >> f, "Enable CUDA:", self.enable_cuda
+ print >> f, "Libtoolize:", self.libtoolize
++ print >> f, "Use System Libraries:", self.use_system_libs
+ print >> f, "Use opt_resources if available:", self.opt_resources
+ print >> f, "Use environment flags:", self.use_environment_flags
+ if( self.use_environment_flags ):
+@@ -1955,6 +1958,10 @@ class pre_process_args:
+ action="store_true",
+ default=False,
+ help="build all shared libraries with libtool. Optionally set --rpath")
++ parser.option(None, "--use_system_libs",
++ action="store_true",
++ default=False,
++ help="Use system Libraries to build.")
+ parser.option(None, "--rpath",
+ type="string",
+ action="store",
+--
diff --git a/debian/patches/series b/debian/patches/series
index 7728ae1..7bbc147 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@
0005-adding-shlib-versioning.patch
0006-upstream-fix-for-declaration-errors-in-gcc4.7.patch
0007-fix-for-gcc4.7-compilation-error.patch
+0008-upstream-fix-to-use-system-libraries.patch
diff --git a/debian/rules b/debian/rules
index a7dbc5f..47b6b1e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -32,6 +32,7 @@ build-py%:
cd $(BUILDDIR)$*; python$* $(SRCDIR)/libtbx/configure.py \
--libtoolize \
--rpath "/usr/lib" \
+ --use_system_libs \
annlib_adaptbx \
boost_adaptbx \
cbflib_adaptbx \
--
Packaging for cctbx
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