[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-61-gd9e4007
Radostan Riedel
raybuntu at googlemail.com
Fri Aug 3 20:48:46 UTC 2012
The following commit has been merged in the master branch:
commit d9e400716410dfe8af60c23f440d81015437e25c
Author: Radostan Riedel <raybuntu at googlemail.com>
Date: Fri Aug 3 19:58:09 2012 +0200
Fix to use systems gpp4, mmdb instead of ccp4.
diff --git a/debian/patches/0001-remove-hardcoded-libtbx_build-env.patch b/debian/patches/0001-remove-hardcoded-libtbx_build-env.patch
index fde9d5e..14d3f09 100644
--- a/debian/patches/0001-remove-hardcoded-libtbx_build-env.patch
+++ b/debian/patches/0001-remove-hardcoded-libtbx_build-env.patch
@@ -22,4 +22,3 @@ index 9c01e0f..8a62446 100644
set_preferred_sys_prefix_and_sys_executable(build_path=build_path)
libtbx_env = open(op.join(build_path, "libtbx_env"), "rb")
env = pickle.load(libtbx_env)
---
diff --git a/debian/patches/0002-fix-opengl-header-missing-gltbx.patch b/debian/patches/0002-fix-opengl-header-missing-gltbx.patch
index 670fb33..d3684a5 100644
--- a/debian/patches/0002-fix-opengl-header-missing-gltbx.patch
+++ b/debian/patches/0002-fix-opengl-header-missing-gltbx.patch
@@ -49,4 +49,3 @@ index d02e7a5..4b2213d 100644
if (not env_etc.gltbx_has_usable_opengl):
print "gltbx: OpenGL headers and/or libraries not available."
print "gltbx: Compilation skipped."
---
diff --git a/debian/patches/0003-correct-paths-in-dispatcher-creation.patch b/debian/patches/0003-correct-paths-in-dispatcher-creation.patch
index 284ee38..4fe0ea3 100644
--- a/debian/patches/0003-correct-paths-in-dispatcher-creation.patch
+++ b/debian/patches/0003-correct-paths-in-dispatcher-creation.patch
@@ -83,4 +83,3 @@ index 8a62446..c3e1c7d 100644
precall_commands = self.dispatcher_precall_commands()
if (precall_commands is not None):
for line in precall_commands:
---
diff --git a/debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch b/debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
index f9f92f2..ac9de30 100644
--- a/debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
+++ b/debian/patches/0004-upstream-fix-for-declaration-errors-in-gcc4.7.patch
@@ -453,4 +453,3 @@ index 6959f18..0be075f 100644
template <typename DataType, typename TagType>
void
---
diff --git a/debian/patches/0005-fix-for-gcc4.7-compilation-error.patch b/debian/patches/0005-fix-for-gcc4.7-compilation-error.patch
index 708cf5e..f2b9523 100644
--- a/debian/patches/0005-fix-for-gcc4.7-compilation-error.patch
+++ b/debian/patches/0005-fix-for-gcc4.7-compilation-error.patch
@@ -81,4 +81,3 @@ index e430cad..3d16a9c 100644
}
};
---
diff --git a/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
index 2b1f35d..6c058d7 100644
--- a/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
+++ b/debian/patches/0006-options-for-system-libs-installtarget-and-prefix.patch
@@ -3,16 +3,18 @@ Date: Mon, 23 Jul 2012 18:28:04 +0200
Subject: options for system libs installtarget and prefix
---
- cctbx_sources/boost_adaptbx/SConscript | 26 ++++--
+ cctbx_sources/boost_adaptbx/SConscript | 26 +-
+ cctbx_sources/ccp4io_adaptbx/SConscript | 284 ++++++++++----------
+ cctbx_sources/ccp4io_adaptbx/ext.cpp | 2 +-
cctbx_sources/cctbx/SConscript | 2 +-
- cctbx_sources/clipper_adaptbx/SConscript | 86 +++++++++++---------
+ cctbx_sources/clipper_adaptbx/SConscript | 86 +++---
cctbx_sources/clipper_adaptbx/clipper/SConscript | 2 +-
- cctbx_sources/gltbx/SConscript | 20 +++--
- cctbx_sources/iotbx/cif/boost_python/SConscript | 13 +--
+ cctbx_sources/gltbx/SConscript | 20 +-
+ cctbx_sources/iotbx/cif/boost_python/SConscript | 13 +-
cctbx_sources/iotbx/mtz/SConscript | 3 +-
cctbx_sources/iotbx/pdb/SConscript | 2 +-
- cctbx_sources/libtbx/SConscript | 79 +++++++++++++++++-
- cctbx_sources/libtbx/env_config.py | 21 +++++
+ cctbx_sources/libtbx/SConscript | 79 +++++-
+ cctbx_sources/libtbx/env_config.py | 21 ++
cctbx_sources/mmtbx/den/SConscript | 2 +-
cctbx_sources/mmtbx/geometry_restraints/SConscript | 2 +-
cctbx_sources/mmtbx/secondary_structure/SConscript | 2 +-
@@ -22,7 +24,7 @@ Subject: options for system libs installtarget and prefix
.../smtbx/refinement/boost_python/SConscript | 4 +-
.../refinement/constraints/boost_python/SConscript | 4 +-
cctbx_sources/spotfinder/SConscript | 2 +-
- 19 files changed, 201 insertions(+), 77 deletions(-)
+ 21 files changed, 348 insertions(+), 216 deletions(-)
diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
index 866b1c1..ed21fb4 100644
@@ -82,6 +84,333 @@ index 866b1c1..ed21fb4 100644
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/ccp4io_adaptbx/SConscript b/cctbx_sources/ccp4io_adaptbx/SConscript
+index f55cc92..300c54f 100644
+--- a/cctbx_sources/ccp4io_adaptbx/SConscript
++++ b/cctbx_sources/ccp4io_adaptbx/SConscript
+@@ -36,118 +36,152 @@ else:
+ # clean out after completely removing support for
+ # old CCP4 directory structure above
+
+-build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
+-if (not op.isdir(build_ccp4io_adaptbx)):
+- os.mkdir(build_ccp4io_adaptbx)
+- assert op.isdir(build_ccp4io_adaptbx)
+-
+-def replace_printf(file_name):
+- full_path = op.join(path_lib_src, file_name)
+- if (not op.isfile(full_path)):
+- full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
+- result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
+- for line in open(full_path).read().splitlines():
+- for key in ["printf", "fprintf"]:
+- matches = list(re.finditer(
+- pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
+- if (len(matches) != 0):
+- for m in reversed(matches):
+- s,e = m.start(), m.end()
+- line = line[:s] \
+- + line[s:e].replace(key, "ccp4io_%s" % key) \
+- + line[e:]
+- result.append(line)
+- return "\n".join(result)
+-
+-env = env_base.Clone(
+- SHLINKFLAGS=env_etc.shlinkflags)
+-env.Append(CCFLAGS=env_etc.ccp4io_defines)
+-env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
+-env_etc.include_registry.append(
+- env=env,
+- paths=[
+- "#",
+- op.dirname(env_etc.ccp4io_include),
+- env_etc.ccp4io_include,
+- op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
+- op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
+-env.Append(LIBS=env_etc.libm)
+-if ( op.normcase(op.dirname(env_etc.ccp4io_dist))
+- != op.normcase("ccp4io")):
+- env.Repository(op.dirname(env_etc.ccp4io_dist))
+ source = []
+-
+ c_files = []
+-c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-library_err.c
+-library_file.c
+-library_utils.c
+-ccp4_array.c
+-ccp4_parser.c
+-ccp4_unitcell.c
+-cvecmat.c
+-cmtzlib.c
+-""".splitlines()])
+-open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
+- open(op.join(path_lib_src, "csymlib.c")).read()
+- .replace(
+- "static int reported_syminfo = 0",
+- "static int reported_syminfo = 1"))
+-source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
++if not env_etc.check_syslib('gpp4', extra_libs=env_etc.py_lib)\
++ or not env_etc.check_syslib('mmdb'):
++ build_ccp4io_adaptbx = libtbx.env.under_build("ccp4io_adaptbx")
++ if (not op.isdir(build_ccp4io_adaptbx)):
++ os.mkdir(build_ccp4io_adaptbx)
++ assert op.isdir(build_ccp4io_adaptbx)
++
++ def replace_printf(file_name):
++ full_path = op.join(path_lib_src, file_name)
++ if (not op.isfile(full_path)):
++ full_path = op.join(op.dirname(path_lib_src), "fortran", file_name)
++ result = ["#include <ccp4io_adaptbx/printf_wrappers.h>"]
++ for line in open(full_path).read().splitlines():
++ for key in ["printf", "fprintf"]:
++ matches = list(re.finditer(
++ pattern="[^A-Za-z0-9_]%s[^A-Za-z0-9_]" % key, string=line))
++ if (len(matches) != 0):
++ for m in reversed(matches):
++ s,e = m.start(), m.end()
++ line = line[:s] \
++ + line[s:e].replace(key, "ccp4io_%s" % key) \
++ + line[e:]
++ result.append(line)
++ return "\n".join(result)
++ env = env_base.Clone(
++ SHLINKFLAGS=env_etc.shlinkflags)
++ env.Append(CCFLAGS=env_etc.ccp4io_defines)
++ env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++ env_etc.include_registry.append(
++ env=env,
++ paths=[
++ "#",
++ op.dirname(env_etc.ccp4io_include),
++ env_etc.ccp4io_include,
++ op.join(env_etc.ccp4io_dist, "lib", mmdb_src),
++ op.join(env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb")])
++ env.Append(LIBS=env_etc.libm)
++ if ( op.normcase(op.dirname(env_etc.ccp4io_dist))
++ != op.normcase("ccp4io")):
++ env.Repository(op.dirname(env_etc.ccp4io_dist))
+
+-probe_file_name = op.join(path_lib_src, "cmaplib.h")
+-env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
+-if (env_etc.ccp4io_has_cmaplib):
+ c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
+-cmap_accessor.c
+-cmap_close.c
+-cmap_data.c
+-cmap_header.c
+-cmap_labels.c
+-cmap_open.c
+-cmap_skew.c
+-cmap_stats.c
+-cmap_symop.c
+-""".splitlines()])
++ library_err.c
++ library_file.c
++ library_utils.c
++ ccp4_array.c
++ ccp4_parser.c
++ ccp4_unitcell.c
++ cvecmat.c
++ cmtzlib.c
++ """.splitlines()])
++ open(op.join(build_ccp4io_adaptbx, "csymlib.c"), "w").write(
++ open(op.join(path_lib_src, "csymlib.c")).read()
++ .replace(
++ "static int reported_syminfo = 0",
++ "static int reported_syminfo = 1"))
++ source.append(op.join("#ccp4io_adaptbx", "csymlib.c"))
+
+-c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
+-bfgs_min
+-file_
+-hybrid_36
+-linalg_
+-machine_
+-math_
+-mattype_
+-mmdb_align
+-mmdb_atom
+-mmdb_bondmngr
+-mmdb_chain
+-mmdb_cifdefs
+-mmdb_coormngr
+-mmdb_cryst
+-mmdb_ficif
+-mmdb_file
+-mmdb_graph
+-mmdb_manager
+-mmdb_mask
+-mmdb_mmcif
+-mmdb_model
+-mmdb_rwbrook
+-mmdb_sbase
+-mmdb_sbase0
+-mmdb_selmngr
+-mmdb_symop
+-mmdb_tables
+-mmdb_title
+-mmdb_uddata
+-mmdb_utils
+-mmdb_xml
+-random_n
+-stream_
+-""".splitlines()])
+-prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
+-for file_name in c_files:
+- source.append(op.join(prefix, file_name))
++ probe_file_name = op.join(path_lib_src, "cmaplib.h")
++ env_etc.ccp4io_has_cmaplib = op.isfile(probe_file_name)
++ if (env_etc.ccp4io_has_cmaplib):
++ c_files.extend(["%s/%s" % (ccp4_src, bn ) for bn in """\
++ cmap_accessor.c
++ cmap_close.c
++ cmap_data.c
++ cmap_header.c
++ cmap_labels.c
++ cmap_open.c
++ cmap_skew.c
++ cmap_stats.c
++ cmap_symop.c
++ """.splitlines()])
++
++ c_files.extend(["%s/mmdb/%s.cpp" % ( mmdb_src, bn ) for bn in """\
++ bfgs_min
++ file_
++ hybrid_36
++ linalg_
++ machine_
++ math_
++ mattype_
++ mmdb_align
++ mmdb_atom
++ mmdb_bondmngr
++ mmdb_chain
++ mmdb_cifdefs
++ mmdb_coormngr
++ mmdb_cryst
++ mmdb_ficif
++ mmdb_file
++ mmdb_graph
++ mmdb_manager
++ mmdb_mask
++ mmdb_mmcif
++ mmdb_model
++ mmdb_rwbrook
++ mmdb_sbase
++ mmdb_sbase0
++ mmdb_selmngr
++ mmdb_symop
++ mmdb_tables
++ mmdb_title
++ mmdb_uddata
++ mmdb_utils
++ mmdb_xml
++ random_n
++ stream_
++ """.splitlines()])
++ prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib")
++ for file_name in c_files:
++ source.append(op.join(prefix, file_name))
++
++ need_f_c = (
++ libtbx.env.has_module("solve_resolve")
++ or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
++ if (need_f_c or os.name != "nt"):
++ source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
++ for file_name in """\
++ ccp4_diskio_f.c
++ ccp4_general.c
++ ccp4_general_f.c
++ ccp4_parser_f.c
++ ccp4_program.c
++ ccp4_unitcell_f.c
++ cmaplib_f.c
++ cmtzlib_f.c
++ csymlib_f.c
++ library_f.c
++ """.splitlines():
++ open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
++ replace_printf(file_name=file_name))
++ source.append(op.join("#ccp4io_adaptbx", file_name))
++ source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
++ env_etc.ccp4io_lib = "ccp4io"
++ mmdb_path= [ os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
++ os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
++ ]
++else:
++ env = env_base.Clone(
++ SHLINKFLAGS=env_etc.shlinkflags)
++ env.Append(CCFLAGS=env_etc.ccp4io_defines)
++ env.Append(SHCCFLAGS=env_etc.ccp4io_defines)
++ env_etc.ccp4io_lib = ["ccp4io", "mmdb", "gpp4"]
++ mmdb_path= []
+
+ ssm_prefix = "#"+op.join(op.basename(env_etc.ccp4io_dist), "lib", "ssm")
+ ssm_sources = """\
+@@ -159,46 +193,20 @@ ssm_superpose.cpp
+ """.splitlines()
+ source.extend( [ op.join( ssm_prefix, f ) for f in ssm_sources ] )
+
+-need_f_c = (
+- libtbx.env.has_module("solve_resolve")
+- or libtbx.env.find_in_repositories(relative_path="mosflm_fable"))
+-if (need_f_c or os.name != "nt"):
+- source.append(op.join("#ccp4io_adaptbx", "fortran_call_stubs.c"))
+- for file_name in """\
+-ccp4_diskio_f.c
+-ccp4_general.c
+-ccp4_general_f.c
+-ccp4_parser_f.c
+-ccp4_program.c
+-ccp4_unitcell_f.c
+-cmaplib_f.c
+-cmtzlib_f.c
+-csymlib_f.c
+-library_f.c
+-""".splitlines():
+- open(op.join(build_ccp4io_adaptbx, file_name), "w").write(
+- replace_printf(file_name=file_name))
+- source.append(op.join("#ccp4io_adaptbx", file_name))
+- source.append(op.join("#ccp4io_adaptbx", "printf_wrappers.c"))
+-
+ # static library for solve_resolve
+ env.StaticLibrary(target='#lib/ccp4io', source=source)
+-env_etc.ccp4io_lib = "ccp4io"
+
+ if ( libtbx.env.has_module("boost")
+ and not env_etc.no_boost_python):
+ Import( "env_no_includes_boost_python_ext" )
+ sources = [ "#ccp4io_adaptbx/ext.cpp" ]
+ env_ext = env_no_includes_boost_python_ext.Clone()
+- env_ext.Prepend( LIBS = "ccp4io" )
++ env_ext.Prepend( LIBS = env_etc.ccp4io_lib )
+ env_etc.include_registry.append(
+ env = env_ext,
+- paths = [
+- os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src ),
+- os.path.join( env_etc.ccp4io_dist, "lib", mmdb_src, "mmdb" ),
+- os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
+- env_etc.boost_include,
+- env_etc.python_include,
+- ]
++ paths = mmdb_path + [ os.path.join( env_etc.ccp4io_dist, "lib", "ssm"),
++ env_etc.boost_include,
++ env_etc.python_include,
++ ]
+ )
+ env_ext.SharedLibrary( target = "#lib/ccp4io_adaptbx_ext", source = sources )
+diff --git a/cctbx_sources/ccp4io_adaptbx/ext.cpp b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+index ce21568..e507515 100644
+--- a/cctbx_sources/ccp4io_adaptbx/ext.cpp
++++ b/cctbx_sources/ccp4io_adaptbx/ext.cpp
+@@ -1,5 +1,5 @@
+ #include <boost/python.hpp>
+-#include <mmdb_manager.h>
++#include <mmdb/mmdb_manager.h>
+ #include <ssm_align.h>
+
+ namespace ccp4io_adaptbx { namespace boost_python {
diff --git a/cctbx_sources/cctbx/SConscript b/cctbx_sources/cctbx/SConscript
index af767ae..6ce770c 100644
--- a/cctbx_sources/cctbx/SConscript
@@ -589,4 +918,3 @@ index 1d280d4..1d73677 100644
env_etc.include_registry.append(
env=env_spotfinder_boost_python_ext,
paths=env_etc.spotfinder_common_includes + [env_etc.python_include])
---
diff --git a/debian/patches/0007-adding-shlib-versioning.patch b/debian/patches/0007-adding-shlib-versioning.patch
index ec6cf1d..b721969 100644
--- a/debian/patches/0007-adding-shlib-versioning.patch
+++ b/debian/patches/0007-adding-shlib-versioning.patch
@@ -203,4 +203,3 @@ index 5efad84..e1cc775 100644
parser.option(None, "--scan_boost",
action="store_true",
default=False,
---
diff --git a/debian/patches/0008-add-with_pycbf-option.patch b/debian/patches/0008-add-with_pycbf-option.patch
index 08adff7..f6469f0 100644
--- a/debian/patches/0008-add-with_pycbf-option.patch
+++ b/debian/patches/0008-add-with_pycbf-option.patch
@@ -75,4 +75,3 @@ index e1cc775..7c0cbc4 100644
parser.option(None, "--install_destdir",
type="string",
action="store",
---
diff --git a/debian/patches/0009-build-libann-statically.patch b/debian/patches/0009-build-libann-statically.patch
index 6508c9b..77ba2b2 100644
--- a/debian/patches/0009-build-libann-statically.patch
+++ b/debian/patches/0009-build-libann-statically.patch
@@ -25,4 +25,3 @@ index 31b4da6..f217b3f 100644
source = ["../annlib/src/ANN.cpp",
"../annlib/src/bd_fix_rad_search.cpp",
"../annlib/src/bd_pr_search.cpp",
---
diff --git a/debian/patches/0010-adding-setup_py.patch b/debian/patches/0010-adding-setup_py.patch
index 8ca9a9e..525e554 100644
--- a/debian/patches/0010-adding-setup_py.patch
+++ b/debian/patches/0010-adding-setup_py.patch
@@ -560,4 +560,3 @@ index 0000000..09b5759
+ py_modules = MODS,
+ data_files = [('share/cctbx/%s'%(py_str), ['%LIBTBXENV%'])], # special treatment from install_data
+ )
---
diff --git a/debian/patches/0011-fix-missing-python-lib-during-linking.patch b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
index 1f00252..f158f4c 100644
--- a/debian/patches/0011-fix-missing-python-lib-during-linking.patch
+++ b/debian/patches/0011-fix-missing-python-lib-during-linking.patch
@@ -44,4 +44,3 @@ index 1f396e5..b906eb3 100644
env_etc.include_registry.append(
env=env,
paths=env_etc.scitbx_common_includes + [env_etc.python_include])
---
diff --git a/debian/patches/0012-fix-to-remove-cctbx.python-interpreter.patch b/debian/patches/0012-fix-to-remove-cctbx.python-interpreter.patch
index 55584ed..ec9a216 100644
--- a/debian/patches/0012-fix-to-remove-cctbx.python-interpreter.patch
+++ b/debian/patches/0012-fix-to-remove-cctbx.python-interpreter.patch
@@ -27,4 +27,3 @@ index c07c015..8eebd49 100644
#
# Biostruct-X Data Reduction Use Case 1.2:
#
---
diff --git a/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch b/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
index 620740d..55d1375 100644
--- a/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
+++ b/debian/patches/0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
@@ -88,4 +88,3 @@ index 7c0cbc4..82dd261 100644
parser.option(None, "--force_32bit",
action="store_true",
default=False,
---
diff --git a/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch b/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
index 05dd02b..e5e5f45 100644
--- a/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
+++ b/debian/patches/0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
@@ -19,4 +19,3 @@ index 7c7471d..dcd888a 100644
""" ************************ Custom Builders and Emitters ********************************* """
---
diff --git a/debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch b/debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
index 54b4888..199d590 100644
--- a/debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
+++ b/debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
@@ -21,4 +21,3 @@ index c10a192..e70dcb6 100644
input_string.size(),
pANTLR3_UINT8(filename.c_str()));
lxr = cifLexerNew(input);
---
diff --git a/debian/patches/0016-adapt-test_utils-in-libtbx-for-setup_py-test.patch b/debian/patches/0016-adapt-test_utils-in-libtbx-for-setup_py-test.patch
index eadcf26..6e3b61d 100644
--- a/debian/patches/0016-adapt-test_utils-in-libtbx-for-setup_py-test.patch
+++ b/debian/patches/0016-adapt-test_utils-in-libtbx-for-setup_py-test.patch
@@ -47,4 +47,3 @@ index 13b6e67..c93867f 100644
else:
if (co.valgrind):
cmd = os.environ.get(
---
diff --git a/debian/repack.local b/debian/repack.local
index bd5d091..ffc093b 100755
--- a/debian/repack.local
+++ b/debian/repack.local
@@ -2,6 +2,7 @@
shopt -s extglob
rm rf cctbx_sources/boost/*
rm rf cctbx_sources/clipper/!(clipper)
+rm rf cctbx_sources/ccp4io/lib/!(ssm)
rm rf cctbx_sources/clipper/clipper/!(cctbx)
rm rf cctbx_sources/scons/*
rm rf cctbx_sources/ucif/antlr3
--
Packaging for cctbx
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