[SCM] Packaging for cctbx branch, master, updated. upstream/2012.05.08.2305-53-gbb12f37

[Radostan Riedel]

The following commit has been merged in the master branch:
commit bb12f37d269d21331303f75b3091b38cf2c2f239
Author: Radostan Riedel <raybuntu at googlemail.com>
Date:   Thu Jul 26 00:33:58 2012 +0200

    Fix to avoid building antlr3c symbols.

diff --git a/debian/control b/debian/control
index 7d3a0eb..cba768b 100644
--- a/debian/control
+++ b/debian/control
@@ -6,6 +6,7 @@ Priority: extra
 Build-Depends: debhelper (>= 9),
                python-all-dev,
                libfftw3-dev,
+               libantlr3c-dev (<= 3.2),
                libcbf-dev,
                libgl2ps-dev,
                libann-dev,
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 363c987..2b1f35d 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
@@ -8,6 +8,7 @@ Subject: options for system libs installtarget and prefix
  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/iotbx/mtz/SConscript                 |    3 +-
  cctbx_sources/iotbx/pdb/SConscript                 |    2 +-
  cctbx_sources/libtbx/SConscript                    |   79 +++++++++++++++++-
@@ -21,7 +22,7 @@ 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 +-
- 18 files changed, 193 insertions(+), 72 deletions(-)
+ 19 files changed, 201 insertions(+), 77 deletions(-)
 
 diff --git a/cctbx_sources/boost_adaptbx/SConscript b/cctbx_sources/boost_adaptbx/SConscript
 index 866b1c1..ed21fb4 100644
@@ -262,6 +263,34 @@ index 4b2213d..04e0654 100644
      env_util.SharedLibrary(
        target="#lib/gltbx_util_ext",
        source=source)
+diff --git a/cctbx_sources/iotbx/cif/boost_python/SConscript b/cctbx_sources/iotbx/cif/boost_python/SConscript
+index 49837af..2833ff1 100644
+--- a/cctbx_sources/iotbx/cif/boost_python/SConscript
++++ b/cctbx_sources/iotbx/cif/boost_python/SConscript
+@@ -34,15 +34,18 @@ antlr3_src_files = [
+ ]
+ 
+ prefix = "#ucif/antlr3/src"
+-source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++if not env_etc.check_syslib('antlr3c'):
++  source = [os.path.join(prefix, file_name) for file_name in antlr3_src_files]
++  env_etc.include_registry.append(
++    env=env,
++    paths=[antlr3_include, antlr3_dist])
++else:
++  source = []
++  env.Append(LIBS=['antlr3c'])
+ source.extend([
+   "cif_ext.cpp",
+   "#ucif/cifParser.cpp",
+   "#ucif/cifLexer.cpp",
+ ])
+ 
+-env_etc.include_registry.append(
+-  env=env,
+-  paths=[antlr3_include, antlr3_dist])
+-
+ env.SharedLibrary(target="#lib/iotbx_cif_ext", source=source)
 diff --git a/cctbx_sources/iotbx/mtz/SConscript b/cctbx_sources/iotbx/mtz/SConscript
 index c0a4bb0..cd539e6 100644
 --- a/cctbx_sources/iotbx/mtz/SConscript
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
new file mode 100644
index 0000000..54b4888
--- /dev/null
+++ b/debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
@@ -0,0 +1,24 @@
+From: Radostan Riedel <raybuntu at googlemail.com>
+Date: Thu, 26 Jul 2012 03:48:36 +0200
+Subject: fix cif parser to work with antlr3c 3.2
+
+---
+ cctbx_sources/ucif/parser.h |    3 +--
+ 1 file changed, 1 insertion(+), 2 deletions(-)
+
+diff --git a/cctbx_sources/ucif/parser.h b/cctbx_sources/ucif/parser.h
+index c10a192..e70dcb6 100644
+--- a/cctbx_sources/ucif/parser.h
++++ b/cctbx_sources/ucif/parser.h
+@@ -24,9 +24,8 @@ class parser
+            std::string input_string,
+            std::string filename="memory", bool strict=true)
+     {
+-      input = antlr3StringStreamNew(
++      input = antlr3NewAsciiStringInPlaceStream(
+         pANTLR3_UINT8(input_string.c_str()),
+-        ANTLR3_ENC_8BIT,
+         input_string.size(),
+         pANTLR3_UINT8(filename.c_str()));
+       lxr = cifLexerNew(input);
+-- 
diff --git a/debian/patches/series b/debian/patches/series
index 397d2be..7c163b7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -12,3 +12,4 @@
 0012-fix-to-remove-cctbx.python-interpreter.patch
 0013-fix-to-support-LDFLAGS-in-use_enviroment_flags.patch
 0014-Fix-to-append-CPPFLAGS-to-CXXFLAGS.patch
+0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch

-- 
Packaging for cctbx