[med-svn] [ball] 01/01: Mass commit of NMU changes of 1.4.2+20140406-1.1
Andreas Tille
tille at debian.org
Fri Jul 10 16:50:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ball.
commit be10cf8a93b4233e2831dd9c1a37f0ff24830b39
Author: Andreas Tille <tille at debian.org>
Date: Fri Jul 10 18:49:47 2015 +0200
Mass commit of NMU changes of 1.4.2+20140406-1.1
---
debian/ballview.menu | 2 +-
debian/changelog | 32 +++++-----
debian/control | 15 ++---
debian/patches/0101-cmake-syntax.patch | 4 --
.../0102-fix-boost-compatibility-issue.patch | 8 ++-
..._OPTIONS-CMake-macro-changed-in-CMake-2.8.patch | 6 +-
debian/patches/HelpSipAmbiguity.patch | 13 ++++
debian/patches/findsip.patch | 70 ++++++++++++++++++++++
debian/patches/gcc5.diff | 69 +++++++++++++++++++++
debian/patches/link_against_x11.patch | 18 ++++++
debian/patches/nopsboxit.patch | 16 +++++
debian/patches/series | 8 ++-
debian/rules | 7 +--
13 files changed, 225 insertions(+), 43 deletions(-)
diff --git a/debian/ballview.menu b/debian/ballview.menu
index 55c52bd..81807f8 100644
--- a/debian/ballview.menu
+++ b/debian/ballview.menu
@@ -3,5 +3,5 @@
section="Applications/Science/Chemistry"\
title="BALLView"\
command="/usr/bin/BALLView"\
- icon="/usr/share/pixmaps/ballview_32x32.xpm"\
+ icon="ballview_32x32.xpm"\
longtitle="BALLView: A Molecular modeling and molecular graphics tool"
diff --git a/debian/changelog b/debian/changelog
index d8d1656..74ad8a8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,22 +1,18 @@
-ball (1.4.2+20140406-2) UNRELEASED; urgency=medium
-
- * Unique naming of patches
- * Fix build problem with clang compiler (Thanks for the patch to
- Alexander <sanek23994 at gmail.com>)
- Closes: #755225
- * debian/rules: remove empty directories to silence lintian
- * debian/ballview.menu: absolute path to icon
- * debian/control:
- - do not repeat Section
- - s/python-support/dh-python/
- * debian/rules:
- - s/dh_pysupport/dh_python2/
- - s/dh_clean -k/dh_prep/
- - s/Conflicts: \(.*<<\)/Breaks: \1/ according to Debian Policy Manual
- section 7.4
- * Update patches and add DEP3 description
+ball (1.4.2+20140406-1.1) unstable; urgency=medium
+
+ [ Lisandro Damián Nicanor Pérez Meyer ]
+ * Non-maintainer upload.
+ * Remove qt4-related non-development build dependencies (Closes: #787746).
+ * Force linking against libX11 with link_against_x11.patch. It seems that
+ now we require to manually explicit it.
+ * Add findsip.patch by Dmitry Shachnev to fix sip library detection.
+
+ [ Matthias Klose ]
+ * Fix some build errors with GCC 5 and clang++. Closes: #755225.
+ Addresses #777791.
+ * Build using dh-python. Closes: #785941.
- -- Andreas Tille <tille at debian.org> Wed, 23 Jul 2014 11:51:26 +0200
+ -- Matthias Klose <doko at debian.org> Thu, 09 Jul 2015 12:17:06 +0200
ball (1.4.2+20140406-1) unstable; urgency=medium
diff --git a/debian/control b/debian/control
index 0462b51..c5320b8 100644
--- a/debian/control
+++ b/debian/control
@@ -8,11 +8,7 @@ Priority: optional
Build-Depends: debhelper (>= 9),
qt4-dev-tools,
libqt4-dev,
- libqt4-gui,
- libqt4-opengl,
libqt4-opengl-dev,
- libqt4-sql,
- libqt4-network,
python-sip-dev,
flex,
bison,
@@ -32,9 +28,10 @@ Build-Depends: debhelper (>= 9),
libboost-regex-dev,
libxmu-dev,
libglew-dev,
+ libx11-dev,
tidy,
chrpath,
- dh-python,
+ dh-python,
libqt4-dev-bin
Build-Depends-Indep: doxygen,
graphviz,
@@ -51,6 +48,7 @@ X-Python-Version: all
Package: libball1.4-data
Architecture: all
+Section: science
Depends: ${misc:Depends}
Description: Biochemical Algorithms Library
BALL (Biochemical Algorithms Library) is an application framework
@@ -69,6 +67,7 @@ Description: Biochemical Algorithms Library
Package: libball1.4
Architecture: any
+Section: science
Depends: ${shlibs:Depends},
${misc:Depends},
libball1.4-data
@@ -101,6 +100,7 @@ Description: Header files for the Biochemical Algorithms Library
Package: libballview1.4
Architecture: any
+Section: science
Depends: ${shlibs:Depends},
${misc:Depends}
Description: Biochemical Algorithms Library, VIEW framework
@@ -140,7 +140,7 @@ Depends: ${shlibs:Depends},
${sip:Depends},
libball1.4,
${misc:Depends}
-Breaks: python-ball (<< ${binary:Version})
+Conflicts: python-ball (<< ${binary:Version})
Description: Python bindings for the Biochemical Algorithms Library
BALL (Biochemical Algorithms Library) is an application framework
in C++ that has been specifically designed for rapid software
@@ -158,7 +158,7 @@ Depends: ${shlibs:Depends},
libballview1.4,
python-ball (= ${binary:Version}),
${misc:Depends}
-Breaks: python-ballview (<< ${binary:Version})
+Conflicts: python-ballview (<< ${binary:Version})
Description: Python bindings for VIEW-parts of the Biochemical Algorithms Library
BALL (Biochemical Algorithms Library) is an application framework
in C++ that has been specifically designed for rapid software
@@ -168,6 +168,7 @@ Description: Python bindings for VIEW-parts of the Biochemical Algorithms Librar
Package: ballview
Architecture: any
+Section: science
Depends: ${shlibs:Depends},
libball1.4,
libballview1.4,
diff --git a/debian/patches/0101-cmake-syntax.patch b/debian/patches/0101-cmake-syntax.patch
index f7df0de..91d4c1e 100644
--- a/debian/patches/0101-cmake-syntax.patch
+++ b/debian/patches/0101-cmake-syntax.patch
@@ -1,7 +1,3 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 12 Dec 2013 16:55:11 +0100
-Description: Fix some cmake syntax issues
-
--- a/cmake/BALLDoc.cmake
+++ b/cmake/BALLDoc.cmake
@@ -30,15 +30,15 @@ IF (DOXYGEN_FOUND)
diff --git a/debian/patches/0102-fix-boost-compatibility-issue.patch b/debian/patches/0102-fix-boost-compatibility-issue.patch
index 8adb0f7..3d8113d 100644
--- a/debian/patches/0102-fix-boost-compatibility-issue.patch
+++ b/debian/patches/0102-fix-boost-compatibility-issue.patch
@@ -3,9 +3,11 @@ Last-Update: Thu, 12 Dec 2013 19:43:34 +0100
Bug-Debian: http://bugs.debian.org/720681
Description: Fix build issue with more recent boost versions
---- a/source/FORMAT/PDBFileDetails.C
-+++ b/source/FORMAT/PDBFileDetails.C
-@@ -901,7 +901,7 @@ namespace BALL
+Index: ball/source/FORMAT/PDBFileDetails.C
+===================================================================
+--- ball.orig/source/FORMAT/PDBFileDetails.C
++++ ball/source/FORMAT/PDBFileDetails.C
+@@ -901,7 +901,7 @@
{
if (!(current_protein_->hasProperty("CRYSTALINFO")))
{
diff --git a/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
index d4e261d..2aa9b2e 100644
--- a/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
+++ b/debian/patches/0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
@@ -8,8 +8,10 @@ Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12;
cmake/BALLMacros.cmake | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
---- a/cmake/BALLMacros.cmake
-+++ b/cmake/BALLMacros.cmake
+Index: ball/cmake/BALLMacros.cmake
+===================================================================
+--- ball.orig/cmake/BALLMacros.cmake
++++ ball/cmake/BALLMacros.cmake
@@ -6,16 +6,22 @@
### minor modifications (marked with ## BALL ###)
###
diff --git a/debian/patches/HelpSipAmbiguity.patch b/debian/patches/HelpSipAmbiguity.patch
new file mode 100644
index 0000000..9869b18
--- /dev/null
+++ b/debian/patches/HelpSipAmbiguity.patch
@@ -0,0 +1,13 @@
+Index: ball/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
+===================================================================
+--- ball.orig/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
++++ ball/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
+@@ -26,7 +26,7 @@
+ ModularWidget(const ModularWidget&) throw();
+ ~ModularWidget() throw();
+
+- virtual void destroy() throw();
++ //virtual void destroy() throw(); // Steffen
+ virtual void clear() throw();
+
+ static void registerWidget(ModularWidget*) throw(NullPointer);
diff --git a/debian/patches/findsip.patch b/debian/patches/findsip.patch
new file mode 100644
index 0000000..78ee7fa
--- /dev/null
+++ b/debian/patches/findsip.patch
@@ -0,0 +1,70 @@
+Description: fix sip library detection
+ The old algorithm used hard-coded library names and thus could not
+ detect our multi-arched name.
+ .
+ Instead of that, just import sip from Python script and use the
+ __file__ property to find the library.
+Author: Dmitry Shachnev <mitya57 at debian.org>
+Forwarded: no
+Last-Update: 2015-06-13
+
+--- a/cmake/FindSIP.cmake
++++ b/cmake/FindSIP.cmake
+@@ -69,6 +69,7 @@ ELSE(SIP_VERSION)
+ STRING(REGEX REPLACE ".*\nsip_bin:([^\n]+).*$" "\\1" SIP_EXECUTABLE ${sip_config})
+ STRING(REGEX REPLACE ".*\ndefault_sip_dir:([^\n]+).*$" "\\1" SIP_DEFAULT_SIP_DIR ${sip_config})
+ STRING(REGEX REPLACE ".*\nsip_inc_dir:([^\n]+).*$" "\\1" SIP_INCLUDE_DIR ${sip_config})
++ STRING(REGEX REPLACE ".*\nsip_library:([^\n]+).*$" "\\1" SIP_LIBRARIES ${sip_config})
+ SET(SIP_FOUND TRUE)
+ ENDIF(sip_config)
+
+@@ -100,12 +101,6 @@ IF(NOT SIP_VERSION)
+
+ SET(OLD_CMAKE_FIND_LIBRARY_PREFIXES "${CMAKE_FIND_LIBRARY_PREFIXES}" CACHE INTERNAL "")
+ SET(CMAKE_FIND_LIBRARY_PREFIXES "")
+- FIND_LIBRARY(SIP_LIBRARIES
+- NAMES sip libsip
+- PATHS ${SIP_POSSIBLE_LIB_DIRS} ${PYTHON_SITE_PACKAGES}
+- PATH_SUFFIXES lib dlls
+- DOC "SIP module")
+- SET(CMAKE_FIND_LIBRARY_PREFIXES "${OLD_CMAKE_FIND_LIBRARY_PREFIXES}")
+
+ # (c) Try to find the sip executable:
+
+@@ -134,27 +129,6 @@ IF(NOT SIP_VERSION)
+ STRING(REGEX REPLACE "define SIP_VERSION_STR[ \t]+\"([^\"]*)\"" "\\1" SIP_VERSION_STR "${SIP_VERSION_STR}")
+ ENDIF(NOT SIP_VERSION)
+
+-IF(NOT SIP_LIBRARIES)
+- # Try to find the sip library:
+- EXECUTE_PROCESS ( COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()"
+- OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
+- OUTPUT_STRIP_TRAILING_WHITESPACE
+- )
+-
+- # Use the path to the python installation as a hint for finding sip
+- GET_FILENAME_COMPONENT(SIP_POSSIBLE_LIB_DIRS "${PYTHON_LIBRARIES}" PATH)
+- LIST(APPEND SIP_POSSIBLE_LIB_DIRS "/usr/lib/pyshared/python${PYTHON_VERSION}")
+-
+- SET(OLD_CMAKE_FIND_LIBRARY_PREFIXES "${CMAKE_FIND_LIBRARY_PREFIXES}" CACHE INTERNAL "")
+- SET(CMAKE_FIND_LIBRARY_PREFIXES "")
+- FIND_LIBRARY(SIP_LIBRARIES
+- NAMES sip libsip
+- PATHS ${SIP_POSSIBLE_LIB_DIRS} ${PYTHON_SITE_PACKAGES}
+- PATH_SUFFIXES lib dlls
+- DOC "SIP module")
+- SET(CMAKE_FIND_LIBRARY_PREFIXES "${OLD_CMAKE_FIND_LIBRARY_PREFIXES}")
+-ENDIF()
+-
+ INCLUDE(FindPackageHandleStandardArgs)
+ FIND_PACKAGE_HANDLE_STANDARD_ARGS(SIP DEFAULT_MSG
+ SIP_EXECUTABLE
+--- a/cmake/FindSIP.py
++++ b/cmake/FindSIP.py
+@@ -13,3 +13,6 @@ print("sip_version_str:%s" % sipcfg.sip_
+ print("sip_bin:%s" % sipcfg.sip_bin)
+ print("default_sip_dir:%s" % sipcfg.default_sip_dir)
+ print("sip_inc_dir:%s" % sipcfg.sip_inc_dir)
++
++import sip
++print("sip_library:%s" % sip.__file__)
diff --git a/debian/patches/gcc5.diff b/debian/patches/gcc5.diff
new file mode 100644
index 0000000..ef20351
--- /dev/null
+++ b/debian/patches/gcc5.diff
@@ -0,0 +1,69 @@
+--- a/include/BALL/DATATYPE/string.h 2013-03-07 21:15:10.000000000 +0400
++++ b/include/BALL/DATATYPE/string.h 2014-07-31 02:12:03.770913795 +0400
+@@ -47,6 +47,9 @@
+ {
+ // forward declaration
+ class Substring;
++ class String;
++ BALL_EXPORT
++ std::istream& getline(std::istream& s, String& string, char delimiter = '\n');
+
+ /** \defgroup String String
+ An improved version of STL string.
+@@ -998,7 +1001,7 @@
+
+ ///
+ BALL_EXPORT
+- friend std::istream& getline(std::istream& s, String& string, char delimiter = '\n');
++ friend std::istream& getline(std::istream& s, String& string, char delimiter);
+
+ //@}
+
+--- a/source/FORMAT/molFileFactory.C
++++ b/source/FORMAT/molFileFactory.C
+@@ -39,7 +39,7 @@
+ try
+ {
+ string s;
+- ok = std::getline(in,s);
++ if (std::getline(in,s)) ok = true;
+ }
+ catch (const boost::iostreams::gzip_error& e)
+ {
+--- a/source/STRUCTURE/binaryFingerprintMethods.C
++++ b/source/STRUCTURE/binaryFingerprintMethods.C
+@@ -10,7 +10,7 @@
+ #include <BALL/SYSTEM/timer.h>
+
+ #include <boost/foreach.hpp>
+-
++#include <boost/unordered_map.hpp>
+
+ using namespace std;
+ using namespace boost;
+@@ -1604,13 +1604,13 @@ bool BinaryFingerprintMethods::connectedComponents(const vector<unsigned int>& s
+ {
+
+ // STEP 1: Get connected components and member indices
+- unordered_map<unsigned int, unordered_map<unsigned int, unsigned int> > ccs_tmp;
+- unordered_map<unsigned int, unordered_map<unsigned int, unsigned int> >::iterator ccs_iter;
++ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, unsigned int> > ccs_tmp;
++ boost::unordered_map<unsigned int, boost::unordered_map<unsigned int, unsigned int> >::iterator ccs_iter;
+ BOOST_FOREACH(Vertex current_vertex, vertices(sim_graph))
+ {
+ if (ccs_tmp.find(ds->find_set(current_vertex)) == ccs_tmp.end())
+ {
+- ccs_tmp[ds->find_set(current_vertex)] = unordered_map<unsigned int, unsigned int>();
++ ccs_tmp[ds->find_set(current_vertex)] = boost::unordered_map<unsigned int, unsigned int>();
+ }
+
+ // ccs_tmp[ds->find_set(current_vertex)][current_vertex] = ccs_tmp[ds->find_set(current_vertex)].size();
+@@ -1628,7 +1628,7 @@ bool BinaryFingerprintMethods::connectedComponents(const vector<unsigned int>& s
+ }
+
+ // STEP 3: Write information in return data structures
+- unordered_map<unsigned int, unsigned int>::iterator cc_iter;
++ boost::unordered_map<unsigned int, unsigned int>::iterator cc_iter;
+ for (size_iter=cc_sizes.begin(); size_iter!=cc_sizes.end(); ++size_iter)
+ {
+ ccs.push_back(vector<unsigned int>(size_iter->first, 0));
diff --git a/debian/patches/link_against_x11.patch b/debian/patches/link_against_x11.patch
new file mode 100644
index 0000000..d0e3dc9
--- /dev/null
+++ b/debian/patches/link_against_x11.patch
@@ -0,0 +1,18 @@
+Description: Link against libx11
+ Something has changed since Jessie and now we need to explicitely link
+ against X11.
+Author: Lisandro Damián Nicanor Pérez Meyer <lisandro at debian.org>
+Forwarded: no
+Last-Update: 2015-06-05.
+
+--- ball-1.4.2+20140406.orig/CMakeLists.txt
++++ ball-1.4.2+20140406/CMakeLists.txt
+@@ -550,7 +550,7 @@ TARGET_LINK_LIBRARIES(BALL ${BALL_DEP_LI
+ ${QT_QTCORE_LIBRARY}
+ ${QT_QTSQL_LIBRARY}
+ ${QT_QTNETWORK_LIBRARY}
+- ${QT_QTXML_LIBRARY})
++ ${QT_QTXML_LIBRARY} -lX11)
+
+
+ IF(BALL_HAS_VIEW)
diff --git a/debian/patches/nopsboxit.patch b/debian/patches/nopsboxit.patch
new file mode 100644
index 0000000..06cea8a
--- /dev/null
+++ b/debian/patches/nopsboxit.patch
@@ -0,0 +1,16 @@
+Index: ball/doc/TUTORIAL/macros.tex
+===================================================================
+--- ball.orig/doc/TUTORIAL/macros.tex
++++ ball/doc/TUTORIAL/macros.tex
+@@ -11,8 +11,9 @@
+ \usepackage{times}
+ % use postscript fonts
+
+-\usepackage{psboxit}
+-\newcommand{\graybox}[1]{\psboxit{box .85 setgray fill}{\fbox{#1}}}
++%\usepackage{psboxit}
++%\newcommand{\graybox}[1]{\psboxit{box .85 setgray fill}{\fbox{#1}}}
++\newcommand{\graybox}[1]{\fbox{#1}}
+ % display gray shaded boxes using postscript commands
+ %
+
diff --git a/debian/patches/series b/debian/patches/series
index 500e0b9..0b8451a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,6 +5,8 @@
0101-cmake-syntax.patch
0102-fix-boost-compatibility-issue.patch
0103-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
-0104-nopsboxit.patch
-0105-HelpSipAmbiguity.patch
-0106-clang.patch
+nopsboxit.patch
+HelpSipAmbiguity.patch
+link_against_x11.patch
+findsip.patch
+gcc5.diff
diff --git a/debian/rules b/debian/rules
index a7dc7c1..b44932e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -92,7 +92,7 @@ clean:
install-arch: build-arch
dh_testdir
dh_testroot
- dh_prep
+ dh_clean -k
dh_installdirs
mkdir -p debian/libball$(SOVERSION)/usr/lib \
@@ -147,7 +147,7 @@ install-arch: build-arch
install-indep: build-indep
dh_testdir
dh_testroot
- dh_prep
+ dh_clean -k
dh_installdirs
mkdir -p debian/libball$(SOVERSION)-doc/usr/share/doc/libball$(SOVERSION)/html \
@@ -180,8 +180,6 @@ install-indep: build-indep
dh_python2 -i
dh_sip -i
- # remove empty directories to silence lintian
- find debian/libball*-doc/usr/share/doc -type d -empty -delete
binary-common:
@@ -192,7 +190,6 @@ binary-common:
dh_installexamples
dh_install
dh_installmenu
-# dh_python
dh_installman
dh_link
dh_strip --dbg-package=ballview-dbg
--
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