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commit be10cf8a93b4233e2831dd9c1a37f0ff24830b39 Author: Andreas Tille <[email protected]> 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 <[email protected]>) - 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 <[email protected]> Wed, 23 Jul 2014 11:51:26 +0200 + -- Matthias Klose <[email protected]> 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 <[email protected]> -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 <[email protected]> +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 <[email protected]> +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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ball.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
