Control: tags 954351 + patch
Control: tags 954351 + pending
Dear maintainer,
I've prepared an NMU for rdkit (versioned as 201909.1-4.1) and uploaded
it to DELAYED/2. Please feel free to tell me if I should cancel it.
cu
Adrian
diff -Nru rdkit-201909.1/debian/changelog rdkit-201909.1/debian/changelog
--- rdkit-201909.1/debian/changelog 2020-05-12 13:21:19.000000000 +0300
+++ rdkit-201909.1/debian/changelog 2020-06-10 16:07:07.000000000 +0300
@@ -1,3 +1,10 @@
+rdkit (201909.1-4.1) unstable; urgency=high
+
+ * Non-maintainer upload.
+ * Add patch for FTBFS with Boost 1.71. (Closes: #954351)
+
+ -- Adrian Bunk <b...@debian.org> Wed, 10 Jun 2020 16:07:07 +0300
+
rdkit (201909.1-4) unstable; urgency=medium
* Team upload.
diff -Nru rdkit-201909.1/debian/patches/fix-ftbfs.patch rdkit-201909.1/debian/patches/fix-ftbfs.patch
--- rdkit-201909.1/debian/patches/fix-ftbfs.patch 1970-01-01 02:00:00.000000000 +0200
+++ rdkit-201909.1/debian/patches/fix-ftbfs.patch 2020-06-10 16:06:58.000000000 +0300
@@ -0,0 +1,307 @@
+Description: fix all of boost detections
+Author: Dimitri John Ledkov <x...@ubuntu.com>
+
+
+--- rdkit-201909.1.orig/CMakeLists.txt
++++ rdkit-201909.1/CMakeLists.txt
+@@ -223,6 +223,12 @@ if(RDK_BUILD_INCHI_SUPPORT)
+ find_package(Inchi)
+ endif(RDK_BUILD_INCHI_SUPPORT)
+
++find_package(Boost 1.56.0 COMPONENTS "python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}" system serialization iostreams regex REQUIRED)
++add_definitions("-DRDKIT_USE_BOOST_REGEX")
++add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
++ADD_DEFINITIONS("-DRDK_USE_BOOST_IOSTREAMS")
++
++
+ if(RDK_BUILD_PYTHON_WRAPPERS)
+ #-------
+ # pull in python:
+@@ -240,29 +246,6 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
+ find_package(NumPy REQUIRED)
+ target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH})
+
+- if(PYTHON_VERSION_MAJOR EQUAL 3)
+- # Find boost-python3 using name specified as command line option then fall back to commonly used names
+- set(RDK_BOOST_PYTHON3_NAME "python3" CACHE STRING "Name of the boost python3 library. If installed as libboost_python-xxx.so, use python-xxx.")
+- list(APPEND Boost_Python_Names "${RDK_BOOST_PYTHON3_NAME}" "python-py3${PYTHON_VERSION_MINOR}" "python3")
+- endif(PYTHON_VERSION_MAJOR EQUAL 3)
+-
+- # Boost 1.67+ uses a version suffix like "python36" or "python27"
+- list(APPEND Boost_Python_Names "python${PYTHON_VERSION_MAJOR}${PYTHON_VERSION_MINOR}")
+-
+- # Try each potential boost-python name until one works
+- foreach(Boost_Python_Lib ${Boost_Python_Names})
+- find_package(Boost 1.56.0 COMPONENTS "${Boost_Python_Lib}" QUIET)
+- if(Boost_FOUND)
+- break()
+- endif()
+- endforeach()
+-
+- # Finally just try "python" and hope it is a compatible version
+- if(NOT Boost_FOUND)
+- find_package(Boost 1.56.0 COMPONENTS python REQUIRED)
+- endif()
+-
+-
+ if(RDK_INSTALL_INTREE)
+ set(RDKit_PythonDir "${CMAKE_SOURCE_DIR}/rdkit")
+ else(RDK_INSTALL_INTREE)
+@@ -322,8 +305,6 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
+ message("PYTHON Py_ENABLE_SHARED: ${Py_ENABLE_SHARED}")
+ message("PYTHON USING LINK LINE: ${PYTHON_LDSHARED}")
+ endif()
+-else(RDK_BUILD_PYTHON_WRAPPERS)
+- find_package(Boost 1.56.0 REQUIRED)
+ endif(RDK_BUILD_PYTHON_WRAPPERS)
+
+ # Detect clang, which masquerades as gcc. CMake 2.6 doesn't know how to
+@@ -357,11 +338,7 @@ else()
+ endif()
+
+ if(RDK_USE_BOOST_SERIALIZATION)
+- set(T_LIBS ${Boost_LIBRARIES})
+- find_package(Boost 1.56.0 COMPONENTS serialization)
+- if (Boost_SERIALIZATION_LIBRARY)
+- set(Boost_LIBRARIES ${T_LIBS} ${Boost_LIBRARIES})
+- endif()
++
+ endif()
+
+
+@@ -369,7 +346,7 @@ endif()
+ target_include_directories(rdkit_base INTERFACE
+ $<BUILD_INTERFACE:${RDKit_CodeDir}>
+ $<INSTALL_INTERFACE:${RDKit_HdrDir}>
+- ${Boost_INCLUDE_DIR}
++ ${Boost_INCLUDE_DIRS}
+ )
+ target_link_libraries(rdkit_base INTERFACE ${BOOST_LIBRARIES})
+
+--- rdkit-201909.1.orig/Code/GraphMol/FileParsers/CMakeLists.txt
++++ rdkit-201909.1/Code/GraphMol/FileParsers/CMakeLists.txt
+@@ -2,35 +2,11 @@
+ remove_definitions(-DRDKIT_GRAPHMOL_BUILD)
+ add_definitions(-DRDKIT_FILEPARSERS_BUILD)
+
+-if(RDK_USE_BOOST_IOSTREAMS)
+-if(WIN32)
+- find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+- find_package(Boost 1.56.0 COMPONENTS zlib)
+- set (link_iostreams ${Boost_LIBRARIES})
+- if (NOT Boost_USE_STATIC_LIBS)
+- add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+- endif()
+-else()
+- find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+- set (link_iostreams ${Boost_LIBRARIES})
+- if (NOT Boost_USE_STATIC_LIBS)
+- add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+- endif()
+-endif()
+-ADD_DEFINITIONS("-DRDK_USE_BOOST_IOSTREAMS")
+-endif(RDK_USE_BOOST_IOSTREAMS)
+-
+ if(RDK_BUILD_COORDGEN_SUPPORT)
+ include_directories(${maeparser_INCLUDE_DIRS})
+ set (maesupplier MaeMolSupplier.cpp)
+ endif()
+
+-if(RDK_USE_BOOST_REGEX)
+- add_definitions(-DRDKIT_USE_BOOST_REGEX)
+- find_package(Boost 1.58.0 COMPONENTS regex REQUIRED)
+- set(regex_lib Boost::regex)
+-endif()
+-
+ rdkit_library(FileParsers
+ Mol2FileParser.cpp MolFileParser.cpp
+ MolSGroupParsing.cpp MolSGroupWriting.cpp
+@@ -45,7 +21,7 @@ rdkit_library(FileParsers
+ ProximityBonds.cpp
+ SequenceParsers.cpp SequenceWriters.cpp
+ SVGParser.cpp
+- LINK_LIBRARIES Depictor SmilesParse GraphMol ${RDK_COORDGEN_LIBS} ${regex_lib} ${link_iostreams})
++ LINK_LIBRARIES Depictor SmilesParse GraphMol ${RDK_COORDGEN_LIBS})
+
+ rdkit_headers(FileParsers.h
+ FileParserUtils.h
+--- rdkit-201909.1.orig/Code/GraphMol/MolDraw2D/QTDemo/CMakeLists.txt
++++ rdkit-201909.1/Code/GraphMol/MolDraw2D/QTDemo/CMakeLists.txt
+@@ -1,9 +1,3 @@
+-
+-set(Boost_USE_STATIC_LIBS ON)
+-set(Boost_USE_MULTITHREADED OFF)
+-set(Boost_USE_STATIC_RUNTIME ON)
+-find_package( Boost 1.46.0 COMPONENTS program_options iostreams filesystem )
+-
+ # Instruct CMake to run moc automatically when needed.
+ set(CMAKE_AUTOMOC ON)
+
+@@ -31,7 +25,7 @@ set( RDKitSV_INCS MolDisplay2DWidget.H
+ QTGet2Strings.H
+ QT4SelectItems.H )
+
+-set( LIBS Boost::program_options Boost::iostreams Boost::filesystem
++set( LIBS
+ ${RDKit_THREAD_LIBS}
+ FileParsers SmilesParse Depictor RDGeometryLib
+ RDGeneral SubstructMatch Subgraphs GraphMol RDGeometryLib
+--- rdkit-201909.1.orig/Code/GraphMol/MolStandardize/CMakeLists.txt
++++ rdkit-201909.1/Code/GraphMol/MolStandardize/CMakeLists.txt
+@@ -67,9 +67,4 @@ rdkit_catch_test(molStandardizeCatchTest
+ Catalogs SmilesParse RDGeneral GraphMol SubstructMatch FileParsers
+ ChemTransforms Descriptors)
+
+-#find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+-#if (NOT Boost_USE_STATIC_LIBS)
+-# add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+-#endif()
+-
+-# rdkit_test(compareMolVSTest testPCS.cpp LINK_LIBRARIES RDGeneral SmilesParse RDGeneral GraphMol MolStandardize ${Boost_LIBRARIES})
++# rdkit_test(compareMolVSTest testPCS.cpp LINK_LIBRARIES RDGeneral SmilesParse RDGeneral GraphMol MolStandardize)
+--- rdkit-201909.1.orig/Code/GraphMol/Wrap/CMakeLists.txt
++++ rdkit-201909.1/Code/GraphMol/Wrap/CMakeLists.txt
+@@ -27,25 +27,12 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
+ include_directories(${maeparser_INCLUDE_DIRS})
+ endif()
+
+-if(RDK_BUILD_COMPRESSED_SUPPLIERS)
+-find_package(Boost 1.56.0 COMPONENTS iostreams REQUIRED)
+-if (NOT Boost_USE_STATIC_LIBS)
+- add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+-endif()
+ set(rdmolfiles_sources rdmolfiles.cpp
+ ForwardSDMolSupplier.cpp ${maesupplier}
+ SDMolSupplier.cpp TDTMolSupplier.cpp
+ SmilesMolSupplier.cpp SmilesWriter.cpp SDWriter.cpp
+ TDTWriter.cpp CompressedSDMolSupplier.cpp
+ PDBWriter.cpp )
+-else(RDK_BUILD_COMPRESSED_SUPPLIERS)
+-set(rdmolfiles_sources rdmolfiles.cpp
+- ForwardSDMolSupplier.cpp ${maesupplier}
+- SDMolSupplier.cpp TDTMolSupplier.cpp
+- SmilesMolSupplier.cpp SmilesWriter.cpp SDWriter.cpp
+- TDTWriter.cpp
+- PDBWriter.cpp )
+-endif(RDK_BUILD_COMPRESSED_SUPPLIERS)
+
+ rdkit_python_extension(rdmolfiles
+ ${rdmolfiles_sources}
+--- rdkit-201909.1.orig/Code/JavaWrappers/CMakeLists.txt
++++ rdkit-201909.1/Code/JavaWrappers/CMakeLists.txt
+@@ -38,32 +38,14 @@ set(swigRDKitLibs "")
+ foreach(swigRDKitLib ${swigRDKitLibList})
+ set(swigRDKitLibs "${swigRDKitLibs}${swigRDKitLib}${swigRDKitLibSuffix};")
+ endforeach()
+-set(swigRDKitLibs "${swigRDKitLibs}${Boost_SERIALIZATION_LIBRARY};")
+
+-if(RDK_USE_BOOST_IOSTREAMS)
+ ADD_DEFINITIONS("-DRDK_USE_BOOST_IOSTREAMS")
+-if(WIN32)
+- find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+- set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_SYSTEM_LIBRARY};")
+-
+- find_package(Boost 1.56.0 COMPONENTS zlib)
+- if(Boost_zlib_FOUND)
+- set(swigRDKitLibs "${swigRDKitLibs}${Boost_ZLIB_LIBRARY};")
+- endif()
+-else()
+- find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+- set(swigRDKitLibs "${swigRDKitLibs}${Boost_IOSTREAMS_LIBRARY};${Boost_SYSTEM_LIBRARY};")
+-endif()
+-endif(RDK_USE_BOOST_IOSTREAMS)
+-
+-
+
+ set(RDKit_Wrapper_Libs ${swigRDKitLibs})
+
+ message("SUFFIX: ${swigRDKitLibSuffix}")
+ message("JAVA_LIBS: ${RDKit_Wrapper_Libs}")
+
+-
+ if(RDK_BUILD_SWIG_JAVA_WRAPPER)
+ add_subdirectory(gmwrapper)
+ endif()
+--- rdkit-201909.1.orig/Code/RDStreams/CMakeLists.txt
++++ rdkit-201909.1/Code/RDStreams/CMakeLists.txt
+@@ -1,28 +1,8 @@
+ if(RDK_USE_BOOST_IOSTREAMS)
+ ADD_DEFINITIONS("-DRDK_USE_BOOST_IOSTREAMS")
+-
+-find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+-set (link_iostreams ${Boost_LIBRARIES})
+-if (NOT Boost_USE_STATIC_LIBS)
+- add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+-endif()
+-
+-if (WIN32)
+- find_package(Boost 1.58.0 COMPONENTS zlib)
+- if(Boost_zlib_FOUND)
+- set(zlib_lib Boost::zlib)
+- endif()
+-else()
+- if(Boost_USE_STATIC_LIBS)
+- # when we're doing static linkage of boost
+- # to also link against zlib (due to iostreams)
+- find_package(ZLIB)
+- set(zlib_lib ${ZLIB_LIBRARIES})
+- endif()
+-endif()
+-
+-add_definitions(-DRDKIT_RDSTREAMS_BUILD)
++add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
++add_definitions("-DRDKIT_RDSTREAMS_BUILD")
+ endif(RDK_USE_BOOST_IOSTREAMS)
+ rdkit_library(RDStreams streams.cpp
+- LINK_LIBRARIES ${Boost_LIBRARIES} ${link_iostreams} ${zlib_lib})
++ LINK_LIBRARIES ${Boost_LIBRARIES})
+ rdkit_headers(streams.h DEST RDStreams)
+--- rdkit-201909.1.orig/Docs/Book/C++Examples/CMakeLists.txt
++++ rdkit-201909.1/Docs/Book/C++Examples/CMakeLists.txt
+@@ -9,7 +9,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}
+ set(Boost_USE_STATIC_LIBS ON)
+ set(Boost_USE_MULTITHREADED OFF)
+ set(Boost_USE_STATIC_RUNTIME ON)
+-find_package( Boost COMPONENTS iostreams filesystem system)
++find_package( Boost COMPONENTS iostreams filesystem system REQUIRED)
+
+ find_package( Cairo REQUIRED )
+
+@@ -23,9 +23,9 @@ set(EXECUTABLE_OUTPUT_PATH ${CMAKE_SOURC
+ find_package (Threads)
+ set(RDKit_THREAD_LIBS Threads::Threads)
+
+-set( LIBS ${RDKIT_LIBRARIES} Boost::iostreams ${RDKit_THREAD_LIBS} z )
++set( LIBS ${RDKIT_LIBRARIES} ${Boost_LIBRARIES} ${RDKit_THREAD_LIBS} z )
+
+-include_directories(${RDKIT_INCLUDE_DIR})
++include_directories(${RDKIT_INCLUDE_DIRS})
+ foreach( exnum RANGE 1 16 )
+ message( "Example : ${exnum}" )
+ set( exe "example${exnum}" )
+--- rdkit-201909.1.orig/External/CoordGen/CMakeLists.txt
++++ rdkit-201909.1/External/CoordGen/CMakeLists.txt
+@@ -10,23 +10,10 @@ if(RDK_BUILD_COORDGEN_SUPPORT)
+ add_definitions(-DIN_COORDGEN)
+ endif(MSVC AND (NOT RDK_INSTALL_DLLS_MSVC))
+
+- find_package(Boost 1.56.0 COMPONENTS system iostreams REQUIRED)
+- set (link_iostreams ${Boost_LIBRARIES})
+- if (NOT Boost_USE_STATIC_LIBS)
+- add_definitions("-DBOOST_IOSTREAMS_DYN_LINK")
+- endif()
+-
+ if (WIN32)
+ set( T_LIBS ${Boost_LIBRARIES})
+ find_package(Boost 1.58.0 COMPONENTS zlib)
+ set( Boost_LIBRARIES ${T_LIBS} ${Boost_LIBRARIES})
+-
+- else()
+- if(Boost_USE_STATIC_LIBS)
+- # when we're doing static linkage of boost
+- # to also link against zlib (due to iostreams)
+- find_package(ZLIB)
+- endif()
+ endif()
+
+ find_package(maeparser MODULE)
diff -Nru rdkit-201909.1/debian/patches/series rdkit-201909.1/debian/patches/series
--- rdkit-201909.1/debian/patches/series 2020-05-12 13:21:19.000000000 +0300
+++ rdkit-201909.1/debian/patches/series 2020-06-10 16:06:58.000000000 +0300
@@ -4,3 +4,4 @@
sphinx_imgconverter.patch
catch2_header.patch
postgres_alternative_test_outputs.patch
+fix-ftbfs.patch
