Remove boost::regex support rdkit#6817 (rdkit#6913)

Made the following changes * removed RDK_USE_BOOST_REGEX cmake option and its references * removed usage of RDKIT_USE_BOOST_REGEX macro * removed install instructions related to boost regex
e-kwsm · Nov 21, 2023 · ab7b8dd · ab7b8dd
1 parent 2a68050
commit ab7b8dd
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Showing 17 changed files with 12 additions and 76 deletions.
diff --git a/.azure-pipelines/linux_build.yml b/.azure-pipelines/linux_build.yml
@@ -25,7 +25,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF \
     -DRDK_BUILD_CPP_TESTS=ON \
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
-    -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \
@@ -70,7 +69,7 @@ steps:
 - bash: |
     source ${CONDA}/etc/profile.d/conda.sh
     conda activate rdkit_build
-    conda install ipython matplotlib-base 
+    conda install ipython matplotlib-base
     conda install -c conda-forge sphinx myst-parser
     export RDBASE=`pwd`
     export PYTHONPATH=${RDBASE}:${PYTHONPATH}

diff --git a/.azure-pipelines/linux_build_cartridge.yml b/.azure-pipelines/linux_build_cartridge.yml
@@ -16,7 +16,6 @@ steps:
     -DRDK_INSTALL_INTREE=ON \
     -DRDK_BUILD_CPP_TESTS=OFF \
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
-    -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/linux_build_java.yml b/.azure-pipelines/linux_build_java.yml
@@ -14,7 +14,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=ON \
     -DRDK_BUILD_CPP_TESTS=OFF \
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
-    -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/linux_build_limitexternal.yml b/.azure-pipelines/linux_build_limitexternal.yml
@@ -26,7 +26,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF \
     -DRDK_BUILD_CPP_TESTS=ON \
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
-    -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=OFF \
     -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/linux_build_py311.yml b/.azure-pipelines/linux_build_py311.yml
@@ -24,7 +24,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF \
     -DRDK_BUILD_CPP_TESTS=ON \
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
-    -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \
@@ -67,7 +66,7 @@ steps:
 - bash: |
     source ${CONDA}/etc/profile.d/conda.sh
     conda activate rdkit_build
-    conda install ipython matplotlib-base 
+    conda install ipython matplotlib-base
     conda install -c conda-forge sphinx myst-parser
     export RDBASE=`pwd`
     export PYTHONPATH=${RDBASE}:${PYTHONPATH}

diff --git a/.azure-pipelines/linux_build_py37.yml b/.azure-pipelines/linux_build_py37.yml
@@ -23,7 +23,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF \
     -DRDK_BUILD_CPP_TESTS=ON \
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
-    -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/mac_build.yml b/.azure-pipelines/mac_build.yml
@@ -40,7 +40,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF \
     -DRDK_BUILD_CPP_TESTS=ON \
     -DRDK_BUILD_PYTHON_WRAPPERS=ON \
-    -DRDK_USE_BOOST_REGEX=ON \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/mac_build_java.yml b/.azure-pipelines/mac_build_java.yml
@@ -34,7 +34,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=ON \
     -DRDK_BUILD_CPP_TESTS=OFF \
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
-    -DRDK_USE_BOOST_REGEX=OFF \
     -DRDK_BUILD_COORDGEN_SUPPORT=ON \
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON \
     -DRDK_OPTIMIZE_POPCNT=ON \

diff --git a/.azure-pipelines/vs_build.yml b/.azure-pipelines/vs_build.yml
@@ -25,7 +25,6 @@ steps:
     -DRDK_INSTALL_STATIC_LIBS=OFF ^
     -DRDK_BUILD_CPP_TESTS=ON ^
     -DRDK_BUILD_PYTHON_WRAPPERS=ON ^
-    -DRDK_USE_BOOST_REGEX=ON ^
     -DRDK_BUILD_COORDGEN_SUPPORT=ON ^
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON ^
     -DRDK_OPTIMIZE_POPCNT=ON ^

diff --git a/.azure-pipelines/vs_build_dll.yml b/.azure-pipelines/vs_build_dll.yml
@@ -25,7 +25,6 @@ steps:
     -DRDK_INSTALL_DLLS_MSVC=ON ^
     -DRDK_BUILD_CPP_TESTS=ON ^
     -DRDK_BUILD_PYTHON_WRAPPERS=OFF ^
-    -DRDK_USE_BOOST_REGEX=ON ^
     -DRDK_BUILD_COORDGEN_SUPPORT=ON ^
     -DRDK_BUILD_MAEPARSER_SUPPORT=ON ^
     -DRDK_OPTIMIZE_POPCNT=ON ^

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -60,7 +60,6 @@ option(RDK_BUILD_XYZ2MOL_SUPPORT "build in support for the RDKit's implementatio
 option(RDK_BUILD_STRUCTCHECKER_SUPPORT "build in support for the StructChecker alpha (not recommended, use the MolVS integration instead)" OFF )
 option(RDK_USE_URF "Build support for Florian Flachsenberg's URF library" ON)
 option(RDK_INSTALL_DEV_COMPONENT "install libraries and headers" ON)
-option(RDK_USE_BOOST_REGEX "use boost::regex instead of std::regex (needed for systems with g++-4.8)" OFF)
 option(RDK_USE_BOOST_IOSTREAMS "use boost::iostreams" ON)
 option(RDK_BUILD_MINIMAL_LIB "build the minimal RDKit wrapper (for the JS bindings)" OFF)
 option(RDK_MINIMAL_LIB_SUPPORT_LEGACY_BROWSERS "build the minimal RDKit JS wrapper such that it supports legacy browsers" OFF)
@@ -313,7 +312,7 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
   if(WIN32 OR "${Py_ENABLE_SHARED}" STREQUAL "1")
     target_link_libraries(rdkit_py_base INTERFACE ${PYTHON_LIBRARIES} )
   endif()
-  
+
   find_package(NumPy REQUIRED)
   target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH})
 
@@ -488,12 +487,6 @@ if(RDK_USE_BOOST_IOSTREAMS)
     target_link_libraries(rdkit_base INTERFACE ${zlib_lib})
 endif()
 
-if(RDK_USE_BOOST_REGEX)
-  add_definitions(-DRDKIT_USE_BOOST_REGEX)
-  find_package(Boost ${RDK_BOOST_VERSION} COMPONENTS regex REQUIRED)
-  target_link_libraries(rdkit_base INTERFACE ${Boost_LIBRARIES})
-endif()
-
 
 # set the boost include directories and linkage:
 target_include_directories(rdkit_base INTERFACE

diff --git a/Code/Demos/RDKit/Draw/qtDemo/qtdraw_demo.pro b/Code/Demos/RDKit/Draw/qtDemo/qtdraw_demo.pro
@@ -9,8 +9,8 @@ CONFIG += qt
 INCLUDEPATH += ${RDBASE}/Code
 
 RD_STATIC_LIBS = -lSmilesParse_static -lDepictor_static -lGraphMol_static \
--lRDGeometryLib_static -lRDGeneral_static 
+-lRDGeometryLib_static -lRDGeneral_static
 
 LIBS += -L${RDBASE}/lib $${RD_STATIC_LIBS}
 
-LIBS += -L${BOOST}/lib -lboost_regex -lboost_system
+LIBS += -L${BOOST}/lib -lboost_system
diff --git a/Code/GraphMol/FileParsers/MolFileParser.cpp b/Code/GraphMol/FileParsers/MolFileParser.cpp
@@ -37,25 +37,18 @@
 #include <typeinfo>
 #include <exception>
 #include <charconv>
-
-#ifdef RDKIT_USE_BOOST_REGEX
-#include <boost/regex.hpp>
-using boost::regex;
-using boost::regex_match;
-using boost::smatch;
-#else
 #include <regex>
-using std::regex;
-using std::regex_match;
-using std::smatch;
-#endif
 #include <sstream>
 #include <locale>
 #include <cstdlib>
 #include <cstdio>
 #include <string_view>
 
 using namespace RDKit::SGroupParsing;
+using std::regex;
+using std::regex_match;
+using std::smatch;
+
 
 namespace RDKit {
 

diff --git a/Code/cmake/rdkit_valgrind.suppressions b/Code/cmake/rdkit_valgrind.suppressions
@@ -21,7 +21,6 @@
 #    -DRDK_BUILD_THREADSAFE_SSS=ON \
 #    -DRDK_TEST_MULTITHREADED=ON \
 #    -DRDK_BUILD_FREESASA_SUPPORT=ON \
-#    -DRDK_USE_BOOST_REGEX=ON \
 #    -DPYTHON_NUMPY_INCLUDE_PATH="$CONDA_PREFIX/lib/python3.6/site-packages/numpy/core/include"
 #
 {

diff --git a/Docs/Book/Install.md b/Docs/Book/Install.md
@@ -358,26 +358,6 @@ In each case I've replaced specific pieces of the path with `...`.
 
 *Problem:* :
 
-```
-Linking CXX shared library libSLNParse.so
-/usr/bin/ld: .../libboost_regex.a(cpp_regex_traits.o): relocation R_X86_64_32S against `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage' can not be used when making a shared object; recompile with -fPIC
-.../libboost_regex.a: could not read symbols: Bad value
-collect2: ld returned 1 exit status
-make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
-make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
-make: *** [all] Error 2
-```
-
-*Solution:*
-
-Add this to the arguments when you call cmake: `-DBoost_USE_STATIC_LIBS=OFF`
-
-More information here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html
-
-* * * * *
-
-*Problem:* :
-
 ```
 .../Code/GraphMol/Wrap/EditableMol.cpp:114:   instantiated from here
 .../boost/type_traits/detail/cv_traits_impl.hpp:37: internal compiler error: in make_rtl_for_nonlocal_decl, at cp/decl.c:5067
@@ -479,15 +459,15 @@ This section assumes that python is installed in `C:\Python36 that the boost lib
 #### Building from the command line (recommended)
 
 -   Create a directory `C:\RDKit\build` and cd into it
--   Run cmake. Here's an example basic command line for 64bit windows that will download the InChI and Avalon toolkit sources from the InChI Trust and SourceForge repositories, respectively, and build the PostgreSQL cartridge for the installed version of PostgreSQL:  
+-   Run cmake. Here's an example basic command line for 64bit windows that will download the InChI and Avalon toolkit sources from the InChI Trust and SourceForge repositories, respectively, and build the PostgreSQL cartridge for the installed version of PostgreSQL:
   `cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/boost -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\9.5" -G"Visual Studio 14 2015 Win64" ..`
--   Build the code. Here's an example command line:  
+-   Build the code. Here's an example command line:
   `C:/Windows/Microsoft.NET/Framework64/v4.0.30319/MSBuild.exe /m:4 /p:Configuration=Release INSTALL.vcxproj`
 -   If you have built in PostgreSQL support, you will need to open a shell with administrator privileges, stop the PostgreSQL service, run the `pgsql_install.bat` installation script, then restart the PostgreSQL service (please refer to `%RDBASE%\Code\PgSQL\rdkit\README` for further details):
     -   `"C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresql-9.5" -D "C:\Program Files\PostgreSQL\9.5\data" -w stop`
     -   `C:\RDKit\build\Code\PgSQL\rdkit\pgsql_install.bat`
     -   `"C:\Program Files\PostgreSQL\9.5\bin\pg_ctl.exe" -N "postgresql-9.5" -D "C:\Program Files\PostgreSQL\9.5\data" -w start`
-    -   Before restarting the PostgreSQL service, make sure that the Boost libraries the RDKit was built against are in the system PATH, or PostgreSQL will fail to create the `rdkit` extension with a deceptive error message such as:  
+    -   Before restarting the PostgreSQL service, make sure that the Boost libraries the RDKit was built against are in the system PATH, or PostgreSQL will fail to create the `rdkit` extension with a deceptive error message such as:
       `ERROR: could not load library "C:/Program Files/PostgreSQL/9.5/lib/rdkit.dll": The specified module could not be found.`
 
 

diff --git a/Docs/Book_jp/Installation_jp.rst b/Docs/Book_jp/Installation_jp.rst
@@ -423,24 +423,6 @@ JAVAラッパーのビルド
 
 *問題:*
 
-.. code:: console
-
-   Linking CXX shared library libSLNParse.so
-   /usr/bin/ld: .../libboost_regex.a(cpp_regex_traits.o): relocation R_X86_64_32S against `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage' can not be used when making a shared object; recompile with -fPIC
-   .../libboost_regex.a: could not read symbols: Bad value
-   collect2: ld returned 1 exit status
-   make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1
-   make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2
-   make: *** [all] Error 2
-
-*解決方法:*
-
-cmakeを呼び出すときに次を引数に加えてください:\ ``-DBoost_USE_STATIC_LIBS=OFF``\
-
-さらに情報が欲しい場合はこちら：http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html
-
-*問題:*
-
 .. code:: console
 
    .../Code/GraphMol/Wrap/EditableMol.cpp:114:   instantiated from here

diff --git a/rdkit-config.cmake.in b/rdkit-config.cmake.in
@@ -25,7 +25,6 @@ set(RDKit_USE_OPTIMIZED_POPCNT @RDK_OPTIMIZE_POPCNT@)
 set(RDKit_USE_STRICT_ROTOR_DEFINITION @RDK_USE_STRICT_ROTOR_DEFINITION@)
 set(RDKit_USE_BOOST_VERSION @Boost_VERSION_STRING@)
 set(RDKit_USE_BOOST_SERIALIZATION @RDK_USE_BOOST_SERIALIZATION@)
-set(RDKit_USE_BOOST_REGEX @RDK_USE_BOOST_REGEX@)
 set(RDKit_USE_BOOST_IOSTREAMS @RDK_USE_BOOST_IOSTREAMS@)
 
 # Find the RDKit dependencies