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#1149286 rdkit: FTBFS with boost 1.92 #1149286

Package:: src:rdkit

Source:: src:rdkit

Submitter:: Anton Gladky

Date:: 2026-10-21 05:21:01 UTC

Severity:: normal

Tags:

#1149286#5

Date:: 2026-09-29 05:31:53 UTC

From:

To:

Dear Maintainer,

Boost 1.92 will most likely be the default boost version in the
upcoming Debian 14 (forky) release.

rdkit FTBFS with boost 1.92. Note that the FTBFS may not necessarily be
connected to boost - please check the build log for the actual cause.

boost-defaults pointing to 1.92 is available in experimental, so you can
rebuild your package against it to reproduce the failure and test the fix.

Note: This ticket severity will be increased to RC bug when
boost-defaults is switched to 1.92.

If your package depends on versioned boost packages (e.g. libboost1.90-dev),
please switch to the unversioned (default) ones (e.g. libboost-dev), so the
package follows future boost transitions automatically.

Here is the most probably relevant part of the failing build log:

==================== build log ====================
[  3%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o
cd /build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/x86_64-linux-gnu-g++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_CONTAINER_DYN_LINK -DBOOST_CONTAINER_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_EXCEPTION_NO_LIB=1 -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_RANDOM_DYN_LINK -DBOOST_RANDOM_NO_LIB -DBOOST_REGEX_DYN_LINK -DBOOST_REGEX_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -DBOOST_THREAD_USE_DLL -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202603.4/External -I/build/reproducible-path/rdkit
 -202603.4/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202603.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++20 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202603.4/Code/DataStructs/testDatastructs.cpp
In file included from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9,
                 from /build/reproducible-path/rdkit-202603.4/Code/RDBoost/python.h:5,
                 from /build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:10:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<int>; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>; bool NoProxy = true; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<int>; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>; bool NoProxy = true; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>, true, false, int, long unsigned int, int> >; classT = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>, true, false, int, long unsigned int, int>]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>, true, false, int, long unsigned int, int>; W = std::__cxx11::list<int>; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:125:13:   required from ‘void RegisterListConverter(bool) [with T = int]’
  124 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |         .def(python::list_indexing_suite<std::list<T>, 1>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:360:29:   required from here
  360 |   RegisterListConverter<int>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, true>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<int>; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>; bool NoProxy = false; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<int>; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>; bool NoProxy = false; bool NoSlice = false; Data = int; Index = long unsigned int; Key = int]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>, false, false, int, long unsigned int, int> >; classT = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>, false, false, int, long unsigned int, int>]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<int>, boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>, false, false, int, long unsigned int, int>; W = std::__cxx11::list<int>; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<int>, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:128:13:   required from ‘void RegisterListConverter(bool) [with T = int]’
  127 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  128 |         .def(python::list_indexing_suite<std::list<T>>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:360:29:   required from here
  360 |   RegisterListConverter<int>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<int>, false>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<std::vector<int> >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>; bool NoProxy = true; bool NoSlice = false; Data = std::vector<int>; Index = long unsigned int; Key = std::vector<int>]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<std::vector<int> >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>; bool NoProxy = true; bool NoSlice = false; Data = std::vector<int>; Index = long unsigned int; Key = std::vector<int>]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>, true, false, std::vector<int>, long unsigned int, std::vector<int> > >; classT = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>, true, false, std::vector<int>, long unsigned int, std::vector<int> >]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>, true, false, std::vector<int>, long unsigned int, std::vector<int> >; W = std::__cxx11::list<std::vector<int> >; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:125:13:   required from ‘void RegisterListConverter(bool) [with T = std::vector<int>]’
  124 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |         .def(python::list_indexing_suite<std::list<T>, 1>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:361:42:   required from here
  361 |   RegisterListConverter<std::vector<int>>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, true>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<std::vector<int> >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>; bool NoProxy = false; bool NoSlice = false; Data = std::vector<int>; Index = long unsigned int; Key = std::vector<int>]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<std::vector<int> >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>; bool NoProxy = false; bool NoSlice = false; Data = std::vector<int>; Index = long unsigned int; Key = std::vector<int>]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>, false, false, std::vector<int>, long unsigned int, std::vector<int> > >; classT = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>, false, false, std::vector<int>, long unsigned int, std::vector<int> >]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<std::vector<int> >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>, false, false, std::vector<int>, long unsigned int, std::vector<int> >; W = std::__cxx11::list<std::vector<int> >; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<std::vector<int> >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:128:13:   required from ‘void RegisterListConverter(bool) [with T = std::vector<int>]’
  127 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  128 |         .def(python::list_indexing_suite<std::list<T>>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:361:42:   required from here
  361 |   RegisterListConverter<std::vector<int>>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<int> >, false>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>; bool NoProxy = true; bool NoSlice = false; Data = std::vector<unsigned int>; Index = long unsigned int; Key = std::vector<unsigned int>]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>; bool NoProxy = true; bool NoSlice = false; Data = std::vector<unsigned int>; Index = long unsigned int; Key = std::vector<unsigned int>]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>, true, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> > >; classT = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>, true, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> >]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>, true, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> >; W = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::
 python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:125:13:   required from ‘void RegisterListConverter(bool) [with T = std::vector<unsigned int>]’
  124 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  125 |         .def(python::list_indexing_suite<std::list<T>, 1>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:362:51:   required from here
  362 |   RegisterListConverter<std::vector<unsigned int>>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, true>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp: In instantiation of ‘static void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::base_clear(Container&) [with Container = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>; bool NoProxy = false; bool NoSlice = false; Data = std::vector<unsigned int>; Index = long unsigned int; Key = std::vector<unsigned int>]’:
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:187:31:   required from ‘void boost::python::indexing_suite<Container, DerivedPolicies, NoProxy, NoSlice, Data, Index, Key>::visit(Class&) const [with Class = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; Container = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; DerivedPolicies = boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>; bool NoProxy = false; bool NoSlice = false; Data = std::vector<unsigned int>; Index = long unsigned int; Key = std::vector<unsigned int>]’
  187 |                 .def("clear", &base_clear)
      |                               ^~~~~~~~~~~
/usr/include/boost/python/def_visitor.hpp:31:34:   required from ‘static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor<boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>, false, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> > >; classT = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>]’
   31 |         v.derived_visitor().visit(c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~
/usr/include/boost/python/def_visitor.hpp:67:34:   required from ‘void boost::python::def_visitor<DerivedVisitor>::visit(classT&) const [with classT = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost::python::detail::not_specified>; DerivedVisitor = boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>, false, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> >]’
   67 |         def_visitor_access::visit(*this, c);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
/usr/include/boost/python/class.hpp:221:22:   required from ‘boost::python::class_<T, X1, X2, X3>::self& boost::python::class_<T, X1, X2, X3>::def(const boost::python::def_visitor<Derived>&) [with Derived = boost::python::indexing_suite<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>, false, false, std::vector<unsigned int>, long unsigned int, std::vector<unsigned int> >; W = std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, boost::python::detail::not_specified, boost::python::detail::not_specified, boost
 ::python::detail::not_specified>]’
  221 |         visitor.visit(*this);
      |         ~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap.h:128:13:   required from ‘void RegisterListConverter(bool) [with T = std::vector<unsigned int>]’
  127 |     python::class_<std::list<T>>(name.c_str())
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  128 |         .def(python::list_indexing_suite<std::list<T>>());
      |         ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/rdkit-202603.4/Code/RDBoost/Wrap/RDBase.cpp:362:51:   required from here
  362 |   RegisterListConverter<std::vector<unsigned int>>();
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/usr/include/boost/python/suite/indexing/indexing_suite.hpp:296:42: error: ‘clear’ is not a member of ‘boost::python::detail::final_list_derived_policies<std::__cxx11::list<std::vector<unsigned int>, std::allocator<std::vector<unsigned int> > >, false>’
  296 |             return DerivedPolicies::clear(container);
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
make[4]: *** [Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make:82: Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o] Error 1
make[4]: Leaving directory '/build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:5344: Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/all] Error 2
make[3]: *** Waiting for unfinished jobs....
[  3%] Linking CXX executable testDataStructs
cd /build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1
/usr/bin/x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202603.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs  ../RDGeneral/librdkitCatch.a ../../lib/libRDKitDataStructs.so.1.2026.03.4 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeneral.so.1.2026.03.4 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_date_time.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_container.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_excep
 tion.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_random.so.1.92.0 /usr/lib/x86_64-linux-gnu/libboost_regex.so.1.92.0 -ldl
make[4]: Leaving directory '/build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu'
[  3%] Built target testDataStructs
make[3]: Leaving directory '/build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/build/reproducible-path/rdkit-202603.4/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 INSTALL="install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:103: override_dh_auto_build] Error 25
make[1]: Leaving directory '/build/reproducible-path/rdkit-202603.4'
make: *** [debian/rules:49: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2

==================== end of build log =============

Thanks,

Anton Gladky

#1149286#16

Date:: 2026-10-21 05:19:19 UTC

From:

To:

We believe that the bug you reported is fixed in the latest version of
rdkit, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1149286@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andrius Merkys <merkys@debian.org> (supplier of updated rdkit package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 21 Oct 2026 00:47:41 -0400
Source: rdkit
Architecture: source
Version: 202609.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Closes: 1149286
Changes:
 rdkit (202609.1-1) unstable; urgency=medium
 .
   * New upstream version 202609.1 (Closes: #1149286)
Checksums-Sha1:
 6e4b2aca90f34a038f2e38eeb6f0f558b67a3316 2551 rdkit_202609.1-1.dsc
 51cd7f7bb9bb05a7e8091a08274b10156c854222 65618536 rdkit_202609.1.orig.tar.xz
 6b136082eb6441b37439cacabaee80b07b962a37 50576 rdkit_202609.1-1.debian.tar.xz
 1601ffa4101532412e63e4b173f15671c6d0e710 17402 rdkit_202609.1-1_source.buildinfo
Checksums-Sha256:
 2e131e4b36c5b436e2e50fcd341208fc1dfa035dfb8542356758d1b355247438 2551 rdkit_202609.1-1.dsc
 cb3e9aa74b5a6ba679f9c2d794f2c3b78ca185078dc3ef184f2d16039571b802 65618536 rdkit_202609.1.orig.tar.xz
 610cddd665e830de765a033c22163fb7e4402b6bd3e2bafb74f371b891d5472e 50576 rdkit_202609.1-1.debian.tar.xz
 964f722ac6349f14ecab98b914206b434c132572bb20d0f22d6ba1f0e12c2058 17402 rdkit_202609.1-1_source.buildinfo
Files:
 2cafbf2d0e7460205e9ca34fbf3de40b 2551 science optional rdkit_202609.1-1.dsc
 783ee07b1b0bc8efbb4cda4c2d7bd008 65618536 science optional rdkit_202609.1.orig.tar.xz
 ab046abe7200801a3b01b99274c683a5 50576 science optional rdkit_202609.1-1.debian.tar.xz
 31aa294cfe374564df9d8aefe0272ea9 17402 science optional rdkit_202609.1-1_source.buildinfo
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#1149286 rdkit: FTBFS with boost 1.92 #1149286

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