build issue

[Mike31415]

I have installed all dependencies via conda (as suggested). But I am getting errors in the build all around this line in the file cast.h
This looks like the first one, can you help?

In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h: In function 'std::string pybind11::detail::error_string()':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:446:36: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
446 | " " + handle(frame->f_code->co_filename).caststd::string() +
| ^~

[AlanKerstjens]

Hi @Mike31415,
In order to investigate this further I need to reproduce the issue. Could you provide me with some additional information?

• What operating system are you using?
• What compiler and version are you using?
• What's your version of Python?
• What's your version of pybind11?
• Can you post the whole compilation output?

[Mike31415]

The operating system is centos 7
compiler:
g++ (conda-forge gcc 11.3.0-19) 11.3.0
Copyright (C) 2021 Free Software Foundation, Inc.
python:
Python 3.11.0
pybind11: should be using the one that came with your distro? This is the header
pybind11/pybind11.h: Main header file of the C++11 python
binding generator library

Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>

Cmake output:
-- The CXX compiler identification is GNU 11.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /bfhome/mlipkin/anaconda3/envs/LEADD/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Boost: /bfhome/mlipkin/anaconda3/envs/LEADD/lib/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0") found components: serialization program_options
-- Found HDF5: /bfhome/mlipkin/anaconda3/envs/LEADD/lib/libhdf5_cpp.so;/bfhome/mlipkin/anaconda3/envs/LEADD/lib/libhdf5.so;/bfhome/mlipkin/anaconda3/envs/LEADD/lib/libcrypto.so;/bfhome/mlipkin/anaconda3/envs/LEADD/lib/libcurl.so;/bfhome/mlipkin/anaconda3/envs/LEADD/x86_64-conda-linux-gnu/sysroot/usr/lib/librt.so;/bfhome/mlipkin/anaconda3/envs/LEADD/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so;/bfhome/mlipkin/anaconda3/envs/LEADD/lib/libsz.so;/bfhome/mlipkin/anaconda3/envs/LEADD/lib/libz.so;/bfhome/mlipkin/anaconda3/envs/LEADD/x86_64-conda-linux-gnu/sysroot/usr/lib/libdl.so;/bfhome/mlipkin/anaconda3/envs/LEADD/x86_64-conda-linux-gnu/sysroot/usr/lib/libm.so (found version "1.14.0") found components: CXX
-- Found SQLite3: /bfhome/mlipkin/anaconda3/envs/LEADD/include (found version "3.40.0")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5") found components: CXX
-- Extra compilation flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /bfhome/mlipkin/anaconda3/envs/LEADD/include
-- pybind11 v2.6.2
-- Found PythonInterp: /bfhome/mlipkin/anaconda3/envs/LEADD/bin/python (found version "3.11")
-- Found PythonLibs: /bfhome/mlipkin/anaconda3/envs/LEADD/lib/libpython3.11.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Found Python: /bfhome/mlipkin/anaconda3/envs/LEADD/bin/python3.11 (found version "3.11.0") found components: Interpreter Development Development.Module Development.Embed
-- Configuring done
-- Generating done
-- Build files have been written to: /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/build

compilation output:
[ 2%] Building CXX object CMakeFiles/Graph.dir/source/Graph.cpp.o
[ 4%] Linking CXX shared library libGraph.so
[ 4%] Built target Graph
[ 6%] Building CXX object CMakeFiles/Connection.dir/source/Connection.cpp.o
[ 8%] Linking CXX shared library libConnection.so
[ 8%] Built target Connection
[ 10%] Building CXX object CMakeFiles/Pseudofragment.dir/source/Pseudofragment.cpp.o
[ 12%] Linking CXX shared library libPseudofragment.so
[ 12%] Built target Pseudofragment
[ 14%] Building CXX object CMakeFiles/PseudofragmentDB.dir/source/PseudofragmentDB.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/config/header_deprecated.hpp:18,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:22,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/PseudofragmentDB.hpp:7,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/PseudofragmentDB.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 16%] Linking CXX shared library libPseudofragmentDB.so
[ 16%] Built target PseudofragmentDB
[ 18%] Building CXX object CMakeFiles/FragmentationSettings.dir/source/FragmentationSettings.cpp.o
[ 20%] Linking CXX shared library libFragmentationSettings.so
[ 20%] Built target FragmentationSettings
[ 22%] Building CXX object CMakeFiles/Fragmentation.dir/source/Fragmentation.cpp.o
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Fragmentation.cpp: In function 'std::vector GetAtomTypes(const RDKit::ROMol&, const FragmentationSettings&)':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Fragmentation.cpp:143:1: warning: control reaches end of non-void function [-Wreturn-type]
143 | };
| ^
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Fragmentation.cpp: In function 'std::vector<boost::shared_ptrRDKit::ROMol > FragmentSystematically(RDKit::ROMol&, const FragmentationSettings&, bool)':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Fragmentation.cpp:331:1: warning: control reaches end of non-void function [-Wreturn-type]
331 | };
| ^
[ 25%] Linking CXX shared library libFragmentation.so
[ 25%] Built target Fragmentation
[ 27%] Building CXX object CMakeFiles/ReconstructionSettings.dir/source/ReconstructionSettings.cpp.o
[ 29%] Linking CXX shared library libReconstructionSettings.so
[ 29%] Built target ReconstructionSettings
[ 31%] Building CXX object CMakeFiles/ConnectionCompatibilities.dir/source/ConnectionCompatibilities.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/config/header_deprecated.hpp:18,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:22,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/PseudofragmentDB.hpp:7,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConnectionCompatibilities.hpp:8,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConnectionCompatibilities.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 33%] Linking CXX shared library libConnectionCompatibilities.so
[ 33%] Built target ConnectionCompatibilities
[ 35%] Building CXX object CMakeFiles/ConnectionQueryResults.dir/source/ConnectionQueryResults.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/config/header_deprecated.hpp:18,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:22,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/PseudofragmentDB.hpp:7,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConnectionCompatibilities.hpp:8,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConnectionQueryResults.hpp:9,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConnectionQueryResults.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 37%] Linking CXX shared library libConnectionQueryResults.so
[ 37%] Built target ConnectionQueryResults
[ 39%] Building CXX object CMakeFiles/Reconstruction.dir/source/Reconstruction.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr.hpp:19,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/Numerics/Vector.h:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/Geometry/point.h:24,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h:30,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h:21,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Reconstruction.hpp:10,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Reconstruction.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 41%] Linking CXX shared library libReconstruction.so
[ 41%] Built target Reconstruction
[ 43%] Building CXX object CMakeFiles/SAScore.dir/source/SAScore.cpp.o
[ 45%] Linking CXX shared library libSAScore.so
[ 45%] Built target SAScore
[ 47%] Building CXX object CMakeFiles/LEADD.dir/source/LEADD.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/property_map/vector_property_map.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/property_map/property_map.hpp:606,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/graph/adjacency_list.hpp:27,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/ROMol.h:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/RWMol.h:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/SmilesParse/SmilesParse.h:14,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/LEADD.hpp:5,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/LEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 50%] Linking CXX shared library libLEADD.so
[ 50%] Built target LEADD
[ 52%] Building CXX object CMakeFiles/DecodeConnection.dir/source/DecodeConnection.cpp.o
[ 54%] Linking CXX executable DecodeConnection
[ 54%] Built target DecodeConnection
[ 56%] Building CXX object CMakeFiles/EncodeConnection.dir/source/EncodeConnection.cpp.o
[ 58%] Linking CXX executable EncodeConnection
[ 58%] Built target EncodeConnection
[ 60%] Building CXX object CMakeFiles/Fragment.dir/source/Fragment.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/Fragment.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 62%] Linking CXX executable Fragment
[ 62%] Built target Fragment
[ 64%] Building CXX object CMakeFiles/MakeFragmentSimilarityMatrix.dir/source/MakeFragmentSimilarityMatrix.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp:2:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp: In function 'int main(int, const char**)':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp:73:36: warning: narrowing conversion of 'n_pseudofragments' from 'sqlite3_int64' {aka 'long long int'} to 'hsize_t' {aka 'long unsigned int'} [-Wnarrowing]
73 | hsize_t memory_dimensions[1] = { n_pseudofragments };
| ^~~~~~~~~~~~~~~~~
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp:74:34: warning: narrowing conversion of 'n_pseudofragments' from 'sqlite3_int64' {aka 'long long int'} to 'hsize_t' {aka 'long unsigned int'} [-Wnarrowing]
74 | hsize_t file_dimensions[2] = { n_pseudofragments, n_pseudofragments };
| ^~~~~~~~~~~~~~~~~
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp:74:53: warning: narrowing conversion of 'n_pseudofragments' from 'sqlite3_int64' {aka 'long long int'} to 'hsize_t' {aka 'long unsigned int'} [-Wnarrowing]
74 | hsize_t file_dimensions[2] = { n_pseudofragments, n_pseudofragments };
| ^~~~~~~~~~~~~~~~~
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFragmentSimilarityMatrix.cpp:83:41: warning: narrowing conversion of 'n_pseudofragments' from 'sqlite3_int64' {aka 'long long int'} to 'hsize_t' {aka 'long unsigned int'} [-Wnarrowing]
83 | hsize_t hyperslab_dimensions[2] = {1, n_pseudofragments};
| ^~~~~~~~~~~~~~~~~
[ 66%] Linking CXX executable MakeFragmentSimilarityMatrix
[ 66%] Built target MakeFragmentSimilarityMatrix
[ 68%] Building CXX object CMakeFiles/PrecalculateConnectionQueryResults.dir/source/PrecalculateConnectionQueryResults.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/PrecalculateConnectionQueryResults.cpp:2:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 70%] Linking CXX executable PrecalculateConnectionQueryResults
[ 70%] Built target PrecalculateConnectionQueryResults
[ 72%] Building CXX object CMakeFiles/InspectConnectionQueryResults.dir/source/InspectConnectionQueryResults.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/InspectConnectionQueryResults.cpp:4:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 75%] Linking CXX executable InspectConnectionQueryResults
[ 75%] Built target InspectConnectionQueryResults
[ 77%] Building CXX object CMakeFiles/BinAtomPairFrequencies.dir/source/BinAtomPairFrequencies.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/BinAtomPairFrequencies.cpp:4:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 79%] Linking CXX executable BinAtomPairFrequencies
[ 79%] Built target BinAtomPairFrequencies
[ 81%] Building CXX object CMakeFiles/MakeFeatureLibrary.dir/source/MakeFeatureLibrary.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/config/header_deprecated.hpp:18,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:22,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/MakeFeatureLibrary.cpp:3:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 83%] Linking CXX executable MakeFeatureLibrary
[ 83%] Built target MakeFeatureLibrary
[ 85%] Building CXX object CMakeFiles/CalculateSAScore.dir/source/CalculateSAScore.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/config/header_deprecated.hpp:18,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:22,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/CalculateSAScore.cpp:3:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 87%] Linking CXX executable CalculateSAScore
[ 87%] Built target CalculateSAScore
[ 89%] Building CXX object CMakeFiles/ConvertToReconstruction.dir/source/ConvertToReconstruction.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/ConvertToReconstruction.cpp:4:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 91%] Linking CXX executable ConvertToReconstruction
[ 91%] Built target ConvertToReconstruction
[ 93%] Building CXX object CMakeFiles/StandaloneLEADD.dir/source/StandaloneLEADD.cpp.o
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/shared_ptr.hpp:17,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options/options_description.hpp:16,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/program_options.hpp:15,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/StandaloneLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 95%] Linking CXX executable StandaloneLEADD
[ 95%] Built target StandaloneLEADD
[ 97%] Building CXX object CMakeFiles/pyLEADD.dir/source/pyLEADD.cpp.o
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h: In function 'std::string pybind11::detail::error_string()':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:446:36: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
446 | " " + handle(frame->f_code->co_filename).caststd::string() +
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:446:75: error: expected primary-expression before '>' token
446 | " " + handle(frame->f_code->co_filename).caststd::string() +
| ^
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:446:77: error: expected primary-expression before ')' token
446 | " " + handle(frame->f_code->co_filename).caststd::string() +
| ^
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:448:29: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
448 | handle(frame->f_code->co_name).caststd::string() + "\n";
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:448:64: error: expected primary-expression before '>' token
448 | handle(frame->f_code->co_name).caststd::string() + "\n";
| ^
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:448:66: error: expected primary-expression before ')' token
448 | handle(frame->f_code->co_name).caststd::string() + "\n";
| ^
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:449:26: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
449 | frame = frame->f_back;
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h: In function 'pybind11::function pybind11::detail::get_type_override(const void*, const pybind11::detail::type_info*, const char*)':
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2291:49: error: 'PyThreadState' {aka 'struct _ts'} has no member named 'frame'; did you mean 'cframe'?
2291 | PyFrameObject *frame = PyThreadState_Get()->frame;
| ^~~~~
| cframe
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2292:41: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
2292 | if (frame && (std::string) str(frame->f_code->co_name) == name &&
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2293:14: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
2293 | frame->f_code->co_argcount > 0) {
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2296:18: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:35,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2296:30: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~~~~~~~~~~~~~~~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:38,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:2296:30: error: invalid use of incomplete type 'PyFrameObject' {aka 'struct _frame'}
2296 | frame->f_locals, PyTuple_GET_ITEM(frame->f_code->co_varnames, 0));
| ^~~~~~~~~~~~~~~~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/Python.h:42,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/detail/common.h:124,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pytypes.h:12,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/cast.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/attr.h:13,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/pybind11/include/pybind11/pybind11.h:45,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:1:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'PyFrameObject' {aka 'struct _frame'}
22 | typedef struct _frame PyFrameObject;
| ^~~~~~
In file included from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/smart_ptr/shared_ptr.hpp:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/property_map/vector_property_map.hpp:14,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/property_map/property_map.hpp:606,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/graph/adjacency_list.hpp:27,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/ROMol.h:29,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/RWMol.h:22,
from /bfhome/mlipkin/anaconda3/envs/LEADD/include/rdkit/GraphMol/SmilesParse/SmilesParse.h:14,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/LEADD.hpp:5,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/LEADD.cpp:1,
from /bfprojects/Development/Scripts/mlipkin/LEADD/LEADD/source/pyLEADD.cpp:3:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp: At global scope:
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/bfhome/mlipkin/anaconda3/envs/LEADD/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/pyLEADD.dir/build.make:76: CMakeFiles/pyLEADD.dir/source/pyLEADD.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:820: CMakeFiles/pyLEADD.dir/all] Error 2
make: *** [Makefile:136: all] Error 2

Thanks for your help

[AlanKerstjens]

@Mike31415,
Apparently the pybind11 version the corresponding submodule was pointing to (2.6.2) was not compatible with Python 3.11. I've updated the version to 2.10.3. You can do the same by either cloning LEADD again or just updating pybind11:

cd ${LEADD}/pybind11
git pull origin stable

Then you need to rerun the cmake and make commands:

cd ${LEADD}/build
cmake -DRDKit_INCLUDE_DIRS=${CONDA_PREFIX}/include/rdkit -DRDKit_LIBRARY_DIRS=${CONDA_PREFIX}/lib ..
make install clean

With the new pybind11 version the code compiled on a fresh install of Centos7. Please let me know if this isn't the case for you.