Hi, I tried using the cmake integration on python 3.10, M1 MacOS 12.5.1, but I can't reproduce the example repo jclay/cppyy-knearestneighbors-example; I get a missing symbols error.

I understand this is not a configuration easy to support, but I would be thankful for some steps or resources to get started debugging it.

Steps to reproduce

System: M1, MacOS 12.5.1.

Clone cppyy-knearestneighbors-example.

Create a conda environment: mamba create -n cppyy cppyy python cmake ninja python-clang

Activate it: conda activate cppyy

Save/export with: mamba list > mamba_list.txt mamba env export -n cppyy > env.yml.txt

(instead of creating as above, exactly reproduce the one I had by running mamba create -n cppyy -f env.yml).

By trial and error I figured out that python-clang was required otherwise FindLibClang would fail in the cmake config step.

Dump environment variables: env > env.txt.

Home directory and conda base environment path replaced by $HOME and $CONDA_BASE_DIR, respectively.

Perform successfully the check in README.md:

$ ( python -c "from clang.cindex import Config; print(Config().lib)" )
<CDLL 'libclang.dylib', handle 20a59e2e0 at 0x1056a8700>

Attempt to build it: (rm -rdf build && mkdir build && cd build && cmake -G Ninja .. && cmake --build . ) > build_log.txt 2>&1

build_log.txt is attached. Excerpt:

[...]
Undefined symbols for architecture arm64:
  "CppyyLegacy::kAssertMsg", referenced from:
      CppyyLegacy::Detail::TCollectionProxyInfo::Iterators<std::__1::vector<Point, std::__1::allocator<Point> >, false>::next(void*, void const*) in knn_example.cpp.o
[...]

mamba_list.txt env.txt env.yml.txt build_log.txt

Aug 25 '22 09:08 LunarLanding

That symbol is lives in libCoreLegacy.so, which should certainly not be linked with, so I'm not understanding that step.

Could you give the PyPI M1 builds a try instead (python -m pip install cppyy), just to be able to figure out whether the issue is with the conda builds or the example?

Aug 25 '22 17:08 wlav

Thanks, did just that, yet I keep gettting the same error. I have updated this post with a more verbose build log, including the compilation commands and linker invocations. I'm not familiar with C++ and compilation, so I'm likely missing something basic.

Environment

OSX 12.5.1 Xcode installed.

mamba create -n cppyy python python-clang libclang compilers  cmake ninja

$ mamba list
# packages in environment at $CONDA_DIR:
#
# Name                    Version                   Build  Channel
boost-cpp                 1.74.0               h1cb353e_8    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
c-compiler                1.5.0                h5008568_0    conda-forge
ca-certificates           2022.6.15            h4653dfc_0    conda-forge
cctools                   973.0.1             hcbb26d4_10    conda-forge
cctools_osx-arm64         973.0.1             he930820_10    conda-forge
cgal-cpp                  5.5                  h97fd3db_0    conda-forge
clang                     14.0.4               hce30654_0    conda-forge
clang-14                  14.0.4          default_h81a5282_0    conda-forge
clang_osx-arm64           14.0.4               hc634a12_2    conda-forge
clangxx                   14.0.4          default_hb7ecf47_0    conda-forge
clangxx_osx-arm64         14.0.4               hb7a33d8_2    conda-forge
cmake                     3.24.1               h967666c_0    conda-forge
compiler-rt               14.0.4               h4418234_0    conda-forge
compiler-rt_osx-arm64     14.0.4               hb07f8d1_0    conda-forge
compilers                 1.5.0                hce30654_0    conda-forge
cppyy                     2.4.0                    pypi_0    pypi
cppyy-backend             1.14.9                   pypi_0    pypi
cppyy-cling               6.27.0                   pypi_0    pypi
cpycppyy                  1.12.11                  pypi_0    pypi
cxx-compiler              1.5.0                hffc8910_0    conda-forge
eigen                     3.4.0                hc021e02_0    conda-forge
expat                     2.4.8                h6b3803e_0    conda-forge
fortran-compiler          1.5.0                h2ccabda_0    conda-forge
gfortran                  11.3.0               h1ca8e4b_0    conda-forge
gfortran_impl_osx-arm64   11.3.0              h95416cd_25    conda-forge
gfortran_osx-arm64        11.3.0               h57527a5_0    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
icu                       70.1                 h6b3803e_0    conda-forge
isl                       0.22.1               hb904e53_2    conda-forge
krb5                      1.19.3               he492e65_0    conda-forge
ld64                      609                 h619f069_10    conda-forge
ld64_osx-arm64            609                 h132958c_10    conda-forge
libclang                  14.0.4          default_h81a5282_0    conda-forge
libclang-cpp14            14.0.4          default_h81a5282_0    conda-forge
libclang13                14.0.4          default_he70ec0d_0    conda-forge
libcurl                   7.83.1               h7965298_0    conda-forge
libcxx                    14.0.6               h04bba0f_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           11_3_0_hd922786_25    conda-forge
libgfortran-devel_osx-arm64 11.3.0              hfe9555d_25    conda-forge
libgfortran5              11.3.0              hdaf2cc0_25    conda-forge
libiconv                  1.16                 h642e427_0    conda-forge
libllvm14                 14.0.4               h37c5ba8_0    conda-forge
libnghttp2                1.47.0               h519802c_1    conda-forge
libsqlite                 3.39.2               h2c9beb0_1    conda-forge
libssh2                   1.10.0               h7a5bd25_3    conda-forge
libuv                     1.44.2               he4db4b2_0    conda-forge
libzlib                   1.2.12               ha287fd2_2    conda-forge
llvm-openmp               14.0.4               hd125106_0    conda-forge
llvm-tools                14.0.4               h37c5ba8_0    conda-forge
mpc                       1.2.1                h309154c_0    conda-forge
mpfr                      4.1.0                h6d7a090_1    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
ninja                     1.11.0               hf86a087_0    conda-forge
openssl                   3.0.5                h7aea29f_1    conda-forge
pip                       22.2.2             pyhd8ed1ab_0    conda-forge
python                    3.10.6          hae75cb6_0_cpython    conda-forge
python-clang              14.0.4          default_hccd1708_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
readline                  8.1.2                h46ed386_0    conda-forge
rhash                     1.4.3                he4db4b2_0    conda-forge
setuptools                65.3.0          py310hbe9552e_0    conda-forge
sigtool                   0.1.3                h44b9a77_0    conda-forge
tapi                      1100.0.11            he4954df_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tzdata                    2022c                h191b570_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zlib                      1.2.12               ha287fd2_2    conda-forge
zstd                      1.5.2                h8128057_4    conda-forge

Some software versions

`cppyy` components

Each of these cppyy components merits some entry. For now we just have this listing:

$ mamba list | grep pypi
cppyy                     2.4.0                    pypi_0    pypi
cppyy-backend             1.14.9                   pypi_0    pypi
cppyy-cling               6.27.0                   pypi_0    pypi
cpycppyy                  1.12.11                  pypi_0    pypi

Compiler

$ which $CXX
$CONDA_DIR/bin/arm64-apple-darwin20.0.0-clang++
$ ls -lha $(which $CXX)
lrwxr-xr-x 1 ma staff 8 Aug 26 05:05 $CONDA_DIR/bin/arm64-apple-darwin20.0.0-clang++ -> clang-14
$ clang-14 --version
clang version 14.0.4
Target: arm64-apple-darwin21.6.0
Thread model: posix
InstalledDir: $CONDA_DIR/bin

$CXX points to arm64-apple-darwin20.0.0-clang++ which points to clang-14, and clang14 --version shows arm64-apple-darwin21.6.0. Is this a problem? According to Wikipedia, darwin21.6 corresponds to macOS 12.5. Assuming for now that darwin21.6 is compatible with darwin20.0.

Build command

( \
    rm -rdf build && \
    mkdir build && \
    cd build && \
    ( cmake -DCMAKE_VERBOSE_MAKEFILE=ON --trace-source=CMakeLists.txt -G Ninja .. && cmake --build . ) > log.txt 2>&1 \
)

It's easier to read by postprocessing to replace project directory by $PROJECT_DIR, conda prefix by $CONDA_PREFIX, home folder by $HOME.

Just the log:

(PROJECT_DIR=$(pwd) ; SDK_ROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"; sed -i '' "s@${CONDA_PREFIX}@\$CONDA_PREFIX@g; s@${PROJECT_DIR}@\$PROJECT_DIR@g; s@${HOME}@\$HOME@g; s@${SDK_ROOT}@\$SDK_ROOT@g" build/log.txt)

All files:

(PROJECT_DIR=$(pwd) ; cd build && LC_ALL=C find . -type f -exec sed -i '' "s@${CONDA_PREFIX}@\$CONDA_PREFIX@g; s@${PROJECT_DIR}@\$PROJECT_DIR@g; s@${HOME}@\$HOME@g" {} \; )

Current cmake script

Original script + policies + -v flag for the compiler.

cmake version 3.24.1.

# these three policies were set
set(CMAKE_POLICY_DEFAULT_CMP0102 NEW)
set(CMAKE_POLICY_DEFAULT_CMP0128 NEW)
set(CMAKE_POLICY_DEFAULT_CMP0126 NEW)
cmake_minimum_required(VERSION 3.10)

# this flag enables verbose output from the compiler
set(CMAKE_CXX_FLAGS  "-v")


project(cppyy_example LANGUAGES CXX)


execute_process(COMMAND cling-config --cmake OUTPUT_VARIABLE CPPYY_MODULE_PATH OUTPUT_STRIP_TRAILING_WHITESPACE)
# Make sure this is set to something like:
# ~/.local/lib/python2.7/site-packages/cpyy_backend/cmake 

message("CPYY_MODULE_PATH: " ${CPPYY_MODULE_PATH})
list(INSERT CMAKE_MODULE_PATH 0 ${CPPYY_MODULE_PATH})

find_package(Cppyy)

set(SOURCES nearest_neighbors.cpp)
set(HEADERS nearest_neighbors.h)

# It seems like this library has to be shared...
add_library(knn_lib SHARED ${SOURCES})
# Note this is a necessary compile flag for cppyy bindings to work.
set_target_properties(knn_lib PROPERTIES POSITION_INDEPENDENT_CODE ON)
target_include_directories(knn_lib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

cppyy_add_bindings(
   "knn_example" "0.0.1" "Joel" "[email protected]"
   LANGUAGE_STANDARD "14"
   GENERATE_OPTIONS "-D__PIC__;-Wno-macro-redefined"
   INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
   LINK_LIBRARIES knn_lib
   H_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
   H_FILES ${HEADERS})

add_executable(knn main.cpp)
target_link_libraries(knn PUBLIC knn_lib)

Going through the compilation log

How to generate:

( \
    ( \
        export VERBOSE=1 ; \
        rm -rdf build && \
        mkdir build && \
        cd build && \
        ( cmake -DCMAKE_VERBOSE_MAKEFILE=ON --trace-source=CMakeLists.txt -G Ninja .. && cmake --build . ) > log.txt 2>&1 \
    )
    ( \
        PROJECT_DIR=$(pwd) ; \
        SDK_ROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"; \
        sed -i '' "s@${CONDA_PREFIX}@\$CONDA_PREFIX@g; s@${PROJECT_DIR}@\$PROJECT_DIR@g; s@${HOME}@\$HOME@g; s@${SDK_ROOT}@\$SDK_ROOT@g" build/log.txt \
    ) \
)

Below, the resulting build/log.txt is included. It consists of the following sections:

cmake configuration
1/9 Compile main.cpp
2/9 Compile nearest_neighbors.cpp
3/9 ? nearest_neighbors.cpp.o
4/9 ? libknn_lib.dylib
5/9 cppyy-generator nearest_neighbors.h
6/9 rootcling ?
7/9 Compile knn_example.cpp
8/9 ? libknn_lib.dylib

The last step fails.

Re-run cmake no build system arguments
$PROJECT_DIR/CMakeLists.txt(1):  set(CMAKE_POLICY_DEFAULT_CMP0102 NEW )
$PROJECT_DIR/CMakeLists.txt(2):  set(CMAKE_POLICY_DEFAULT_CMP0128 NEW )
$PROJECT_DIR/CMakeLists.txt(3):  set(CMAKE_POLICY_DEFAULT_CMP0126 NEW )
$PROJECT_DIR/CMakeLists.txt(4):  cmake_minimum_required(VERSION 3.10 )
$PROJECT_DIR/CMakeLists.txt(11):  set(CMAKE_CXX_FLAGS -v )
$PROJECT_DIR/CMakeLists.txt(14):  project(cppyy_example LANGUAGES CXX )
-- The CXX compiler identification is Clang 14.0.4
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
$PROJECT_DIR/CMakeLists.txt(17):  execute_process(COMMAND cling-config --cmake OUTPUT_VARIABLE CPPYY_MODULE_PATH OUTPUT_STRIP_TRAILING_WHITESPACE )
$PROJECT_DIR/CMakeLists.txt(24):  message(CPYY_MODULE_PATH:  ${CPPYY_MODULE_PATH} )
CPYY_MODULE_PATH: $CONDA_PREFIX/lib/python3.10/site-packages/cppyy_backend/cmake
$PROJECT_DIR/CMakeLists.txt(25):  list(INSERT CMAKE_MODULE_PATH 0 ${CPPYY_MODULE_PATH} )
$PROJECT_DIR/CMakeLists.txt(27):  find_package(Cppyy )
-- Found Cppyy: $CONDA_PREFIX/bin/rootcling (found version "6.20.04") 
$PROJECT_DIR/CMakeLists.txt(29):  set(SOURCES nearest_neighbors.cpp )
$PROJECT_DIR/CMakeLists.txt(30):  set(HEADERS nearest_neighbors.h )
$PROJECT_DIR/CMakeLists.txt(33):  add_library(knn_lib SHARED ${SOURCES} )
$PROJECT_DIR/CMakeLists.txt(35):  set_target_properties(knn_lib PROPERTIES POSITION_INDEPENDENT_CODE ON )
$PROJECT_DIR/CMakeLists.txt(36):  target_include_directories(knn_lib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} )
$PROJECT_DIR/CMakeLists.txt(38):  cppyy_add_bindings(knn_example 0.0.1 Joel [email protected] LANGUAGE_STANDARD 14 GENERATE_OPTIONS -D__PIC__;-Wno-macro-redefined INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR} LINK_LIBRARIES knn_lib H_DIRS ${CMAKE_CURRENT_SOURCE_DIR} H_FILES ${HEADERS} )
-- Found LibClang: $CONDA_PREFIX/lib/libclang.dylib (found version "$CONDA_PREFIX/lib/libclang.dylib") 
-- $CONDA_PREFIX/lib/python3.10/site-packages/cppyy_backend/pkg_templates/initializor.py
$PROJECT_DIR/CMakeLists.txt(48):  add_executable(knn main.cpp )
$PROJECT_DIR/CMakeLists.txt(49):  target_link_libraries(knn PUBLIC knn_lib )
-- Configuring done
-- Generating done
-- Build files have been written to: $PROJECT_DIR/build
[0/2] $CONDA_PREFIX/bin/cmake -P $PROJECT_DIR/build/CMakeFiles/VerifyGlobs.cmake
[1/9] $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -Dknn_lib_EXPORTS -I$PROJECT_DIR -v -arch arm64 -isysroot $SDK_ROOT -fPIC -MD -MT CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o -MF CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o.d -o CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o -c $PROJECT_DIR/nearest_neighbors.cpp
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 (in-process)
 "$CONDA_PREFIX/bin/clang-14" -cc1 -triple arm64-apple-macosx12.0.0 -Wundef-prefix=TARGET_OS_ -Werror=undef-prefix -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all --mrelax-relocations -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name nearest_neighbors.cpp -mrelocation-model pic -pic-level 2 -mframe-pointer=non-leaf -ffp-contract=on -fno-rounding-math -funwind-tables=2 -target-sdk-version=12.3 -fcompatibility-qualified-id-block-type-checking -fvisibility-inlines-hidden-static-local-var -target-cpu apple-m1 -target-feature +v8.5a -target-feature +fp-armv8 -target-feature +neon -target-feature +crc -target-feature +crypto -target-feature +dotprod -target-feature +fp16fml -target-feature +ras -target-feature +lse -target-feature +rdm -target-feature +rcpc -target-feature +zcm -target-feature +zcz -target-feature +fullfp16 -target-feature +sha2 -target-feature +aes -target-abi darwinpcs -fallow-half-arguments-and-returns -mllvm -treat-scalable-fixed-error-as-warning -debugger-tuning=lldb -target-linker-version 609 -v -fcoverage-compilation-dir=$PROJECT_DIR/build -resource-dir $CONDA_PREFIX/lib/clang/14.0.4 -dependency-file CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o.d -MT CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o -sys-header-deps -isysroot $SDK_ROOT -D knn_lib_EXPORTS -I $PROJECT_DIR -stdlib=libc++ -internal-isystem $CONDA_PREFIX/bin/../include/c++/v1 -internal-isystem $SDK_ROOT/usr/local/include -internal-isystem $CONDA_PREFIX/lib/clang/14.0.4/include -internal-externc-isystem $SDK_ROOT/usr/include -fdeprecated-macro -fdebug-compilation-dir=$PROJECT_DIR/build -ferror-limit 19 -stack-protector 1 -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fcxx-exceptions -fexceptions -fmax-type-align=16 -D__GCC_HAVE_DWARF2_CFI_ASM=1 -o CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o -x c++ $PROJECT_DIR/nearest_neighbors.cpp
clang -cc1 version 14.0.4 based upon LLVM 14.0.4 default target arm64-apple-darwin21.6.0
ignoring nonexistent directory "$SDK_ROOT/usr/local/include"
ignoring nonexistent directory "$SDK_ROOT/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 $PROJECT_DIR
 $CONDA_PREFIX/bin/../include/c++/v1
 $CONDA_PREFIX/lib/clang/14.0.4/include
 $SDK_ROOT/usr/include
 $SDK_ROOT/System/Library/Frameworks (framework directory)
End of search list.
[2/9] $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++  -I$PROJECT_DIR -v -arch arm64 -isysroot $SDK_ROOT -MD -MT CMakeFiles/knn.dir/main.cpp.o -MF CMakeFiles/knn.dir/main.cpp.o.d -o CMakeFiles/knn.dir/main.cpp.o -c $PROJECT_DIR/main.cpp
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 (in-process)
 "$CONDA_PREFIX/bin/clang-14" -cc1 -triple arm64-apple-macosx12.0.0 -Wundef-prefix=TARGET_OS_ -Werror=undef-prefix -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all --mrelax-relocations -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name main.cpp -mrelocation-model pic -pic-level 2 -mframe-pointer=non-leaf -ffp-contract=on -fno-rounding-math -funwind-tables=2 -target-sdk-version=12.3 -fcompatibility-qualified-id-block-type-checking -fvisibility-inlines-hidden-static-local-var -target-cpu apple-m1 -target-feature +v8.5a -target-feature +fp-armv8 -target-feature +neon -target-feature +crc -target-feature +crypto -target-feature +dotprod -target-feature +fp16fml -target-feature +ras -target-feature +lse -target-feature +rdm -target-feature +rcpc -target-feature +zcm -target-feature +zcz -target-feature +fullfp16 -target-feature +sha2 -target-feature +aes -target-abi darwinpcs -fallow-half-arguments-and-returns -mllvm -treat-scalable-fixed-error-as-warning -debugger-tuning=lldb -target-linker-version 609 -v -fcoverage-compilation-dir=$PROJECT_DIR/build -resource-dir $CONDA_PREFIX/lib/clang/14.0.4 -dependency-file CMakeFiles/knn.dir/main.cpp.o.d -MT CMakeFiles/knn.dir/main.cpp.o -sys-header-deps -isysroot $SDK_ROOT -I $PROJECT_DIR -stdlib=libc++ -internal-isystem $CONDA_PREFIX/bin/../include/c++/v1 -internal-isystem $SDK_ROOT/usr/local/include -internal-isystem $CONDA_PREFIX/lib/clang/14.0.4/include -internal-externc-isystem $SDK_ROOT/usr/include -fdeprecated-macro -fdebug-compilation-dir=$PROJECT_DIR/build -ferror-limit 19 -stack-protector 1 -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fcxx-exceptions -fexceptions -fmax-type-align=16 -D__GCC_HAVE_DWARF2_CFI_ASM=1 -o CMakeFiles/knn.dir/main.cpp.o -x c++ $PROJECT_DIR/main.cpp
clang -cc1 version 14.0.4 based upon LLVM 14.0.4 default target arm64-apple-darwin21.6.0
ignoring nonexistent directory "$SDK_ROOT/usr/local/include"
ignoring nonexistent directory "$SDK_ROOT/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 $PROJECT_DIR
 $CONDA_PREFIX/bin/../include/c++/v1
 $CONDA_PREFIX/lib/clang/14.0.4/include
 $SDK_ROOT/usr/include
 $SDK_ROOT/System/Library/Frameworks (framework directory)
End of search list.
[3/9] : && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -v -arch arm64 -isysroot $SDK_ROOT -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib -o libknn_lib.dylib -install_name @rpath/libknn_lib.dylib CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o   && :
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 "$CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-ld" -demangle -lto_library $CONDA_PREFIX/lib/libLTO.14.dylib -dynamic -dylib -arch arm64 -dylib_install_name @rpath/libknn_lib.dylib -platform_version macos 12.0.0 12.3 -syslibroot $SDK_ROOT -o libknn_lib.dylib -L$CONDA_PREFIX/lib -headerpad_max_install_names -pie -headerpad_max_install_names -dead_strip_dylibs -rpath $CONDA_PREFIX/lib CMakeFiles/knn_lib.dir/nearest_neighbors.cpp.o -lc++ -lSystem $CONDA_PREFIX/lib/clang/14.0.4/lib/darwin/libclang_rt.osx.a
ld: warning: -pie being ignored. It is only used when linking a main executable
[4/9] : && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -v -arch arm64 -isysroot $SDK_ROOT -Wl,-search_paths_first -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib CMakeFiles/knn.dir/main.cpp.o -o knn  -Wl,-rpath,$PROJECT_DIR/build  libknn_lib.dylib && :
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 "$CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-ld" -demangle -lto_library $CONDA_PREFIX/lib/libLTO.14.dylib -dynamic -arch arm64 -platform_version macos 12.0.0 12.3 -syslibroot $SDK_ROOT -o knn -L$CONDA_PREFIX/lib -search_paths_first -headerpad_max_install_names -pie -headerpad_max_install_names -dead_strip_dylibs -rpath $CONDA_PREFIX/lib CMakeFiles/knn.dir/main.cpp.o -rpath $PROJECT_DIR/build libknn_lib.dylib -lc++ -lSystem $CONDA_PREFIX/lib/clang/14.0.4/lib/darwin/libclang_rt.osx.a
[5/9] cd $PROJECT_DIR/build/knn_example && python $CONDA_PREFIX/bin/cppyy-generator --libclang $CONDA_PREFIX/lib/libclang.dylib --flags "\-D__PIC__;\-Wno-macro-redefined;\-std=c++14;\-I$PROJECT_DIR;\-I$PROJECT_DIR" $PROJECT_DIR/build/knn_example/knn_example.map $PROJECT_DIR/nearest_neighbors.h
[6/9] cd $PROJECT_DIR/build/knn_example && $CONDA_PREFIX/bin/rootcling -f $PROJECT_DIR/build/knn_example.cpp -s knn_example -rmf $PROJECT_DIR/build/knn_example/knn_example.rootmap -rml libknn_exampleCppyy.dylib -cxxflags='-D__PIC__ -Wno-macro-redefined -std=c++14 -I$PROJECT_DIR -I$PROJECT_DIR' $PROJECT_DIR/nearest_neighbors.h $PROJECT_DIR/build/linkdef.h
[7/9] $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -Dknn_exampleCppyy_EXPORTS -I$CONDA_PREFIX/lib/python3.10/site-packages/cppyy_backend/cmake/../include -I$PROJECT_DIR -v -arch arm64 -isysroot $SDK_ROOT -fPIC -MD -MT CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o -MF CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o.d -o CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o -c $PROJECT_DIR/build/knn_example.cpp
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 (in-process)
 "$CONDA_PREFIX/bin/clang-14" -cc1 -triple arm64-apple-macosx12.0.0 -Wundef-prefix=TARGET_OS_ -Werror=undef-prefix -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all --mrelax-relocations -disable-free -clear-ast-before-backend -disable-llvm-verifier -discard-value-names -main-file-name knn_example.cpp -mrelocation-model pic -pic-level 2 -mframe-pointer=non-leaf -ffp-contract=on -fno-rounding-math -funwind-tables=2 -target-sdk-version=12.3 -fcompatibility-qualified-id-block-type-checking -fvisibility-inlines-hidden-static-local-var -target-cpu apple-m1 -target-feature +v8.5a -target-feature +fp-armv8 -target-feature +neon -target-feature +crc -target-feature +crypto -target-feature +dotprod -target-feature +fp16fml -target-feature +ras -target-feature +lse -target-feature +rdm -target-feature +rcpc -target-feature +zcm -target-feature +zcz -target-feature +fullfp16 -target-feature +sha2 -target-feature +aes -target-abi darwinpcs -fallow-half-arguments-and-returns -mllvm -treat-scalable-fixed-error-as-warning -debugger-tuning=lldb -target-linker-version 609 -v -fcoverage-compilation-dir=$PROJECT_DIR/build -resource-dir $CONDA_PREFIX/lib/clang/14.0.4 -dependency-file CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o.d -MT CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o -sys-header-deps -isysroot $SDK_ROOT -D knn_exampleCppyy_EXPORTS -I $CONDA_PREFIX/lib/python3.10/site-packages/cppyy_backend/cmake/../include -I $PROJECT_DIR -stdlib=libc++ -internal-isystem $CONDA_PREFIX/bin/../include/c++/v1 -internal-isystem $SDK_ROOT/usr/local/include -internal-isystem $CONDA_PREFIX/lib/clang/14.0.4/include -internal-externc-isystem $SDK_ROOT/usr/include -fdeprecated-macro -fdebug-compilation-dir=$PROJECT_DIR/build -ferror-limit 19 -stack-protector 1 -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fcxx-exceptions -fexceptions -fmax-type-align=16 -D__GCC_HAVE_DWARF2_CFI_ASM=1 -o CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o -x c++ $PROJECT_DIR/build/knn_example.cpp
clang -cc1 version 14.0.4 based upon LLVM 14.0.4 default target arm64-apple-darwin21.6.0
ignoring nonexistent directory "$SDK_ROOT/usr/local/include"
ignoring nonexistent directory "$SDK_ROOT/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 $CONDA_PREFIX/lib/python3.10/site-packages/cppyy_backend/cmake/../include
 $PROJECT_DIR
 $CONDA_PREFIX/bin/../include/c++/v1
 $CONDA_PREFIX/lib/clang/14.0.4/include
 $SDK_ROOT/usr/include
 $SDK_ROOT/System/Library/Frameworks (framework directory)
End of search list.
[8/9] : && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -v -arch arm64 -isysroot $SDK_ROOT -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib -o knn_example/libknn_exampleCppyy.dylib -install_name @rpath/libknn_exampleCppyy.dylib CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o  -Wl,-rpath,$PROJECT_DIR/build  libknn_lib.dylib && :
FAILED: knn_example/libknn_exampleCppyy.dylib 
: && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -v -arch arm64 -isysroot $SDK_ROOT -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib -o knn_example/libknn_exampleCppyy.dylib -install_name @rpath/libknn_exampleCppyy.dylib CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o  -Wl,-rpath,$PROJECT_DIR/build  libknn_lib.dylib && :
clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 "$CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-ld" -demangle -lto_library $CONDA_PREFIX/lib/libLTO.14.dylib -dynamic -dylib -arch arm64 -dylib_install_name @rpath/libknn_exampleCppyy.dylib -platform_version macos 12.0.0 12.3 -syslibroot $SDK_ROOT -o knn_example/libknn_exampleCppyy.dylib -L$CONDA_PREFIX/lib -headerpad_max_install_names -pie -headerpad_max_install_names -dead_strip_dylibs -rpath $CONDA_PREFIX/lib CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o -rpath $PROJECT_DIR/build libknn_lib.dylib -lc++ -lSystem $CONDA_PREFIX/lib/clang/14.0.4/lib/darwin/libclang_rt.osx.a
ld: warning: -pie being ignored. It is only used when linking a main executable
Undefined symbols for architecture arm64:
  "CppyyLegacy::kAssertMsg", referenced from:
      CppyyLegacy::Detail::TCollectionProxyInfo::Iterators<std::__1::vector<Point, std::__1::allocator<Point> >, false>::next(void*, void const*) in knn_example.cpp.o
  "CppyyLegacy::TDictionary::CreateAttributeMap()", referenced from:
      CppyyLegacy::Point_TClassManip(CppyyLegacy::TClass*) in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_TClassManip(CppyyLegacy::TClass*) in knn_example.cpp.o
  "CppyyLegacy::TVersionCheck::TVersionCheck(int)", referenced from:
      ___cxx_global_var_init in knn_example.cpp.o
  "CppyyLegacy::TDictAttributeMap::AddProperty(char const*, char const*)", referenced from:
      CppyyLegacy::Point_TClassManip(CppyyLegacy::TClass*) in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_TClassManip(CppyyLegacy::TClass*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetNewArray(void* (*)(long, void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDestructor(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDeleteArray(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::AdoptCollectionProxyInfo(CppyyLegacy::Detail::TCollectionProxyInfo*)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetNew(void* (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::GetClass()", referenced from:
      CppyyLegacy::Point_Dictionary() in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_Dictionary() in knn_example.cpp.o
      CppyyLegacy::stdcLcLvectorlEPointgR_Dictionary() in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDelete(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::TGenericClassInfo(char const*, char const*, int, std::type_info const&, CppyyLegacy::Internal::TInitBehavior const*, CppyyLegacy::TClass* (*)(), CppyyLegacy::TVirtualIsAProxy*, int, int)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::TGenericClassInfo(char const*, int, char const*, int, std::type_info const&, CppyyLegacy::Internal::TInitBehavior const*, CppyyLegacy::TClass* (*)(), CppyyLegacy::TVirtualIsAProxy*, int, int)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::~TGenericClassInfo()", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::Fatal(char const*, char const*, ...)", referenced from:
      CppyyLegacy::Detail::TCollectionProxyInfo::Iterators<std::__1::vector<Point, std::__1::allocator<Point> >, false>::next(void*, void const*) in knn_example.cpp.o
  "CppyyLegacy::TROOT::RegisterModule(char const*, char const**, char const**, char const*, char const*, void (*)(), std::__1::vector<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int>, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int> > > const&, char const**, bool)", referenced from:
      (anonymous namespace)::TriggerDictionaryInitialization_knn_example_Impl() in knn_example.cpp.o
  "CppyyLegacy::Internal::DefineBehavior(void*, void*)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TIsAProxy::TIsAProxy(std::type_info const&)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
ld: symbol(s) not found for architecture arm64
clang-14: error: linker command failed with exit code 1 (use -v to see invocation)
ninja: build stopped: subcommand failed.

8/9 ? libknn_lib.dylib

[8/9] : && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $CONDA_PREFIX/include -arch arm64 -isysroot $SDK_ROOT -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib -o knn_example/libknn_exampleCppyy.dylib -install_name @rpath/libknn_exampleCppyy.dylib CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o  -Wl,-rpath,$PROJECT_DIR/build  libknn_lib.dylib && :
FAILED: knn_example/libknn_exampleCppyy.dylib 
: && $CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem $CONDA_PREFIX/include -arch arm64 -isysroot $SDK_ROOT -dynamiclib -Wl,-headerpad_max_install_names -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$CONDA_PREFIX/lib -L$CONDA_PREFIX/lib -o knn_example/libknn_exampleCppyy.dylib -install_name @rpath/libknn_exampleCppyy.dylib CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o  -Wl,-rpath,$PROJECT_DIR/build  libknn_lib.dylib && :
ld: warning: -pie being ignored. It is only used when linking a main executable
Undefined symbols for architecture arm64:
  "CppyyLegacy::kAssertMsg", referenced from:
      CppyyLegacy::Detail::TCollectionProxyInfo::Iterators<std::__1::vector<Point, std::__1::allocator<Point> >, false>::next(void*, void const*) in knn_example.cpp.o
  "CppyyLegacy::TDictionary::CreateAttributeMap()", referenced from:
      CppyyLegacy::Point_Dictionary() in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_Dictionary() in knn_example.cpp.o
  "CppyyLegacy::TVersionCheck::TVersionCheck(int)", referenced from:
      __GLOBAL__sub_I_knn_example.cpp in knn_example.cpp.o
  "CppyyLegacy::TDictAttributeMap::AddProperty(char const*, char const*)", referenced from:
      CppyyLegacy::Point_Dictionary() in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_Dictionary() in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetNewArray(void* (*)(long, void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDestructor(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDeleteArray(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::AdoptCollectionProxyInfo(CppyyLegacy::Detail::TCollectionProxyInfo*)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetNew(void* (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::GetClass()", referenced from:
      CppyyLegacy::Point_Dictionary() in knn_example.cpp.o
      CppyyLegacy::NearestNeighbors_Dictionary() in knn_example.cpp.o
      CppyyLegacy::stdcLcLvectorlEPointgR_Dictionary() in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::SetDelete(void (*)(void*))", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::TGenericClassInfo(char const*, char const*, int, std::type_info const&, CppyyLegacy::Internal::TInitBehavior const*, CppyyLegacy::TClass* (*)(), CppyyLegacy::TVirtualIsAProxy*, int, int)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::TGenericClassInfo(char const*, int, char const*, int, std::type_info const&, CppyyLegacy::Internal::TInitBehavior const*, CppyyLegacy::TClass* (*)(), CppyyLegacy::TVirtualIsAProxy*, int, int)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TGenericClassInfo::~TGenericClassInfo()", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::Fatal(char const*, char const*, ...)", referenced from:
      CppyyLegacy::Detail::TCollectionProxyInfo::Iterators<std::__1::vector<Point, std::__1::allocator<Point> >, false>::next(void*, void const*) in knn_example.cpp.o
  "CppyyLegacy::TROOT::RegisterModule(char const*, char const**, char const**, char const*, char const*, void (*)(), std::__1::vector<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int>, std::__1::allocator<std::__1::pair<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, int> > > const&, char const**, bool)", referenced from:
      (anonymous namespace)::TriggerDictionaryInitialization_knn_example_Impl() in knn_example.cpp.o
  "CppyyLegacy::Internal::DefineBehavior(void*, void*)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
  "CppyyLegacy::TIsAProxy::TIsAProxy(std::type_info const&)", referenced from:
      CppyyLegacy::GenerateInitInstanceLocal(Point const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(NearestNeighbors const*) in knn_example.cpp.o
      CppyyLegacy::GenerateInitInstanceLocal(std::__1::vector<Point, std::__1::allocator<Point> > const*) in knn_example.cpp.o
ld: symbol(s) not found for architecture arm64
clang-14: error: linker command failed with exit code 1 (use -v to see invocation)
ninja: build stopped: subcommand failed.

Understanding the command

( \
PROJECT_DIR=$(pwd) ; \
SDK_ROOT="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"; \
cd build ; \
$CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-clang++ \
 -v
 -ftree-vectorize \
 -fPIC \
 -fPIE \
 -fstack-protector-strong \
 -O2 \
 -pipe \
 -stdlib=libc++ \
 -fvisibility-inlines-hidden \
 -fmessage-length=0 \
 -isystem \
 $CONDA_PREFIX/include \
 -arch \
 arm64 \
 -isysroot \
 $SDK_ROOT \
 -dynamiclib \
 -Wl,-headerpad_max_install_names \
 -Wl,-pie \
 -Wl,-headerpad_max_install_names \
 -Wl,-dead_strip_dylibs \
 -Wl,-rpath,$CONDA_PREFIX/lib \
 -L$CONDA_PREFIX/lib \
 -o \
 knn_example/libknn_exampleCppyy.dylib \
 -install_name \
 @rpath/libknn_exampleCppyy.dylib \
 CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o \
 \
 -Wl,-rpath,$PROJECT_DIR/build \
 \
 libknn_lib.dylib \
 \
)

List of files involved:

knn_example/libknn_exampleCppyy.dylib
CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o
libknn_li.dylib

At this point we added the -v option to the CXX compiler via CMakeLists.txt. This prints some extra information and the linker invocation, which for the bugged command is (replacing by \n):

clang version 14.0.4
Target: arm64-apple-darwin20.0.0
Thread model: posix
InstalledDir: $CONDA_PREFIX/bin
 "$CONDA_PREFIX/bin/arm64-apple-darwin20.0.0-ld" 
 -demangle 
 -lto_library 
 $CONDA_PREFIX/lib/libLTO.14.dylib 
 -dynamic 
 -dylib 
 -arch 
 arm64 
 -dylib_install_name 
 @rpath/libknn_exampleCppyy.dylib 
 -platform_version 
 macos 
 12.0.0 
 12.3 
 -syslibroot 
 $SDK_ROOT 
 -o 
 knn_example/libknn_exampleCppyy.dylib 
 -L$CONDA_PREFIX/lib 
 -headerpad_max_install_names 
 -pie 
 -headerpad_max_install_names 
 -dead_strip_dylibs 
 -rpath 
 $CONDA_PREFIX/lib 
 CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o 
 -rpath 
 $PROJECT_DIR/build 
 libknn_lib.dylib 
 -lc++ 
 -lSystem 
 $CONDA_PREFIX/lib/clang/14.0.4/lib/darwin/libclang_rt.osx.a

Current reasoning

The compiler complains symbols refered in CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o are missing.

CppyyLegacy is a namespace that is defined in build/knn_example.cpp. No other file in the build directory refers to it. It includes several files that define the missing symbols.

Yet, somehow it was built into CMakeFiles/knn_exampleCppyy.dir/knn_example.cpp.o.

Which command created this file?
Where did it obtain kAssertMsg and others?
And why are these not available to the last command?

Aug 25 '22 20:08 LunarLanding

Just updated the previous comment with a more verbose build log, using pypi cppyy.

Aug 31 '22 21:08 LunarLanding

Just adding that I'm on macOS 12.6 on an Intel MacBook, and I have the same error with CppyyLegacy , so it seems not limited to M1 silicon.

Sep 26 '22 08:09 torfinnberset

I added this to the CMakeLists.txt, and now it's at least linking:

link_directories(<home>/micromamba/envs/cppyy/lib/python3.10/site-packages)
link_libraries(CoreLegacy)

Sep 26 '22 08:09 torfinnberset

I added this to the CMakeLists.txt, and now it's at least linking:
link_directories(<home>/micromamba/envs/cppyy/lib/python3.10/site-packages)
link_libraries(CoreLegacy)

I tried it and the linker complains it cannot find CoreLegacy:

[build] ld: library not found for -lCoreLegacy

From the listing in site-packages, seems only libcppyy.cpython-310-darwin.so is contained within. Can you post which libraries you have in this folder? Either way thanks for the info. Below is the contents of my sitepackages and also the current build script.

site-packages$ ls -lha
total 828K
drwxr-xr-x  20 ma staff  640 Aug 26 06:14 .
drwxr-xr-x 209 ma staff 6.6K Aug 26 01:36 ..
drwxr-xr-x   8 ma staff  256 Aug 26 01:36 CPyCppyy-1.12.11.dist-info
-rw-rw-r--   4 ma staff  119 Aug 22 22:42 README.txt
drwxr-xr-x   5 ma staff  160 Aug 26 06:14 clang
drwxr-xr-x  15 ma staff  480 Aug 26 01:36 cppyy
drwxr-xr-x  10 ma staff  320 Aug 26 01:36 cppyy-2.4.0.dist-info
drwxr-xr-x  19 ma staff  608 Aug 26 01:36 cppyy_backend
drwxr-xr-x   8 ma staff  256 Aug 26 01:36 cppyy_backend-1.14.9.dist-info
drwxr-xr-x   9 ma staff  288 Aug 26 01:36 cppyy_cling-6.27.0.dist-info
-rw-rw-r--   2 ma staff  151 Aug 24 23:16 distutils-precedence.pth
-rwxr-xr-x   1 ma staff 820K Aug 26 01:36 libcppyy.cpython-310-darwin.so
drwxr-xr-x   9 ma staff  288 Aug 29 16:52 pip
drwxr-xr-x   8 ma staff  256 Aug 26 01:36 pip-22.2.2-py3.10.egg-info
drwxr-xr-x   6 ma staff  192 Aug 26 01:36 pkg_resources
drwxr-xr-x  48 ma staff 1.5K Aug 26 01:36 setuptools
drwxr-xr-x   8 ma staff  256 Aug 26 01:36 setuptools-65.3.0-py3.10.egg-info
drwxr-xr-x  12 ma staff  384 Aug 26 01:36 wheel
drwxr-xr-x   9 ma staff  288 Aug 26 01:36 wheel-0.37.1-py3.8.egg-info
drwxr-xr-x   5 ma staff  160 Aug 26 01:36 _distutils_hack

CMakeLists

set(CMAKE_POLICY_DEFAULT_CMP0102 NEW)
set(CMAKE_POLICY_DEFAULT_CMP0128 NEW)
set(CMAKE_POLICY_DEFAULT_CMP0126 NEW)
cmake_minimum_required(VERSION 3.10)


# add_link_options("LINKER:-v")
# set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -Xlinker -v")
# set(CMAKE_SHARED_LINKER_FLAGS  "${CMAKE_SHARED_LINKER_FLAGS} -Xlinker -v")

set(CMAKE_CXX_FLAGS  "-v")




project(cppyy_example LANGUAGES CXX)


execute_process(COMMAND cling-config --cmake OUTPUT_VARIABLE CPPYY_MODULE_PATH OUTPUT_STRIP_TRAILING_WHITESPACE)
# Make sure this is set to something like:
# ~/.local/lib/python2.7/site-packages/cpyy_backend/cmake 




message("CPYY_MODULE_PATH: " ${CPPYY_MODULE_PATH})
list(INSERT CMAKE_MODULE_PATH 0 ${CPPYY_MODULE_PATH})

find_package(Cppyy)


link_directories($ENV{CONDA_PREFIX}/lib/python3.10/site-packages)
link_libraries(CoreLegacy)

set(SOURCES nearest_neighbors.cpp)
set(HEADERS nearest_neighbors.h)

# It seems like this library has to be shared...
add_library(knn_lib SHARED ${SOURCES})
# Note this is a necessary compile flag for cppyy bindings to work.
set_target_properties(knn_lib PROPERTIES POSITION_INDEPENDENT_CODE ON)
target_include_directories(knn_lib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

cppyy_add_bindings(
   "knn_example" "0.0.1" "Joel" "[email protected]"
   LANGUAGE_STANDARD "14"
   GENERATE_OPTIONS "-D__PIC__;-Wno-macro-redefined"
   # COMPILE_OPTIONS "-v"
   INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
   LINK_LIBRARIES knn_lib
   H_DIRS ${CMAKE_CURRENT_SOURCE_DIR}
   H_FILES ${HEADERS})

add_executable(knn main.cpp)
target_link_libraries(knn PUBLIC knn_lib)




# set_property(TARGET knn PROPERTY CXX_STANDARD 14)
# set_property(TARGET knn_lib PROPERTY CXX_STANDARD 14)

Sep 26 '22 11:09 LunarLanding

Ok, so adding this directory works: link_directories($ENV{CONDA_PREFIX}/lib/python3.10/site-packages/cppyy_backend/lib) That's where libCoreLegacy.so is on my install.

PS: nicer cmake commands:

get_filename_component(PYTHON_SITE_PACKAGES ${CPPYY_MODULE_PATH} DIRECTORY)
set(CPPYY_LIB_SO ${PYTHON_SITE_PACKAGES}/lib)
message("CPYY_LIB_SO: " ${CPPYY_LIB_SO})


link_directories(${CPPYY_LIB_SO})
link_libraries(CoreLegacy)

Sep 26 '22 11:09 LunarLanding

`cppyy` components

Each of these cppyy components merits some entry. For now we just have this listing:

$ mamba list | grep pypi
cppyy                     2.4.0                    pypi_0    pypi
cppyy-backend             1.14.9                   pypi_0    pypi
cppyy-cling               6.27.0                   pypi_0    pypi
cpycppyy                  1.12.11                  pypi_0    pypi

@wlav just to clarify, in case it was not clear, in this comment I describe an environment where cppyy was installed via pip, while python was installed via conda. I could further try to install python/ other base dependencies via homebrew and then install cppyy via pip. It worries me a bit I might run into further issues by working around it and linking to CoreLegacy, as I am doing now that I have found where it is.

Sep 26 '22 12:09 LunarLanding

M1 cmake interface example repo not working

Steps to reproduce

Meta

Environment

Some software versions

`cppyy` components

Compiler

Build command

Current cmake script

Going through the compilation log

8/9 ? libknn_lib.dylib

Understanding the command

Current reasoning

`cppyy` components