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vanderschaarlab / temporai

TemporAI: ML-centric Toolkit for Medical Time Series
https://www.temporai.vanderschaar-lab.com/
Apache License 2.0
100 stars 19 forks source link

[Bug] Catboost is required, but fails to build (macOS 13.5) #93

Closed JulianKlug closed 1 year ago

JulianKlug commented 1 year ago

Describe the bug Building the temporai package from pip or from github fails as catboost is required. This is probably linked to #72 were the catboost dependency should have been removed and to https://github.com/catboost/catboost/issues/2371#issue-1692320252

Platform:

To Reproduce pip install temporai or pip install "temporai @ git+https://github.com/vanderschaarlab/temporai@daa4af2e3943e5639098a4459464012c007245a3"

Expected behavior Build should not fail, and catboost should probably not be required.

Results temporai build fails.

Collecting catboost>=1.0.5 (from hyperimpute>=0.1.17->temporai@ git+https://github.com/vanderschaarlab/temporai@daa4af2e3943e5639098a4459464012c007245a3)
  Using cached catboost-1.2.2.tar.gz (60.1 MB)
``` Building wheel for catboost (pyproject.toml) ... error error: subprocess-exited-with-error × Building wheel for catboost (pyproject.toml) did not run successfully. │ exit code: 1 ╰─> [218 lines of output] running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.9-x86_64-cpython-311 creating build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/monoforest.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/plot_helpers.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/metrics.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/version.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/text_processing.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/datasets.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/core.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/utils.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost copying catboost/dev_utils.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost creating build/lib.macosx-10.9-x86_64-cpython-311/catboost/widget copying catboost/widget/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/widget copying catboost/widget/metrics_plotter.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/widget copying catboost/widget/ipythonwidget.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/widget copying catboost/widget/callbacks.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/widget creating build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/catboost_evaluation.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/_fold_model.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/_readers.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/log_config.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/_splitter.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/execution_case.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/_fold_storage.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/factor_utils.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/utils.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/evaluation_result.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval copying catboost/eval/_fold_models_handler.py -> build/lib.macosx-10.9-x86_64-cpython-311/catboost/eval running build_ext Buildling _catboost with cmake and ninja target_platform=darwin-x86_64. Building targets _catboost with PIC Running "cmake /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src -B /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/build/temp.macosx-10.9-x86_64-cpython-311 -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src/build/toolchains/clang.toolchain --log-level=VERBOSE -DCMAKE_POSITION_INDEPENDENT_CODE=On -DCATBOOST_COMPONENTS=python-package -DCMAKE_OSX_DEPLOYMENT_TARGET=11.0 -DHAVE_CUDA=no -DPython3_ROOT_DIR=/Users/jk1/opt/anaconda3/envs/treatment_effects" -- The C compiler identification is AppleClang 14.0.3.14030022 -- The CXX compiler identification is AppleClang 14.0.3.14030022 -- The ASM compiler identification is Clang -- Found assembler: /Library/Developer/CommandLineTools/usr/bin/clang -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/clang - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/clang++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /Users/jk1/opt/anaconda3/envs/treatment_effects/bin/python3.1 (found version "3.11.5") found components: Interpreter -- CMAKE_C_FLAGS = " -fexceptions -fno-common -fcolor-diagnostics -faligned-allocation -fdebug-default-version=4 -ffunction-sections -fdata-sections -Wall -Wextra -Wno-parentheses -Wno-implicit-const-int-float-conversion -Wno-unknown-warning-option -pipe -D_THREAD_SAFE -D_PTHREADS -D_REENTRANT -D_LARGEFILE_SOURCE -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D__LONG_LONG_SUPPORTED -DLIBCXX_BUILDING_LIBCXXRT -D_FILE_OFFSET_BITS=64 -m64 -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mpopcnt -mcx16 -DSSE_ENABLED=1 -DSSE3_ENABLED=1 -DSSSE3_ENABLED=1 -DSSE41_ENABLED=1 -DSSE42_ENABLED=1 -DPOPCNT_ENABLED=1 -DCX16_ENABLED=1" -- CMAKE_CXX_FLAGS = " -fexceptions -fno-common -fcolor-diagnostics -faligned-allocation -fdebug-default-version=4 -ffunction-sections -fdata-sections -Wall -Wextra -Wno-parentheses -Wno-implicit-const-int-float-conversion -Wno-unknown-warning-option -pipe -D_THREAD_SAFE -D_PTHREADS -D_REENTRANT -D_LARGEFILE_SOURCE -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D__LONG_LONG_SUPPORTED -DLIBCXX_BUILDING_LIBCXXRT -D_FILE_OFFSET_BITS=64 -m64 -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -mpopcnt -mcx16 -Woverloaded-virtual -Wimport-preprocessor-directive-pedantic -Wno-undefined-var-template -Wno-return-std-move -Wno-defaulted-function-deleted -Wno-pessimizing-move -Wno-deprecated-anon-enum-enum-conversion -Wno-deprecated-enum-enum-conversion -Wno-deprecated-enum-float-conversion -Wno-ambiguous-reversed-operator -Wno-deprecated-volatile -DSSE_ENABLED=1 -DSSE3_ENABLED=1 -DSSSE3_ENABLED=1 -DSSE41_ENABLED=1 -DSSE42_ENABLED=1 -DPOPCNT_ENABLED=1 -DCX16_ENABLED=1" -- Conan: checking conan executable -- Conan: Found program /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/bin/conan -- Conan: Version found Conan version 1.59.0 -- Conan executing: /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/bin/conan install /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src --remote conancenter --install-folder /private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/build/temp.macosx-10.9-x86_64-cpython-311 --build missing --env CONAN_CMAKE_GENERATOR=Ninja --settings build_type=Release --settings compiler=apple-clang --settings compiler.version=14.0 --settings compiler.libcxx=libc++ --settings compiler.cppstd=20 --conf tools.cmake.cmaketoolchain:generator=Ninja Configuration: [settings] arch=x86_64 arch_build=x86_64 build_type=Release compiler=apple-clang compiler.cppstd=20 compiler.libcxx=libc++ compiler.version=14.0 os=Macos os_build=Macos [options] [build_requires] [env] CONAN_CMAKE_GENERATOR=Ninja [conf] tools.cmake.cmaketoolchain:generator=Ninja Version ranges solved Version range '>=1.2.11 <2' required by 'pcre/8.45' resolved to 'zlib/1.3' in local cache conanfile.txt: Installing package Requirements libiconv/1.15 from 'conancenter' - Cache openssl/1.1.1t from 'conancenter' - Cache Packages libiconv/1.15:e1ef30a7ac2ff8c218173fdf49ec961a5c046a36 - Cache openssl/1.1.1t:a319f556f93546f2dff1b70922784b70e7cba919 - Cache Build requirements bzip2/1.0.8 from 'conancenter' - Cache pcre/8.45 from 'conancenter' - Cache ragel/6.10 from 'conancenter' - Cache swig/4.0.2 from 'conancenter' - Cache yasm/1.3.0 from 'conancenter' - Cache zlib/1.3 from 'conancenter' - Cache Build requirements packages bzip2/1.0.8:b9b85a7c8f543b96385e1da9e174853f1fb08e0c - Cache pcre/8.45:842afe377248eac66b64b538531df2b005d57959 - Cache ragel/6.10:801752c0480319b8e090188c566245a78e9abcf4 - Cache swig/4.0.2:099d7b9cd06e9bd11e92b9a2ddf3b29cd986fdcb - Cache yasm/1.3.0:801752c0480319b8e090188c566245a78e9abcf4 - Cache zlib/1.3:a319f556f93546f2dff1b70922784b70e7cba919 - Cache Installing (downloading, building) binaries... bzip2/1.0.8: Already installed! libiconv/1.15: Already installed! openssl/1.1.1t: Already installed! ragel/6.10: Already installed! ragel/6.10: Appending PATH environment variable: /Users/jk1/.conan/data/ragel/6.10/_/_/package/801752c0480319b8e090188c566245a78e9abcf4/bin yasm/1.3.0: Already installed! yasm/1.3.0: Appending PATH environment variable: /Users/jk1/.conan/data/yasm/1.3.0/_/_/package/801752c0480319b8e090188c566245a78e9abcf4/bin zlib/1.3: Already installed! pcre/8.45: Already installed! swig/4.0.2: Already installed! swig/4.0.2: Appending PATH environment variable: /Users/jk1/.conan/data/swig/4.0.2/_/_/package/099d7b9cd06e9bd11e92b9a2ddf3b29cd986fdcb/bin conanfile.txt: Applying build-requirement: ragel/6.10 conanfile.txt: Applying build-requirement: swig/4.0.2 conanfile.txt: Applying build-requirement: yasm/1.3.0 conanfile.txt: Applying build-requirement: pcre/8.45 conanfile.txt: Applying build-requirement: bzip2/1.0.8 conanfile.txt: Applying build-requirement: zlib/1.3 conanfile.txt: Generator cmake_find_package created Findragel.cmake conanfile.txt: Generator cmake_find_package created FindSWIG.cmake conanfile.txt: Generator cmake_find_package created Findyasm.cmake conanfile.txt: Generator cmake_find_package created FindIconv.cmake conanfile.txt: Generator cmake_find_package created FindOpenSSL.cmake conanfile.txt: Generator cmake_find_package created FindPCRE.cmake conanfile.txt: Generator cmake_find_package created FindBZip2.cmake conanfile.txt: Generator cmake_find_package created FindZLIB.cmake conanfile.txt: Generator cmake_paths created conan_paths.cmake conanfile.txt: Generator txt created conanbuildinfo.txt conanfile.txt: Aggregating env generators conanfile.txt: Generated conaninfo.txt conanfile.txt: Generated graphinfo conanfile.txt imports(): Copied 434 '.i' files conanfile.txt imports(): Copied 273 '.swg' files conanfile.txt imports(): Copied 1 '.swig' file: Makefile.swig conanfile.txt imports(): Copied 2 '.ml' files: swig.ml, swigp4.ml conanfile.txt imports(): Copied 1 '.pl' file: Makefile.pl conanfile.txt imports(): Copied 6 files conanfile.txt imports(): Copied 1 '.rb' file: extconf.rb conanfile.txt imports(): Copied 1 '.h' file: noembed.h conanfile.txt imports(): Copied 1 '.scm' file: common.scm conanfile.txt imports(): Copied 1 '.mli' file: swig.mli conanfile.txt imports(): Copied 1 '.hpp' file: octheaders.hpp CMake Error at /usr/local/Cellar/cmake/3.21.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) Call Stack (most recent call first): /usr/local/Cellar/cmake/3.21.3/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /usr/local/Cellar/cmake/3.21.3/share/cmake/Modules/FindPython/Support.cmake:3166 (find_package_handle_standard_args) /usr/local/Cellar/cmake/3.21.3/share/cmake/Modules/FindPython3.cmake:485 (include) catboost/python-package/catboost/CMakeLists.darwin-x86_64.txt:9 (find_package) catboost/python-package/catboost/CMakeLists.txt:20 (include) -- Configuring incomplete, errors occurred! See also "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/build/temp.macosx-10.9-x86_64-cpython-311/CMakeFiles/CMakeOutput.log". See also "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/build/temp.macosx-10.9-x86_64-cpython-311/CMakeFiles/CMakeError.log". Traceback (most recent call last): File "/Users/jk1/opt/anaconda3/envs/treatment_effects/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in main() File "/Users/jk1/opt/anaconda3/envs/treatment_effects/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main json_out['return_val'] = hook(**hook_input['kwargs']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/jk1/opt/anaconda3/envs/treatment_effects/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel return _build_backend().build_wheel(wheel_directory, config_settings, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 434, in build_wheel return self._build_with_temp_dir( ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir self.run_setup() File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 507, in run_setup super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in run_setup exec(code, locals()) File "", line 731, in File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup return distutils.core.setup(**attrs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup return run_commands(dist) ^^^^^^^^^^^^^^^^^^ File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands dist.run_commands() File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands self.run_command(cmd) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command super().run_command(command) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command cmd_obj.run() File "", line 397, in run File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 364, in run self.run_command("build") File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command self.distribution.run_command(command) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command super().run_command(command) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command cmd_obj.run() File "", line 332, in run File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run self.run_command(cmd_name) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command self.distribution.run_command(command) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/dist.py", line 989, in run_command super().run_command(command) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-build-env-itfn3d2q/overlay/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command cmd_obj.run() File "", line 444, in run File "", line 462, in build_with_cmake_and_ninja File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src/build/build_native.py", line 517, in build cmd_runner.run(cmake_cmd, env=build_environ) File "/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src/build/build_native.py", line 164, in run subprocess.run(cmd, check=True, **subprocess_run_kwargs) File "/Users/jk1/opt/anaconda3/envs/treatment_effects/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['cmake', '/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src', '-B', '/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/build/temp.macosx-10.9-x86_64-cpython-311', '-G', 'Ninja', '-DCMAKE_BUILD_TYPE=Release', '-DCMAKE_TOOLCHAIN_FILE=/private/var/folders/9v/1s329cwj32jc2kkx24p8jp980000gp/T/pip-install-pvf83pvv/catboost_978ae68fc7434fc3857f456b847dec21/catboost_all_src/build/toolchains/clang.toolchain', '--log-level=VERBOSE', '-DCMAKE_POSITION_INDEPENDENT_CODE=On', '-DCATBOOST_COMPONENTS=python-package', '-DCMAKE_OSX_DEPLOYMENT_TARGET=11.0', '-DHAVE_CUDA=no', '-DPython3_ROOT_DIR=/Users/jk1/opt/anaconda3/envs/treatment_effects']' returned non-zero exit status 1. [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for catboost Successfully built temporai Failed to build catboost ERROR: Could not build wheels for catboost, which is required to install pyproject.toml-based projects ```
DrShushen commented 1 year ago

Thank you for reporting this! We will investigate.

This may also be related to the fact that you are using Python 3.11 (which would affect dependencies), which we do not yet fully support. Could you try with Python 3.10 to see if that resolves the issue?

JulianKlug commented 1 year ago

The build works with python 3.10.