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Posted to issues@arrow.apache.org by "orliac (via GitHub)" <gi...@apache.org> on 2023/05/25 11:37:02 UTC
[GitHub] [arrow] orliac opened a new issue, #35586: [Python] Fails to build PyArrow@12.0.0 on RH8
orliac opened a new issue, #35586:
URL: https://github.com/apache/arrow/issues/35586
### Describe the bug, including details regarding any error messages, version, and platform.
When installing arrow@12.0.0 from source using GCC 11.3.0 on a RH8 machine (pip 22.3.1, Python 3.9, using Spack) I bump into the following issue:
```
-- Running cmake --build for PyArrow
cmake --build . --config release --
[ 1%] Compiling Cython CXX source for lib...
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "Python.h":
int PySlice_Check(object)
cdef int check_status(const CStatus& status) except -1 nogil
^
------------------------------------------------------------
pyarrow/lib.pxd:67:55: Syntax error in C variable declaration
```
Can someone see what the issue could be? Thank you.
Below the full log.
```
-- Running cmake for PyArrow
cmake -DCMAKE_INSTALL_PREFIX=/tmp/orliac/spack-stage/spack-stage-py-pyarrow-12.0.0-ghhdfuencjj7ztv4eywxmqn6emhq56u7/spack-src/build/lib.linux-x86_64-3.9/pyarrow -DPYTHON_EXECUTABLE=/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/python-3.9.15-zsmss6eznpwn5qtkdkxpli3qhsr54fld/bin/python3.9 -DPython3_EXECUTABLE=/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/python-3.9.15-zsmss6eznpwn5qtkdkxpli3qhsr54fld/bin/python3.9 -DPYARROW_CXXFLAGS= -DPYARROW_BUILD_CUDA=off -DPYARROW_BUILD_SUBSTRAIT=off -DPYARROW_BUILD_FLIGHT=off -DPYARROW_BUILD_GANDIVA=off -DPYARROW_BUILD_ACERO=on -DPYARROW_BUILD_DATASET=on -DPYARROW_BUILD_ORC=off -DPYARROW_BUILD_PARQUET=on -DPYARROW_BUILD_PARQUET_ENCRYPTION=off -DPYARROW_BUILD_GCS=off -DPYARROW_BUILD_S3=off -DPYARROW_BUILD_HDFS=off -DPYARROW_BUNDLE_ARROW_CPP=off -DPYARROW_BUNDLE_CYTHON_CPP=off -DPYARROW_GENERATE_COVERAGE=off -DCMAKE_BUILD_TYPE=release /tmp/orliac/spack-stage/spack-stage-py-pyarrow-12.0.0-ghhdfue
ncjj7ztv4eywxmqn6emhq56u7/spack-src
-- The C compiler identification is GNU 11.3.0
-- The CXX compiler identification is GNU 11.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /work/backup/ska/orliac/spack/lib/spack/env/gcc/gcc - 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: /work/backup/ska/orliac/spack/lib/spack/env/gcc/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Using ccache: /usr/bin/ccache
-- System processor: x86_64
-- Performing Test CXX_SUPPORTS_SSE4_2
-- Performing Test CXX_SUPPORTS_SSE4_2 - Success
-- Performing Test CXX_SUPPORTS_AVX2
-- Performing Test CXX_SUPPORTS_AVX2 - Success
-- Performing Test CXX_SUPPORTS_AVX512
-- Performing Test CXX_SUPPORTS_AVX512 - Success
-- Arrow build warning level: PRODUCTION
-- Using ld linker
-- Build Type: RELEASE
-- CMAKE_C_FLAGS: -Wall -fno-semantic-interposition -msse4.2 -fdiagnostics-color=always -fno-omit-frame-pointer -Wno-unused-variable -Wno-maybe-uninitialized
-- CMAKE_CXX_FLAGS: -Wno-noexcept-type -Wall -fno-semantic-interposition -msse4.2 -fdiagnostics-color=always -fno-omit-frame-pointer -Wno-unused-variable -Wno-maybe-uninitialized
-- Generator: Unix Makefiles
-- Build output directory: /tmp/orliac/spack-stage/spack-stage-py-pyarrow-12.0.0-ghhdfuencjj7ztv4eywxmqn6emhq56u7/spack-src/build/temp.linux-x86_64-3.9/release
-- Found Python3: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/python-3.9.15-zsmss6eznpwn5qtkdkxpli3qhsr54fld/bin/python3.9 (found version "3.9.15") found components: Interpreter Development.Module NumPy
-- Found Python3Alt: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/python-3.9.15-zsmss6eznpwn5qtkdkxpli3qhsr54fld/bin/python3.9
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
CMake Warning at /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/cmake/Arrow/FindThriftAlt.cmake:56 (find_package):
By not providing "FindThrift.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Thrift", but
CMake did not find one.
Could not find a package configuration file provided by "Thrift" with any
of the following names:
ThriftConfig.cmake
thrift-config.cmake
Add the installation prefix of "Thrift" to CMAKE_PREFIX_PATH or set
"Thrift_DIR" to a directory containing one of the above files. If "Thrift"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/cmake-3.24.3-5pf3twpa3mag2ln3cgxu3mkjbarasb4a/share/cmake-3.24/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/cmake/Arrow/ArrowConfig.cmake:105 (find_dependency)
CMakeLists.txt:261 (find_package)
-- Checking for module 'thrift'
-- Found thrift, version 0.16.0
-- Found ThriftAlt: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/thrift-0.16.0-aahpf6q4yv4lvcypwegxj3xh2bjsehb4/lib/libthrift.so (found version "0.16.0")
-- Found utf8proc: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/utf8proc-2.8.0-36yitvl7cdvcnzgepfzbaddy2pr4dqaq/lib64/libutf8proc.so (found version "2.8.0")
-- Arrow version: 12.0.0
-- Found the Arrow shared library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow.so.1200.0.0
-- Found the Arrow import library: ARROW_IMPORT_LIB-NOTFOUND
-- Found the Arrow static library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow.a
-- Parquet version: 12.0.0
-- Found the Parquet shared library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libparquet.so.1200.0.0
-- Found the Parquet import library: PARQUET_IMPORT_LIB-NOTFOUND
-- Found the Parquet static library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libparquet.a
-- ArrowAcero version: 12.0.0
-- Found the ArrowAcero shared library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow_acero.so.1200.0.0
-- Found the ArrowAcero import library: ARROW_ACERO_IMPORT_LIB-NOTFOUND
-- Found the ArrowAcero static library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow_acero.a
-- ArrowDataset version: 12.0.0
-- Found the ArrowDataset shared library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow_dataset.so.1200.0.0
-- Found the ArrowDataset import library: ARROW_DATASET_IMPORT_LIB-NOTFOUND
-- Found the ArrowDataset static library: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/arrow-12.0.0-b6lftge64at2hocynsnwm2u5m3u6bcce/lib64/libarrow_dataset.a
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/orliac/spack-stage/spack-stage-py-pyarrow-12.0.0-ghhdfuencjj7ztv4eywxmqn6emhq56u7/spack-src/build/temp.linux-x86_64-3.9
-- Finished cmake for PyArrow
-- Running cmake --build for PyArrow
cmake --build . --config release --
[ 1%] Compiling Cython CXX source for lib...
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "Python.h":
int PySlice_Check(object)
cdef int check_status(const CStatus& status) except -1 nogil
^
------------------------------------------------------------
pyarrow/lib.pxd:67:55: Syntax error in C variable declaration
Error compiling Cython file:
------------------------------------------------------------
...
ArrowIOError = IOError
# This function could be written directly in C++ if we didn't
# define Arrow-specific subclasses (ArrowInvalid etc.)
cdef int check_status(const CStatus& status) except -1 nogil:
^
------------------------------------------------------------
pyarrow/error.pxi:82:55: Syntax error in C variable declaration
gmake[2]: *** [CMakeFiles/lib_pyx.dir/build.make:71: CMakeFiles/lib_pyx] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:146: CMakeFiles/lib_pyx.dir/all] Error 2
gmake: *** [Makefile:136: all] Error 2
error: command '/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/cmake-3.24.3-5pf3twpa3mag2ln3cgxu3mkjbarasb4a/bin/cmake' failed with exit code 2
error: subprocess-exited-with-error
× Building wheel for pyarrow (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
full command: /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/python-3.9.15-zsmss6eznpwn5qtkdkxpli3qhsr54fld/bin/python3.9 /work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/py-pip-22.3.1-oiljmniioyay6w4x6nlhbge3uqexfzyu/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmp4vqpbc1n
cwd: /tmp/orliac/spack-stage/spack-stage-py-pyarrow-12.0.0-ghhdfuencjj7ztv4eywxmqn6emhq56u7/spack-src
Building wheel for pyarrow (pyproject.toml): finished with status 'error'
ERROR: Failed building wheel for pyarrow
Failed to build pyarrow
ERROR: Could not build wheels for pyarrow, which is required to install pyproject.toml-based projects
Exception information:
Traceback (most recent call last):
File "/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/py-pip-22.3.1-oiljmniioyay6w4x6nlhbge3uqexfzyu/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper
status = run_func(*args)
File "/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/py-pip-22.3.1-oiljmniioyay6w4x6nlhbge3uqexfzyu/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 247, in wrapper
return func(self, options, args)
File "/work/backup/ska/orliac/spack/opt/spack/linux-rhel8-icelake/gcc-11.3.0/py-pip-22.3.1-oiljmniioyay6w4x6nlhbge3uqexfzyu/lib/python3.9/site-packages/pip/_internal/commands/install.py", line 464, in run
raise InstallationError(
pip._internal.exceptions.InstallationError: Could not build wheels for pyarrow, which is required to install pyproject.toml-based projects
Removed build tracker: '/tmp/pip-build-tracker-il8ou_m6'
```
### Component(s)
C++, Python
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[GitHub] [arrow] jorisvandenbossche commented on issue #35586: [Python] Fails to build PyArrow@12.0.0 on RH8
Posted by "jorisvandenbossche (via GitHub)" <gi...@apache.org>.
jorisvandenbossche commented on issue #35586:
URL: https://github.com/apache/arrow/issues/35586#issuecomment-1562751214
@orliac do you know which version of cython you used before? (when it was failing)
Because we currently have "cython >= 0.29.31" specified in our build dependencies, and so wondering if we need to bump that version there
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[GitHub] [arrow] westonpace commented on issue #35586: Fails to build PyArrow@12.0.0
Posted by "westonpace (via GitHub)" <gi...@apache.org>.
westonpace commented on issue #35586:
URL: https://github.com/apache/arrow/issues/35586#issuecomment-1552980983
Hmm, do you know what version of cython you have installed? To support cython 3 we moved from:
```
cdef int check_status(const CStatus& status) nogil except -1:
```
to...
```
cdef int check_status(const CStatus& status) except -1 nogil:
```
I wonder if some older versions of cython don't recognize the "nogil at the end" syntax.
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[GitHub] [arrow] orliac commented on issue #35586: [Python] Fails to build PyArrow@12.0.0 on RH8
Posted by "orliac (via GitHub)" <gi...@apache.org>.
orliac commented on issue #35586:
URL: https://github.com/apache/arrow/issues/35586#issuecomment-1554300260
Thanks @westonpace
Indeed, I could solve the issue using a more recent version of Cython. With version 0.29.33 it compiles smoothly.
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[GitHub] [arrow] orliac closed issue #35586: [Python] Fails to build PyArrow@12.0.0 on RH8
Posted by "orliac (via GitHub)" <gi...@apache.org>.
orliac closed issue #35586: [Python] Fails to build PyArrow@12.0.0 on RH8
URL: https://github.com/apache/arrow/issues/35586
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