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Posted to issues@arrow.apache.org by GitBox <gi...@apache.org> on 2022/12/12 15:43:03 UTC
[GitHub] [arrow] sdy72 opened a new issue, #14920: [Python] wheel cmake error on Raspberry PI
sdy72 opened a new issue, #14920:
URL: https://github.com/apache/arrow/issues/14920
### Describe the usage question you have. Please include as many useful details as possible.
Dear Arrow
When I try to install pyarrow on my Raspberry PI 3 using pip I get this error
` CMake Error at /usr/local/share/cmake-3.25/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find Python3 (missing: Python3_NumPy_INCLUDE_DIRS NumPy) (found
suitable version "3.9.2", minimum required is "3.7")
Call Stack (most recent call first):
/usr/local/share/cmake-3.25/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE)
/usr/local/share/cmake-3.25/Modules/FindPython/Support.cmake:3245 (find_package_handle_standard_args)
/usr/local/share/cmake-3.25/Modules/FindPython3.cmake:490 (include)
/tmp/pip-install-h0q930xi/pyarrow_e68ff656d2a84a388a1cc31acfc338a9/cmake_modules/FindPython3Alt.cmake:60 (find_package)`
Full output attached. I didn't know where to ask or if it should be a bug report instead. So I start here.
System is "Raspbian GNU/Linux 11 (bullseye) on Raspberry PI 3 armhf.
I tried both with numpy installed from apt and pip, and cmake install from apt and latest build from source.
Same error message.
Please let me know if I should provide info or how I can help you help me.
My main objective is to install streamlit which has a dependency to pyarrow via pip.
[pyarrow_install_stdout.txt](https://github.com/apache/arrow/files/10209463/pyarrow_install_stdout.txt)
### Component(s)
Python
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1358923787
My bad. That works both places.
Another observation:
After https://gitlab.kitware.com/cmake/cmake/-/blob/v3.25.1/Modules/FindPython/Support.cmake
lines 3170-3176
`_Python3_NumPy_PATH` is empty when pyarrow installer runs.
`_Python3_NumPy_PATH = /usr/lib/python3/dist-packages/numpy/core/include` when I run the toy example.
I'll try to put more message output and share here.
Do you have suggestions to something specific you wanna see?
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1371399924
Ah, we need to add `-latomic` to our CMake package because PyArrow uses CMake package not pkg-config package. Could you try the following patch?
```diff
diff --git a/cpp/src/arrow/CMakeLists.txt b/cpp/src/arrow/CMakeLists.txt
index 3bf5ebb9b9..4c784f2bb8 100644
--- a/cpp/src/arrow/CMakeLists.txt
+++ b/cpp/src/arrow/CMakeLists.txt
@@ -578,6 +578,8 @@ endif()
# See also: https://issues.apache.org/jira/browse/ARROW-12860
if(${CMAKE_SYSTEM_NAME} STREQUAL "Linux" AND ${CMAKE_SYSTEM_PROCESSOR} MATCHES "armv7")
string(APPEND ARROW_PC_LIBS_PRIVATE " -latomic")
+ list(APPEND ARROW_SHARED_INSTALL_INTERFACE_LIBS "-latomic")
+ list(APPEND ARROW_STATIC_INSTALL_INTERFACE_LIBS "-latomic")
endif()
# If libarrow.a is only built, "pkg-config --cflags --libs arrow"
```
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1368918814
I got it.
Your CMake is 3.18.4 but `cmake --preset` is available since 3.19.
Could you use `cmake -DARROW_BUILD_STATIC=OFF -DARROW_COMPUTE=ON -DARROW_CSV=ON -DARROW_FILESYSTEM=ON -DARROW_JSON=ON -DCMAKE_BUILD_TYPE=Release -GNinja .` instead?
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[GitHub] [arrow] westonpace commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
westonpace commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1371048067
Yes, arrow will need to be linked with `-latomic`. However, that should be happening here:
https://github.com/apache/arrow/blob/a0d16306229fc08f9dc64361f9459806e02b5932/cpp/src/arrow/CMakeLists.txt#L577-L581
Is there any reason this check might not be working?
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1374695906
Thanks for confirming it.
I've opened a pull request: https://github.com/apache/arrow/pull/15251
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1366418317
Sure
[pyarrow-pip-output.txt](https://github.com/apache/arrow/files/10312697/pyarrow-pip-output.txt)
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1365436592
Could you share the output of `ls -la /home/pi/arrow/apache-arrow-10.0.1/cpp/jemalloc_ep-prefix/src/jemalloc_ep-stamp/`?
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1367565821
Could you show the output of `sudo cmake --build . --target install` that is mentioned in https://github.com/apache/arrow/issues/14920#issuecomment-1360479081 ?
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1366004832
Thanks. My bad. I wiped and re-unpacked arrow source code and the above cmake commands completed with success.
(I also went back to use cmake 3.18 installed with apt).
Now I get this error when I try to install pyarrow with pip:
```
-- Build files have been written to: /tmp/pip-install-lmhsbdp3/pyarrow_0897d7658651493cb858488552932daa/build/cpp
-- Finished CMake for PyArrow C++
-- Running CMake build and install for PyArrow C++
cmake --build . --config release --target install
Scanning dependencies of target arrow_python_objlib
[ 4%] Building CXX object CMakeFiles/arrow_python_objlib.dir/arrow/python/arrow_to_pandas.cc.o
/tmp/pip-install-lmhsbdp3/pyarrow_0897d7658651493cb858488552932daa/pyarrow/src/arrow/python/arrow_to_pandas.cc:49:10: fatal error: arrow/compute/api.h: No such file or directory
49 | #include "arrow/compute/api.h"
| ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
gmake[2]: *** [CMakeFiles/arrow_python_objlib.dir/build.make:82: CMakeFiles/arrow_python_objlib.dir/arrow/python/arrow_to_pandas.cc.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:174: CMakeFiles/arrow_python_objlib.dir/all] Error 2
gmake: *** [Makefile:149: all] Error 2
error: command '/usr/bin/cmake' failed with exit code 2
----------------------------------------
ERROR: Failed building wheel for pyarrow
Failed to build pyarrow
ERROR: Could not build wheels for pyarrow which use PEP 517 and cannot be installed directly
```
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1360203950
`cmake .`
[install_manifest.txt](https://github.com/apache/arrow/files/10272580/install_manifest.txt)
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[GitHub] [arrow] westonpace commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
westonpace commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1371148481
I think that's ok. `MATCHES` should still match true if the pattern is a substring in the variable. Perhaps the issue is that this only applies to static builds? @kou might know more here.
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1374427442
It works now all the way. Thank you kou.
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[GitHub] [arrow] kou closed issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou closed issue #14920: [Python] wheel cmake error on Raspberry PI
URL: https://github.com/apache/arrow/issues/14920
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1360160583
Great!
Could you show the `cmake` command line used for Apache Arrow C++?
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1358710167
Thanks! Could you show the output of the following `CMakeLists.txt`?
```cmake
cmake_minimum_required(VERSION 3.20)
project(hello LANGUAGES CXX)
## this works:
find_package(Python 3.7 REQUIRED COMPONENTS Interpreter Development NumPy)
message(STATUS "#### Python_NumPy_VERSION = ${Python_NumPy_VERSION} ")
message(STATUS "#### Python_NumPy_FOUND = ${Python_NumPy_FOUND} ")
message(STATUS "#### Python_NumPy_INCLUDE_DIRS = ${Python_NumPy_INCLUDE_DIRS} ")
message(STATUS "#### Python_EXECUTABLE = ${Python_EXECUTABLE} ")
## this leaves Python_NumPy_INCLUDE_DIRS and the other variables empty
find_package(Python3 3.7 REQUIRED COMPONENTS Interpreter Development NumPy)
message(STATUS "#### Python3_NumPy_VERSION = ${Python3_NumPy_VERSION} ")
message(STATUS "#### Python3_NumPy_FOUND = ${Python3_NumPy_FOUND} ")
message(STATUS "#### Python3_NumPy_INCLUDE_DIRS = ${Python3_NumPy_INCLUDE_DIRS} ")
message(STATUS "#### Python3_EXECUTABLE = ${Python3_EXECUTABLE} ")
add_executable(hello "hello.cpp")
```
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1366196187
Could you the show full output of `pip install pyarrow`?
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1365276235
Thanks.
I also got some hints about dependencies here:
https://gist.github.com/renjieliu/b86f14e648cac7ddf582cb6ceb164d32
I had to fetch xsimd source manually and set this prior to the cmake commands:
```
export xsimd_DIR=/home/pi/xsimd/xsimd
```
But I could not get rid of this error:
```
[1/233] Creating directories for 'jemalloc_ep'
FAILED: jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-mkdir /home/pi/arrow/apache-arrow-10.0.1/cpp/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-mkdir
cd /home/pi/arrow/apache-arrow-10.0.1/cpp && /usr/local/bin/cmake -Dcfgdir= -P /home/pi/arrow/apache-arrow-10.0.1/cpp/jemalloc_ep-prefix/tmp/jemalloc_ep-mkdirs.cmake && /usr/local/bin/cmake -E touch /home/pi/arrow/apache-arrow-10.0.1/cpp/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-mkdir
cmake -E touch: failed to update "/home/pi/arrow/apache-arrow-10.0.1/cpp/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-mkdir".
ninja: build stopped: subcommand failed.
```
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1370590788
That worked. It least after I also added dataset on:
`cmake -DARROW_BUILD_STATIC=OFF -DARROW_COMPUTE=ON -DARROW_CSV=ON -DARROW_FILESYSTEM=ON -DARROW_JSON=ON -DARROW_DATASET=ON -DCMAKE_BUILD_TYPE=Release -GNinja .`
I successfully installed pyarrow. Thank you :-)
Then when I try to import pyarrow I get this error:
```
>>> import pyarrow
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.9/dist-packages/pyarrow/__init__.py", line 65, in <module>
import pyarrow.lib as _lib
ImportError: /usr/local/lib/libarrow.so.1000: undefined symbol: __atomic_fetch_add_8
```
Could that be related to this?
https://github.com/pytorch/pytorch/issues/22898#issuecomment-511692921
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1367084119
[find_arrow_include.txt](https://github.com/apache/arrow/files/10317734/find_arrow_include.txt)
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1347261439
Could you show the output of `/usr/bin/python3 -c 'import numpy; print(numpy.get_include())'`?
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1368461493
[cmake_build_output.txt](https://github.com/apache/arrow/files/10328957/cmake_build_output.txt)
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1366910533
Thanks.
Could you show `find /usr/local/include/arrow/`?
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1368530969
Hmm. Did you really use `cmake --preset=ninja-release-python-minimal .`?
Could you also show the output of `cmake --preset=ninja-release-python-minimal .`
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1360479081
OK. We need to specify some options to enable Apache Arrow C++ components that are used by pyarrow.
Could you try the following?
```bash
cmake --preset=ninja-release-python-minimal .
cmake --build .
sudo cmake --build . --target install
```
See also: https://arrow.apache.org/docs/dev/developers/python.html#build-and-test
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1359632892
New finding. I removed the try: ... except: pass in
https://gitlab.kitware.com/cmake/cmake/-/blob/v3.25.1/Modules/FindPython/Support.cmake#L3172
and got this error:
```
from numpy.core._multiarray_umath import (
ImportError: libcblas.so.3: cannot open shared object file: No such file or directory
```
I then followed the recommendation in https://numpy.org/devdocs/user/troubleshooting-importerror.html
and installed `sudo apt-get install libatlas-base-dev`
Then find_package(Python3... ran with the success.
` _Python3_NumPy_PATH = /tmp/pip-build-env-rlrroqfr/overlay/lib/python3.9/site-packages/numpy/core/include`
Now I get the following error instead. Attached output.
[pyarrow_install_make_error.txt](https://github.com/apache/arrow/files/10270070/pyarrow_install_make_error.txt)
---
Btw, I also installed arrow from source apache-arrow-10.0.1/cpp
cmake -> make -> sudo make install
Prior to all this, otherwise I got this error
```
CMake Error at CMakeLists.txt:63 (find_package):
By not providing "FindArrow.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Arrow", but
CMake did not find one.
```
Is this intended?
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1347854744
Sure:
`pi@raspberrypi:~ $ /usr/bin/python3 -c 'import numpy; print(numpy.get_include())'`
`/usr/lib/python3/dist-packages/numpy/core/include`
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[GitHub] [arrow] kou commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
kou commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1354025240
Hmm. there is no problem for it...
Can you add debug prints (`message("...")`) to /usr/local/share/cmake-3.25/Modules/FindPython/Support.cmake (line 3145-3226) https://gitlab.kitware.com/cmake/cmake/-/blob/v3.25.1/Modules/FindPython/Support.cmake#L3154-3226 ?
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1358087952
Thanks kou
I played around with messages you suggested and found something that could be the issue.
I attached a little cmake toy example and I was able to reproduce an error on both my Ubuntu/22.04 LTS (cmake 3.22.1)
as well as my Raspberry PI described above.
I looked at this:
https://github.com/apache/arrow/blob/16d40c844a98129299224d871b65f258d5ec8741/cpp/cmake_modules/FindPython3Alt.cmake#L60
It makes a difference whether you put this
`find_package(Python3 ...`
or
`find_package(Python ...`
Please check this toy example:
[CMakeLists.txt](https://github.com/apache/arrow/files/10261809/CMakeLists.txt)
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1371140341
Could it be this?
`message(STATUS "#### CMAKE_SYSTEM_PROCESSOR = ${CMAKE_SYSTEM_PROCESSOR} ")`
outputs:
`CMAKE_SYSTEM_PROCESSOR = armv7l `
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[GitHub] [arrow] sdy72 commented on issue #14920: [Python] wheel cmake error on Raspberry PI
Posted by GitBox <gi...@apache.org>.
sdy72 commented on issue #14920:
URL: https://github.com/apache/arrow/issues/14920#issuecomment-1368675576
I just verified it, yes. Output attached.
I just tried with this option:
-DARROW_COMPUTE=ON
but got out of memory error during build. I'll adding some swap
[cmake_ninja_output.txt](https://github.com/apache/arrow/files/10330199/cmake_ninja_output.txt)
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