-L/usr/lib... can leak onto linker command line

[being-ak-70]

I'm trying to build .so file for Android abi arm64-v8a

I run this command on Linux terminal

sudo ./build-wheel.py --python 3.11 --abi arm64-v8a packages/cython-example

And I'm getting this error :

ld: error: --fix-cortex-a53-843419 is only supported on AArch64 targets
clang: error: linker command failed with exit code 1 (use -v to see invocation)

This is the complete output from the build-wheel

build-wheel.py: python3.11 -m pip --disable-pip-version-check install cython==0.29.36
Requirement already satisfied: cython==0.29.36 in /usr/local/lib/python3.11/dist-packages (0.29.36)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
build-wheel.py: cd /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0
build-wheel.py: rm -rf /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a
build-wheel.py: mkdir -p /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a
build-wheel.py: cp -a /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/src /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/src
build-wheel.py: mkdir -p /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements
build-wheel.py: mkdir -p /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include
build-wheel.py: mkdir -p /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib
build-wheel.py: unzip -q -d /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy /home/aniket/Desktop/chaquopy/maven/com/chaquo/python/target/3.11.0-2/target-3.11.0-2-arm64-v8a.zip include/* jniLibs/*
build-wheel.py: mv /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/jniLibs/arm64-v8a/* /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib
build-wheel.py: rm -r /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/jniLibs
build-wheel.py: ln -s libcrypto_chaquopy.so /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/libcrypto.so
build-wheel.py: ln -s libpython3.11.so /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/libpython3..so
build-wheel.py: ln -s libsqlite3_chaquopy.so /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/libsqlite3.so
build-wheel.py: ln -s libssl_chaquopy.so /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/libssl.so
build-wheel.py: abi=arm64-v8a; api_level=21; prefix=/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy; . /home/aniket/Desktop/chaquopy/server/pypi/../../target/build-common.sh; export
/home/aniket/Desktop/chaquopy/server/pypi/../../target/build-common.sh: line 14: /home/aniket/Android/Sdk/ndk/22.1.7171670: Is a directory
build-wheel.py: /home/aniket/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/llvm-ar rc /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/libpthread.a
build-wheel.py: /home/aniket/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/llvm-ar rc /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib/librt.a
build-wheel.py: cd /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/src
build-wheel.py: python3.11 -m pip --disable-pip-version-check wheel --no-deps -v -e .
/usr/local/lib/python3.11/dist-packages/_distutils_hack/init.py:33: UserWarning: Setuptools is replacing distutils.
warnings.warn("Setuptools is replacing distutils.")
Obtaining file:///home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/src
Running command python setup.py egg_info
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future np.bytes will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
/usr/local/lib/python3.11/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/src/hello.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling hello.pyx because it changed.
[1/1] Cythonizing hello.pyx
running egg_info
creating /tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info
writing /tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/PKG-INFO
writing dependency_links to /tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/dependency_links.txt
writing top-level names to /tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/top_level.txt
writing manifest file '/tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/SOURCES.txt'
reading manifest file '/tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/SOURCES.txt'
writing manifest file '/tmp/pip-pip-egg-info-btb74xjr/cython_example.egg-info/SOURCES.txt'
Preparing metadata (setup.py) ... done
Building wheels for collected packages: cython-example
Running command python setup.py bdist_wheel
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future np.bytes will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running bdist_wheel
running build
running build_ext
building 'hello' extension
INFO: C compiler: /home/aniket/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/aarch64-linux-android21-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include -idirafter /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include/python3.11 -fPIC

creating build
creating build/temp.linux_aarch64-cpython-311
INFO: compile options: '-c'
INFO: aarch64-linux-android21-clang: hello.c
creating build/lib.linux_aarch64-cpython-311
INFO: /home/aniket/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/aarch64-linux-android21-clang -shared -L/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib -Wl,--exclude-libs,libgcc.a -Wl,--exclude-libs,libgcc_real.a -Wl,--exclude-libs,libunwind.a -Wl,--build-id=sha1 -Wl,--no-rosegment -lm -Wl,--no-undefined -lpython3.11 -I/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include -idirafter /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include/python3.11 build/temp.linux_aarch64-cpython-311/hello.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux_aarch64-cpython-311/hello.cpython-311-x86_64-linux-gnu.so
ld: error: --fix-cortex-a53-843419 is only supported on AArch64 targets
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: Command "/home/aniket/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/aarch64-linux-android21-clang -shared -L/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/lib -Wl,--exclude-libs,libgcc.a -Wl,--exclude-libs,libgcc_real.a -Wl,--exclude-libs,libunwind.a -Wl,--build-id=sha1 -Wl,--no-rosegment -lm -Wl,--no-undefined -lpython3.11 -I/home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include -idirafter /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/requirements/chaquopy/include/python3.11 build/temp.linux_aarch64-cpython-311/hello.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux_aarch64-cpython-311/hello.cpython-311-x86_64-linux-gnu.so" failed with exit status 1
error: subprocess-exited-with-error

× python setup.py bdist_wheel 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.

cwd: /home/aniket/Desktop/chaquopy/server/pypi/packages/cython-example/build/1.0/cp311-cp311-android_21_arm64_v8a/src/
Building wheel for cython-example (setup.py) ... error
ERROR: Failed building wheel for cython-example
Running setup.py clean for cython-example
Running command python setup.py clean
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future np.bytes will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
Chaquopy: clean command disabled
Failed to build cython-example
ERROR: Failed to build one or more wheels
Traceback (most recent call last):
File "/home/aniket/Desktop/chaquopy/server/pypi/./build-wheel.py", line 812, in
BuildWheel().main()
File "/home/aniket/Desktop/chaquopy/server/pypi/./build-wheel.py", line 98, in main
self.unpack_and_build()
File "/home/aniket/Desktop/chaquopy/server/pypi/./build-wheel.py", line 145, in unpack_and_build
wheel_filename = self.build_wheel()
^^^^^^^^^^^^^^^^^^
File "/home/aniket/Desktop/chaquopy/server/pypi/./build-wheel.py", line 313, in build_wheel
return self.build_with_pip()
^^^^^^^^^^^^^^^^^^^^^
File "/home/aniket/Desktop/chaquopy/server/pypi/./build-wheel.py", line 402, in build_with_pip
wheel_filename, = glob("*.whl") # Note comma
^^^^^^^^^^^^^^^
ValueError: not enough values to unpack (expected 1, got 0)

[being-ak-70]

Please reply sir @mhsmith it's been a week.

[mhsmith]

Sorry for the slow reply.

This is another instance of -L/usr/lib... leaking onto a linker command line. I haven't reproduced this myself yet, but it's been reported by several users, with various resulting errors:

• -L/usr/lib... can leak onto linker command line #909
  • ld: error: --fix-cortex-a53-843419 is only supported on AArch64 targets
• Trying to build a wheel file for netcdf4 and getting errors #823 (comment)
  • build-wheel.py: Error: /home/me/WHEEL-TEST/chaquopy/server/pypi/packages/chaquopy-netcdf4-python/build/1.6.3/cp38-cp38-android_21_x86_64/fix_wheel/netCDF4/_netCDF4.so is linked against unknown library 'libm.so.6'.
• Astropy & Photutils Libraries #812 (comment)
  • ld: error: /home/deniz/Android/Sdk/ndk/22.1.7171670/toolchains/llvm/prebuilt/linux-x86_64/bin/../sysroot/usr/lib/arm-linux-androideabi/21/crtbegin_so.o is incompatible with elf64-x86-64
ld: error: /home/deniz/dev/fork/chaquopy/server/pypi/packages/astropy/build/5.1/cp38-cp38-android_21_armeabi_v7a/requirements/chaquopy/lib/libpython3.8.so is incompatible with elf64-x86-64
• No matching distribution found for lameenc #773 (comment)
  • Same error as previous
• Building lz4 library #915
  • Same error as previous
• Add package: miniaudio #896 (comment)
  • Same error as previous, but not yet confirmed to have the same command line problem

I'll look into this further and get back to you.

[being-ak-70]

I tried to build cython-example with Python 3.8.13 and it got built successfully.

Thank you sir @mhsmith for your support

[mhsmith]

So it works with Python 3.8 but not with 3.11? Where did you get each version of Python?

For example, I see that your Python 3.11 is in /usr/local. Is that because you compiled it yourself?

Or if you got either of them from your distribution, please let me know the distribution name and version.

[being-ak-70]

I'm using Kali Linux in Virtual Machine, Python 3.11 came pre-installed with it.

When it didn't work with 3.11 then I installed 3.8 following this article

https://tecadmin.net/install-python-3-8-ubuntu/

then again I tried to build the cython-example with 3.8 and it built successfully

Then I re-installed 3.11 following the same article and now it builds successfully with 3.11 also

I think the problem was with Python's configuration not with build-wheel tool.

[mhsmith]

I think most if not all of these were caused by this block in setuptools/_distutils/command/build_ext.py:

        if sysconfig.get_config_var('Py_ENABLE_SHARED'):
            if not sysconfig.python_build:
                # building third party extensions
                self.library_dirs.append(sysconfig.get_config_var('LIBDIR'))

Py_ENABLE_SHARED is 0 in Python builds from miniconda, as well as pyenv before version 2.3.10 (which is what I was using myself). However, it's set to 1 in Python builds from Debian, as well as pyenv since version 2.3.10.

I fixed this by updating the distutils monkey patch to filter lib dirs in the same way as we already do for include dirs. I also limited both of them to known safe locations, specifically the src and requirements subdirectories of the build dir. This may be too strict, but we'll see.