BUG: Cannot install SciPy using pip on Raspberry Pi

Describe your issue.

Tried to install scipy through pip3 install -3 requirements.txt with the following: librosa==0.6.3 numpy pandas soundfile==0.9.0 wave scikit-learn==0.24.2 tqdm==4.28.1 matplotlib==2.2.3 pyaudio==0.2.11 but it gave an error. Already tried using sudo apt-get install python3-scipy, but still the same issue happens.

Reproducing Code Example

N/A - all I did is run sudo LLVM_CONFIG=`which llvm-config-11` pip3 install -r requirements.txt

Error message

Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
  
  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [55 lines of output]
      The Meson build system
      Version: 0.62.2
      Source dir: /tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821
      Build dir: /tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-b9th5ncm/build
      Build type: native build
      Project name: SciPy
      Project version: 1.9.0
      C compiler for the host machine: cc (gcc 8.3.0 "cc (Raspbian 8.3.0-6+rpi1) 8.3.0")
      C linker for the host machine: cc ld.bfd 2.31.1
      C++ compiler for the host machine: c++ (gcc 8.3.0 "c++ (Raspbian 8.3.0-6+rpi1) 8.3.0")
      C++ linker for the host machine: c++ ld.bfd 2.31.1
      Host machine cpu family: arm
      Host machine cpu: armv7l
      Compiler for C supports arguments -Wno-unused-but-set-variable: YES
      Library m found: YES
      Fortran compiler for the host machine: gfortran (gcc 8.3.0 "GNU Fortran (Raspbian 8.3.0-6+rpi1) 8.3.0")
      Fortran linker for the host machine: gfortran ld.bfd 2.31.1
      Program cython found: YES (/tmp/pip-build-env-wco6m20p/overlay/bin/cython)
      Program pythran found: YES (/tmp/pip-build-env-wco6m20p/overlay/bin/pythran)
      Program cp found: YES (/usr/bin/cp)
      Program python3 found: YES (/usr/local/bin/python3.9)
      Found pkg-config: /usr/bin/pkg-config (0.29)
      
      ../../scipy/meson.build:40:0: ERROR: Command "/usr/local/bin/python3.9 -c import os; os.chdir(".."); import numpy; print(numpy.get_include())" failed with status 1.
      
      A full log can be found at /tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-b9th5ncm/build/meson-logs/meson-log.txt
      + meson setup --native-file=/tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-native-file.ini -Ddebug=false -Doptimization=2 --prefix=/usr/local /tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821 /tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-b9th5ncm/build
      Traceback (most recent call last):
        File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 909, in get_requires_for_build_wheel
          with _project(config_settings) as project:
        File "/usr/local/lib/python3.9/contextlib.py", line 119, in __enter__
          return next(self.gen)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 888, in _project
          with Project.with_temp_working_dir(
        File "/usr/local/lib/python3.9/contextlib.py", line 119, in __enter__
          return next(self.gen)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 547, in with_temp_working_dir
          yield cls(source_dir, tmpdir, build_dir)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 463, in __init__
          self._configure(reconfigure=bool(build_dir) and not native_file_mismatch)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 494, in _configure
          self._meson(
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 477, in _meson
          return self._proc('meson', *args)
        File "/tmp/pip-build-env-wco6m20p/overlay/lib/python3.9/site-packages/mesonpy/__init__.py", line 472, in _proc
          subprocess.check_call(list(args))
        File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command '['meson', 'setup', '--native-file=/tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-native-file.ini', '-Ddebug=false', '-Doptimization=2', '--prefix=/usr/local', '/tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821', '/tmp/pip-install-93y57wnw/scipy_34185744f91f4e619985e97d31e27821/.mesonpy-b9th5ncm/build']' returned non-zero exit status 1.
      [end of output]

SciPy/NumPy/Python version information

Python 3.9 - NumPy 1.22.4

[rekkitcwts]

Just a thought, but looking at that meson log, this is a Raspberry Pi, right? The compiler toolchain seems to suggest that, and it would be consistent with a bunch of source build failures because compatible binaries may not be available on default PyPI.

If my guess is right, you might try something like https://www.raspberrypi.com/news/piwheels/ perhaps? To check maybe do uname -m and let us know what it says? I think Pi boards use something other than the ARMv8/aarch64 that we support/provide binaries for? @rgommers or @h-vetinari may know better than I.

Yep – it’s a raspberry pi 3b+ with Buster in it – and it fixed itself when I downgraded the Python from 3.9 to 3.7 due to some “glibc” errors.

[yumemio]

Thanks @rgommers, and sorry for replying late. The Meson log revealed the actual issue: libcblas.so.3 was missing.

$ pip install --config-settings=builddir=/home/me/scipy/build scipy==1.9.3
...
$ cat scipy/build/meson-logs/meson-log.txt
...
(truncated)
...
Run-time dependency threads found: YES
Running command: /usr/bin/python3 -c import os; os.chdir(".."); import numpy; print(numpy.get_include())
--- stdout ---

--- stderr ---
Traceback (most recent call last):
  File "/tmp/pip-build-env-y7tf5n1e/overlay/lib/python3.9/site-packages/numpy/core/__init__.py", line 22, in <module>
    from . import multiarray
  File "/tmp/pip-build-env-y7tf5n1e/overlay/lib/python3.9/site-packages/numpy/core/multiarray.py", line 12, in <module>
    from . import overrides
  File "/tmp/pip-build-env-y7tf5n1e/overlay/lib/python3.9/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ImportError: libcblas.so.3: cannot open shared object file: No such file or directory

...
(truncated)
...

I have uploaded the complete log without truncation here for reference.

After running apt install libatlas-base-dev (as described in this StackOverflow answer), scipy==1.9.3 was installed successfully.

Therefore the complete installation process for RPi4 would be:

# apt install gfortran cmake libopenblas-base libopenblas-dev libatlas-base-dev
$ pip install scipy==1.9.3