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[Docker on Debian 11] Could not build wheels for psutil #2192

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wasabipesto opened this issue Jan 15, 2023 · 7 comments
Open

[Docker on Debian 11] Could not build wheels for psutil #2192

wasabipesto opened this issue Jan 15, 2023 · 7 comments
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bug doc linux wheels

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@wasabipesto
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Summary

  • OS: Debian GNU/Linux 11 (bullseye)
  • Docker Image OS: Alpine 3
  • Architecture: x86_64
  • Psutil version: 5.9.4
  • Python version: 3.10.9-r1
  • Type: Installation via pip in Dockerfile

Description

In this Dockerfile, I use the latest version of alpine 3, install python 3, and then attempt to install jupyter. The build fails when attempting to install psutil as a dependency.

justin@kalak:/opt/hephaestus/test$ cat Dockerfile 
FROM alpine:3
RUN apk add --update --no-cache python3 python3-dev
RUN python3 -m ensurepip
RUN pip3 install --no-cache-dir --upgrade pip
RUN pip3 install --no-cache-dir jupyterjustin@kalak:/opt/hephaestus/test$ 
justin@kalak:/opt/hephaestus/test$ cat Dockerfile 
FROM alpine:3
RUN apk add --update --no-cache python3 python3-dev
RUN python3 -m ensurepip
RUN pip3 install --no-cache-dir --upgrade pip
RUN pip3 install --no-cache-dir jupyter
justin@kalak:/opt/hephaestus/test$ docker build --no-cache .
Sending build context to Docker daemon  2.048kB
Step 1/5 : FROM alpine:3
 ---> 042a816809aa
Step 2/5 : RUN apk add --update --no-cache python3 python3-dev
 ---> Running in 627b1de47fcd
fetch https://dl-cdn.alpinelinux.org/alpine/v3.17/main/x86_64/APKINDEX.tar.gz
fetch https://dl-cdn.alpinelinux.org/alpine/v3.17/community/x86_64/APKINDEX.tar.gz
(1/15) Installing libbz2 (1.0.8-r4)
(2/15) Installing libexpat (2.5.0-r0)
(3/15) Installing libffi (3.4.4-r0)
(4/15) Installing gdbm (1.23-r0)
(5/15) Installing xz-libs (5.2.9-r0)
(6/15) Installing libgcc (12.2.1_git20220924-r4)
(7/15) Installing libstdc++ (12.2.1_git20220924-r4)
(8/15) Installing mpdecimal (2.5.1-r1)
(9/15) Installing ncurses-terminfo-base (6.3_p20221119-r0)
(10/15) Installing ncurses-libs (6.3_p20221119-r0)
(11/15) Installing readline (8.2.0-r0)
(12/15) Installing sqlite-libs (3.40.1-r0)
(13/15) Installing python3 (3.10.9-r1)
(14/15) Installing pkgconf (1.9.3-r0)
(15/15) Installing python3-dev (3.10.9-r1)
Executing busybox-1.35.0-r29.trigger
OK: 107 MiB in 30 packages
Removing intermediate container 627b1de47fcd
 ---> 37c22c0d420a
Step 3/5 : RUN python3 -m ensurepip
 ---> Running in da41305318a8
Looking in links: /tmp/tmpi9dqhuph
Processing /tmp/tmpi9dqhuph/setuptools-65.5.0-py3-none-any.whl
Processing /tmp/tmpi9dqhuph/pip-22.3.1-py3-none-any.whl
Installing collected packages: setuptools, pip
Successfully installed pip-22.3.1 setuptools-65.5.0
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
Removing intermediate container da41305318a8
 ---> 79a9aefa5266
Step 4/5 : RUN pip3 install --no-cache-dir --upgrade pip
 ---> Running in 4a284b1fda82
Requirement already satisfied: pip in /usr/lib/python3.10/site-packages (22.3.1)
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
Removing intermediate container 4a284b1fda82
 ---> 217dac38a4c1
Step 5/5 : RUN pip3 install --no-cache-dir jupyter
 ---> Running in a28cf131228e
Collecting jupyter
  Downloading jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
Collecting notebook
  Downloading notebook-6.5.2-py3-none-any.whl (439 kB)
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Collecting ipywidgets
  Downloading ipywidgets-8.0.4-py3-none-any.whl (137 kB)
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Collecting nbconvert
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Collecting jupyter-console
  Downloading jupyter_console-6.4.4-py3-none-any.whl (22 kB)
Collecting ipykernel
  Downloading ipykernel-6.20.1-py3-none-any.whl (149 kB)
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Collecting psutil
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  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting comm>=0.1.1
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Collecting traitlets>=5.4.0
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Collecting packaging
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Collecting jupyter-client>=6.1.12
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Collecting widgetsnbextension~=4.0
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Collecting jupyterlab-widgets~=3.0
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Collecting pygments
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Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
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Collecting jupyter-core>=4.7
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Collecting pandocfilters>=1.4.1
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  Downloading cffi-1.15.1-cp310-cp310-musllinux_1_1_x86_64.whl (464 kB)
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Collecting pure-eval
  Downloading pure_eval-0.2.2-py3-none-any.whl (11 kB)
Collecting asttokens>=2.1.0
  Downloading asttokens-2.2.1-py2.py3-none-any.whl (26 kB)
Collecting executing>=1.2.0
  Downloading executing-1.2.0-py2.py3-none-any.whl (24 kB)
Collecting sniffio>=1.1
  Downloading sniffio-1.3.0-py3-none-any.whl (10 kB)
Collecting idna>=2.8
  Downloading idna-3.4-py3-none-any.whl (61 kB)
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Collecting pycparser
  Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 118.7/118.7 kB 95.1 MB/s eta 0:00:00
Collecting python-json-logger>=2.0.4
  Downloading python_json_logger-2.0.4-py3-none-any.whl (7.8 kB)
Collecting rfc3339-validator
  Downloading rfc3339_validator-0.1.4-py2.py3-none-any.whl (3.5 kB)
Collecting pyyaml>=5.3
  Downloading PyYAML-6.0.tar.gz (124 kB)
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  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting rfc3986-validator>=0.1.1
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Building wheels for collected packages: psutil, pyyaml
  Building wheel for psutil (pyproject.toml): started
  Building wheel for psutil (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Building wheel for psutil (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [41 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-310
      creating build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_pslinux.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_psosx.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_pswindows.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_compat.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_pssunos.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_psbsd.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/__init__.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_psposix.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_common.py -> build/lib.linux-x86_64-cpython-310/psutil
      copying psutil/_psaix.py -> build/lib.linux-x86_64-cpython-310/psutil
      creating build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_system.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/__main__.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_memleaks.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/runner.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/__init__.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_testutils.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      copying psutil/tests/test_process.py -> build/lib.linux-x86_64-cpython-310/psutil/tests
      running build_ext
      building 'psutil._psutil_linux' extension
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/psutil
      gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Os -fomit-frame-pointer -g -O2 -Os -fomit-frame-pointer -g -O2 -Os -fomit-frame-pointer -g -O2 -DTHREAD_STACK_SIZE=0x100000 -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_SIZEOF_PID_T=4 -DPSUTIL_VERSION=594 -DPy_LIMITED_API=0x03060000 -DPSUTIL_LINUX=1 -DPSUTIL_ETHTOOL_MISSING_TYPES=1 -I/usr/include/python3.10 -c psutil/_psutil_common.c -o build/temp.linux-x86_64-cpython-310/psutil/_psutil_common.o
      error: command 'gcc' failed: No such file or directory
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for psutil
  Building wheel for pyyaml (pyproject.toml): started
  Building wheel for pyyaml (pyproject.toml): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-6.0-cp310-cp310-linux_x86_64.whl size=45330 sha256=530d140ff46eb0876732f00e31cb6c5fa8e121965881c9f0f33bc3e5471ddae5
  Stored in directory: /tmp/pip-ephem-wheel-cache-__y6ht9z/wheels/06/72/f6/3f89f64cf1943a82e42cdd8e59d7b2aa98769fd48b08019fc7
Successfully built pyyaml
Failed to build psutil
ERROR: Could not build wheels for psutil, which is required to install pyproject.toml-based projects
The command '/bin/sh -c pip3 install --no-cache-dir jupyter' returned a non-zero code: 1

Related Issues

I searched for related issues and found the following:
@ben9923
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ben9923 commented Jan 18, 2023 •
edited

Wheels for musllinux (which Alpine is using, unlike the commonly used glibc [== manylinux]) are not available for psutil, see #2126.
As they are not yet available, you'll need to have all necessary build tools/libraries to install it, rather than a minimal Python installation.

You can see the changes in mentioned PR also include whatever you need to install for a successful build on Alpine:

apk add gcc musl-dev linux-headers python3-dev

IIRC @giampaolo once mentioned he's still not sure whether he'd like to provide musllinux wheels, so until then you'll need to install the system packages mentioned above.

Another option would be using a glibc-based base image, like python:slim.
BTW, for Alpine, consider the python:alpine base image over manually installing python3 on top of the base alpine image.

@basebandit
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Am just confirming here that installing the following gcc musl-dev linux-headers python3-dev as instructed above worked for me. Thank you @ben9923

@MrMino
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MrMino commented Aug 2, 2023

IIRC @giampaolo once mentioned he's still not sure whether he'd like to provide musllinux wheels, so until then you'll need to install the system packages mentioned above.

Would be nice to hear from @giampaolo the rationale behind this. For all modern versions of pip the wheel will be built anyway during installation, so unless psutil is planning to explicitly drop support for Musl-based distributions, there is no reason not to put the said wheel on PyPI.

It saves electricity 🥬 😉.

@guidopetri
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@giampaolo I'm running into this issue as well with Python 3.11, Debian 12, psutil 5.9.6.

@baggiponte
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Me too, same issue with python:3.10-slim.

sgoggins added a commit to chaoss/augur that referenced this issue Jan 26, 2024
@sgoggins
Update Dockerfile
d5dcce5 
Resolving ps_utils error: 

```
giampaolo/psutil#2192
```

Signed-off-by: Sean P. Goggins <outdoors@acm.org>
sgoggins added a commit to chaoss/augur that referenced this issue Jan 26, 2024
@sgoggins
Update Dockerfile
79d74a1 
Fixing PS_UTIL issue on python3.10

gcc musl-dev linux-headers python3-dev

giampaolo/psutil#2192

Signed-off-by: Sean P. Goggins <outdoors@acm.org>
@NFeruch
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NFeruch commented Feb 11, 2024

Can confirm that going from python:3.10-alpine to python:3.10-slim allowed me to install psutil in docker

@weiglszonja weiglszonja mentioned this issue Feb 26, 2024
Merged
2 tasks
@hadiawahab
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Not only alpine, but python:3.12-slim also gave me the error mentioned in the post and for cffi too

adding these lines solved the issue
RUN apk add gcc musl-dev linux-headers python3-dev
RUN apk add libffi-dev

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@MrMino @basebandit @guidopetri @ben9923 @wasabipesto @NFeruch @baggiponte @hadiawahab