can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS #1106

sanboton · 2024-04-20T19:23:56Z

Describe the issue or bug

I can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS

To Reproduce

Open cmd as administrator

pip3 install rpy2 or pip install rpy2

Expected behavior
install rpy2

Error

pip3 install rpy2
Defaulting to user installation because normal site-packages is not writeable
Collecting rpy2
  Using cached rpy2-3.5.16.tar.gz (220 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      Traceback (most recent call last):
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 162, in get_requires_for_build_wheel
          return self._get_build_requires(
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 143, in _get_build_requires
          self.run_setup()
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 158, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 23, in <module>
          import setuptools.command.build
      ModuleNotFoundError: No module named 'setuptools.command.build'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build 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.

The text was updated successfully, but these errors were encountered:

sanboton · 2024-04-20T19:24:18Z

I had to go down to version 3.5.2 to be able to install it

lgautier · 2024-04-20T19:37:33Z

What is your version of setuptools?

sanboton · 2024-04-20T20:14:28Z

Hi, it's 69.5.1.

pip3 show setuptools
Name: setuptools
Version: 69.5.1
Summary: Easily download, build, install, upgrade, and uninstall Python packages
Home-page: https://github.com/pypa/setuptools
Author: Python Packaging Authority
Author-email: distutils-sig@python.org
License:
Location: /home/NAME/.local/lib/python3.10/site-packages
Requires:
Required-by: APScheduler

lgautier · 2024-04-20T20:58:18Z

I can't reproduce with Ubuntu 22.04, Python 3.10, and the same setuptools. It installs fine. What is your Python version?

sanboton · 2024-04-21T08:59:31Z

My version is 3.10.12:

python3 -V
Python 3.10.12

lgautier · 2024-04-21T17:22:51Z

The error traceback says that the path is /usr/lib/python3/dist-packages/setuptools/build_meta.py while pip3 show setuptools says that the path is /home/NAME/.local/lib/python3.10/site-packages.

Hasnae12 · 2024-05-01T17:22:06Z

Describe the issue or bug

I can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS

To Reproduce

Open cmd as administrator

pip3 install rpy2 or pip install rpy2

Expected behavior install rpy2

Error

pip3 install rpy2
Defaulting to user installation because normal site-packages is not writeable
Collecting rpy2
  Using cached rpy2-3.5.16.tar.gz (220 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error

  × Getting requirements to build wheel did not run successfully.
  │ exit code: 1
  ╰─> [16 lines of output]
      Traceback (most recent call last):
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
          main()
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/lib/python3/dist-packages/pip/_vendor/pep517/in_process/_in_process.py", line 130, in get_requires_for_build_wheel
          return hook(config_settings)
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 162, in get_requires_for_build_wheel
          return self._get_build_requires(
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 143, in _get_build_requires
          self.run_setup()
        File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 158, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 23, in <module>
          import setuptools.command.build
      ModuleNotFoundError: No module named 'setuptools.command.build'
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× Getting requirements to build 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.

Hi, I have the same issue on Ubuntu 20.04.6 LTS

lgautier · 2024-05-05T14:49:12Z

The last mentions

Open cmd as administrator

while the traceback has

Defaulting to user installation because normal site-packages is not writeable

There is a contradiction.

I believe that both error reports result from invalid assumptions by the operators about what Python+libraries are used, or the system ID running the installation process.

D3SL · 2024-05-11T00:07:45Z

Had this as well. Using rocker/r2u:jammy as a base I couldn't get the latest version of rpy2 to install, only 3.5.2.

Edit: I solved this with RUN pip3 install --upgrade pip wheel setuptools>51 prior to trying to install rpy2.

Yunuuuu · 2024-05-16T16:08:26Z

The same problem

Yunuuuu · 2024-05-16T16:11:39Z

Had this as well. Using rocker/r2u:jammy as a base I couldn't get the latest version of rpy2 to install, only 3.5.2.

Edit: I solved this with RUN pip3 install --upgrade pip wheel setuptools>51 prior to trying to install rpy2.

This works well

amano-takahisa · 2024-05-17T17:56:59Z

Same issues on Ubuntu 24.04.

To reproduce, build container with following Dockerfile:

FROM ubuntu:24.04

RUN apt-get update \
    && apt-get install -y --no-install-recommends \
    r-base \
    r-base-dev \
    python3 \
    python3-pip \
    python3-venv

USER ubuntu
WORKDIR /home/ubuntu

Build and enter the container with docker build -t test_rpy2 . && docker run -it --rm test_rpy2 /bin/bash, and in that container, run:

python3 -m venv .venv
source .venv/bin/activate
pip install -U pip setuptools 
pip install rpy2

Raise the following error.

Details

$ pip install rpy2
Collecting rpy2
  Downloading rpy2-3.5.16.tar.gz (220 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 220.0/220.0 kB 8.1 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... error
  error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.

│ exit code: 1

╰─> [37 lines of output]

/usr/bin/ld: cannot find -ltirpc: No such file or directory

collect2: error: ld returned 1 exit status

Traceback (most recent call last):

File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/_distutils/unixccompiler.py", line 269, in link

self.spawn(linker + ld_args)

File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/_distutils/ccompiler.py", line 1041, in spawn

spawn(cmd, dry_run=self.dry_run, **kwargs)

File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/_distutils/spawn.py", line 68, in spawn

raise DistutilsExecError(f"command {cmd!r} failed with exit code {exitcode}")

distutils.errors.DistutilsExecError: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/home/ubuntu/.venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
      main()
    File "/home/ubuntu/.venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/ubuntu/.venv/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
      return hook(config_settings)
             ^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
      return self._get_build_requires(config_settings, requirements=['wheel'])
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 311, in run_setup
      exec(code, locals())
    File "<string>", line 141, in <module>
    File "<string>", line 121, in get_r_c_extension_status
    File "<string>", line 82, in get_c_extension_status
    File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/_distutils/ccompiler.py", line 781, in link_executable
      self.link(
    File "/tmp/pip-build-env-3em6ull7/overlay/lib/python3.12/site-packages/setuptools/_distutils/unixccompiler.py", line 271, in link
      raise LinkError(msg)
  distutils.errors.LinkError: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: subprocess-exited-with-error
× Getting requirements to build 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.

pip install 'rpy2<=3.5.12' worked, but not pip install 'rpy2>=3.5.13'.

setuptools is as follows:

$ pip3 show setuptools
Name: setuptools
Version: 69.5.1
Summary: Easily download, build, install, upgrade, and uninstall Python packages
Home-page: https://github.com/pypa/setuptools
Author: Python Packaging Authority
Author-email: distutils-sig@python.org
License:
Location: /home/ubuntu/.venv/lib/python3.12/site-packages
Requires:
Required-by:

amano-takahisa · 2024-05-18T08:49:50Z

I solved my issue with apt-get install libtirpc-dev beforehand.

lgautier · 2024-05-24T16:45:22Z

Had this as well. Using rocker/r2u:jammy as a base I couldn't get the latest version of rpy2 to install, only 3.5.2.

Edit: I solved this with RUN pip3 install --upgrade pip wheel setuptools>51 prior to trying to install rpy2.

@D3SL - This seems odd. rpy2 already requires setuptools>=61:

rpy2/pyproject.toml

Line 3 in ae74c26

"setuptools >= 61",

lgautier · 2024-05-24T16:53:06Z

I solved my issue with apt-get install libtirpc-dev beforehand.

@amano-takahisa - The library is a dependency for R builds (see https://archlinux.org/packages/extra/x86_64/r/) but I was not aware that the headers were also necessary (when build C extensions for rpy2). Did you identify where those headers are required?

amano-takahisa · 2024-05-28T15:13:34Z

@lgautier I'm not sure where that the header is required.
I just guessed from the following part of error message.

/usr/bin/ld: cannot find -ltirpc: No such file or directory

sanboton added the bug Something isn't working label Apr 20, 2024

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can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS #1106

can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS #1106

sanboton commented Apr 20, 2024

sanboton commented Apr 20, 2024

lgautier commented Apr 20, 2024

sanboton commented Apr 20, 2024

lgautier commented Apr 20, 2024

sanboton commented Apr 21, 2024

lgautier commented Apr 21, 2024

Hasnae12 commented May 1, 2024

lgautier commented May 5, 2024

D3SL commented May 11, 2024 •

edited

Yunuuuu commented May 16, 2024

Yunuuuu commented May 16, 2024

amano-takahisa commented May 17, 2024 •

edited

amano-takahisa commented May 18, 2024 •

edited

lgautier commented May 24, 2024

lgautier commented May 24, 2024

amano-takahisa commented May 28, 2024

can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS #1106

can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS #1106

Comments

sanboton commented Apr 20, 2024

sanboton commented Apr 20, 2024

lgautier commented Apr 20, 2024

sanboton commented Apr 20, 2024

lgautier commented Apr 20, 2024

sanboton commented Apr 21, 2024

lgautier commented Apr 21, 2024

Hasnae12 commented May 1, 2024

lgautier commented May 5, 2024

D3SL commented May 11, 2024 • edited

Yunuuuu commented May 16, 2024

Yunuuuu commented May 16, 2024

amano-takahisa commented May 17, 2024 • edited

amano-takahisa commented May 18, 2024 • edited

lgautier commented May 24, 2024

lgautier commented May 24, 2024

amano-takahisa commented May 28, 2024

D3SL commented May 11, 2024 •

edited

amano-takahisa commented May 17, 2024 •

edited

amano-takahisa commented May 18, 2024 •

edited