can't install rpy2 3.5.16 on Ubuntu 22.04.3 LTS about rpy2 HOT 16 OPEN

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

from rpy2.

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

from rpy2.

What is your version of setuptools?

from rpy2.

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: [email protected]
License:
Location: /home/NAME/.local/lib/python3.10/site-packages
Requires:
Required-by: APScheduler

from rpy2.

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

from rpy2.

My version is 3.10.12:

python3 -V
Python 3.10.12

from rpy2.

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.

from rpy2.

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

from rpy2.

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.

from rpy2.

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.

from rpy2.

The same problem

from rpy2.

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.

$ 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: [email protected]
License:
Location: /home/ubuntu/.venv/lib/python3.12/site-packages
Requires:
Required-by:

from rpy2.

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

from rpy2.

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:

from rpy2.

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?

from rpy2.

@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

from rpy2.