Unable to install rpy2 in centos7/rhel7 with R4.4.0

[kelli-rstudio]

Describe the issue or bug
I am unable to install rpy2 on centos7/rhel7 when using R4.4.0. But I can install rpy2 on centos/rhel7 on earlier versions of R (eg R4.3.2) and on other linux operating systems (eg. ubuntu22, rhel8/9) when using R4.4.0.

To Reproduce

I'm using Python 3.10.9 and I installed R4.4.0 with:

curl -O https://cdn.rstudio.com/r/centos-7/pkgs/R-4.4.0-1-1.x86_64.rpm
sudo yum install -y R-4.4.0-1-1.x86_64.rpm
sudo rm /usr/local/bin/R
sudo rm /usr/local/bin/Rscript
sudo ln -s /opt/R/4.4.0/bin/R /usr/local/bin/R
sudo ln -s /opt/R/4.4.0/bin/Rscript /usr/local/bin/Rscript

Then ran pip install -v -U rpy2.

Expected behavior
I expect to be able to install rpy2 on centos/rhel7 when using R4.4.0.

Error

pip install -v -U rpy2
Using pip 22.3.1 from /opt/python/3.10.9/lib/python3.10/site-packages/pip (python 3.10)
Defaulting to user installation because normal site-packages is not writeable
Collecting rpy2
  Downloading rpy2-3.5.16.tar.gz (220 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 220.0/220.0 kB 10.3 MB/s eta 0:00:00
  Running command pip subprocess to install build dependencies
  Ignoring packaging: markers 'platform_system == "Windows"' don't match your environment
  Collecting setuptools>=61
    Using cached setuptools-69.5.1-py3-none-any.whl (894 kB)
  Collecting wheel
    Using cached wheel-0.43.0-py3-none-any.whl (65 kB)
  Collecting cffi>=1.15.0
    Downloading cffi-1.16.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB)
       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 443.9/443.9 kB 1.9 MB/s eta 0:00:00
  Collecting pycparser
    Downloading pycparser-2.22-py3-none-any.whl (117 kB)
       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.6/117.6 kB 26.0 MB/s eta 0:00:00
  Installing collected packages: wheel, setuptools, pycparser, cffi
  Successfully installed cffi-1.16.0 pycparser-2.22 setuptools-69.5.1 wheel-0.43.0

  [notice] A new release of pip available: 22.3.1 -> 24.0
  [notice] To update, run: /opt/python/3.10.9/bin/python3.10 -m pip install --upgrade pip
  Installing build dependencies ... done
  Running command Getting requirements to build wheel
  /usr/bin/ld: warning: libRblas.so, needed by /opt/R/4.4.0/lib/R/lib/libR.so, not found (try using -rpath or -rpath-link)
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `drot_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `drotg_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dswap_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dgemm_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dnrm2_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dscal_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `zgemm_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dtrsm_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `daxpy_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dcopy_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dsyrk_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dasum_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `ddot_'
  /opt/R/4.4.0/lib/R/lib/libR.so: undefined reference to `dgemv_'
  collect2: error: ld returned 1 exit status
  Traceback (most recent call last):
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 269, in link
      self.spawn(linker + ld_args)
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 1041, in spawn
      spawn(cmd, dry_run=self.dry_run, **kwargs)
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/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/gcc' failed with exit code 1

  During handling of the above exception, another exception occurred:

  Traceback (most recent call last):
    File "/opt/python/3.10.9/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 351, in <module>
      main()
    File "/opt/python/3.10.9/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 333, in main
      json_out['return_val'] = hook(**hook_input['kwargs'])
    File "/opt/python/3.10.9/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 118, in get_requires_for_build_wheel
      return hook(config_settings)
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/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-hv1b_832/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
      self.run_setup()
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/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-hv1b_832/overlay/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 781, in link_executable
      self.link(
    File "/tmp/pip-build-env-hv1b_832/overlay/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 271, in link
      raise LinkError(msg)
  distutils.errors.LinkError: command '/usr/bin/gcc' failed with exit code 1
  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.
  full command: /opt/python/3.10.9/bin/python3.10 /opt/python/3.10.9/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /tmp/tmprgac1v87
  cwd: /tmp/pip-install-memgunyq/rpy2_961064ee4f144ec09b45576b360b941c
  Getting requirements to build wheel ... error
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.

[lgautier]

You have:

sudo rm /usr/local/bin/R
sudo rm /usr/local/bin/Rscript
sudo ln -s /opt/R/4.4.0/bin/R /usr/local/bin/R
sudo ln -s /opt/R/4.4.0/bin/Rscript /usr/local/bin/Rscript

I suggest instead:

export PATH=/opt/R/4.4.0/bin/:${PATH}
pip install -v -U rpy2