Installation error when pip updates rpy2

[ThomasAkam]

I just tried installing pymer4 on windows 7 in a newly created conda environment using the follwing commands:

conda create --name pymer4
activate pymer4
conda install pip
conda install -c conda-forge r r-base r-lmertest r-lsmeans rpy2
pip install pymer4

The final command gave the following error:

(pymer4) C:\Users\takam>pip install pymer4
Collecting pymer4
  Using cached https://files.pythonhosted.org/packages/fe/81/a5a639614c22b901905
418f1f7f5364ae23c97ae4b081904665308ff233a/pymer4-0.6.0-py2.py3-none-any.whl
Collecting numpy>=1.12.0 (from pymer4)
  Downloading https://files.pythonhosted.org/packages/00/0e/5a8c34adb97fc1cd6636
d78050e575945e874c8516d501421d5a0f377a6c/numpy-1.15.4-cp37-none-win_amd64.whl (1
3.5MB)
    100% |████████████████████████████████| 13.5MB 1.5MB/s
Collecting rpy2>=2.9.4 (from pymer4)
  Using cached https://files.pythonhosted.org/packages/02/d1/074ffbbe7b4bf74c60b
75d74c8e67a1e4515b0d85f85cd6540e39610754a/rpy2-2.9.5.tar.gz
    Complete output from command python setup.py egg_info:
    R version 3.5.1 (2018-07-02) -- "Feather Spray"
    Copyright (C) 2018 The R Foundation for Statistical Computing
    Platform: x86_64-w64-mingw32/x64 (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY.
    You are welcome to redistribute it under the terms of the
    GNU General Public License versions 2 or 3.
    For more information about these matters see
    http://www.gnu.org/licenses/.

    'sh' is not recognized as an internal or external command,
    operable program or batch file.
    R version 3.5.1 (2018-07-02) -- "Feather Spray"
    C:\Users\takam\Anaconda3\envs\pymer4\lib\R\bin\x64\R CMD config --ldflags
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\takam\AppData\Local\Temp\pip-install-li1spxm4\rpy2\setup.py
", line 374, in <module>
        ri_ext = getRinterface_ext()
      File "C:\Users\takam\AppData\Local\Temp\pip-install-li1spxm4\rpy2\setup.py
", line 269, in getRinterface_ext
        ldf = shlex.split(' '.join(rexec.cmd_config('--ldflags')))
      File "C:\Users\takam\AppData\Local\Temp\pip-install-li1spxm4\rpy2\setup.py
", line 222, in cmd_config
        universal_newlines = True)
      File "C:\Users\takam\Anaconda3\envs\pymer4\lib\subprocess.py", line 389, i
n check_output
        **kwargs).stdout
      File "C:\Users\takam\Anaconda3\envs\pymer4\lib\subprocess.py", line 481, i
n run
        output=stdout, stderr=stderr)
    subprocess.CalledProcessError: Command '('C:\\Users\\takam\\Anaconda3\\envs\
\pymer4\\lib\\R\\bin\\x64\\R', 'CMD', 'config', '--ldflags')' returned non-zero
exit status 1.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\Users\takam\Ap
pData\Local\Temp\pip-install-li1spxm4\rpy2\

As the error occured when pip was trying to upgrade rpy2 to, I tried upgrading rpy2 using conda before trying to install pymer4:

conda install rpy2=2.9.4

I was then able to install pymer4 successfully with pip, but am posting this here in case anyone encounters the same issue.

[ejolly]

@ThomasAkam I know this is pretty late but hopefully the new version (just released) should address these compatibility issues