installation issue for pymer4 #38

jagadavk · 2019-04-03T08:35:27Z

base) C:\Users\j.siddaramanna>conda install pymer4
Collecting package metadata: done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

pymer4

Current channels:

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(base) C:\Users\j.siddaramanna>pip install pymer4
Collecting pymer4
Using cached https://files.pythonhosted.org/packages/fe/81/a5a639614c22b901905418f1f7f5364ae23c97ae4b081904665308ff233a/pymer4-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: patsy>=0.4.1 in c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages (from pymer4) (0.5.1)
Requirement already satisfied: pandas>=0.19.1 in c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages (from pymer4) (0.23.4)
Requirement already satisfied: matplotlib>=2.0 in c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages (from pymer4) (3.0.2)
Collecting rpy2>=2.9.4 (from pymer4)
Using cached https://files.pythonhosted.org/packages/9c/81/86f9ba26b4fb27c17a143c064301f4928681c96c09c59edb23a44767c3d6/rpy2-3.0.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\cparser.py", line 276, in _parse
ast = _get_parser().parse(fullcsource)
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\c_parser.py", line 152, in parse
debug=debuglevel)
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\ply\yacc.py", line 331, in parse
return self.parseopt_notrack(input, lexer, debug, tracking, tokenfunc)
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\ply\yacc.py", line 1199, in parseopt_notrack
tok = call_errorfunc(self.errorfunc, errtoken, self)
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\ply\yacc.py", line 193, in call_errorfunc
r = errorfunc(token)
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\c_parser.py", line 1848, in p_error
column=self.clex.find_tok_column(p)))
File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\pycparser\plyparser.py", line 67, in _parse_error
raise ParseError("%s: %s" % (coord, msg))
pycparser.plyparser.ParseError: :23:5: before: blah1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\JA6F5~1.SID\AppData\Local\Temp\pip-install-sj6qv50w\rpy2\setup.py", line 185, in <module>
    'rpy2': ['doc/source/rpy2_logo.png', ]}
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\setuptools\__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\distutils\core.py", line 108, in setup
    _setup_distribution = dist = klass(attrs)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\setuptools\dist.py", line 447, in __init__
    k: v for k, v in attrs.items()
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\distutils\dist.py", line 292, in __init__
    self.finalize_options()
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\setuptools\dist.py", line 739, in finalize_options
    ep.load()(self, ep.name, value)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\setuptools_ext.py", line 204, in cffi_modules
    add_cffi_module(dist, cffi_module)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\setuptools_ext.py", line 49, in add_cffi_module
    execfile(build_file_name, mod_vars)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\setuptools_ext.py", line 25, in execfile
    exec(code, glob, glob)
  File "rpy/_rinterface_cffi_build.py", line 546, in <module>
    """ if os.name == 'nt' else ''
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\api.py", line 107, in cdef
    self._cdef(csource, override=override, packed=packed)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\api.py", line 121, in _cdef
    self._parser.parse(csource, override=override, **options)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\cparser.py", line 315, in parse
    self._internal_parse(csource)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\cparser.py", line 320, in _internal_parse
    ast, macros, csource = self._parse(csource)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\cparser.py", line 278, in _parse
    self.convert_pycparser_error(e, csource)
  File "c:\users\j.siddaramanna\appdata\local\continuum\anaconda3\lib\site-packages\cffi\cparser.py", line 307, in convert_pycparser_error
    raise CDefError(msg)
cffi.error.CDefError: cannot parse "blah1 ReadConsole;"
<cdef source string>:23:5: before: blah1

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in C:\Users\JA6F5~1.SID\AppData\Local\Temp\pip-install-sj6qv50w\rpy2\

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

james-morrison-mowi · 2019-04-15T08:05:25Z

See #33.

If you call:
conda install rpy2=2.9.4

then:

pip install pymer4

It should install without out the above error.

ejolly · 2019-10-30T21:18:49Z

@jagadavk sorry for being so late to get to this, but please try with the latest release of pymer4. Lots of bug fixes and compatibility issues solved in that version

@james-morrison-mowi Thanks for addressing this and providing support!

moritz-gerster · 2023-07-31T05:51:00Z

@ejolly I get the same error

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

pymer4

Current channels:

https://conda.anaconda.org/ejolly/label/pre-release/osx-arm64

https://conda.anaconda.org/ejolly/label/pre-release/noarch

https://conda.anaconda.org/conda-forge/osx-arm64

https://conda.anaconda.org/conda-forge/noarch

https://repo.anaconda.com/pkgs/main/osx-arm64

https://repo.anaconda.com/pkgs/main/noarch

https://repo.anaconda.com/pkgs/r/osx-arm64

https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.

I have tried all these commands:

conda install -c ejolly/label/pre-release -c conda-forge -c defaults pymer4
conda install -c ejolly -c conda-forge -c defaults pymer4
conda install -c "ejolly/label/pre-release" pymer4
conda install -c ejolly pymer4
conda install pymer4
conda install -c ejolly -c defaults pymer4

Should I use pip? I am on Mac OS Ventura with M1 chip.

ejolly · 2023-07-31T12:33:51Z

Hmm you're likely running into this because I've never made no-arch or arm64 builds of pymer as I don't have access to an m1 for building. I can try to make a no-arch build but won't have time until the end of this month or next month.

You can try pip in the mean time if you can get all the other dependencies working, but it's a bit tricky with the required R packages which conda handles well. If you do get a pip only install working it would be very helpful if you could share your steps!

moritz-gerster · 2023-07-31T13:06:57Z

Alright, thanks for the feedback! I'll check how I'll proceed

ejolly · 2023-09-08T20:33:40Z

Hi @moritz-gerster I've finally had time to circle back to this and version 0.8.1 includes a no-arch build of pymer4 that's installable and working on m1/m2 macs. Feel free to try that out!

moritz-gerster · 2023-09-13T09:03:26Z

Now it works, thank you @ejolly!

ejolly closed this as completed Oct 30, 2019

ejolly mentioned this issue Apr 26, 2020

Package updates for dependencies compatibility #58

Closed

ejolly reopened this Sep 8, 2023

ejolly closed this as completed Sep 8, 2023

noahcreany mentioned this issue Mar 20, 2024

Issue with r-matrix package? #136

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installation issue for pymer4 #38

installation issue for pymer4 #38

jagadavk commented Apr 3, 2019

james-morrison-mowi commented Apr 15, 2019

ejolly commented Oct 30, 2019

moritz-gerster commented Jul 31, 2023 •

edited

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ejolly commented Jul 31, 2023

moritz-gerster commented Jul 31, 2023

ejolly commented Sep 8, 2023

moritz-gerster commented Sep 13, 2023

installation issue for pymer4 #38

installation issue for pymer4 #38

Comments

jagadavk commented Apr 3, 2019

james-morrison-mowi commented Apr 15, 2019

ejolly commented Oct 30, 2019

moritz-gerster commented Jul 31, 2023 • edited Loading

ejolly commented Jul 31, 2023

moritz-gerster commented Jul 31, 2023

ejolly commented Sep 8, 2023

moritz-gerster commented Sep 13, 2023

moritz-gerster commented Jul 31, 2023 •

edited

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