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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
44 stars 6 forks source link

UnsatisfiableError: The following specifications were found to be incompatible with each other: #145

Closed dputhier closed 3 years ago

dputhier commented 3 years ago

Got this message ("UnsatisfiableError: The following specifications were found to be incompatible with each other") but without any listed dependency....

      $ conda create -n ologram python=3.7
      $ conda activate ologram
      $ conda install -c bioconda pygtftk
      Collecting package metadata (current_repodata.json): done
      Solving environment: failed with initial frozen solve. Retrying with flexible solve.
      Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
      Collecting package metadata (repodata.json): done
      Solving environment: failed with initial frozen solve. Retrying with flexible solve.
      Solving environment: - 
      Found conflicts! Looking for incompatible packages.
      This can take several minutes.  Press CTRL-C to abort.
      failed                                                                                                        

      UnsatisfiableError: The following specifications were found to be incompatible with each other:

      Output in format: Requested package -> Available versions

I tried to remove any Python lib installed in my home directory but without success (rm -rf .local/lib/python*).

  $ uname -a

  Linux V-PP-30-LUM-003 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

@guillaumecharbonnier do you have any idea ?

guillaumecharbonnier commented 3 years ago

Hi @dputhier, I have just tried to install it with no issue as described below. The installed python is 3.7. Installing software after the creation of the conda environment often lead to failures.

$ conda env create -f pygtftk.yaml
$ cat pygtftk.yaml 
name:
  pygtftk
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pygtftk
dputhier commented 3 years ago

@guillaumecharbonnier Hi Guillaume, I also managed to install it on a Linux and OSX machine. But for unknown reason I was unable to install it on this specific machine (which correspond to student machines @ AMU...). I was unable to get additional information regarding the issue...

guillaumecharbonnier commented 3 years ago

Any insight with increased verbosity?

  -v, --verbose         Use once for info, twice for debug, three times for
                        trace.
dputhier commented 3 years ago

Thank you Guillaume... But nothing really meaningful...

$ python --version
Python 3.7.9
(ologram_py37) V-PP-30-LUM-003 puthier ~
$ conda config --set unsatisfiable_hints True
(ologram_py37) V-PP-30-LUM-003 puthier ~
$ conda install -v -c bioconda pygtftk  
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                             
Traceback (most recent call last):
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 261, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 281, in solve_final_state
    ssc = self._run_sat(ssc)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 815, in _run_sat
    ssc.solution_precs = ssc.r.solve(tuple(final_environment_specs),
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/resolve.py", line 1320, in solve
    raise UnsatisfiableError({})
conda.exceptions.UnsatisfiableError: 
Did not find conflicting dependencies. If you would like to know which
packages conflict ensure that you have enabled unsatisfiable hints.

conda config --set unsatisfiable_hints True

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 308, in install
    raise e
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 295, in install
    unlink_link_transaction = solver.solve_for_transaction(
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 114, in solve_for_transaction
    unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 157, in solve_for_diff
    final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 275, in solve_final_state
    ssc = self._add_specs(ssc)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/core/solve.py", line 704, in _add_specs
    ssc.r.find_conflicts(spec_set)
  File "/amuhome/puthier/miniconda3/lib/python3.8/site-packages/conda/resolve.py", line 352, in find_conflicts
    raise UnsatisfiableError(bad_deps, strict=strict_channel_priority)
conda.exceptions.UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions