conda install: UnsatisfiableError:?

Question

I installed conda (conda 4.10.1) on macOS BigSur (11.2.3). I am trying to install some bioinformatics tools, but I always get the same error:

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

Output in format: Requested package -> Available versions

But there are no packages with errors! Does somebody have an idea what to do? The error is not informative at all, I don't have any idea about the incompatibility errors!

In this case, this error comes from a python-based package called liftoff:

conda install -c bioconda liftoff -vv

Edited: OUTPUT in -vv mode:

Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
DEBUG conda.resolve:get_reduced_index(574): Retrieving packages for: 
  - @/osx-64::__unix==0=0
DEBUG conda.resolve:get_reduced_index(574): Retrieving packages for: 
  - @/osx-64::__osx==10.16=0
DEBUG conda.resolve:get_reduced_index(574): Retrieving packages for: 
  - python=3.7
DEBUG conda.resolve:filter_group(635): python: pruned from 98 -> 14
DEBUG conda.resolve:filter_group(635): libffi: pruned from 9 -> 8
DEBUG conda.resolve:filter_group(635): ncurses: pruned from 6 -> 4
DEBUG conda.resolve:filter_group(635): openssl: pruned from 31 -> 26
DEBUG conda.resolve:filter_group(635): pip: pruned from 96 -> 24
DEBUG conda.resolve:filter_group(635): setuptools: pruned from 168 -> 46
DEBUG conda.resolve:filter_group(635): certifi: pruned from 76 -> 22
DEBUG conda.resolve:filter_group(635): wheel: pruned from 50 -> 16
DEBUG conda.resolve:filter_group(635): readline: pruned from 6 -> 5
DEBUG conda.resolve:filter_group(635): sqlite: pruned from 25 -> 19
DEBUG conda.resolve:filter_group(635): xz: pruned from 5 -> 2
DEBUG conda.resolve:get_reduced_index(574): Retrieving packages for: 
  - @/osx-64::__archspec==1=x86_64
failed                                                                                                                                                                                                                                                             
Traceback (most recent call last):
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/install.py", line 265, in install
    should_retry_solve=(_should_retry_unfrozen or repodata_fn != repodata_fns[-1]),
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
    ssc = self._run_sat(ssc)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 818, in _run_sat
    should_retry_solve=ssc.should_retry_solve
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/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 "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/install.py", line 308, in install
    raise e
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/cli/install.py", line 299, in install
    should_retry_solve=(repodata_fn != repodata_fns[-1]),
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
    should_retry_solve)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
    force_remove, should_retry_solve)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 275, in solve_final_state
    ssc = self._add_specs(ssc)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/site-packages/conda/core/solve.py", line 704, in _add_specs
    ssc.r.find_conflicts(spec_set)
  File "/Users/francisco/opt/anaconda3/lib/python3.7/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

Please rerun with verbose flags, e.g., `-vv`, and add output to question. Also, include the command you tried to run. — merv, Apr 24 '21 at 07:21
Are you trying to install this in the **base** environment of an Anaconda install? That’s usually a bad idea. Bioconda requires prioritization of the Conda Forge channel (e.g., you need `conda install -c conda-forge -c bioconda -c defaults liftoff` to install as designed), whereas the `anaconda` package (in **base**) is designed with having **defaults** channel installed. If you regularly use bioinformatics software, I would strongly encourage uninstalling Anaconda and replacing it with Miniforge or Mambaforge, then follow the Bioconda configuration directions. — merv, Apr 25 '21 at 00:23
Many thanks for your suggestion, I have been using conda for at least three years without any problem, but after updating to BigSur the problems started, do you have any advice, or can recommend any tutorial to configure bioconda as you suggest? — Fcallejas, Apr 26 '21 at 02:09
Documentation: https://bioconda.github.io/user/install.html And again, I’d emphasize installing Miniforge or Mambaforge instead of Miniconda. I anticipate the Bioconda docs will eventually start recommending this too. — merv, Apr 26 '21 at 04:25

SeaJane · Answer 1 · 2022-03-05T01:08:51.480

I got this same error when trying to install the bioinformatic tool ppanggolin. The problem seems to be that the version of python in your conda environment is too recent for the tool you are trying to install. I solved this by creating a new conda environment and using an earlier version of python:

conda create -n ppanggolin01 python=3.8
conda activate ppangolin01
conda clean --packages --tarballs
conda install -c bioconda ppanggolin

I added in a package clean up step for good measure. Hopefully this works for your tool, too.

Alternatively, using Mamba to install seems to solve this problem when package conflicts occur and has been described previously: How to interpret conda package conflicts?

conda install: UnsatisfiableError:?

1 Answers1