Cannot even start installation of biobakery workflows on Mac M1

Infrastructure and utilities bioBakery workflows
1

Hi there,
have python 2.7 and biobakery in the top list but still getting error about Requested package → Available versions. Any clue why it so?
max@maxs-Mac-mini ~ % conda install -c biobakery biobakery_workflows
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

max@maxs-Mac-mini ~ %

2

Sorry I do not have a solution to you problem. I have a more general question on the topic. Are the two programs, KneadData and HUMANN3 compatible with the new Mac M1 or M1 Max chips in new MacBooks that have replaced the old Intel chips?

Guy

3

Hello, Have you tried installing the conda package with python 3? It might make it easier for conda to resolve the conflicts that it is seeing in python 2.7 on the Mac M1.

Thanks!
Lauren

4

Hello @Guy , Both programs should be compatible with the new chips. Neither program was developed on a specific architecture. They should both work on various platforms including Mac, Linux, and Windows.

Thanks!
Lauren

5

Hi I think I am having a similar issue to above. I am on an M1 mac using Rosetta mode.

I am trying to install Phylophlan 3.0. I started by creating an env and specifying a newer version of python:

(base) rachelmizzi@Rachels-Air miniconda3 % conda create -n phylophlan python=3.11

Then I ran:
(phylophlan) rachelmizzi@Rachels-Air phylophlan % conda install -c bioconda phylophlan=3.0 --verbose

and got:
(phylophlan) rachelmizzi@Rachels-Air phylophlan % conda install -c bioconda phylophlan=3.0 --verbose
Collecting package metadata (current_repodata.json): …working… done
Solving environment: …working… unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: …working… unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): …working… done
Solving environment: …working… unsuccessful initial attempt using 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 “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/install.py”, line 309, in install*
  • unlink_link_transaction = solver.solve_for_transaction(*
  •                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 153, in solve_for_transaction*
  • unlink_precs, link_precs = self.solve_for_diff(*
  •                           ^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 214, in solve_for_diff*
  • final_precs = self.solve_final_state(*
  •              ^^^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 387, in solve_final_state*
  • ssc = self._run_sat(ssc)*
  •      ^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/common/io.py”, line 83, in decorated*
  • return f(*args, *kwds) 
  •       ^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 1048, in _run_sat*
  • ssc.solution_precs = ssc.r.solve(*
  •                     ^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/common/io.py”, line 83, in decorated*
  • return f(*args, *kwds) 
  •       ^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/resolve.py”, line 1507, 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/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/exception_handler.py”, line 16, in call*
  • return func(*args, *kwargs) 
  •       ^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/main.py”, line 84, in main_subshell*
  • exit_code = do_call(args, p)*
  •            ^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/conda_argparse.py”, line 126, in do_call*
  • return getattr(module, func_name)(args, parser)*
  •       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/notices/core.py”, line 123, in wrapper*
  • return func(*args, *kwargs) 
  •       ^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/main_install.py”, line 22, in execute*
  • install(args, parser, “install”)*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/install.py”, line 378, in install*
  • raise e*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/cli/install.py”, line 361, in install*
  • unlink_link_transaction = solver.solve_for_transaction(*
  •                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 153, in solve_for_transaction*
  • unlink_precs, link_precs = self.solve_for_diff(*
  •                           ^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 214, in solve_for_diff*
  • final_precs = self.solve_final_state(*
  •              ^^^^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 379, in solve_final_state*
  • ssc = self._add_specs(ssc)*
  •      ^^^^^^^^^^^^^^^^^^^^*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/core/solve.py”, line 915, in _add_specs*
  • ssc.r.find_conflicts(spec_set)*
  • File “/Users/rachelmizzi/miniconda3/lib/python3.11/site-packages/conda/resolve.py”, line 418, 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
Note that strict channel priority may have removed packages required for satisfiability.

Assistance appreciated!
R

6

Hello, Thank you for the detailed post and error message. If you are flexible on your python version, try requesting just python 3 instead of 3.11 (ie no specific minor version requested) as this will give conda more flexibility and it should hopefully resolve your errors.

Thanks!
Lauren