Cannot install bioconda-utils: UnsatisfiableError

[mzytnicki]

Please accept my apologies for this newbie question.

I cannot intall bioconda-utils, and I always get this error:

(base) $ conda install -c bioconda bioconda-utils                                                                                                                              

UnsatisfiableError: The following specifications were found to be incompatible with each other:                                                                                                                    
                                                                                                                                                                                                               
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:                                                                              
                                                                                                                                                                                                               
  - feature:/linux-64::__glibc==2.35=0                       
  - feature:|@/linux-64::__glibc==2.35=0
                                                                                                                                                                                                                                                                                                                     
Your installed version is: 2.35                                                                                                                                                                                    
                                                                                                                                                                                                               
Note that strict channel priority may have removed packages required for satisfiability.                                                                                                                           

What I tried:

• Uninstall miniconda (I tried to remove everything).
• conda activate & conda deactivate several times
• conda update conda

Actually, this last operation changed the feature:|@/linux-64::__glibc==2.35=0 to

  - python=3.10 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']        

What are my options now?

(BTW: thank you for the wonderful work @(bio)conda!)

[daler]

@mzytnicki have you set up your channels using the instructions at https://bioconda.github.io/?

If you don't want to do that, you'll need to use --channel conda-forge --channel bioconda --strict-channel-priority instead of just -c bioconda.

[mzytnicki]

@daler thanks for the help!
Yes, I forgot to mention that I typed this beforehand:

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict

The result is still

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
                                                                                                                                                                                                           
  - feature:/linux-64::__glibc==2.35=0 
  - feature:|@/linux-64::__glibc==2.35=0
                                                                                                                                                                                                                                                                                                                 
Your installed version is: 2.35

Which I cannot make sense of...

[daler]

Ok, next thing to try is to put bioconda-utils in its own environment, and while you're at it, install with mamba. That way the environment is created the same way as we do on the CI infrastructure.

e.g.,

mamba create -n bioconda bioconda-utils

It is likely that whatever environment you're installing into has some existing packages that are incompatible with bioconda-utils dependencies.

[mzytnicki]

Works like a charm!

What I did:

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh 
$ source ~/.bashrc
$ mamba create -n bioconda bioconda-utils
$ bioconda-utils -h
  [...]