CheckM installation fails due to "incompatible with your system: - feature:/linux-64::__glibc==2.28=0"

[annaedlund]

Hello,
I am trying to install checkM using 'conda install -c bioconda/label/cf201901 checkm-genome' however the installation fails as I get the error message shown below.

Any input on how to solve this problem is highly appreciated!
Thank you!

Anna

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 the existing python installation in your environment:

Specifications:

• checkm-genome -> python[version='2.7.|3.5.|3.6.*|<3|>=2.7,<2.8.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.28=0
• feature:|@/linux-64::__glibc==2.28=0

Your installed version is: 2.28

[charles-bernard]

Hello @anna,

Had the same issue.
Here was the fix for me:

conda install -c rmg glibc

[mallen6]

Hi there,
I have the same problem as Anna but

conda install -c rmg glibc

does not fix it. Is there anything else I can try?

[charles-bernard]

Hi @mallen6,
You may want to find a better solution that works with the latest version of checkm, but just in case you're struggling too much to install checkm with python 3, here is a solution for installing the latest version of checkm compatible with python 2:

conda create -n checkm python=2
conda activate checkm
conda install numpy matplotlib
conda install -c bioconda hmmer prodigal pplacer pysam
pip install checkm-genome==v1.0.18

mkdir checkm_db
cd checkm_db
wget "https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz"
tar -xvzf checkm_data_2015_01_16.tar.gz
rm checkm_data_2015_01_16.tar.gz
checkm data setRoot checkm_db

[mallen6]

Thanks @charles-bernard, its working now!