Pyrhon version issue of HUMAnN4.0.0a

Microbial community profiling HUMAnN
1

Dear bioBakery team,

I am using HUMAnN3 series very well and have recently tried to use HUMAnN4.0.0a.
When I install and run HUMAnN4.0.0a in the conda environment, I get an error TypeError: super() argument 1 must be type, not classobj.
I found that this error cause by the version of python in conda environment was python2, so I rebuilt the environment with specifying python=3.7 according to the manual.
But during the installation of HUMAnN4.0.0a, it stopped since HUMAnN4.0.0a required python=2.7.
this is the error message:

conda install humann=4.0.0a1 -c biobakery -c bioconda
Channels:
 - biobakery
 - bioconda
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: / warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package humann-4.0.0a1-py_0 requires python_abi 2.7.* *_cp27mu, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ humann 4.0.0a1**  is installable and it requires
│  └─ python_abi 2.7.* *_cp27mu, which requires
│     └─ python 2.7.* , which can be installed;
└─ pin-1 is not installable because it requires
   └─ python 3.7.* , which conflicts with any installable versions previously reported.

Would you kindly fix this problem?

Thanks,
Kirby

1 Like
2

I experience the same error. Would be great to have a solution

Thanks!

1 Like
3

@G-Molano-LA Hello,

I detour this problem by using pip (it is suggested in the manual).

After installing HUMAnN4a using pip, it works fine in my environment.

However, I use conda for stable environment management, so I would like the team to correct the conda version of HUMAnN4a.

4

Related to this, when I try to install humann via:
conda create --prefix /my/path/conda_environment/humann4.0.0.alpha-1 -c biobakery humann=4.0.0a1 it has python 2.7 as a dependancy and instead of Metaphlan 4 it has
bioconda/noarch::metaphlan-2.8.1-py_1

1 Like
5

I’m seeing some differences in the commands above relative to the installation recommendations in the 4.0.0.alpha.1 release notes. Can you verify that you still encounter this error when following those instructions verbatim, including setting the channel priorities? Our HUMAnN 4 recipe should not require anything from Python 2, so I’m wondering if you’re pulling from an unexpected channel / recipe?

6

Same issue here

Screenshot 2025-02-16 at 01.24.34
Screenshot 2025-02-16 at 01.24.341758×728 61.5 KB

7

Sorry for late check.

In my case, conda install humann=4.0.0.alpha-1 -c biobakery was not working.
this is the error message:

conda install humann=4.0.0.alpha-1 -c biobakery
Retrieving notices: done
Channels:
 - biobakery
 - bioconda
 - conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - humann=4.0.0.alpha-1*

Current channels:

  - https://conda.anaconda.org/biobakery
  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

So I checked the package version in Files | Anaconda.org and tried conda install humann=4.0.0a1 -c biobakery -c bioconda.

but this returns the error message I previously mentioned.