conda/mamba installation not working with python=3.11

[aminakur]

I tried to install hicexplorer inside a Singularity container with conda, and it didn't work due to incompatibility:

Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using 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 versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:/linux-64::__linux==4.18.0=0
  - feature:|@/linux-64::__glibc==2.31=0
  - hicexplorer -> ipykernel[version='>=5.3.0'] -> __linux
  - hicexplorer -> ipykernel[version='>=5.3.0'] -> __osx
  - python=3.11 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31

Then following advice found here, I tried mamba:

mamba install hicexplorer -c bioconda -c conda-forge

Didn't work either.

Looking for: ['hicexplorer']

warning  libmamba Could not parse mod/etag header
bioconda/linux-64 (check zst)                      Checked  0.0s
warning  libmamba Could not parse mod/etag header
bioconda/noarch (check zst)                        Checked  0.0s
warning  libmamba Could not parse mod/etag header
warning  libmamba Could not parse mod/etag header
warning  libmamba Could not parse mod/etag header
pkgs/main/linux-64 (check zst)                     Checked  0.0s
warning  libmamba Could not parse mod/etag header
pkgs/main/noarch (check zst)                       Checked  0.0s
warning  libmamba Could not parse mod/etag header
pkgs/r/linux-64 (check zst)                        Checked  0.0s
warning  libmamba Could not parse mod/etag header
pkgs/r/noarch (check zst)                          Checked  0.0s
pkgs/main/linux-64                                   5.2MB @  50.0MB/s  0.1s
pkgs/main/noarch                                   696.1kB @   3.7MB/s  0.0s
pkgs/r/linux-64                                      1.2MB @   4.4MB/s  0.1s
conda-forge/noarch                                  11.7MB @  30.0MB/s  0.4s
pkgs/r/noarch                                        1.3MB @   2.1MB/s  0.3s
conda-forge/linux-64                                29.2MB @  39.3MB/s  0.8s
bioconda/linux-64                                    5.1MB @   5.3MB/s  1.0s
bioconda/noarch                                      4.6MB @   4.6MB/s  1.0s


Pinned packages:
  - python 3.11.*



warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ hicexplorer is installable with the potential options
   ├─ hicexplorer [0.1|1.1a|...|2.2beta] would require
   │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
   ├─ hicexplorer [2.0|2.1|...|2.1alpha1] would require
   │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
   ├─ hicexplorer [2.0|2.1|...|2.1alpha1] would require
   │  └─ python 3.6* , which can be installed;
   ├─ hicexplorer [2.1.4|2.2|2.2beta] would require
   │  └─ python >=3.6,<3.7.0a0 , which can be installed;
   ├─ hicexplorer [2.2|2.2.1|2.2.2|2.2.3] would require
   │  └─ python <3.7 , which can be installed;
   ├─ hicexplorer [3.0.1|3.5|...|3.7.2] would require
   │  └─ pysam with the potential options
   │     ├─ pysam [0.10.0|0.11.0|...|0.9.1.4] would require
   │     │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
   │     ├─ pysam [0.10.0|0.11.0|...|0.9.1.4] would require
   │     │  └─ python 3.4* , which can be installed;
   │     ├─ pysam [0.10.0|0.11.0|...|0.9.1.4] would require
   │     │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
   │     ├─ pysam [0.10.0|0.11.1|...|0.9.1] would require
   │     │  └─ python 3.6* , which can be installed;
   │     ├─ pysam [0.10.0|0.14.1|...|0.9.1] would require
   │     │  └─ python >=3.6,<3.7.0a0 , which can be installed;
   │     ├─ pysam [0.15.2|0.15.3|...|0.9.1] would require
   │     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
   │     ├─ pysam [0.15.2|0.16.0.1|...|0.9.1] would require
   │     │  └─ python >=3.8,<3.9.0a0 , which can be installed;
   │     ├─ pysam [0.16.0.1|0.17.0|...|0.9.1] would require
   │     │  └─ python >=3.9,<3.10.0a0 , which can be installed;
   │     ├─ pysam [0.19.1|0.20.0|0.21.0] would require
   │     │  └─ python >=3.10,<3.11.0a0 , which can be installed;
   │     └─ pysam 0.7.7 would require
   │        └─ python <3.0.0 , which can be installed;
   ├─ hicexplorer [3.0.2|3.1] would require
   │  └─ matplotlib 3.0.*  with the potential options
   │     ├─ matplotlib 3.0.1 would require
   │     │  └─ matplotlib-base 3.0.1 py37hc2fb212_1001, which does not exist (perhaps a missing channel);
   │     ├─ matplotlib 3.0.2 would require
   │     │  └─ matplotlib-base 3.0.2 py36h167e16e_1000, which does not exist (perhaps a missing channel);
   │     ├─ matplotlib [3.0.0|3.0.1|...|3.1.3] would require
   │     │  └─ python >=3.6,<3.7.0a0 , which can be installed;
   │     ├─ matplotlib 3.0.2 would require
   │     │  └─ matplotlib-base 3.0.2 py36h167e16e_1001, which does not exist (perhaps a missing channel);
   │     ├─ matplotlib [3.0.0|3.0.1|...|3.1.3] would require
   │     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
   │     ├─ matplotlib 3.0.2 would require
   │     │  └─ matplotlib-base 3.0.2 py37h167e16e_1001, which does not exist (perhaps a missing channel);
   │     └─ matplotlib 3.0.0 would require
   │        └─ python >=3.5,<3.6.0a0 , which can be installed;
   └─ hicexplorer [3.2|3.3|...|3.4.3] would require
      ├─ matplotlib 3.1.*  with the potential options
      │  ├─ matplotlib [3.0.0|3.0.1|...|3.1.3], which can be installed (as previously explained);
      │  ├─ matplotlib [3.0.0|3.0.1|...|3.1.3], which can be installed (as previously explained);
      │  └─ matplotlib [3.1.1|3.1.2|3.1.3] would require
      │     └─ python >=3.8,<3.9.0a0 , which can be installed;
      └─ pandas 0.25.*  with the potential options
         ├─ pandas [0.25.0|0.25.1|0.25.2|0.25.3] would require
         │  └─ python >=3.6,<3.7.0a0 , which can be installed;
         ├─ pandas [0.25.0|0.25.1|0.25.2|0.25.3] would require
         │  └─ python >=3.7,<3.8.0a0 , which can be installed;
         └─ pandas 0.25.3 would require
            └─ python >=3.8,<3.9.0a0 , which can be installed.

How should I proceed?

[thomasmanke]

I suggest you specify the version explicitly:

mamba create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge

[katecycho]

I also get the same error installing on conda.

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

• feature:/osx-arm64::__osx==13.3=0
• feature:|@/osx-arm64::__osx==13.3=0
• hicexplorer=3.5 -> ipykernel[version='>=5.3.0'] -> __linux
• hicexplorer=3.5 -> ipykernel[version='>=5.3.0'] -> __osx

Your installed version is: 13.3`

I even tried to uninstall conda and re-install conda and start a fresh new environment but get the same error.

[joachimwolff]

Hi,

we do not support Python 3.11 because some dependencies are not for this python version available. With the today released maintenance update 3.7.3 Python 3.8, 3.9 or 3.10 are supported.

Also consider that not all updates might be available for ARM platform. In this case please use the x86 version of conda and Rosetta2.