Installation problem from conda

[bvalot]

Hello,

I have some problems to install MOB Suite using conda:

ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::mob_suite-3.1.8-pyhdfd78af_1'.
Rolling back transaction: done

LinkError: post-link script failed for package bioconda::mob_suite-3.1.8-pyhdfd78af_1
location of failed script: /home/bvalot3/.local/opt/miniconda3/envs/mobsuite/bin/.mob_suite-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: Traceback (most recent call last):
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/bin/mob_init", line 6, in <module>
    from mob_suite.mob_init import main
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.9/site-packages/mob_suite/mob_init.py", line 13, in <module>
    from mob_suite.utils import init_console_logger
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.9/site-packages/mob_suite/utils.py", line 2, in <module>
    from Bio.SeqUtils import gc_fraction
ImportError: cannot import name 'gc_fraction' from 'Bio.SeqUtils' (/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.9/site-packages/Bio/SeqUtils/__init__.py)

return code: 1

Here my configuration:

    active environment : mobsuite
    active env location : /home/bvalot3/.local/opt/miniconda3/envs/mobsuite
            shell level : 2
       user config file : /home/bvalot3/.condarc
 populated config files : /home/bvalot3/.condarc
          conda version : 23.11.0
    conda-build version : not installed
         python version : 3.9.18.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=23.11.0=0
                          __glibc=2.36=0
                          __linux=6.1.0=0
                          __unix=0=0
       base environment : /home/bvalot3/.local/opt/miniconda3  (writable)
      conda av data dir : /home/bvalot3/.local/opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/bvalot3/.local/opt/miniconda3/pkgs
                          /home/bvalot3/.conda/pkgs
       envs directories : /home/bvalot3/.local/opt/miniconda3/envs
                          /home/bvalot3/.conda/envs
               platform : linux-64
             user-agent : conda/23.11.0 requests/2.31.0 CPython/3.9.18 Linux/6.1.0-20-amd64 debian/12.5 glibc/2.36 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.6
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

[kbessonov1984]

Hi, try to have the Biopython to version >= 1.80. Inside your conda environment run conda install biopython=1.81 or you can install it via pip3 pip3 install "biopython==1.81". You might need to remove previous biopython version via conda remove biopython. To fix this we would need to release a new conda recipe that would specify min biopython version >=1.80 since this is when the gc_fraction function was first introduced

[bvalot]

Thanks for the reply.
I try the workaround, but get a new error linking to panda

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(945): An error occurred while installing package 'bioconda::mob_suite-3.0.0-py_1'.
Rolling back transaction: done

LinkError: post-link script failed for package bioconda::mob_suite-3.0.0-py_1
location of failed script: /home/bvalot3/.local/opt/miniconda3/envs/mobsuite/bin/.mob_suite-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: Traceback (most recent call last):
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/bin/mob_init", line 7, in <module>
    from mob_suite.mob_init import main
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.12/site-packages/mob_suite/mob_init.py", line 8, in <module>
    from mob_suite.blast import BlastRunner
  File "/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.12/site-packages/mob_suite/blast/__init__.py", line 9, in <module>
    from pandas.io.common import EmptyDataError
ImportError: cannot import name 'EmptyDataError' from 'pandas.io.common' (/home/bvalot3/.local/opt/miniconda3/envs/mobsuite/lib/python3.12/site-packages/pandas/io/common.py)

return code: 1

()

[kbessonov1984]

Now it seems that you are installing mob_suite version 3.0.0 which does not support pandas > 2.0. For mob-suite version 3.0.0 you need pandas 1.0.5. I would recommend using the newest version of mob-suite which is 3.1.8. Install it via conda/mamba and then update to the biopython package to >= 1.80 via pip3 as with conda it will try to solve all dependencies and would then downgrade mob-suite.

I am working on new build for version 3.1.8 that would restrict biopython version as a permanent fix for now. Also working on a new release 3.1.9 that would also have this issue fixed

[bvalot]

Hello,

It seems that 3.1.8 version could only be install on python 3.12

(mobsuite) bvalot3@hp7490-bv:~$ conda install -c bioconda mob_suite=3.1.8
Channels:
 - bioconda
 - defaults
 - 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 mob_suite-3.1.8-pyhdfd78af_0 requires pandas >=0.22.0,<2, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ mob_suite 3.1.8**  is installable and it requires
│  └─ pandas [>=0.22,<=1.5.3 |>=0.22.0,<2 ] with the potential options
│     ├─ pandas [0.22.0|0.23.0|...|0.24.2] would require
│     │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
│     ├─ pandas [0.22.0|0.23.0|...|0.23.4] would require
│     │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
│     ├─ pandas [0.22.0|0.23.0|...|1.1.5] would require
│     │  └─ python >=3.6,<3.7.0a0 , which can be installed;
│     ├─ pandas [0.23.2|0.23.3|...|1.3.5] would require
│     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
│     ├─ pandas [0.24.2|0.25.3|...|1.5.3] would require
│     │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│     ├─ pandas [1.1.3|1.1.4|...|1.5.3] would require
│     │  └─ python >=3.9,<3.10.0a0 , which can be installed;
│     ├─ pandas 1.3.0 would require
│     │  └─ python >=3.7.1,<3.8.0a0 , which can be installed;
│     ├─ pandas [1.3.4|1.3.5|...|1.5.3] would require
│     │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│     ├─ pandas [1.5.1|1.5.2|1.5.3] would require
│     │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│     └─ pandas 0.22.0 would require
│        └─ python 3.6* , which can be installed;
└─ pin-1 is not installable because it requires
   └─ python 3.12.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.12.* (labeled as 'pin-1')

[bvalot]

If I make conda env with python 3.12, I get same message when try to install the 3.1.8 mob_suite version.

[kbessonov1984]

Hello,

There seems to be an issue with channels as pandas <2 is required and can not be installed. The error message reads:
package mob_suite-3.1.8-pyhdfd78af_0 requires pandas >=0.22.0,<2, but none of the providers can be installed

Try to install the latest build 1 in a fresh clean environment by simply running conda install bioconda::mob_suite which will pick the latest release and build. You can install manually pandas <2

Here is a conda recipe with minimum requirements (in run section)
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/mob_suite/meta.yaml

[kbessonov1984]

I hope it worked for you, we are releasing this week new conda build and perhaps a new version with guaranteed contig ordering independent of input issue #160 and asking for biopython >= 1.80 solving your issue