Installation error with conda create

[c2997108]

I want to install syri and typed the following command.

$conda create -n syri_env -c bioconda syri

But I got the following error.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
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:

Package pysam conflicts for:
syri -> pysam
Package python conflicts for:
syri -> python[version='>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
Package python_abi conflicts for:
syri -> python_abi[version='3.8.*|3.9.*',build='*_cp39|*_cp38']
Package longestrunsubsequence conflicts for:
syri -> longestrunsubsequence
Package pulp conflicts for:
syri -> pulp
Package psutil conflicts for:
syri -> psutil
Package scipy conflicts for:
syri -> scipy
Package libgcc-ng conflicts for:
syri -> libgcc-ng[version='>=10.3.0|>=12']
Package python-igraph conflicts for:
syri -> python-igraph
Package libstdcxx-ng conflicts for:
syri -> libstdcxx-ng[version='>=10.3.0|>=12']
Package numpy conflicts for:
syri -> numpy[version='>=1.20,>=1.22.3,<2.0a0|>=1.20,>=1.23.2,<2.0a0']
Package pandas conflicts for:
syri -> pandas

[NovaYz]

the same question

[comery]

I met the same problem.

[mnshgl0110]

Sorry for a delayed response. I tried to install syri using conda (v4.12.0 and v22.9.0) and it installed without errors both times. What conda version are you using? I am guessing, as the error suggests, that there are indeed conflicts in the environment. Maybe you can try by first creating an empty environment and then installing syri in it using:

conda create -n syri_env
conda activate syri_env
conda install -c bioconda syri

You can also try to first remove the conflicting packages as mentioned above and then try to install syri.

If that does not work then, then you can try in a new clean conda environment.

Unfortunately, as I am currently unable to reproduce the error, I do not know the exact solution.

[hrwang]

I tried the installation in separate steps, still have the error.

creating the env is ok, but had problem with conda install -c bioconda syri:

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: 

[mnshgl0110]

What conda and python version are you using? Have you tried installing by downloading syri from github and then using python setup.py install?

[hrwang]

I solved this with the solution from another issue: https://github.com/schneebergerlab/syri/issues/134

[c2997108]

Thanks mnshgl0110 for your reply. I tried again on Rocky Linux 8.6. I installed the latest miniconda - Conda 4.12.0 Python 3.9.7 and typed the following command.

$conda create -n syri_env -c bioconda syri

But I got the following error.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
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 your system:

  - feature:/linux-64::__glibc==2.28=0
  - syri -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.28

Then I tried the following command, it looked good.

conda install python3 numpy cython
git clone https://github.com/schneebergerlab/syri.git
cd syri
python setup.py install

[mnshgl0110]

Hi @hrwang and @c2997108, thanks for sharing your solutions. I suspect that there are some inconsistencies in how cython is handled by conda and that might be resulting in these errors. So, for the future users, reinstalling it could be a solution as well.