conda installation error in hypo
Entering edit mode
16 months ago
takoyaki ▴ 90

Hi !
I wanted to polish long read by hypo and meet error when installing through conda.
I couldn't solve this problem, so I want to ask you for help. Below are error messages.

(base) $ conda install -c bioconda hypo

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.

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package zlib conflicts for:
hypo -> zlib[version='>=1.2.11,<1.3.0a0']
hypo -> kmc[version='>=3.0'] -> zlib[version='1.2.11.*|1.2.8.*']

Package libstdcxx-ng conflicts for:
hypo -> kmc[version='>=3.0'] -> libstdcxx-ng[version='>=7.2.0']
hypo -> libstdcxx-ng[version='>=7.3.0']

Package libgcc-ng conflicts for:
hypo -> kmc[version='>=3.0'] -> libgcc-ng[version='>=7.2.0']
hypo -> libgcc-ng[version='>=7.3.0']

Package _libgcc_mutex conflicts for:
python=3.7 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]
hypo -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]

I couldn't understand this error message meanings because these doesn't seem to conflict.
Also, I checked these packages from conda list command.

$ conda list
# packages in environment at /home/user/anaconda3:
# Name                    Version                   Build  Channel
zlib                      1.2.11               h7b6447c_3  
kmc                       3.1.2rc1             h2d02072_0    bioconda
libstdcxx-ng              9.1.0                hdf63c60_0  
libgcc-ng                 9.1.0                hdf63c60_0
_libgcc_mutex             0.1                        main

From these version information, I think all packages meet conditions.
How do you think ? What should I do ??

Below are my environment information.

conda version : 4.8.3
conda-build version : 3.18.11
python version :
platform : linux-64

Thanks in advance.

anaconda sequencing assembly longread hypo • 963 views
Entering edit mode
16 months ago
  1. Please remember to use the conda-forge channel as well, we use it in Bioconda for many dependencies.
  2. It's highly recommended to create environments for different tools.


conda create -n hypo -c conda-forge -c bioconda hypo
Entering edit mode

Thanks, Devon. So, it is better to use different virtual environments to avoid these conflict problem.

Please let me ask you one more question. I think that we use a lot of tools in bioinformatics, so will we create many virtual environments, like hypo, busco, flye, medaka ... and so on ?

Entering edit mode

Yes, it's good practice to keep tools in separate versioned environments when possible, or at the very least create project-specific environments that you then do not ever change.


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