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.
failed
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 : 3.7.6.final.0
platform : linux-64
Thanks in advance.
•
written
by
takoyaki
.
conda create -n hypo -c conda-forge -c bioconda hypo
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 ?
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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