CODEWITHSUNDEEP
pythonubuntucondaanaconda3
Diana King
Diana King

Reputation: 1

Error installing Scran package using Anaconda

So I try to install the Scran, use conda install -c bioconda bioconductor-scran then got the error like this:

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: bioconductor-scran -> r-base[version='>=3.6,<3.7.0a0'] -> zlib[version='>=1.2.11,<1.3.0a0'] python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0']

Package ncurses conflicts for: python=3.8 -> ncurses[version='>=6.1,<7.0a0|>=6.2,<7.0a0'] python=3.8 -> readline[version='>=7.0,<8.0a0'] -> ncurses[version='6.0.*|>=6.0,<7.0a0']

Package libgcc-ng conflicts for: python=3.8 -> openssl[version='>=1.1.1k,<1.1.2a'] -> libgcc-ng[version='>=7.2.0|>=9.3.0'] python=3.8 -> libgcc-ng[version='>=7.3.0|>=7.5.0']

Package libstdcxx-ng conflicts for: python=3.8 -> libffi[version='>=3.2.1,<3.3a0'] -> libstdcxx-ng[version='>=7.2.0'] python=3.8 -> libstdcxx-ng[version='>=7.3.0']The following specifications were found to be incompatible with your system:

  • feature:/linux-64::__glibc==2.31=0
  • bioconductor-scran -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
  • python=3.8 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31`

I have tried many ways, but didn't work. I still don't know how to fix. Could someone give me a favor?

Upvotes: 0

Views: 1714

Answers (1)

merv
merv

Reputation: 76970

Avoid mixing Python and R in the same environment. Also, Bioconda assumes the following channel priority:

conda-forge > bioconda > defaults

Try creating a dedicated environment for your Bioconductor work, and make sure to pin an r-base:

bioc_r41.yaml

name: bioc_r41
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - r-base=4.1
  - bioconductor-scran

Create the environment with:

conda env create -n bioc_r41 -f bioc_r41.yaml

Alternatively, one can achieve this with an ad hoc command, but it is rather verbose:

conda create -n bioc_r41 -c conda-forge -c bioconda -c defaults r-base=4.1 bioconductor-scran

Upvotes: 0

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