blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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Conda installation fails based on 'glibc' dependency issue #244

Closed timslittle closed 3 years ago

timslittle commented 3 years ago

I tried to install the conda version of TransRate using both conda versions 4.8.4 and 4.9.2, both giving the following error:

Command: conda install -c bioconda transrate

Error:

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 your system:

  - feature:/linux-64::__glibc==2.17=0
  - transrate -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.17

It is unclear why the installed version 2.17 is not considered to be '>=2.17'.

I've seen this error mentioned online for other conda package installations and I couldn't find a consistent fix.

I tried using an env with Python 3.6 but this did not work. I also tried installing libgcc-ng on its own before trying to install transrate, and while the libgcc-ng installation went fine the transrate installation gave the same error.

What did work was the private channel by lmfaber: https://github.com/lmfaber/transrate_conda

What is the difference between these recipes, and can the main anaconda one be remedied?

timslittle commented 3 years ago

Fixed by using conda-forge: conda install -c conda-forge transrate