bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

[eudesbarbosa]

Hello. I'm having some issue installing and running bcftools after the most recent release (v1.15). And pinning the package to the previous version doesn't help.

Anyone faced something similar? Any hints on how to proceed?

Error:

bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Dependency difference
...works (from previous log):

2022-03-03T14:32:50.9725381Z + gsl 2.7 he838d99_0 conda-forge/linux-64 3MB

...breaks (from current log):

2022-03-23T09:01:56.7405052Z + gsl 2.7.1 hd82f3ee_0 pkgs/main/linux-64 2MB

...also forcing gsl ==2.7 or gsl ==2.7.0 just leads to a different error message (log):

bcftools: symbol lookup error: /usr/share/miniconda/envs/__setup_conda/bin/../lib/libgsl.so.25: undefined symbol: cblas_ctrmv

[pd3]

This is a problem with conda installation. Apparently the program was compiled with --enable-libgsl but the dependency on libgsl is not met on your system. I cannot help with conda (failed many times trying to install something myself), but bcftools is easy to obtain and compile from source: http://www.htslib.org/download/

[eudesbarbosa]

@pd3 , thank you for the quick reply. I will transfer the issue to conda people.

[swvanderlaan]

This issue remains (https://www.biostars.org/p/9480029/#9573995). Is there no way of solving this through conda that anyone is aware of?

[jkbonfield]

It's a perennial conda issue. I see the question you posted to biostars has already been answered, but this is a closed issue here already. (Note it would have been good if you'd updated your question here stating you already had a solution.)

Generally, for issues like this which aren't bugs specifically with our software and are instead errors caused by using prebuilt binaries supplied elsewhere with configuration problems, it's best to seek help on either conda-specific forums or biostars before raising (or resurrecting) issues here.