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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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issue installing cnv_facets using conda #55

Open dalalsult opened 1 year ago

dalalsult commented 1 year ago

I've attempted to install cnv_facets package using:

conda create -n facets
conda activate facets
conda install -c bioconda -c conda-forge cnv_facets

It's taking forever to install and is stuck at solving environment (10 hours). Is anyone experiencing the same problem?

dariober commented 1 year ago

Try using mamba instead of conda (I should update the README). After installing it, instead of 

conda install -c bioconda -c conda-forge cnv_facets

use 

mamba install -c bioconda -c conda-forge cnv_facets
dalalsult commented 1 year ago

Thanks, that seemed to work. However, I've come across another issue when trying to run cnv_facets.R -h Error: package or namespace load failed for ‘facets’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/dalal/miniconda3/envs/cnv_facets/lib/R/library/facets/libs/facets.so': libgfortran.so.4: cannot open shared object file: No such file or directory Execution halted

I installed libgfortran but this doesn't seem to solve the issue.

dariober commented 1 year ago

Can you give some details about your system? I googled libgfortran.so.4: cannot open shared object file and there may be some relevant hits you could try to follow.

dalalsult commented 1 year ago

Sure, here's a few details of the shared server: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 20.04.4 LTS Release: 20.04 Codename: focal Kernel: Linux 5.4.0-107-generic Architecture: x86-64

Please let me know if you require any other details.

fgvieira commented 3 months ago

Having the same issue!

dariober commented 3 months ago

Hello- apologies for keeping quiet... At the moment, I cannot reproduce the issue either locally or on github actions. I run the test suite on Ubuntu 20 and 22 and it looks fine see https://github.com/dariober/cnv_facets/actions/runs/10355003504

The workflow executed on github is https://github.com/dariober/cnv_facets/blob/master/.github/workflows/main.yml