libgfortran.so.3: cannot open shared object file: No such file or directory

[AKWB]

Hi there,

I installed confindr via conda and face the error below.

Any suggestions are very welcome. THANKS!

Operating system: Ubuntu 22.04.3 LTS

confindr -h
Traceback (most recent call last):
File "/usr/local/tools/miniconda/envs/confindr/bin/confindr", line 7, in
from confindr_src.confindr import main
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/confindr_src/confindr.py", line 2, in
from confindr_src.methods import check_acceptable_xmx, check_for_databases_and_download, check_valid_base_fraction,
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/confindr_src/methods.py", line 10, in
import numpy as np
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/numpy/init.py", line 142, in
from . import add_newdocs
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/numpy/add_newdocs.py", line 13, in
from numpy.lib import add_newdoc
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/numpy/lib/init.py", line 8, in
from .type_check import *
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/numpy/lib/type_check.py", line 11, in
import numpy.core.numeric as _nx
File "/usr/local/tools/miniconda/envs/confindr/lib/python3.5/site-packages/numpy/core/init.py", line 14, in
from . import multiarray
ImportError: libgfortran.so.3: cannot open shared object file: No such file or directory

[pcrxn]

Hi @AKWB, I'm sorry for the delay in responding to your issue. Thanks for including that error message and your OS. This looks like a broken installation.

Did you install ConFindr using the recommended command in the README (conda create -n confindr -c bioconda confindr=0.8.1)? And have you tried re-installing since then?