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I am using an R script which uses Julia functions to run the code. It works perfectly on my computer, but when I try to set it up in the virtual environment, it gives me an error. I've created a container (ubuntu 22.04) with R and Julia installed inside with all the packages required, and upon testing it worked great. However, once I run a specific code, which calls Julia to interact with R, it gives me this error:

ERROR: LoadError: InitError: could not load library "/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so"
/usr/lib/x86_64-linux-gnu/libcurl.so: version `CURL_4' not found (required by /home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so)

I've looked online, and it says that the main problem is that the script is using the system's lib* files, as opposed to of that from Julia, which creates this error.

So I am trying to modify the last .def file to fix the problem, so far this is what I've added to it:

Bootstrap: localimage
From: ubuntu_R_ResistanceGA.sif

%post


Install system dependencies for Julia


apt-get update && 

apt-get install -y wget tar gnupg lsb-release 

software-properties-common libhdf5-dev libnetcdf-dev 

libcurl4-openssl-dev=7.68.0-1ubuntu2.25 

libgconf-2-4 

libssl-dev


Run ldconfig to update the linker cache


ldconfig


Set environment variable to include the directory where the artifacts are stored


echo "export LD_LIBRARY_PATH=/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib:$LD_LIBRARY_PATH" >> /etc/profile


Clean up the package cache to reduce container size


apt-get clean


Install Julia 1.9.3


wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz
  tar -xvzf julia-1.9.3-linux-x86_64.tar.gz
  mv julia-1.9.3 /usr/local/julia
  ln -s /usr/local/julia/bin/julia /usr/local/bin/julia


Install Circuitscape


julia -e 'using Pkg; Pkg.add("Circuitscape")'
julia -e 'using Pkg; Pkg.build("NetCDF_jll")'


%environment
  export LD_LIBRARY_PATH=/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib:$LD_LIBRARY_PATH
Varvara Vladimirova
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0 Answers0