RCall.jl
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using RCall quits Julia with the error "cannot find system Renviron"
Hi,
I'm trying to call RCall in Julia 1.8.5 but it fails with the following error:
[root@noun ~]# export LD_LIBRARY_PATH=/softs/R/R-4.2.2/lib:$LD_LIBRARY_PATH
[root@noun ~]# julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.8.5 (2023-01-08)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> using RCall
cannot find system Renviron
The operating system is Rocky Linux 8.6. Julia is installed on the folder /softs/julia/julia-1.8.5 and R is installed on the folder /softs/R/R-4.2.2. Before installing RCall in Julia, I define the following environment variables:
export R_HOME=/softs/R/R-4.2.2/
export LD_LIBRARY_PATH=/softs/R/R-4.2.2/lib/:$LD_LIBRARY_PATH
Then in Julia, I launch:
using Pkg
Pkg.add("RCall")
Pkg.build("RCall")
Building Conda → `/softs/julia/julia-1.8.5/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/e32a90da027ca45d84678b826fffd3110bb3fc90/build.log`
Building RCall → `/softs/julia/julia-1.8.5/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/2c0ffd39860c9a48259a0f57214ced2024ab63bc/build.log`
The building of RCall seems to work but I can't use it. Renviron is currently in the folder /softs/R/R-4.2.2/lib64/R/etc/. I tried to add this folder to the LD_LIBRARY_PATH variable or to the PATH variable but it doesn't solve the problem. I also give the largest rights to the file Renviron (chmod 777). But it doesn't solve the issue.
Here is the result of versioninfo() in julia if it helps:
versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 32 × Intel(R) Xeon(R) Silver 4108 CPU @ 1.80GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, skylake-avx512)
Threads: 1 on 32 virtual cores
Environment:
LD_LIBRARY_PATH = /softs/R/R-4.2.2/lib:/softs/R/R-4.2.2/lib:/softs/R/R-4.2.2/lib:/softs/R/R-4.2.2/lib64/R/etc/:/softs/R/R-4.2.2/lib:/opt/ohpc/pub/mpi/libfabric/1.13.0/lib:/opt/ohpc/pub/mpi/ucx-ohpc/1.11.2/lib:/opt/ohpc/pub/libs/hwloc/lib:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.1.1/lib:/opt/ohpc/pub/compiler/gcc/9.4.0/lib64
JULIA_DEPOT_PATH = /softs/julia/julia-1.8.5
JULIA_HISTORY = /root/.julia/logs/repl_history.jl
JULIA_DIR = /softs/julia/julia-1.8.5/