"libR.so: cannot open shared object file: No such file or directory" and associated warnings after Pkg.build()

[mkarikom]

I have the following error, which complains about various libraries not being found.
However, a check shows that they exist:

Steps to reproduce:

Set up the environment:

julia> ENV["JULIA_PROJECT"]="/dfs6/pub/me/myproject" # make sure all workers can access the project enviroment
julia> ENV["R_HOME"]="/opt/apps/R/4.0.4/lib64/R" # make sure JuliaCall/RCall can access R
julia> ENV["R_LIBS"]="/opt/apps/R/4.0.4/lib64/R/library" # make sure that RCall.jl knows what packages are installed

Sanity check:

julia> ENV["R_HOME"]=<cluster R home> # "/opt/apps/R/4.0.4/lib64/R"
julia> readdir(ENV["R_HOME"]) # sanity check for R
  10-element Vector{String}:
   "COPYING"
   "SVN-REVISION"
   "bin"
   "doc"
   "etc"
   "include"
   "lib"
   "library"
   "modules"
   "share"
julia> [findall( x -> occursin(rc_lib, x), readdir(ENV["R_LIBS"])) for rc_lib in ["utils","grDevices","graphics","stats","methods"]] # sanity check for R libs
5-element Vector{Vector{Int64}}:
 [39, 320, 375, 403]
 [190]
 [191]
 [379, 380]
 [37, 253]

Build RCall:

julia> using Pkg
julia> Pkg.build("RCall")
    Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/299304989a5e6473d985212c28928899c74e9421/build.log`
    Building RCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/5108a75602f6a11f7737707dff26461ef02abc66/build.log`

Attempt to use RCall:

julia> using Distributed,RCall
┌ Warning: RCall.jl: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/methods/libs/methods.so':
│   libR.so: cannot open shared object file: No such file or directory
│ Warning message:
│ package "methods" in options("defaultPackages") was not found 
│ Error: package or namespace load failed for ‘utils’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/utils/libs/utils.so':
│   libR.so: cannot open shared object file: No such file or directory
│ Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/grDevices/libs/grDevices.so':
│   libR.so: cannot open shared object file: No such file or directory
│ Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/grDevices/libs/grDevices.so':
│   libR.so: cannot open shared object file: No such file or directory
│ Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/grDevices/libs/grDevices.so':
│   libR.so: cannot open shared object file: No such file or directory
│ Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...):
│  unable to load shared object '/opt/apps/R/4.0.4/lib64/R/library/methods/libs/methods.so':
│   libR.so: cannot open shared object file: No such file or directory
│ During startup - Warning messages:
│ 1: package ‘utils’ in options("defaultPackages") was not found 
│ 2: package ‘grDevices’ in options("defaultPackages") was not found 
│ 3: package ‘graphics’ in options("defaultPackages") was not found 
│ 4: package ‘stats’ in options("defaultPackages") was not found 
│ 5: package ‘methods’ in options("defaultPackages") was not found 
└ @ RCall ~/.julia/packages/RCall/iMDW2/src/io.jl:160

Check that shared libs exist:

julia> isfile("/opt/apps/R/4.0.4/lib64/R/library/utils/libs/utils.so")
true

julia> isfile("/opt/apps/R/4.0.4/lib64/R/library/grDevices/libs/grDevices.so")
true

julia> isfile("/opt/apps/R/4.0.4/lib64/R/library/methods/libs/methods.so")
true

Note on warnings about missing R packages

Also the warnings like package <packagename> in options("defaultPackages") was not found are confusing because they were already verified under # sanity check for R libs above

[fcaira]

Hi @mkarikom, did you ever find a solution to this?

[mkarikom]

Hi @mkarikom, did you ever find a solution to this?

The following is currently working, although some changes to the hpc environment (that I don't fully understand) may also have helped:

      library(JuliaCall)
      julia_setup(JULIA_HOME = Sys.getenv("JULIA_HOME"),verbose=TRUE,rebuild = TRUE,install=FALSE)

[ViralBShah]

Please reopen if this is still an issue.

[AFFFPupu]

I had the same problem and solved by adding R into the PATH.