JuliaInterop
Difficulty installing RCall on a low version of julia
Hi ！ I had to install RCall in Julia 1.4.0 because of the R package dependency, I ran the following code, however I'm having trouble resolving the error
julia> ENV["R_HOME"] = "~/miniconda3/envs/RTIGER/lib/R"
"~/miniconda3/envs/RTIGER/lib/R"
julia> Rhome = "~/miniconda3/envs/RTIGER/lib/R"
"~/miniconda3/envs/RTIGER/lib/R"
julia> libR = "~/miniconda3/envs/RTIGER/lib/R/lib/libR.so"
"~/miniconda3/envs/RTIGER/lib/R/lib/libR.so"
julia> Pkg.build(PackageSpec(name="RCall", version="0.13.2"))
Building Conda → `~/.julia/packages/Conda/sDjAP/deps/build.log`
Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R_HOME is not a directory.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] top-level scope at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:42
│ [3] include(::String) at ./client.jl:439
│ [4] top-level scope at none:5
│ in expression starting at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:10
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:892
R is installed via conda and I have determined that "~/miniconda3/envs/RTIGER/lib/R" is the folder. I specified the RCall version, because the newer versions of RCall don't work on Julia before 1.6.0+, I don't know if 0.13.2 will, I didn't find instructions corresponding to the julia version! I'd like to try it, but the installation comes first!
Seeking help !
Instead of using the ~, can you use the full path? ~ is something that Bash provides and it's not necessarily recognized at the file system level. Looking at the rest of your error message, you need something like
julia> ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
Dear Developer, @palday Firstly, I apologize for the late reply, I’ve been tied up with too many trivial matters! I tried the method you suggested, however, the same error still appears.
[xuruiqiang@login2 ~]$ source ~/miniconda3/bin/activate RTIGER
(RTIGER) [xuruiqiang@login2 ~]$ R RHOME
/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R
(RTIGER) [xuruiqiang@login2 ~]$ which R
~/miniconda3/envs/RTIGER/bin/R
(RTIGER) [xuruiqiang@login2 ~]$ julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.4.0 (2020-03-21)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
"/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
julia> ENV["JULIA_R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/bin/R"
"/public/home/xuruiqiang/miniconda3/envs/RTIGER/bin/R"
julia> using Pkg
julia> Pkg.build(PackageSpec(name="RCall", version="0.13.6"))
Building Conda → `~/.julia/packages/Conda/sDjAP/deps/build.log`
Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] top-level scope at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:47
│ [3] include(::String) at ./client.jl:439
│ [4] top-level scope at none:5
│ in expression starting at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:10
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:892
In addition, I also tried several other methods, all to no avail. As you can see, R is in the conda environment, and Julia is in the system environment variables. I need to install RCall in Julia in order to use a specific R package. I don’t know if you can provide any other suggestions to help identify where the problem lies and how to solve it. Please forgive me as a programming novice and Julia newbie. Any advice is needed !
What happens if you do
ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/bin/R"
using Pkg
Pkg.build(PackageSpec(name="RCall", version="0.13.6"))
?
emmm......it dose not work
julia> ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/bin/R"
"/public/home/xuruiqiang/miniconda3/envs/RTIGER/bin/R"
julia> using Pkg
julia> Pkg.build(PackageSpec(name="RCall", version="0.13.6"))
Building Conda → `~/.julia/packages/Conda/sDjAP/deps/build.log`
Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R_HOME is not a directory.
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] top-level scope at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:42
│ [3] include(::String) at ./client.jl:439
│ [4] top-level scope at none:5
│ in expression starting at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:10
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:892
Any chance it's a problem with the julia install?
One more idea:
(RTIGER) [xuruiqiang@login2 ~]$ LD_LIBRARY_PATH="/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R/lib/:$LD_LIBRARY_PATH" julia
julia> ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
julia> using Pkg
julia> Pkg.build(PackageSpec(name="RCall", version="0.13.6"))
still erro.
(RTIGER) [xuruiqiang@login2 julia-1.4.0]$ LD_LIBRARY_PATH="/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R/lib/:$LD_LIBRARY_PATH" julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.4.0 (2020-03-21)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
julia> ENV["R_HOME"] = "/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
"/public/home/xuruiqiang/miniconda3/envs/RTIGER/lib/R"
julia> using Pkg
julia> Pkg.build(PackageSpec(name="RCall", version="0.13.6"))
Building Conda → `~/.julia/packages/Conda/sDjAP/deps/build.log`
Building RCall → `~/.julia/packages/RCall/ffM0W/deps/build.log`
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
│ Stacktrace:
│ [1] error(::String) at ./error.jl:33
│ [2] top-level scope at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:47
│ [3] include(::String) at ./client.jl:439
│ [4] top-level scope at none:5
│ in expression starting at /public/home/xuruiqiang/.julia/packages/RCall/ffM0W/deps/build.jl:10
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:892