Switch to using Preferences-based RCall

Author: Frankie Robertson

.github/workflows/CI.yml

@@ -73,7 +73,7 @@ jobs:
           R_HOME: '*'
       - name: Make docs
         run: |
-          julia --project=docs/ docs/setup_r.jl &&
+          julia --project=docs/ docs/fix_r_preferences.jl &&
           USE_CAIRO_MAKIE=1 julia --project=docs/ -e '
             include("docs/make.jl")'
         env:

docs/Manifest.toml

@@ -1522,7 +1522,9 @@ version = "0.2.19"
 
 [[deps.RCall]]
 deps = ["CategoricalArrays", "Conda", "DataFrames", "DataStructures", "Dates", "Libdl", "Missings", "REPL", "Random", "Requires", "StatsModels", "WinReg"]
-git-tree-sha1 = "d441bdeea943f8e8f293e0e3a78fe2d7c3aa24e6"
+git-tree-sha1 = "c0cbc8173a6782e19df785a6a12ddfd9e0c31ca7"
+repo-rev = "master"
+repo-url = "https://github.com/frankier/RCall.jl.git#preferences-r-installation"
 uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
 version = "0.13.15"
 

docs/build.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-julia --project=. ./setup_r.jl
+julia --project=. ./fix_r_preferences.jl
 USE_CAIRO_MAKIE=1 julia --project=. make.jl

docs/fix_r_preferences.jl

@@ -0,0 +1,56 @@
+using CondaPkg
+using Preferences
+using Libdl
+using PreferenceTools
+
+"""
+    validate_libR(libR)
+
+Checks that the R library `libR` can be loaded and is satisfies version requirements.
+
+"""
+function validate_libR(libR)
+    if !isfile(libR)
+        error("Could not find library $libR. Make sure that R shared library exists.")
+    end
+    # Issue #143
+    # On linux, sometimes libraries linked from libR (e.g. libRblas.so) won't open unless LD_LIBRARY_PATH is set correctly.
+    libptr = try
+        Libdl.dlopen(libR)
+    catch er
+        Base.with_output_color(:red, stderr) do io
+            print(io, "ERROR: ")
+            showerror(io, er)
+            println(io)
+        end
+        @static if Sys.iswindows()
+            error("Try adding $(dirname(libR)) to the \"PATH\" environmental variable and restarting Julia.")
+        else
+            error("Try adding $(dirname(libR)) to the \"LD_LIBRARY_PATH\" environmental variable and restarting Julia.")
+        end
+    end
+    # R_tryCatchError is only available on v3.4.0 or later.
+    if Libdl.dlsym_e(libptr, "R_tryCatchError") == C_NULL
+        error("R library $libR appears to be too old. RCall.jl requires R 3.4.0 or later.")
+    end
+    Libdl.dlclose(libptr)
+    return true
+end
+
+function locate_libR(Rhome)
+    @static if Sys.iswindows()
+        libR = joinpath(Rhome, "bin", Sys.WORD_SIZE==64 ? "x64" : "i386", "R.dll")
+    else
+        libR = joinpath(Rhome, "lib", "libR.$(Libdl.dlext)")
+    end
+    validate_libR(libR)
+    return libR
+end
+
+CondaPkg.resolve()
+target_rhome = "$(CondaPkg.envdir())/lib/R"
+PreferenceTools.add(
+    "RCall",
+    "Rhome" => target_rhome,
+    "libR" => locate_libR(target_rhome)
+)

docs/make.jl

@@ -1,5 +1,3 @@
-include("./setup_r.jl")
-
 using ComputerAdaptiveTesting
 using CATPlots