Deal with normalization collisions in reimport (#532)

* improve rimport
  * detect name collisions and give a nice warning message
  * use gensym instead of a default name to avoid collisions of hidden module
  * allow custom normalization

* version bump

* use default native arch in CI

.github/workflows/ci.yml

@@ -24,17 +24,14 @@ jobs:
           - '4.0'
           - '3.4'
         os: [ubuntu-latest]
-        arch: [x64]
         experimental: [false]
         include:
           # test macOS and Windows with latest Julia only
           - os: macOS-latest
-            arch: x64
             version: 1
             experimental: false
             R: 'release'
           - os: windows-latest
-            arch: x64
             version: 1
             experimental: false
             R: 'release'
@@ -43,7 +40,6 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: julia-actions/cache@v2
       - uses: r-lib/actions/setup-r@v2
         with:

.gitignore

@@ -5,3 +5,4 @@ docs/gh-pages
 docs/site
 deps/build.log
 lcov.info
+*.cov

Project.toml

@@ -1,7 +1,7 @@
 name = "RCall"
 uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
 authors = ["Douglas Bates <[email protected]>", "Randy Lai <[email protected]>", "Simon Byrne <[email protected]>"]
-version = "0.14.1"
+version = "0.14.2"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
@@ -10,7 +10,6 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
 Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -24,7 +23,6 @@ CategoricalArrays = "0.8, 0.9, 0.10"
 Conda = "1.4"
 DataFrames = "0.21, 0.22, 1.0"
 DataStructures = "0.5, 0.6, 0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
-Missings = "0.2, 0.3, 0.4, 1.0"
 Preferences = "1"
 Requires = "0.5.2, 1"
 StatsModels = "0.6, 0.7"

src/RCall.jl

@@ -6,9 +6,6 @@ using Dates
 using Libdl
 using Random
 using REPL
-if VERSION ≤ v"1.1.1"
-   using Missings
-end
 using CategoricalArrays
 using DataFrames
 using StatsModels

src/namespaces.jl

@@ -7,7 +7,7 @@ const reserved = Set{String}([
     "false", "true", "Tuple", "rmember", "__package__"])
 
 
-cached_namespaces = Dict{String, Module}()
+const cached_namespaces = Dict{String, Module}()
 
 """
 Import an R package as a julia module.
@@ -17,18 +17,27 @@ E.g.: `PerformanceAnalytics::charts.Bar` in R becomes `PerformanceAnalytics.char
 ```
 gg = rimport("ggplot2")
 ```
+
+`normalization` is passed directly to `replace` via splatting.
 """
-function rimport(pkg::String, s::Symbol=:__anonymous__; normalizenames::Bool=true)
+function rimport(pkg::String, s::Symbol=gensym(:rimport);
+                 normalizenames::Bool=true, normalization=['.' => '_'])
     if pkg in keys(cached_namespaces)
         m = cached_namespaces[pkg]
     else
         ns = rcall(:asNamespace, pkg)
+        # XXX note that R is sensitive to definition order, so do not change the order!
         members = rcopy(Vector{String}, rcall(:getNamespaceExports, ns))
 
         m = Module(s, false)
         id = Expr(:const, Expr(:(=), :__package__, pkg))
         if normalizenames
-            exports = [Symbol(replace(x, '.' => '_')) for x in members]
+            exports = [Symbol(replace(x, normalization...)) for x in members]
+            dupes = [k for (k, v) in countmap(exports) if v > 1]
+            if !isempty(dupes)
+                error("Normalized names are no longer unique: " *
+                       join(dupes, ", ", " and "))
+            end
         else
             exports = [Symbol(x) for x in members]
         end
@@ -37,13 +46,21 @@ function rimport(pkg::String, s::Symbol=:__anonymous__; normalizenames::Bool=tru
                                    collect(eachindex(exports)))
         consts = [Expr(:const, Expr(:(=),
                        exports[i],
-                       rcall(Symbol("::"), pkg, members[i]))) for i in filtered_indices ]
+                       rcall(Symbol("::"), pkg, members[i]))) for i in filtered_indices]
         Core.eval(m, Expr(:toplevel, id, consts..., Expr(:export, exports...), :(rmember(x) = ($getindex)($ns, x))))
         cached_namespaces[pkg] = m
     end
-    m
+    return m
+end
+rimport(pkg::Symbol, args...; kwargs...) = rimport(string(pkg), args...; kwargs...)
+
+function countmap(v::Vector{T}) where {T}
+    occurrences = Dict{Symbol,Int}()
+    for el in v
+        occurrences[el] = get(occurrences, el, 0) + 1
+    end
+    return occurrences
 end
-rimport(pkg::Symbol, s::Symbol=:__anonymous__) = rimport(string(pkg), s)
 
 """
 Import an R Package as a Julia module. For example,

test/namespaces.jl

@@ -6,9 +6,7 @@ module NamespaceTests
     using RCall
     using Test
 
-    RCall.R"""
-        has_mass_package = require("MASS")
-    """
+    reval("""has_mass_package = require("MASS")""")
 
     RCall.@rget has_mass_package
 
@@ -23,4 +21,22 @@ module NamespaceTests
         @test rcopy(rcall(ginv, RObject([1 2; 0 4]))) ≈ [1 -0.5; 0 0.25]
     end
 
+    # why exclude Windows? because the tempdir could potentially include
+    # unicode characters and R can't handle that
+    if !Sys.iswindows()
+        if !rcopy(reval("""require("ape")"""))  # 418
+            @info "installing ape to temporary lib"
+            tmp = mktempdir()
+            reval("""lib <- "$(tmp)"
+                     .libPaths(lib)
+                     install.packages("ape", repos="https://cloud.r-project.org", method="wget", lib=lib)
+                     library("ape")""")
+        end
+
+        @test_throws ErrorException rimport("ape")
+
+        rimport(:ape; normalization=["." => "__"])
+    end
+    # stats is always available
+    rimport(:stats; normalizenames=false)
 end