Merge branch 'master' into master

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ on:
   pull_request:
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    name: Julia ${{ matrix.version }} - R ${{ matrix.R }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
@@ -19,6 +19,10 @@ jobs:
           - '1.6'
           - '1'
           - nightly
+        R:
+          - 'release'
+          - '4.0'
+          - '3.4'
         os: [ubuntu-latest]
         arch: [x64]
         experimental: [false]
@@ -28,10 +32,12 @@ jobs:
             arch: x64
             version: 1
             experimental: false
+            R: 'release'
           - os: windows-latest
             arch: x64
             version: 1
             experimental: false
+            R: 'release'
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -42,6 +48,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          r-version: ${{ matrix.R }}
       - run: echo "LD_LIBRARY_PATH=$(R RHOME)/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
         if: matrix.os == 'ubuntu-latest'
       - uses: julia-actions/julia-buildpkg@v1

Project.toml

@@ -1,7 +1,7 @@
 name = "RCall"
 uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
 authors = ["Douglas Bates <dmbates@gmail.com>", "Randy Lai <randy.cs.lai@gmail.com>", "Simon Byrne <simonbyrne@gmail.com>"]
-version = "0.13.15"
+version = "0.13.16"
 
 [deps]
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

docs/src/installation.md

@@ -72,7 +72,7 @@ This problem doesn't affect Julia ≥ 1.6!
 
 ### Other methods
 
-If you have installed R by some other method (e.g. building from scratch, or files copied but not installed in the usual manner), which often happens on cluster installations, then you may need to set `R_HOME` or your `PATH` as described above before running `Pkg.build("RCall")` in order for the build script to find your R installation. RCall requries R to be installed with its shared library. It could be done with the flag `--enable-R-shlib`, consult your server administrator to see if it was the case.
+If you have installed R by some other method (e.g. building from scratch, or files copied but not installed in the usual manner), which often happens on cluster installations, then you may need to set `R_HOME` or your `PATH` as described above before running `Pkg.build("RCall")` in order for the build script to find your R installation. RCall requires R to be installed with its shared library. It could be done with the flag `--enable-R-shlib`, consult your server administrator to see if it was the case.
 
 For some environments, you might also need to specify `LD_LIBRARY_PATH`
 ```sh

src/convert/default.jl

@@ -202,7 +202,7 @@ rcopy(r) = r
 # logic of default sexp
 
 """
-`robject(x)` converts a Julia object `x` to a corresponding RObject implictly. Explict conversions
+`robject(x)` converts a Julia object `x` to a corresponding RObject implicitly. Explicit conversions
 could be called with `robject(<R Class>, x)`.
 """
 robject(s) = RObject(s)

src/ijulia.jl

@@ -1,6 +1,6 @@
 # IJulia hooks for displaying plots with RCall
 
-# TODO: create a special graphics device. This would allow us to not accidently close devices opened by users, and display plots immediately as they appear.
+# TODO: create a special graphics device. This would allow us to not accidentally close devices opened by users, and display plots immediately as they appear.
 
 ijulia_mime = nothing
 

src/language.jl

@@ -19,7 +19,7 @@ function rlang_p(f, args...; kwargs...)
     l
 end
 
-"Create a function call from a function pointer and a list of arguments and return it as an RObject, which can then be evaulated"
+"Create a function call from a function pointer and a list of arguments and return it as an RObject, which can then be evaluated"
 rlang(f, args...; kwargs...) = RObject(rlang_p(f,args...; kwargs...))
 
 

src/methods.jl

@@ -459,13 +459,13 @@ isNA(x::Float64) = is_ieee_na(x)
 isNA(x::Int32) = x == Const.NaInt
 isNA(s::Ptr{CharSxp}) = s === sexp(Const.NaString)
 isNA(s::Ptr{S}) where S<:VectorSxp = length(s) == 1 ? isNA(s[1]) : false
-# all other values are consided as non-NA.
+# all other values are considered as non-NA.
 isNA(s::Any) = false
 
 isna(s::Ptr{S}, i::Integer) where S<:VectorSxp = isNA(s[i])
 isna(s::Ptr{S}) where S<:VectorSxp = reshape(BitArray([isNA(a) for a in s]), size(s))
 """
-Check if the ith member of s coorespond to R's NA values.
+Check if the ith member of s correspond to R's NA values.
 """
 isna(r::RObject, i::Integer) = isna(r.p, i)
 """
@@ -544,7 +544,7 @@ getindex(e::RObject{EnvSxp},s) = RObject(getindex(sexp(e),s))
 function setindex!(e::Ptr{EnvSxp},v::Ptr{S},s::Ptr{StrSxp}) where S<:Sxp
     # `Rf_defineVar` is unsafe to use if the binding is locked.
     # However, `setVarInFrame` is not exported. `base::assign` is
-    # an avaliable alternative.
+    # an available alternative.
     rcall_p(Const.BaseNamespace["assign"], s, v, envir = e)
 end
 function setindex!(e::Ptr{EnvSxp},v,s)

src/render.jl

@@ -98,7 +98,7 @@ function render(script::String)
 end
 
 """
-Prepare code for evaluating the julia expressions. When the code is execulated,
+Prepare code for evaluating the julia expressions. When the code is evaluated,
 the results are stored in the R environment `#JL`.
 """
 function prepare_inline_julia_code(symdict, escape::Bool=false)

src/types.jl

@@ -298,7 +298,7 @@ end
 
 
 """
-Convert a `Ptr{UnknownSxp}` to an approptiate `Ptr{S<:Sxp}`.
+Convert a `Ptr{UnknownSxp}` to an appropriate `Ptr{S<:Sxp}`.
 """
 function sexp(p::Ptr{UnknownSxp})
     typ = sexpnum(p)

test/convert/datetime.jl

@@ -73,7 +73,13 @@ r = RObject(d)
 @test rcopy(r) === d
 @test rcopy(DateTime, r) === d
 @test rcopy(R"as.POSIXct($s, 'UTC', '%Y-%m-%dT%H:%M:%S')") == d
-@test rcopy(R"identical(as.character($d, '%Y-%m-%dT%H:%M:%S'), $s)")
+# previously the second argument to as.character.POSIXt was `format``, now it defaults
+# to `digits`. Using `format` as a named argument gives a deprecation warning
+# this changed in R 4.3.0 but is listed as a bugfix
+# > as.character(<POSIXt>) now behaves more in line with the methods for atomic vectors such as numbers,
+# > and is no longer influenced by options(). Ditto for as.character(<Date>). The as.character() method
+# > gets arguments digits and OutDec with defaults not depending on options(). Use of as.character(*, format = .) now warns.
+@test rcopy(R"identical(format($d, '%Y-%m-%dT%H:%M:%S'), $s)")
 
 
 s = ["2001-01-01T01:01:01", "1111-11-11T11:11:00", "2012-12-12T12:12:12"]
@@ -88,7 +94,7 @@ r = RObject(d)
 @test rcopy(r) == d
 @test rcopy(Array{DateTime}, r) == d
 @test rcopy(R"as.POSIXct($s, 'UTC', '%Y-%m-%dT%H:%M:%S')") == d
-@test rcopy(R"identical(as.character($d, '%Y-%m-%dT%H:%M:%S'), $s)")
+@test rcopy(R"identical(format($d, '%Y-%m-%dT%H:%M:%S'), $s)")
 
 
 # SubArray
@@ -103,7 +109,7 @@ r = RObject(d)
 @test rcopy(r) == d
 @test rcopy(Array{DateTime}, r) == d
 @test rcopy(R"as.POSIXct($s[1:2], 'UTC', '%Y-%m-%dT%H:%M:%S')") == d
-@test rcopy(R"identical(as.character($d, '%Y-%m-%dT%H:%M:%S'), $s[1:2])")
+@test rcopy(R"identical(format($d, '%Y-%m-%dT%H:%M:%S'), $s[1:2])")
 
 
 d = DateTime[]