RCall code for translation back and for to R Rle objects loads when R…

.travis.yml

@@ -15,19 +15,6 @@ matrix:
   allow_failures:
   - julia: nightly
 
-before_install:
-  # linux
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get update -qq -y; fi
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then sudo apt-get install git r-base r-base-dev r-recommended -y; fi
-
-  # osx
-  # faster than using homebrew/science tap
-  # but no permalink to release download
-  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then wget "https://cran.rstudio.com/bin/macosx/$(wget -qO- https://cran.rstudio.com/bin/macosx/ | sed -n 's/.*href="\(R-[^"]*.pkg\)".*/\1/p' | head -n 1)"; fi
-  - if [ "$TRAVIS_OS_NAME" == "osx" ]; then sudo installer -pkg R-*.pkg -target /; fi
-
 script:
   - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
   - julia --color=yes -e 'using Pkg; Pkg.build()'

Manifest.toml

@@ -4,22 +4,21 @@
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[CategoricalArrays]]
-deps = ["Compat", "Future", "Missings", "Printf", "Reexport", "Requires"]
-git-tree-sha1 = "94d16e77dfacc59f6d6c1361866906dbb65b6f6b"
+deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport", "Unicode"]
+git-tree-sha1 = "5f4400b24adb1fbed17a9dcc1e8ab8aaf5b03d1f"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "0.5.2"
+version = "0.6.0"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
 git-tree-sha1 = "84aa74986c5b9b898b0d1acaf3258741ee64754f"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
 version = "2.1.0"
 
-[[Conda]]
-deps = ["Compat", "JSON", "VersionParsing"]
-git-tree-sha1 = "b625d802587c2150c279a40a646fba63f9bd8187"
-uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
-version = "1.2.0"
+[[DataAPI]]
+git-tree-sha1 = "8903f0219d3472543fc4b2f5ebaf675a07f817c0"
+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.0.1"
 
 [[DataFrames]]
 deps = ["CategoricalArrays", "Compat", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Unicode"]
@@ -28,10 +27,15 @@ uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 version = "0.18.1"
 
 [[DataStructures]]
-deps = ["InteractiveUtils", "OrderedCollections", "Random", "Serialization", "Test"]
-git-tree-sha1 = "ca971f03e146cf144a9e2f2ce59674f5bf0e8038"
+deps = ["InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "0809951a1774dc724da22d26e4289bbaab77809a"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.15.0"
+version = "0.17.0"
+
+[[DataValueInterfaces]]
+git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
+uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
+version = "1.0.0"
 
 [[Dates]]
 deps = ["Printf"]
@@ -59,10 +63,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[JSON]]
-deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
-git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa"
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.20.0"
+version = "0.21.0"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -82,10 +86,9 @@ deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[Missings]]
-deps = ["Dates", "InteractiveUtils", "SparseArrays", "Test"]
-git-tree-sha1 = "d1d2585677f2bd93a97cfeb8faa7a0de0f982042"
+git-tree-sha1 = "29858ce6c8ae629cf2d733bffa329619a1c843d0"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "0.4.0"
+version = "0.4.2"
 
 [[Mmap]]
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -96,26 +99,25 @@ git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.1.0"
 
+[[Parsers]]
+deps = ["Dates", "Test"]
+git-tree-sha1 = "ef0af6c8601db18c282d092ccbd2f01f3f0cd70b"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "0.3.7"
+
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[PooledArrays]]
-deps = ["Test"]
-git-tree-sha1 = "6ea4cfb9136d3ff2b9d30d6696cd72166a3b837c"
+git-tree-sha1 = "6e8c38927cb6e9ae144f7277c753714861b27d14"
 uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
-version = "0.5.1"
+version = "0.5.2"
 
 [[Printf]]
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[RCall]]
-deps = ["CategoricalArrays", "Conda", "DataFrames", "DataStructures", "Dates", "Libdl", "Missings", "REPL", "Random", "Requires", "StatsModels", "Test", "WinReg"]
-git-tree-sha1 = "58958d1ce1923a5e5f20999caa4d7f0df38e1ca9"
-uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
-version = "0.13.2"
-
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -169,23 +171,17 @@ git-tree-sha1 = "8a0f4b09c7426478ab677245ab2b0b68552143c7"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 version = "0.30.0"
 
-[[StatsModels]]
-deps = ["Compat", "DataFrames", "StatsBase", "Test"]
-git-tree-sha1 = "b5a735dcd2be05f0af86709750d4d5f62ca4a25d"
-uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.5.0"
-
 [[TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
 git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
 uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 version = "1.0.0"
 
 [[Tables]]
-deps = ["IteratorInterfaceExtensions", "LinearAlgebra", "Requires", "TableTraits", "Test"]
-git-tree-sha1 = "e2abd466ca2f00a1bb8cb80024d59745cc8f91a6"
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
+git-tree-sha1 = "aaed7b3b00248ff6a794375ad6adf30f30ca5591"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "0.2.0"
+version = "0.2.11"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
@@ -197,15 +193,3 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-
-[[VersionParsing]]
-deps = ["Compat"]
-git-tree-sha1 = "c9d5aa108588b978bd859554660c8a5c4f2f7669"
-uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
-version = "1.1.3"
-
-[[WinReg]]
-deps = ["Test"]
-git-tree-sha1 = "808380e0a0483e134081cc54150be4177959b5f4"
-uuid = "1b915085-20d7-51cf-bf83-8f477d6f5128"
-version = "0.3.1"

Project.toml

@@ -5,11 +5,11 @@ version = "0.8.1"
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-julia = "1.0"
 StatsBase = ">= 0.6.0"
-RCall = ">= 0.7.4"
+julia = "1.0"

src/RLEVectors.jl

@@ -1,8 +1,8 @@
 module RLEVectors
 
+using Requires
 using Statistics
 using StatsBase
-using RCall
 using DataFrames
 
 # RLEVector type
@@ -54,9 +54,6 @@ import DataFrames: AbstractDataFrame, DataFrame, Index, index, nrow, ncol
 export RLEDataFrame, nrow, ncol, columns, index, names
 export rowSums, rowMeans, rowMedians, colSums, colMeans, colMedians
 
-# RCall
-import RCall: sexp, rcopy, RClass, rcopytype, @R_str, S4Sxp
-
 ### Includes
 include("utils.jl")
 include("runs.jl")
@@ -69,8 +66,11 @@ include("group_generics.jl")
 include("collections_api.jl")
 include("math.jl")
 include("sorting.jl")
-include("rcall.jl")
 include("precompile.jl")
 _precompile_()
 
-end # Module RLEVectors
+function __init__()
+	 @require RCall="6f49c342-dc21-5d91-9882-a32aef131414" include("rcall.jl")
+end
+
+end # module RLEVectors

src/rcall.jl

@@ -1,12 +1,14 @@
-function sexp(f::RLEVector)
-    R"library(GenomicRanges)"
+using .RCall
+
+function RCall.sexp(f::RLEVector)
+    RCall.R"library(GenomicRanges)"
     v = values(f)
     w = widths(f)
-    R"Rle($v, $w)"
+    RCall.R"Rle($v, $w)"
 end
 
 function rcopy(::Type{RLEVector}, s::Ptr{S4Sxp})
-    RLEVector(rcopy(s[:values]), cumsum(rcopy(s[:lengths])))
+    RLEVector(Rcall.rcopy(s[:values]), cumsum(RCall.rcopy(s[:lengths])))
 end
 
-rcopytype(::Type{RClass{:Rle}}, s::Ptr{S4Sxp}) = RLEVector
+rcopytype(::Type{RCall.RClass{:Rle}}, s::Ptr{RCall.S4Sxp}) = RLEVector