Merge pull request #32 from JuliaStats/only_update_to_0.6

Update to Julia v0.6

.travis.yml

@@ -3,7 +3,7 @@ os:
   - linux
   - osx
 julia:
-  - 0.5
+  - 0.6
   - nightly
 notifications:
   email: false

NEWS.md

@@ -1,3 +1,13 @@
+## RData v0.1.0 Release Notes
+
+Updated to Julia v0.6 (older versions not supported).
+
+##### Changes
+* R logical vectors are converted to `DataVector{Bool}` (instead of `DataVector{Int32}`) [#32]
+* dropped compatibility with Julia versions prior v0.6 [#32]
+
+[#32]: https://github.com/JuliaStats/RData.jl/issues/32
+
 ## RData v0.0.4 Release Notes
 
 Now the recommended way to load `.RData`/`.rda` files is by `FileIO.load()`.

README.md

@@ -1,7 +1,6 @@
 # RData
 
-[![Julia 0.4 Status](http://pkg.julialang.org/badges/RData_0.4.svg)](http://pkg.julialang.org/?pkg=RData&ver=0.4)
-[![Julia 0.5 Status](http://pkg.julialang.org/badges/RData_0.5.svg)](http://pkg.julialang.org/?pkg=RData&ver=0.5)
+[![Julia 0.6 Status](http://pkg.julialang.org/badges/RData_0.6.svg)](http://pkg.julialang.org/?pkg=RData&ver=0.6)
 
 [![Coverage Status](https://coveralls.io/repos/github/JuliaStats/RData.jl/badge.svg)](https://coveralls.io/github/JuliaStats/RData.jl)
 [![Build Status](https://travis-ci.org/JuliaStats/RData.jl.svg?branch=master)](https://travis-ci.org/JuliaStats/RData.jl)

REQUIRE

@@ -1,6 +1,5 @@
-julia 0.5
-DataFrames 0.7
-DataArrays 0.3
+julia 0.6
+DataFrames 0.9
+DataArrays 0.4
 FileIO 0.1.2
 GZip 0.2
-Compat 0.17

appveyor.yml

@@ -1,7 +1,7 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.5/julia-0.5-latest-win32.exe"
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.5/julia-0.5-latest-win64.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.6-latest-win32.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
   - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
   - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
 

src/DictoVec.jl

@@ -11,16 +11,16 @@ function name2index(names::Vector{RString})
 end
 
 """
-    Container that mimics R vector behaviour.
-    Elements could be accessed either by indices as a normal vector,
-    or (optionally) by string keys as a dictionary.
+Container that mimics R vector behaviour.
+Elements could be accessed either by indices as a normal vector,
+or (optionally) by string keys as a dictionary.
 """
-immutable DictoVec{T}
+struct DictoVec{T}
     data::T
     name2index::Dict{RString, Int}
     index2name::Dict{Int, RString}
 
-    @compat function (::Type{DictoVec}){T}(data::T, names::Vector{RString} = Vector{RString}())
+    function (::Type{DictoVec})(data::T, names::Vector{RString} = Vector{RString}()) where T
         n2i, i2n = name2index(names)
         new{T}(data, n2i, i2n)
     end

src/RData.jl

@@ -2,10 +2,8 @@ __precompile__()
 
 module RData
 
-using Compat, DataFrames, GZip, FileIO
-import DataArrays: data
+using DataFrames, DataArrays, GZip, FileIO
 import DataFrames: identifier
-import Compat: unsafe_string
 import FileIO: load
 
 export
@@ -19,7 +17,7 @@ include("sxtypes.jl")
 """
 Abstract RDA format IO stream wrapper.
 """
-@compat abstract type RDAIO end
+abstract type RDAIO end
 
 include("io/XDRIO.jl")
 include("io/ASCIIIO.jl")

src/config.jl

@@ -5,9 +5,9 @@
 ##############################################################################
 
 """
-    Non-standard addition to NaN bit pattern to discriminate NA from NaN.
-    0x000007a2 == UInt32(1954)
-    (I assume 1954 is the year of Ross's birth or something like that.)
+Non-standard addition to NaN bit pattern to discriminate NA from NaN.
+0x000007a2 == UInt32(1954)
+(I assume 1954 is the year of Ross's birth or something like that.)
 """
 const R_NA_FLOAT64_LOW = 0x000007a2
 

src/context.jl

@@ -1,10 +1,10 @@
 """
-    RDA (R data archive) reading context.
+RDA (R data archive) reading context.
 
 * Stores flags that define how R objects are read and converted into Julia objects.
 * Maintains the list of R objects that could be referenced later in the RDA stream.
 """
-type RDAContext{T<:RDAIO}
+struct RDAContext{T<:RDAIO}
     io::T                      # RDA input stream
 
     # RDA format properties
@@ -17,8 +17,10 @@ type RDAContext{T<:RDAIO}
     # intermediate data
     ref_tab::Vector{RSEXPREC}  # SEXP array for references
 end
+
 int2ver(v::Integer) = VersionNumber(v >> 16, (v >> 8) & 0xff, v & 0xff)
-function RDAContext{T<:RDAIO}(io::T, kwoptions::Vector{Any}=Any[])
+
+function RDAContext(io::RDAIO, kwoptions::Vector{Any}=Any[])
     fmtver = readuint32(io)
     rver = int2ver(readint32(io))
     rminver = int2ver(readint32(io))
@@ -27,10 +29,10 @@ function RDAContext{T<:RDAIO}(io::T, kwoptions::Vector{Any}=Any[])
 end
 
 """
-    Registers R object, so that it could be referenced later
-    (by its index in the reference table).
+Register R object, so that it could be referenced later
+(by its index in the reference table).
 """
-function registerref(ctx::RDAContext, obj::RSEXPREC)
+function registerref!(ctx::RDAContext, obj::RSEXPREC)
     push!(ctx.ref_tab, obj)
     obj
 end

src/convert.jl

@@ -40,6 +40,10 @@ function DataArrays.data(ri::RIntegerVector)
     return PooledDataArray(DataArrays.RefArray(refs), pool)
 end
 
+# convert R logical vector (uses Int32 to store values) into DataVector{Bool}
+DataArrays.data(rl::RLogicalVector) =
+    return DataArray(Bool[x != 0 for x in rl.data], namask(rl))
+
 function sexp2julia(rex::RSEXPREC)
     warn("Conversion of $(typeof(rex)) to Julia is not implemented")
     return nothing

src/io/ASCIIIO.jl

@@ -1,10 +1,10 @@
 """
-    ASCII RData format IO stream wrapper.
+ASCII RData format IO stream wrapper.
 """
-type ASCIIIO{T<:IO} <: RDAIO
+struct ASCIIIO{T<:IO} <: RDAIO
     sub::T              # underlying IO stream
 
-    (::Type{ASCIIIO}){T<:IO}(io::T) = new{T}(io)
+    (::Type{ASCIIIO})(io::T) where {T<:IO} = new{T}(io)
 end
 
 readint32(io::ASCIIIO) = parse(Int32, readline(io.sub))

src/io/NativeIO.jl

@@ -1,9 +1,9 @@
 """
-    Native binary RData format IO stream wrapper.
+Native binary RData format IO stream wrapper.
 
-    TODO write readers
+TODO write readers
 """
-type NativeIO{T<:IO} <: RDAIO
+struct NativeIO{T<:IO} <: RDAIO
     sub::T               # underlying IO stream
-    (::Type{NativeIO}){T<:IO}(io::T) = new{T}(io)
+    (::Type{NativeIO})(io::T) where {T<:IO} = new{T}(io)
 end

src/io/XDRIO.jl

@@ -1,10 +1,10 @@
 """
-    XDR (machine-independent binary) RData format IO stream wrapper.
+XDR (machine-independent binary) RData format IO stream wrapper.
 """
-type XDRIO{T<:IO} <: RDAIO
+struct XDRIO{T<:IO} <: RDAIO
     sub::T             # underlying IO stream
     buf::Vector{UInt8} # buffer for strings
-    @compat (::Type{XDRIO}){T <: IO}(io::T) = new{T}(io, Vector{UInt8}(1024))
+    (::Type{XDRIO})(io::T) where {T <: IO} = new{T}(io, Vector{UInt8}(1024))
 end
 
 readint32(io::XDRIO) = ntoh(read(io.sub, Int32))
@@ -25,7 +25,7 @@ function readfloatorNA(io::XDRIO, n::RVecLength)
     reinterpret(Float64, map!(ntoh, v, v))
 end
 
-readuint8(io::XDRIO, n::RVecLength) = readbytes(io.sub, n)
+readuint8(io::XDRIO, n::RVecLength) = read(io.sub, UInt8, n)
 
 function readnchars(io::XDRIO, n::Int32)  # a single character string
     readbytes!(io.sub, io.buf, n)

src/io/utils.jl

@@ -1,12 +1,12 @@
 """
-    Creates `RDAIO` wrapper for `io` stream depending on its format
-    specified by `formatcode`.
+Creates `RDAIO` wrapper for `io` stream depending on its format
+specified by `formatcode`.
 """
 function rdaio(io::IO, formatcode::AbstractString)
     if formatcode == "X" XDRIO(io)
     elseif formatcode == "A" ASCIIIO(io)
     elseif formatcode == "B" NativeIO(io)
-    else error("Unrecognized RDA format \"$formatcode\"")
+    else throw(ArgumentError("Unrecognized RDA format \"$formatcode\""))
     end
 end
 
@@ -41,9 +41,9 @@ else
     end
 end
 
-immutable CHARSXProps # RDA CHARSXP properties
-  levs::UInt32       # level flags (encoding etc) TODO process
-  nchar::Int32       # string length, -1 for NA strings
+struct CHARSXProps # RDA CHARSXP properties
+    levs::UInt32       # level flags (encoding etc) TODO process
+    nchar::Int32       # string length, -1 for NA strings
 end
 
 function readcharsxprops(io::RDAIO) # read character string encoding and length

src/readers.jl

@@ -65,7 +65,7 @@ end
 
 function readsymbol(ctx::RDAContext, fl::RDATag)
     @assert sxtype(fl) == SYMSXP
-    registerref(ctx, RSymbol(readcharacter(ctx.io)))
+    registerref!(ctx, RSymbol(readcharacter(ctx.io)))
 end
 
 function readS4(ctx::RDAContext, fl::RDATag)
@@ -78,7 +78,7 @@ end
 function readenv(ctx::RDAContext, fl::RDATag)
     @assert sxtype(fl) == ENVSXP
     is_locked = readint32(ctx.io)
-    res = registerref(ctx, REnvironment()) # registering before reading the contents
+    res = registerref!(ctx, REnvironment()) # registering before reading the contents
     res.enclosed = readitem(ctx)
     res.frame = readitem(ctx)
     res.hashtab = readitem(ctx)
@@ -98,12 +98,12 @@ end
 
 function readnamespace(ctx::RDAContext, fl::RDATag)
     @assert sxtype(fl) == NAMESPACESXP
-    registerref(ctx, RNamespace(readname(ctx)))
+    registerref!(ctx, RNamespace(readname(ctx)))
 end
 
 function readpackage(ctx::RDAContext, fl::RDATag)
     @assert sxtype(fl) == PACKAGESXP
-    registerref(ctx, RPackage(readname(ctx)))
+    registerref!(ctx, RPackage(readname(ctx)))
 end
 
 # reads single-linked lists R objects
@@ -170,17 +170,17 @@ end
 
 function readextptr(ctx::RDAContext, fl::RDATag)
     @assert sxtype(fl) == EXTPTRSXP
-    res = registerref(ctx, RExtPtr()) # registering before reading the contents
+    res = registerref!(ctx, RExtPtr()) # registering before reading the contents
     res.protected = readitem(ctx)
     res.tag = readitem(ctx)
     res.attr = readattrs(ctx, fl)
     return res
 end
 
 """
-    Context for reading R bytecode.
+Context for reading R bytecode.
 """
-immutable BytecodeContext
+struct BytecodeContext
     ctx::RDAContext         # parent RDA context
     ref_tab::Vector{Any}    # table of bytecode references
 
@@ -251,15 +251,15 @@ function readunsupported(ctx::RDAContext, fl::RDATag)
 end
 
 """
-    Definition of R type.
+Definition of R type.
 """
-immutable SXTypeInfo
+struct SXTypeInfo
     name::String         # R type name
     reader::Function     # function to deserialize R type from RDA stream
 end
 
 """
-    Maps R type id (`SXType`) to its `SXTypeInfo`.
+Maps R type id (`SXType`) to its `SXTypeInfo`.
 """
 const SXTypes = Dict{SXType, SXTypeInfo}(
     NILSXP     => SXTypeInfo("NULL",readdummy),