Ah, sorry. There's a mistake in the highlighting. At the bottom of
read_object, it should actually be highlighted like this:
elseif rType == defaultRType.RAWSXP
rawLength = readInt32(rr.reader)
result = RObject(readbytes(rr.reader, rawLength), is_raw = true)
elseif rType == defaultRType.LANGSXP
result = RObject(None)
att_list = read_attribute_list(rr) # att_list returns nothing DataType
setAttributes(result, att_list)
elseif rType == defaultRType.SYMSXP
symbol = read_symbol_or_string(rr)
push!(rr.symbols, symbol)
return RObject([symbol])
else
error("Unexpected type")
end
if getAttributeFlag(typeTag)
att_list = read_attribute_list(rr)
setAttributes(result, att_list)
end
return result
end
On Tuesday, August 11, 2015 at 5:03:23 PM UTC-4, Sayeed Tasnim wrote:
>
> I'm working on some Julia code to read XDR data/files (something that
> might be generated from R using save).
>
> I have a function read_attribute_list to read the attributes associated
> with an R Object which returns a Dict. I also have a function read_object
> to read an R Object which calls read_attribute_list.
>
> function read_attribute_list(rr::RReader)
> result = Dict{String,RObject}()
> typeTag = get_type_tag(rr)
>
> defaultRType = RType()
> while getRType(typeTag) == defaultRType.LISTSXP
> tagFlag = getTagFlag(typeTag)
> tag = None
>
> if tagFlag
> tag = read_symbol_or_string(rr)
> end
>
> car = read_object(rr)
> if car != None
> result[tag] = car
> end
>
> typeTag = get_type_tag(rr)
>
> end
>
> if getRType(typeTag) != defaultRType.EMPTYTAIL &&
> getRType(typeTag) != defaultRType.STRSXP
> error("Not Implemented")
> end
>
> return result # result remains a Dict here and can be printed right
> before
> end
>
>
> function read_object(rr::RReader)
> typeTag = get_type_tag(rr)
> lengthVar = 0
> result = None
> rType = getRType(typeTag)
>
> defaultRType = RType()
> if rType == defaultRType.LGLSXP
> lengthVar = readInt32(rr.reader)
> boolValues = @data(bitunpack(falses(lengthVar)))
> for i in 1:lengthVar
> flag = read_integer(rr)
> if flag == 0 || flag == 1
> boolValues[i] = !(flag == 0)
> elseif flag == None
> boolValues[i] = NA
> else
> error("Invalid boolean flag from XDR: $(flag)")
> end
> end
>
> result = RObject(boolValues)
>
> elseif rType == defaultRType.INTSXP
> lengthVar = readInt32(rr.reader)
> values = @data(zeros(Int32, lengthVar))
>
> for i in 1:lengthVar
> value = read_integer(rr)
> if value == None
> values[i] = NA
> else
> values[i] = value
> end
> end
>
> result = RObject(values)
>
> elseif rType == defaultRType.REALSXP
> lengthVar = readInt32(rr.reader)
> values = @data(zeros(Float64, lengthVar))
>
> for i in 1:lengthVar
> value = readFloat64(rr.reader)
> if isnan(value)
> values[i] = NA
> else
> values[i] = value
> end
> end
>
> result = RObject(values)
>
> elseif rType == defaultRType.CPLXSXP
> lengthVar = readInt32(rr.reader)
> complexValues = @data(zeros(Complex128,lengthVar))
>
> for i in 1:lengthVar
> realVal = readFloat64(rr.reader)
> imaginaryVal = readFloat64(rr.reader)
> if !isnan(realVal) && !isnan(imaginaryVal)
> complexValues[i] = complex128(realVal, imaginaryVal)
> else
> complexValues[i] = NA
> end
> end
>
> result = RObject(complexValues)
>
> elseif rType == defaultRType.STRSXP
> lengthVar = readInt32(rr.reader)
> stringVector = @data(fill("", lengthVar))
>
> for i in 1:lengthVar
> val = read_symbol_or_string(rr)
> stringVector[i] = val != None ? val : NA
> end
>
> result = RObject(stringVector)
>
> elseif rType == defaultRType.VECSXP
> lengthVar = readInt32(rr.reader)
> vectorObject = @data(fill!(Array(Any,lengthVar),None))
> for i in 1:lengthVar
> vectorObject[i] = read_object(rr)
> end
>
> result = RObject(vectorObject)
>
> elseif rType == defaultRType.EXTPTRSXP
> readInt64(rr.reader)
> result = None
>
> elseif rType == defaultRType.RAWSXP
> rawLength = readInt32(rr.reader)
> result = RObject(readbytes(rr.reader, rawLength), is_raw = true)
>
> elseif rType == defaultRType.LANGSXP
> result = RObject(None)
> att_list = read_attribute_list(rr) # att_list returns nothing DataType
> setAttributes(result, att_list)
>
> elseif rType == defaultRType.SYMSXP
> symbol = read_symbol_or_string(rr)
> push!(rr.symbols, symbol)
> return RObject([symbol])
>
> else
> error("Unexpected type")
> end
>
> if getAttributeFlag(typeTag)
> att_list = read_attribute_list(rr)
> setAttributes(result, att_list)
> end
>
> return result
> end
>
>
> As read_attribute_list is called, the attributes are read correctly and
> the Dict can be viewed by printing it right before the return statement.
> However, in the highlighted code for read_object, the att_list returned is
> a nothing DataType and the Dict that was visible before is lost.
>
> I can't figure out what would be causing this bug. Some things that I
> have tried that might be helpful:
> 1) Turn off gc(). I disable garbage collection and run the code. The
> behavior remains the same and nothing is returned.
> 2) Return a list of tuples instead. Instead of returning a Dict, I return
> Array{(String,RObject)} to serialize the Dict. The behavior remains the
> same and nothing is returned.
> 3) Reproduce the bug outside of the module. I extract the part of the XDR
> file with only the attributes. read_attribute_list reads properly and
> returns the Dict.
>
> Feel free to ask questions about other pieces of the code or
> implementation details. Any help with this would be appreciated!
>
