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Call R from Julia

License: Other

Julia 100.00%

julia r-language

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wildart robertfeldt nagyist ykzhou vlulla tkelman mmaechler islandsofsleep andygreenwell armgong ranjanan abhijithch pallharaldsson lelmiger kaskarn tlyim non-contradiction freeboson funnell kleinschmidt randy3k jngod2011 jayvn juliadocsforks gmontanari cossio gaybro8777 haberdashpi ppalmes stjordanis jing-xinxing juliatagbot andreasnoack hsm207 oxinabox liguoyuan jackdunnnz cgmossa 00mjk thecedarprince diegozea standardgalactic kool7d pitmonticone ianbutterworth playfloor tomhaber terasakisatoshi nicjc juliaepi szcf-weiya chrisrackauckas bernardo-besada rafabench frankier schlichtanders jolin-io asinghvi17

rcall.jl's Issues

ASCIIString Array conversion error

sexp("q")
SEXP{16}(Ptr{Void} @0x000000000ea8f988)

sexp(["p", "q"])
ERROR: `sexp` has no method matching sexp(::Array{ASCIIString,1})

Would be helpful to convert string vectors as well. Here is an example of my attempts to convert DataFrame to R object where this limitation shows up, as a part of this discussion.

PS: Thanks for the very helpful package!

ErrorException after install

Thanks for RCall it looks very useful. I followed the installation steps in the README on a fresh Julia 0.3.4 on Mac OS X Yosemite with all packages updated but then get this when trying to load RCall:

julia> using RCall
Warning: error initializing module RCall:
ErrorException("type cannot be constructed")

The deps.jl file looks fine except for the LD_LIBRARY_PATH:

feldt:~/feldt/bin$ cat /Users/feldt/.julia/v0.3/RCall/deps/deps.jl
# This is an auto-generated file; do not edit

const libR="/usr/local/Cellar/r/3.1.1/R.framework/Resources/lib/libR.dylib"
ENV["R_HOME"]="/usr/local/Cellar/r/3.1.1/R.framework/Resources"
ENV["R_DOC_DIR"]="/usr/local/Cellar/r/3.1.1/R.framework/Resources/doc"
ENV["R_INCLUDE_DIR"]="/usr/local/Cellar/r/3.1.1/R.framework/Resources/include"
ENV["R_SHARE_DIR"]="/usr/local/Cellar/r/3.1.1/R.framework/Resources/share"
ENV["LD_LIBRARY_PATH"]=""

so I changed it to

ENV["LD_LIBRARY_PATH"]="/usr/local/Cellar/r/3.1.1/R.framework/Resources/lib"

but with same error. Any ideas on what is wrong here? Thanks in advance.

New update is not working on Julia v.0.4

I cannot identify the issue, it seems it has something to do with IJulia.jl. But I cannot figure it out. I am running the nightly build on Mac OS via command line.

PS: it is working on v.0.3.7

ERROR: LoadError: LoadError: error compiling anonymous: unsupported or misplaced expression "import" in function anonymous
 in include at /opt/local/julia-dev/lib/julia/sys.dylib
 in include_from_node1 at /opt/local/julia-dev/lib/julia/sys.dylib
 in include at /opt/local/julia-dev/lib/julia/sys.dylib
 in include_from_node1 at /opt/local/julia-dev/lib/julia/sys.dylib
 in reload_path at /opt/local/julia-dev/lib/julia/sys.dylib
 in _require at /opt/local/julia-dev/lib/julia/sys.dylib
 in require at /opt/local/julia-dev/lib/julia/sys.dylib
while loading /Users/Randy/.julia/v0.4/RCall/src/IJulia.jl, in expression starting on line 3
while loading /Users/Randy/.julia/v0.4/RCall/src/RCall.jl, in expression starting on line 75

Create a type for an SEXPREC

Use bitpack, not BitArray constructor, for compatibility with v0.3.x

deps/build.jl fails on Ubuntu/Debian using version 0.4.0-dev+4850

I haven't dug into exactly why this is failing on v"0.4.0-dev" and not on version 0.3.8 but

~/.julia/v0.4/RCall/deps$ julia -e 'println(versioninfo()); include("build.jl")'
Julia Version 0.3.8
Commit 79599ad (2015-04-30 23:40 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: AMD Athlon(tm) II X4 635 Processor
  WORD_SIZE: 64
  BLAS: libopenblas (NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Barcelona)
  LAPACK: liblapack.so.3
  LIBM: libopenlibm
  LLVM: libLLVM-3.3
nothing
bates@thin40:~/.julia/v0.4/RCall/deps$ julia4 -e 'println(versioninfo()); include("build.jl")'
Julia Version 0.4.0-dev+4850
Commit c260ea9* (2015-05-15 15:14 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: AMD Athlon(tm) II X4 635 Processor
  WORD_SIZE: 64
  BLAS: libopenblas (NO_AFFINITY BARCELONA)
  LAPACK: libopenblas
  LIBM: libopenlibm
  LLVM: libLLVM-3.6.0
nothing
ERROR: LoadError: Unable to locate libR.so
Try setting R_HOME, and re-run Pkg.build("RCall").
 in error at ./error.jl:21
 in anonymous at ./no file:44
 in include at ./boot.jl:252
 in include_from_node1 at ./loading.jl:134
 in process_options at ./client.jl:288
 in _start at ./client.jl:409
while loading /home/bates/.julia/v0.4/RCall/deps/build.jl, in expression starting on line 3

Copy the contents of an R object to Julia instead of protecting it?

At present the vec methods preserve the R storage using R_PreserveObject. If vec is called frequently then garbage collection of the Julia objects becomes slow because R_ReleaseObject does a linear search on a long vector.

One way around this is to have the evaluation of a name or expression create the appropriate Julia object and copy the contents of the R object into Julia storage. This seems like a good idea to me right now but I may have missed good reasons to keep things as they are.

Opinions?

Copy arrays from Julia to R

Hi,

Is it possible to copy simple arrays (matrices/vectors) from Julia to R, let R do some work and copy the result back?
In the documentation I have only found examples where R objects are copied to Julia.

RCall fails to load on recent v0.4 builds because of Timer() change

julia> using RCall
ERROR: LoadError: LoadError: Timer(f) is deprecated. Use Timer(f, delay, repeat) instead.
 in call at ./deprecated.jl:524
 in include at ./boot.jl:254
 in include_from_node1 at ./loading.jl:133
 in include at ./boot.jl:254
 in include_from_node1 at ./loading.jl:133
 in reload_path at ./loading.jl:157
 in _require at ./loading.jl:69
 in require at ./loading.jl:52
while loading /home/bates/.julia/v0.4/RCall/src/eventloop.jl, in expression starting on line 16
while loading /home/bates/.julia/v0.4/RCall/src/RCall.jl, in expression starting on line 77

julia> versioninfo()
Julia Version 0.4.0-dev+5383
Commit 993adea (2015-06-15 08:27 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz
  WORD_SIZE: 64
  BLAS: libmkl_rt
  LAPACK: libmkl_rt
  LIBM: libimf
  LLVM: libLLVM-3.6.1

Unfortunately, I don't know enough about the eventloop to investigate this.

Display issue when used from IJulia

I open a new notebook, first cell is

using RCall

Second cell is

"x <- 5" |> rcopy

This returns an empty graph as the first output, and only then the real output of

1-element Array{Float64,1}:
 5.0

If I then add a third cell that has purely julia code, it will also add this empty graph in the out cell.

I attach a screen shot:

I'm on Windows, julia 0.3.11, IPython/Jupyter 3 and all packages updated to the latest version. This happends with RCall from master or the latest registered version.

Any idea?

deal with non-standard evaluation

@simonbyrne
Thanks for the IJulia hooks. The implementation makes RCall.jl more usable.

I see that Julia objects are now implicitly converted to Sexp objects. And we are seeing crazy axis labels (in graphics.ipynb) because there are no R labels associating the numbers. All the numbers are directly passed to the plot function without masking them with a label.

> X = linspace(0,pi,10)
> rprint(RCall.lang(:plot, sexp(X), sexp(sin(X))))
plot(c(0, 0.349065850398866, 0.698131700797732, 1.0471975511966, 
1.39626340159546, 1.74532925199433, 2.0943951023932, 2.44346095279206, 
2.79252680319093, 3.14159265358979), c(0, 0.342020143325669, 
0.642787609686539, 0.866025403784439, 0.984807753012208, 0.984807753012208, 
0.866025403784439, 0.642787609686539, 0.342020143325669, 1.22464679914735e-16
))

To avoid this, we could pass the Julia objects to R and then plot with the R objects.

X = linspace(0,pi,10)
globalEnv[:X] = X
globalEnv[:Y] = sin(X)
rcall(:plot, :X, :Y)

Actually, I am thinking of another way to convert Julia objects. For example, for each rcall call, we create a new environment via new.env(), if an argument is not a Sexp, we convert it to an R object and stored it in the new environment. Perhaps something like

X = linspace(0,pi,10)
E = rcall(symbol("new.env"))
E[:X] = X
E[:Y] = sin(X)
rcall(:plot, :X, :Y, env=E)

PS: in graphics.jl, rprint is used to "print" the rcall. Actually, it is not necessary.

deps.jl should be rebuilt when R updates,

./deps.jl should be rebuilt when R is updated, or wrong dylib will be loaded.

https://github.com/randy3k/RCall.jl/blob/8f1f2144b91f146c659009b7364182b40c304f7e/deps/build.jl#L26

Pkg.test fails on Mac OSX

Pkg.test("Rcall") fails on Mac OSX with the error:

Running tests:
 * basic.jl ...
ERROR: LoadError: LoadError: test failed: "BJsales" == "airmiles"
 in expression: rcopy(lsd[2]) == "airmiles"
 in error at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in default_handler at test.jl:30
 in do_test at test.jl:53
 in include at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in include_from_node1 at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 [inlined code] from /Users/ranjan/.julia/v0.4/RCall/test/runtests.jl:21
 in anonymous at no file:0
 in include at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in include_from_node1 at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in process_options at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in _start at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
while loading /Users/ranjan/.julia/v0.4/RCall/test/basic.jl, in expression starting on line 8
while loading /Users/ranjan/.julia/v0.4/RCall/test/runtests.jl, in expression starting on line 18
================================[ ERROR: RCall ]================================

failed process: Process(`/Applications/Julia-0.4.1.app/Contents/Resources/julia/bin/julia --check-bounds=yes --code-coverage=none --color=yes /Users/ranjan/.julia/v0.4/RCall/test/runtests.jl`, ProcessExited(1)) [1]

================================================================================
ERROR: RCall had test errors
 in error at /Applications/Julia-0.4.1.app/Contents/Resources/julia/lib/julia/sys.dylib
 in test at pkg/entry.jl:803
 in anonymous at pkg/dir.jl:31
 in cd at file.jl:22
 in cd at pkg/dir.jl:31
 in test at pkg.jl:71

Here's my versioninfo()

Julia Version 0.4.1
Commit cbe1bee* (2015-11-08 10:33 UTC)
Platform Info:
  System: Darwin (x86_64-apple-darwin13.4.0)
  CPU: Intel(R) Core(TM) i5-5257U CPU @ 2.70GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.3

RCall gives error "LoadError: MethodError: `convert` has no method matching convert(::Type{DataFrames.DataFrame}, ::Symbol)

Hi,
Thank you for developing the package.
I have installèd RCall v0.3.1, on Windows 10. I am using Julia ver.0.4.1.

Pkg.add("RCall")
using DataArrays,DataFrames,RCall

attenu = DataFrame(:attenu)

which gives error:

oadError: MethodError: `convert` has no method matching convert(::Type{DataFrames.DataFrame}, ::Symbol)
This may have arisen from a call to the constructor DataFrames.DataFrame(...),
since type constructors fall back to convert methods.
Closest candidates are:
  call{T}(::Type{T}, ::Any)
  convert(::Type{DataFrames.DataFrame}, !Matched::Array{T,2})
  convert(::Type{DataFrames.DataFrame}, !Matched::Dict{K,V})
  ...
while loading In[4], in expression starting on line 1

 in call at essentials.jl:56

However,when I typed rprint(:airmiles) then the command works, ang gives the answer

Time Series:
Start = 1937 
End = 1960 
Frequency = 1 
 [1]   412   480   683  1052  1385  1418  1634  2178  3362  5948  6109  5981
[13]  6753  8003 10566 12528 14760 16769 19819 22362 25340 25343 29269 30514

Thank you for your kind help.

rprint and IO

It would be useful to be able to rprint to different IO objects (at the very least, we could then define nicer show methods for SEXPREC objects).

There doesn't seem to be a convenient way to get this directly from R, so I guess we have to use redirect_stdout?

Issues related to subsetting a VectorListSxp, particularly, a StrSxp

@simonbyrne
I notice that when I subset a StrSxp object with multiple indexes, it returns a julia array of CharSxp's. I think most users (at least myself) is expecting a StrSxp object with the corresponding indexes.
Is there any reasons for this implementation?

julia> a = RObject(["a", "b", "c"])
RCall.RObject{RCall.StrSxp}
[1] "a" "b" "c"


julia> a[1:2]
2-element Array{Any,1}:
 RCall.RObject{RCall.CharSxp}
<CHARSXP: "a">

 RCall.RObject{RCall.CharSxp}
<CHARSXP: "b">

Also, when only one element is being extracted from the StrSxp, the element of type CharSxp is returned to the user

julia> a[1]
RCall.RObject{RCall.CharSxp}
<CHARSXP: "a">

To mirror the R behavior, should it be wrapped inside a StrSxp object and then returned to the user? This may be less important.

readthedocs documentation

[For the record]

Finally, I have added the readthedocs support which generates documentation files semi-automatically.

Lexicon is used to extract the function's docstrings and generate the markdowns. See the build script under the docs directory. Running it will generate the markdown files. For example,

julia docs/build.jl

To push the files to readthedocs: right now, we have to trigger the build manually in readthedocs website. When this thing gets more mature, we should turn on the webhook.

NA values are not handled probably

julia> DataArray(reval("c(NA,1)"))
2-element DataArray{Float64,1}:
 NaN  
   1.0

the correct result should be similar to

julia> @data([NA,1.0])
2-element DataArray{Float64,1}:
  NA
 1.0

Error is reported when converting a vector of string containing NA.

julia> DataArray(reval("c(NA,'a')"))
ERROR: `bytestring` has no method matching bytestring(::CharSxp)
 in isNA at /Users/Randy/.julia/v0.3/RCall/src/sexp.jl:148
 in DataArray at /Users/Randy/.julia/v0.3/RCall/src/sexp.jl:150

Automatically install R when required

It would be useful if we could automatically install R when no local installation is found. Here are some thoughts from having spent a morning trying and failing to get this to work:

The R packages on linux distros are woefully out of date. The recommended way to do this is to use the CRAN repositories (e.g. see .travis.yml file). BinDeps can't do this and probably shouldn't anyway.
Installing the CRAN package on OS X requires administrator privileges
- We could use the homebrew/science tap?
CRAN doesn't provide a permalink to the latest downloads (see .travis.tml/appveyor.yml for hack workarounds)

The most promising option seems to be to use Conda.jl (which is what PyCall.jl uses). However:

Windows builds aren't up-to-date.
the library (R.dll/libR.dylib/libR.so) is not located in a findable directory.

Getting this to work is probably going to require changing the conda recipe.

core dump if draw a graph and `dev.off()` at the same line with `ggplot2`

Here is my code:

using RCall
R.library(:ggplot2)
g = globalEnv
x=linspace(-11,8,2000)
y = randn(2000)
g[:x]=x
g[:y]=y

The following line is fine

"""pdf();plot(x=x,y=y, type="l");dev.off()""" |> rparse|>reval

But the following line will cause a core dump

"""pdf();print(ggplot()+geom_line(aes(x=x, y=y)));dev.off()""" |> rparse|>reval

The error message is

Error: VECTOR_ELT() can only be applied to a 'list', not a 'character'
*** stack smashing detected ***: julia terminated

I also tried something else, like

"""plot(x=x,y=y, type="l")""" |> rparse|>reval

will give me a window of graph. But I cannot close the window unless I run

"""dev.off()""" |> rparse|>reval

For ggplot2 case I also tried

"""pdf();print(ggplot()+geom_line(aes(x=x, y=y)))""" |> rparse|>reval
"""dev.off()""" |> rparse|>reval

Then everything is fine. I replicated the bug on two different Linux machine.

julia> versioninfo()
Julia Version 0.4.0-dev+3172
Commit 456b85a* (2015-02-06 21:24 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i5-2467M CPU @ 1.60GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: libopenblas
  LIBM: libopenlibm
  LLVM: libLLVM-3.3

And

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"

P.S. For ggplot2 case, if I do not use print, it will return a broken file.

Use of an R_str, or similar, macro?

I had been wondering for some time how a string modifier like the 'r' in r"my\w+regexp"was defined and whether we could define R"x <- seq(0,1,101)" to mean reval("x <- seq(0,1,101)"), say. It turns out that the magic is defining a macro with the name R_str.

Does it seem worthwhile allowing this kind of simplification of calls to reval(str) or, perhaps, rcopy(reval(str)). I find that when using the RCall package I get tired of writing that sequence of calls over and over.

Getting RCall passing on PkgEval

Hi @dmbates,

With the recent PackageEvaluator rework I think its not only reasonable but possible to support R-based packages like RCall.

Currently RCall is failing its tests:
http://pkg.julialang.org/?pkg=RCall&ver=release

I am installing R:
https://github.com/IainNZ/PackageEvaluator.jl/blob/1428070377795d2b3977e8f768633f862d0c6138/scripts/setup.sh#L71-L72

But I'm wondering if maybe its too old a version?

RCall initiation: could not find symbol R_BlankScalarString

When I run RCall in Julia 0.4.0, it have such problem. I tried Pkg.build("RCall") but it not solved. Previously RCall worked fine but the problem came after I updated anaconda (I have no idea why anaconda will lead this problem, maybe it is just coincident?).

julia> using RCall
ERROR: LoadError: InitError: cglobal: could not find symbol R_BlankScalarString in li
brary /usr/lib64/R/lib/libR.so
in init at /home/jxiong/.julia/v0.4/RCall/src/RCall.jl:71
in include at ./boot.jl:261
in include_from_node1 at ./loading.jl:304
in require at ./loading.jl:243
during initialization of module RCall
while loading /home/jxiong/.julia/v0.4/RCall/src/RCall.jl, in expression starting on
line 53

changes to eventloop.jl for new Timer never released?

julia> Pkg.rm("RCall")
INFO: Removing RCall v0.2.1
INFO: Package database updated

It seems that the changes to eventless.jl for the new Timer never got released. The version that is being installed as of a few minutes ago is still v0.2.1...

julia> Pkg.add("RCall")
INFO: Installing RCall v0.2.1
INFO: Building RCall
INFO: Package database updated

julia> quit()
et-imac-retina:vams sjbespa$ julia
_
_ _ ()_ | A fresh approach to technical computing
() | () () | Documentation: http://docs.julialang.org
_ _ | | __ _ | Type "?help" for help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 0.4.0-dev+6916 (2015-08-23 18:41 UTC)
/ |_'|||__'| | Commit f8c1986* (1 day old master)
|__/ | x86_64-apple-darwin14.5.0

julia> using RCall
ERROR: LoadError: LoadError: Timer(f) is deprecated. Use Timer(f, delay, repeat) instead.
in call at deprecated.jl:523
in include at ./boot.jl:259
in include_from_node1 at ./loading.jl:267
in include at ./boot.jl:259
in include_from_node1 at ./loading.jl:267
in require at ./loading.jl:206
while loading /Users/sjbespa/.julia/v0.4/RCall/src/eventloop.jl, in expression starting on line 16
while loading /Users/sjbespa/.julia/v0.4/RCall/src/RCall.jl, in expression starting on line 77

Add an R module within RCall so names are R.install, etc.

Missing values for R factor objects

Currently there is a mismatch of the way that R codes NA's in a factor (index of R_NaInt) and the way they are encoded in the DataArray package (index of 0). Should be easy to fix. This is just in case I forget.

LoadError: Timer(f) is deprecated.

using RCall fails on Julia 0.4:

ERROR: LoadError: LoadError: Timer(f) is deprecated. Use Timer(f, delay, repeat) instead.
 in call at deprecated.jl:557
 in include at ./boot.jl:261
 in include_from_node1 at ./loading.jl:304
 in include at ./boot.jl:261
 in include_from_node1 at ./loading.jl:304
 in require at ./loading.jl:243
while loading /home/diego/.julia/v0.4/RCall/src/eventloop.jl, in expression starting on line 16
while loading /home/diego/.julia/v0.4/RCall/src/RCall.jl, in expression starting on line 77

julia> versioninfo()
Julia Version 0.4.0-rc2
Commit fa52609* (2015-09-18 17:51 UTC)
Platform Info:
  System: Linux (x86_64-unknown-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU E5-2650L v2 @ 1.70GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: libopenblas
  LIBM: libopenlibm
  LLVM: libLLVM-3.3

Calling R functions with keyword argumets that have attributes

If I was to call R's stars function. It is easy to invoke it with

rprint(rcall(:stars,myDf))

However if I try to set the draw.segments=TRUE as I would in R. The following invocation fails

rprint(rcall(:stars,myDf,draw.segments=true))
ERROR: syntax: keyword argument is not a symbol: "draw.segments"

I saw nothing in the documentation to clarify how this might be handled.

interact with R event loops

In order to get features like graphics windows working correctly, we need to be able to interact with the R event loops. Some details are covered in R-ext §8.

From what I understand, we need to implement (some of) the functionality provided by run_Rmainloop.

need to `PreserveObject` when calling `rawvector`?

follow up #6
When a R memory is referenced by a julia variable, It may be always necessary to execute PreserveObject when rawvector is called.

Issue building RCall on Windows 8

I am trying to get RCall working for Win8/x64. I am working with the latest 0.3.7/x64 version of Julia for Windows. I first manually added the required environment variables as follows-

R_DOC_DIR = C:/PROGRA~~1/R/R-32~~1.0/doc [Full path: C:\Program Files\R\R-3.2.0\doc]
R_HOME = C:/PROGRA~~1/R/R-32~~1.0 [Full path: C:\Program Files\R\R-3.2.0]
R_INCLUDE_DIR = C:/PROGRA~~1/R/R-32~~1.0/include [Full path: C:\Program Files\R\R-3.2.0\include]
R_SHARE_DIR = C:/PROGRA~~1/R/R-32~~1.0/share [Full path: C:\Program Files\R\R-3.2.0\share]
LD_LIBRARY_PATH = C:/PROGRA~~1/R/R-32~~1.0/modules/x64 [Full path: C:\Program Files\R\R-3.2.0\modules\x64]

In going through deps/build.jl, I noticed that it was trying to access [joinpath(ENV["R_HOME"],"lib",string("libR.",BinDeps.shlib_ext))] which expands to [ C:/PROGRA~~1/R/R-32~~1.0/lib/libR.dll] but this file does not exist on Windows install of R. So I created this "lib" in C:/PROGRA~~1/R/R-32~~1.0 and placed the dll "R.dll" from [C:\Program Files\R\R-3.2.0\bin\x64] in the lib directory. I renamed R.dll to libR.dll. This did not help. I get the error message

-- QUOTE --
================================[ ERROR: RCall ]================================

Unable to load C:/PROGRA~~1/R/R-32~~1.0/lib/libR.dll

Please re-run Pkg.build(package), and restart Julia.
while loading C:\Users\Krishna.julia\v0.3\RCall\deps\build.jl, in expression st
arting on line 14

-- UNQUOTE --

Just for good measure, I copied over all the other dlls found in C:\Program Files\R\R-3.2.0\bin\x64 over to the "lib" folder but that did not help either.

If anyone has got a working Windows version of Rcall working, kindly share your setup.

Thanks.

Unable to locate libR.dylib

I have the latest version of R installed via Homebew (homebrew/science/r-3.2.3).
I am on OSX 10.11.1
I manually set ENV["R_HOME"] = "/usr/local/Cellar/r/3.2.3/"

When I call Pkg.build("RCall")
I get the following error

LoadError: Unable to locate libR.dylib
Try setting R_HOME, and re-run Pkg.build("RCall").
while loading /Users/rodonn/.julia/v0.4/RCall/deps/build.jl, in expression starting on line 3

I tried adding

ENV["DYLD_LIBRARY_PATH"] = "/usr/local/Cellar/r/3.2.3/lib"
ENV["LD_LIBRARY_PATH"] = "/usr/local/Cellar/r/3.2.3/lib"

but I still get the same error.

Thanks!

Write a wrapper for R_ParseVector

ttt = ccall((:R_ParseVector,RCall.libR),Ptr{Void},(Ptr{Void},Cint,Ptr{Cint},Ptr{Void}),RCall.mkString("library(lme4)"),1,status,ff)

Float64 converting to complex when using globalEnv

Fantastic package! I was hoping to wrap some R statistical functionality from Julia and this is perfect. One issue I have encountered follows (in Julia):

using RCall
y = randn(10)
globalEnv[:y] = y
rcopy("typeof(y)")

returns "complex". One can easily get around this by inserting the additional line:

reval("y <- Re(y)")

But I thought I would raise it as an issue here just in case there are situations where this work-around will fail.

Cheers.

graphics.ipynb example includes missing function rplot_set

In attempting to execute graphics.ipynb on my Windows test environment (64-bit Windows, 32-bit Julia v0.4.0-rc1, 32-bit R 3.2.2), the current In[4]: example makes a call to rplot_set(MIME("image/svg+xml"), which generated the following error message on my machine:

LoadError: UndefVarError: rplot_set not defined
while loading In[4], in expression starting on line 1

Is the notebook example stale and in need of update, or should this function actually be present in the RCall namespace and went missing at some point?

The RCall namespace currently includes the following:

julia> RCall.
@rget               __init__             rBraceSymbol
@rimport            allocArray           rBracket2Symbol
@rput               allocList            rBracketSymbol
@rusing             anyNA                rClassSymbol
AnySxp              askYesNoCancel       rDeviceSymbol
AnySxpPtr           attributes           rDimNamesSymbol
BcodeSxp            bound                rDimSymbol
BcodeSxpPtr         callJuliaExtPtr      rDollarSymbol
BuiltinSxp          car                  rDotsSymbol
BuiltinSxpPtr       cdr                  rDoubleColonSymbol
CharSxp             dataptr              rDropSymbol
CharSxpPtr          decrefExtPtr         rEmptyEnv
ClosSxp             errorBuffer          rGlobalEnv
ClosSxpPtr          eval                 rJuliaCallback
CplxSxp             eventCallBack        rLastvalueSymbol
CplxSxpPtr          getAttrib            rLevelsSymbol
DotSxp              getClass             rMissingArg
DotSxpPtr           getNames             rModeSymbol
EnvSxp              globalEnv            rNaInt
EnvSxpPtr           ijulia_cleanup       rNaReal
ExprSxp             ijulia_displayfile   rNaRmSymbol
ExprSxpPtr          ijulia_displayplots  rNaString
ExtPtrSxp           ijulia_file_dir      rNameSymbol
ExtPtrSxpPtr        ijulia_init          rNamesSymbol
FunctionSxp         ijulia_mime          rNamespaceEnvSymbol
FunctionSxpPtr      ijulia_setdevice     rNilValue
IntSxp              isArray              rPackageSymbol
IntSxpPtr           isComplex            rPreviousSymbol
LangSxp             isEnvironment        rQuoteSymbol
LangSxpPtr          isExpression         rRowNamesSymbol
LglSxp              isFactor             rSeedsSymbol
LglSxpPtr           isFrame              rSortListSymbol
ListSxp             isFree               rSourceSymbol
ListSxpPtr          isFunction           rSpecSymbol
NAel                isInteger            rTripleColonSymbol
NilSxp              isLanguage           rUnboundValue
NilSxpPtr           isList               rcall
PairListSxp         isLogical            rcall_p
PairListSxpPtr      isMatrix             rcopy
PromSxp             isNA                 rdevicename
PromSxpPtr          isNewList            rdot_Method
RObject             isNull               rdot_defined
RStart              isNumber             rdot_packageName
RawSxp              isNumeric            rdot_target
RawSxpPtr           isObject             registerFinalizer
RealSxp             isOrdered            release
RealSxpPtr          isPairListSxp        reserved
Rinstance           isPrimitiveSxp       reval
Rproc               isReal               reval_p
S4Sxp               isS4                 rgui_start
S4SxpPtr            isString             rgui_stop
SpecialSxp          isSymbol             rlang
SpecialSxpPtr       isTs                 rlang_formula
StrSxp              isUnordered          rlang_p
StrSxpPtr           isUnsorted           rparse
Sxp                 isUserBinop          rparse_p
SxpHead             isValidString        rprint
SxpPtr              isValidStringF       rwrap
SxpPtrInfo          isVector             setAttrib!
SymSxp              isVectorAtomicSxp    setClass!
SymSxpPtr           isVectorListSxp      setNames!
UnknownSxpPtr       isVectorizable       setcar!
VecSxp              jtypExtPtrs          setcdr!
VecSxpPtr           libR                 settag!
VectorAtomicSxp     makeExternalPtr      sexp
VectorAtomicSxpPtr  makeNativeSymbol     sexp_arglist_dots
VectorListSxp       pJuliaCallback       sexpnum
VectorListSxpPtr    pJuliaDecref         tag
VectorNumericSxp    preserve             timeout
VectorNumericSxpPtr printBuffer          typs
VectorSxp           process_events       unprotect
VectorSxpPtr        protect              unsafe_array
WeakRefSxp          rBaseSymbol          unsafe_vec
WeakRefSxpPtr       rBlankScalarString   voffset
__META__            rBlankString         writeConsoleEx

asSEXP may need 'PreserveObject'

https://github.com/JuliaStats/RCall.jl/blob/b4afdd6d76f3e2f690cace4b242b1d9c0643c767/src/sexp.jl#L140

I believe that we have to somehow preserve the object created by Rf_allocVector.
It should be fine if this R object is blinded to some variable in some environment. But it may not be always the case.
For example, the following produces segfault

x  = RCall.asSEXP([1:10^8])
for i in 1:10
   Reval(Rparse("gc()"))
end
Rprint(x)

using RCall changes Pkg.dir() on Windows

While working against the current master for RCall (obtained via Pkg.checkout("RCall")), when executing:

using RCall

from within a either a 32-bit or a 64-bit Julia session on Windows, the value assigned to Pkg.dir() is currently being modified.

This behavior creates problems when attempting to load other packages later in the same Julia session.

Below is an example Julia session:

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0-pre+7067 (2015-08-28 17:05 UTC)
 _/ |\__'_|_|_|\__'_|  |  Commit e82ba0c (11 days old master)
|__/                   |  i686-w64-mingw32

julia> Pkg.dir()
"C:\\Users\\Administrator\\.julia\\v0.4"

julia> using RCall

julia> Pkg.dir()
"C:\\Users\\Administrator\\Documents\\.julia\\v0.4"

julia>

Callbacks

It would be useful to be able to call Julia functions from within R, similar to PyCall's facility, e.g.

rcall(:plot, x -> x*x)

However there doesn't appear to be an immediately obvious way to call C function pointers from R, at least as far as I could tell. Any ideas?

datasets should not be converted to LangSxp's by @rimport

Currently all the objects in an R package are converted to LangSxp's by @rimport, which is not appropriate for R objects that are vectors, in the R sense. There should at least be a check on whether the name evaluates to a CLOSXP before conversion. I'll take a look at this.

julia> using RCall

julia> @rimport MASS as m

julia> typeof m.s
sammon   ships     shrimp    snails    steam     stormer   survey    synth.tr
select   shoes     shuttle   stdres    stepAIC   studres   synth.te
julia> typeof(m.shuttle)
LangSxp (constructor with 2 methods)

julia> rcall(m.shuttle)
Error: attempt to apply non-function
ERROR: Error occurred in R_tryEval
 in reval at /home/bates/.julia/v0.3/RCall/src/iface.jl:5
 in reval at /home/bates/.julia/v0.3/RCall/src/iface.jl:16

High level API?

Looks like it is shaping up to be a great package. Thanks for spearheading this.

Are there plans for a more julian like higher level API maybe using macros?

Check what happens in deps/build.jl

deps/build.jl should create the name of libR but that is not what is recorded in the deps/deps.jl file.

Error in plot.new() : the base graphics system is not registered

Okay, another weird graphics bug. Certain unrelated julia functions will trigger the following error when an R graphics function is subsequently called

Error in plot.new() : the base graphics system is not registered

The following reliably triggers it on the second invocation of plot(1:10) on my system (OS X, v0.3.7) when run at the REPL (though seems fine when in a script, or via include).

using RCall

rprint("png('/tmp/aa.png')")
rprint("plot(1:10)")
rprint("dev.off()")

io = IOBuffer()
write(io,"1,2,3")
seek(io,0)
readall(io) # this seems to be the trigger

rprint("png('/tmp/aa.png')")
rprint("plot(1:10)")
rprint("dev.off()")

sexp(::Matrix) has copy-paste bug?

I can't convert a Julia Matrix{Float64} into sexp:

feldt:~/.julia/v0.3$ julia
               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.3.5 (2015-01-08 22:33 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-apple-darwin13.4.0

julia> using RCall

julia> m = [0.0 1.0; 2.0 3.0]
2x2 Array{Float64,2}:
 0.0  1.0
 2.0  3.0

julia> rm = sexp(m)
ERROR: l not defined
 in sexp at /Users/feldt/.julia/v0.3/RCall/src/sexp.jl:129

Seems to me that l should instead be q (or p?) on line 129.

RCall Build error on windows 7 64

Hello,

I'm getting "Unable to load the LibR.dll" when trying to add and build RCall.

I have set the R exe and RScript in my windows path.

Any help would be appreciated.

Thanks

Julia version 3.5 64 bit for windows

Failure to load RCall in Julia v0.4.0-rc2 compiled with LLVM 3.7.0

I'm not sure if the problem is with RCall or with using LLMV 3.7.0 but trying to load the RCall package results in

   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0-rc2+31 (2015-09-23 01:56 UTC)
 _/ |\__'_|_|_|\__'_|  |  Commit 09f248f* (2 days old release-0.4)
|__/                   |  x86_64-linux-gnu

julia> using DataFrames,DataArrays

julia> using RCall
julia: codegen.cpp:2999: llvm::Value* emit_assignment(llvm::Value*, jl_value_t*, jl_value_t*, bool, bool, jl_codectx_t*): Assertion `rval->getType() == jl_pvalue_llvmt || rval->getType() == NoopType' failed.

signal (6): Aborted
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f2a0b7e303d)
unknown function (ip: 0x7f2a0b7e30f2)
emit_assignment at /home/bates/git/julia/src/codegen.cpp:2999
emit_assignment at /home/bates/git/julia/src/codegen.cpp:3027
emit_function at /home/bates/git/julia/src/codegen.cpp:4681
to_function at /home/bates/git/julia/src/codegen.cpp:639
jl_compile at /home/bates/git/julia/src/codegen.cpp:808
jl_trampoline_compile_function at /home/bates/git/julia/src/builtins.c:1015
jl_apply_generic at /home/bates/git/julia/src/gf.c:1709
__init__ at /home/bates/.julia/v0.4/RCall/src/RCall.jl:117
unknown function (ip: 0x7f27f5c5f02d)
jl_eh_restore_state at /home/bates/git/julia/src/julia.h:1409
jl_eval_module_expr at /home/bates/git/julia/src/toplevel.c:210
jl_toplevel_eval_flex at /home/bates/git/julia/src/toplevel.c:423
jl_toplevel_eval_flex at /home/bates/git/julia/src/toplevel.c:573
jl_load at /home/bates/git/julia/src/toplevel.c:620
include at ./boot.jl:261
jl_apply_generic at /home/bates/git/julia/src/gf.c:1684
include_from_node1 at ./loading.jl:304
jl_apply_generic at /home/bates/git/julia/src/gf.c:1684
do_call at /home/bates/git/julia/src/interpreter.c:66
eval at /home/bates/git/julia/src/interpreter.c:213
jl_toplevel_eval_flex at /home/bates/git/julia/src/toplevel.c:544
jl_eh_restore_state at /home/bates/git/julia/src/julia.h:1409
require at ./loading.jl:243
unknown function (ip: 0x7f2a06660d39)
jl_apply_generic at /home/bates/git/julia/src/gf.c:1684
eval_import_path_ at /home/bates/git/julia/src/toplevel.c:368
jl_toplevel_eval_flex at /home/bates/git/julia/src/toplevel.c:442
jl_eh_restore_state at /home/bates/git/julia/src/julia.h:1409
eval_user_input at ./REPL.jl:63
Aborted (core dumped)

My versioninfo is

julia> versioninfo()
Julia Version 0.4.0-rc2+31
Commit 09f248f* (2015-09-23 01:56 UTC)
Platform Info:
  System: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
  WORD_SIZE: 64
  BLAS: libopenblas (NO_LAPACKE DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: liblapack
  LIBM: libopenlibm
  LLVM: libLLVM-3.7.0

Is anyone else encountering this?

Error on making a Dict

The following code:

using RCall
d = Dict(1=>2, 2=> 3)
RObject(d)

errors out with:

ERROR: UndefVarError: allocVector not defined
 in sexp at /Users/ranjan/.julia/v0.4/RCall/src/convert-base.jl:212
 in call at /Users/ranjan/.julia/v0.4/RCall/src/types.jl:270

Could you please point me to where allocVector is meant to be defined?

julia> using RCall
julia> @time for( i in 1:1000 ) rcopy( string("c(", join( [rand() * j for j in  1:1000], "," ), ")")) end
  1.414018 seconds (6.17 M allocations: 285.378 MB, 2.55% gc time)

julia> @time for( i in 1:1000 ) rcopy( string("c(", join( [rand() * j for j in  1:1000], "," ), ")")) end
  1.300732 seconds (6.05 M allocations: 280.270 MB, 2.04% gc time)

julia> @time for( i in 1:1000 ) rcopy( string("c(", join( [rand() * j for j in  1:1000], "," ), ")")) end
*** stack smashing detected ***: julia terminated

signal (6): Aborted
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f8e142e8394)
__fortify_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
__fortify_fail at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x7f8c00b22641)
unknown function (ip: (nil))
Aborted (core dumped)