Hi all,

This seems like a place to post RLink issues, so even though my question is not an RLink installation issue, I hope it is appropriate here.

I managed to get RLink to work with an external R distribution on Windows and I installed the packages I want in R. I'm now trying to call them in Mathematica and my peculiar issue is that I can't seem to define a variable and use it in the same code cell. See below for an example.

A similar issue is occurring with loading libraries, I would appreciate any help on the issue! -Dmitry

Yeah, you need curly braces as closure to evaluate the compound expression in R, just like what is documented in REvaluate.

I have a very simple problem that I'd like to utilize R for from a Mathematica (12.1) interface. I'd like to avoid using an external R distribution (the old version of R should be fine for my purposes). However,

<< "RLink`"
RLinkResourcesInstall[]
InstallR[]

gives me the error:

InstallR::fail: Failed to install R. The following error was encountered: crash in low-level RLink component or in R runtime

All of the troubleshooting I've seen online considers how to fix the problem with an external R distribution. What might cause this to fail with only the defaults?

Thanks for looking into this.

Regards, Hamood

According to the doc https://www.rdocumentation.org/packages/BB/versions/2019.10-1/topics/spg you can extract the components one by one:

REvaluate["sc2.f <- function(x){ sum((1:length(x)) * (exp(x) - x)) / 10}"];
REvaluate["p0 <- rnorm(50)"];

REvaluate["{
 ans.spg1 <- spg(par=p0, fn=sc2.f)
 ans.spg1$par
 }"]

Hi Shenghui and Leonid,

I posted this question in another post but no one seems to be responding, so I am reposting it here. I think it's an important question regarding R and Mathematica.

I am having trouble transferring complex matrices from Mathematica to R. In particular, the Fourier matrix, mat1, in the following code is presenting a problem.

w0 = N@2 Pi/101
mat1 = Table[(Exp[I w0]^Range[3])^i, {i, 0, 2}]
mat2 = Table[(Exp[I w0]^Range[3]), {3}]

Now the following line presents no problem

In[479]:= RSet["mat2", mat2]

Out[479]= {{0.998066 + 0.0621696 I, 0.99227 + 0.124099 I, 
  0.982635 + 0.185548 I}, {0.998066 + 0.0621696 I, 
  0.99227 + 0.124099 I, 
  0.982635 + 0.185548 I}, {0.998066 + 0.0621696 I, 
  0.99227 + 0.124099 I, 0.982635 + 0.185548 I}}

However, for some reason, mat1 fails to be RSet.

In[486]:= RSet["mat1", mat1]

During evaluation of In[486]:= JLink`JavaNew::argx: Incorrect number or type of arguments to constructor for class com.wolfram.links.rlink.dataTypes.inTypes.RComplexVectorInType. The arguments, shown here in a list, were {{1.,0.998066 +0.0621696 I,0.99227 +0.124099 I,1.,<<19>> +<<20>> I,0.969199 +0.246279 I,1.,0.982635 +0.185548 I,0.931144 +0.364652 I},{},«<<1>>»}.

During evaluation of In[486]:= RSet::puterr: Error putting the expression {{1. +0. I,1. +0. I,1. +0. I},{0.998066 +0.0621696 I,<<19>> +<<20>> I,0.982635 +<<20>> I},{0.99227 +0.124099 I,0.969199 +0.246279 I,0.931144 +0.364652 I}} into a variable mat1 in R. The last error message issued by R was Error: 'list' object cannot be coerced to type 'complex'

Out[486]= $Failed

There seem to be some type conversion issues between lists and complex data types. Why is this issue cropping up?

Regards, Hamood

Dear Shenghui, here is another problem. I think this is malfunctioning with RLink:

mat = Chop@FourierMatrix[10, WorkingPrecision -> MachinePrecision];
RSet["mat", mat];
X = Transpose[{Range[10]}];
RSet["X", Chop@X];
REvaluate["mat%*%X"];

Produces the following error:

REvaluate::rerr: Failed to retrieve the value for variable or piece of code mat%*%X. The following R error was encountered: Error in mat %*% X : requires numeric/complex matrix/vector arguments.

Checking the type of mat gives:

In[61]:= REvaluate["class(mat)"]

Out[61]= {"list"}

While:

In[54]:= REvaluate["class(X)"]

Out[54]= {"matrix"}

Why is that? I think this is the root of the matter.

Regards, Hamood

Thanks a lot.

Hello, I followed all the steps as indicated in the discussion above to use package ODEsensitivity in R using the Mathematica interface. I installed the package and ran library(packagename) It appears the package is found but I am not able to run it. The commands used are given in the attached notebook. Any help would be appreciated. I did not start a new discussion as my problem is related to above discussion. Thanks Vijaya

Attachments:

rlinktest.nb

Thanks Leonid, it works now!

Claude

Hi Leonid!

That's strange. FactoMine works correctly under the R console:

Nevertheless,

In[15]:= REvaluate["R.Version()"]

Out[15]= RObject[{{"x86_64-w64-mingw32"}, {"x86_64"}, {"mingw32"}, \
{"x86_64, mingw32"}, {""}, {"3"}, {"6.1"}, {"2019"}, {"07"}, {"05"}, \
{"76782"}, {"R"}, {"R version 3.6.1 (2019-07-05)"}, {"Action of the \
Toes"}}, RAttributes[
  "names" :> {"platform", "arch", "os", "system", "status", "major", 
    "minor", "year", "month", "day", "svn rev", "language", 
    "version.string", "nickname"}]]

In[26]:= REvaluate["library(\"FactoMineR\")"]

During evaluation of In[26]:= REvaluate::rerr: Failed to retrieve the value for variable or piece of code library("FactoMineR"). The following R error was encountered: Error in library("FactoMineR") : 
  aucun package nommé 'FactoMineR' n'est trouvé

Out[26]= $Failed

I'll try with other packages, later...

Claude

Hi Leonid! It's not completely finished, unfortunately... I'm now able to load R and execute basic R commands:

In[13]:= InstallR["RHomeLocation" -> "C:/Program Files/R/R-3.6.1", 
 "RVersion" -> "3.6.1", 
 "NativeLibLocation" -> 
  "C:\\Users\\Claude\\Documents\\R\\win-library\\3.6\\rJava\\jri\\x64"]
REvaluate["sample(1:100,10)"]

Out[14]= {52, 54, 40, 35, 44, 77, 47, 53, 46, 79}

but I have more ambition! I would like to perform a multivariate analysis with the excellent package "FactoMineR", which I installed today; it is located there:

C:\Users\Claude\Documents\R\win-library\3.6\FactoMineR

but I can't load it:

In[26]:= REvaluate["library(\"FactoMineR\")"]

During evaluation of In[26]:= REvaluate::rerr: Failed to retrieve the value for variable or piece of code library("FactoMineR"). The following R error was encountered: Error in library("FactoMineR") : 
  aucun package nommé 'FactoMineR' n'est trouvé

Out[26]= $Failed

I tried several variants, without any positive result:

In[27]:= (*REvaluate["library(\"C:\Users\Claude\Documents\R\win-\
library\3.6\FactoMineR\R\")"]*)
REvaluate["library(\"C:\\Users\\Claude\\Documents\\R\\win-library\\3.\
6\\FactoMineR\")"]

During evaluation of In[27]:= REvaluate::crash: Crash in low-level RLink component or in R runtime. Please reinstall RLink via InstallR

Out[27]= $Failed

What should I type to load this package? I also tried to alter $Path, with something like

(*REvaluate["install.packages(\"FactoMineR\")"]*)
CLa = "C:\\Users\\Claude\\Documents\\R\\win-library\\3.6\\";
AppendTo[$Path, CLa]

but is it useful?

Regards, Claude

Thanks Lenonid, now it works!

Claude

Claude,

The "NativeLibLocation" option works for all platforms, not just Mac.

Your latest issue was due to picking the wrong (32 bit) version of the JRI library. You need to use the library from /x64 sub-folder (I did mention that). I just tested on Windows, the following works (make sure to execute this on a fresh kernel for a clean test):

InstallR["RHomeLocation" -> "C:/Program Files/R/R-3.6.1", 
 "RVersion" -> "3.6.1", 
 "NativeLibLocation" -> 
  "C:\\Program Files\\R\\R-3.6.1\\library\\rJava\\jri\\x64"]

pay attention to the \x64 part of the path.

Here is a simple test that we get it working:

In[7]:= REvaluate["R.Version()"]

Out[7]= RObject[{{"x86_64-w64-mingw32"}, {"x86_64"}, {"mingw32"}, \
{"x86_64, mingw32"}, {""}, {"3"}, {"6.1"}, {"2019"}, {"07"}, {"05"}, \
{"76782"}, {"R"}, {"R version 3.6.1 (2019-07-05)"}, {"Action of the \
Toes"}}, RAttributes[
  "names" :> {"platform", "arch", "os", "system", "status", "major", 
    "minor", "year", "month", "day", "svn rev", "language", 
    "version.string", "nickname"}]]

HTH,

Leonid

I got it working on Win10 after a lot of trial and error and with your good advice.

In R Console:

> .libPaths()
[1] "D:/Users/Chris/Documents/R/win-library/4.0"
[2] "C:/Program Files/R/R-4.0.3/library" 

In Wolfram:

Exit
JLink`UninstallJava[]
Needs["RLink`"]
InstallR[
"RHomeLocation" -> "C:/Program Files/R/R-4.0.3/",
"RVersion" -> "4.0.3",
"NativeLibLocation" -> 
"D:/Users/Chris/Documents/R/win-library/4.0/rJava/jri/x64"]

Hi Leonid, and thanks a lot, first! Java was not installed on my recent machine.... I just installed everything; here is the (default) location of rJava/jri:

C:\Users\Claude\Documents\R\win-library\3.6\rJava\jri

Unfortunately, it doesn't work, yet:

In[2]:= InstallR[
 "RHomeLocation" -> 
  "C:/Users/Claude/Documents/R/win-library/3.6/rJava/jri", 
 "RVersion" -> "3.6.1"]

During evaluation of In[2]:= InstallR::fail: Failed to install R. The following error was encountered: Unable to load dynamic libraries

Out[2]= $Failed

Any suggestion? Best regards,

Claude

This indeed looks like the problem of incompatible libraries. You will have to go through a number of steps to fix this.

1. Make sure you have JDK

   First, make sure you have some relatively recent JDK (Java development kit) installed. Java 8 and above should do. This can be downloaded from Oracle web site and installed.

2. Start your R distribution interactive console (command line R interface).

3. For your current R session, set the environmental variable JAVA_HOME to the location of your JDK / JRE.

   In my case, the corresponding command looked like

   Sys.setenv(JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/jre").
   

4. Install the rJava R package:

   install.packages('rJava')
   

   You will be prompted by R to pick a mirror, and then the package should get installed.

5. You will need to locate where R installed the rJava / jri package. Normally, it will be installed into the folder given by (execute this in R prompt):

   .libPaths()
   

   In my case, it was located at

   /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/jri
   

   where the part before /rJava/jri was given by .libPaths()

6. You should find the jri.dll library inside the jri sub-folder in rJava package. If there is an x86-64 sub-folder there, you should get the one from there (assuming your architecture is 64 bit). You can either use that file directly or copy it to some more convenient location.

7. Now you are ready to call InstallR. On a fresh Mathematica kernel, the call will look similarly to this (except this is for Mac OS X, but the same should also work for Windows):

   InstallR["RHomeLocation" -> 
         "/Library/Frameworks/R.framework/Versions/3.6/Resources", 
        "RVersion" -> "3.6.1" , 
        "NativeLibLocation" -> 
            "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/jri"
   ]
   

   where an undocumented option "NativeLibLocation" was used to indicate an alternative location of the JRI library, and the value should be the path to the folder containing jri.dll (which you have located previously).

The steps 1 through 6 are only necessary to be performed once. After that, you will always need to call InstallR with this extra option, to use more recent versions of R than those for which the library is available out of the box. Of course, future versions of Mathematica will eventually catch up with more recent R versions.

Hope this helps.

I am working to address multiple RLink issues right now, most likely including the one that causes the failure on some Macs. Have not yet tested on Catalina, but we will certainly do that. With some luck, we may be able to have these fixes in 12.1.1, or may be even earlier as a paclet update.