Interface with R in Mathematica 12 and R 3.6.1?

claudemante · October 15, 2019, 9:19am

Hello everybody!

I wrote a number of notebooks calling R packages. But using up-to-date versions (Mathematica 12 and R 3.6.1), nothing works any more! For instance, it seems the default distribution doesn’t exist now:

In[2]:= InstallR[]
REvaluate["sample(1:100,10)"]

During evaluation of In[2]:= InstallR::invldrhome: The specified path to R home directory does not point to a valid directory

Out[2]= $Failed

I tried to use my own distribution, but it is not recognized!

In[4]:= InstallR["RHomeLocation" -> "C:/PROGRA~1/R/R-36~1.1", 
 "RVersion" -> "3.6.1"]

During evaluation of In[5]:= InstallR::fail: Failed to install R. The following error was encountered: crash in low-level RLink component or in R runtime

Out[5]= $Failed

It seems there is an issue with the R.dll file (dll: 3.6.1, expecting 3.5.0). What can I do? Install an older version of R? Which one?

Best regards,
Claude

leonids · October 15, 2019, 9:39pm

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

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

claudemante · October 16, 2019, 4:18pm

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

leonids · October 16, 2019, 4:22pm

Hi Claude,

I think you missed the option "NativeLibLocation" - it is that one that has to point out to that folder with the library, while "RHomeLocation" should point at the root of your R distribution, as before. Have a look at the example of InstallR[] call I provided, and adopt the right paths for your system - hopefully it should work.

HTH,

Leonid

claudemante · October 16, 2019, 5:12pm

Hi Leonid!

I didn’t understood: I thought “NativeLibLocation” was specific to Mac!
But

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"]

During evaluation of In[13]:= InstallR::fail: Failed to install R. The following error was encountered: Unable to load dynamic libraries

Out[13]= $Failed

is wrong, too… Nevertheless, “jri.dll” is here:

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

I could touch it (but I prefer clean screens)!

Regards,

Claude

leonids · October 16, 2019, 9:32pm

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

claudemante · October 17, 2019, 7:16am

Thanks Lenonid, now it works!

Claude

leonids · October 17, 2019, 10:01am

You are welcome, Claude. I am happy to help.

Leonid

claudemante · October 17, 2019, 5:32pm

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

leonids · October 18, 2019, 3:16pm

Hi Claude,

Make sure you have correctly installed that R library together with all its dependencies (of which there are a lot). To be specific, the following packages were also installed in my case:

{
 "backports", "digest", "glue", "zeallot", "ellipsis", "magrittr",  "vctrs", "R6",
 "clipr", "BH", "rematch", "prettyunits", "assertthat", "utf8", "forcats", "hms",
 "readr", "cellranger", "progress", "zip", "cli", "crayon", "fansi", "pillar", 
 "pkgconfig", "rlang", "SparseM", "MatrixModels", "sp", "haven", "curl", 
 "data.table", "readxl", "openxlsx", "tibble", "minqa", "nloptr", "Rcpp", "RcppEigen",
 "carData", "abind", "pbkrtest", "quantreg", "maptools", "rio", "lme4", "car",
 "ellipse", "flashClust", "leaps", "scatterplot3d", "FactoMineR"
}

Check that first using R console:

> library('FactoMineR')

I am using the same R version as you, also on Windows:

In[12]:= REvaluate["R.Version()"]

Out[12]= 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"}]]

I have installed FactoMineR under Windows, and for me everything works fine, at least as far as just testing the package being loaded is concerned:

In[13]:= REvaluate["library(\"FactoMineR\")"]

Out[13]= {"FactoMineR", "stats", "graphics", "grDevices", "utils",  "datasets", "methods", "base"}

Using long paths or $Path isn’t correct and won’t help.

I hope you will manage to get this working.

Leonid

claudemante · October 18, 2019, 4:25pm

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

leonids · October 20, 2019, 10:34am

Hi Claude,

Looking at your library path, I suspect it isn’t a standard one for R on Windows, so it might be that it is not added automatially when R is started via RLink.

I would try to evaluate REvaluate[".libPaths()"], which for me returns:

In[5]:= REvaluate[".libPaths()"]

Out[5]= {"C:/Program Files/R/R-3.6.1/library"}

Try evaluating this on your system and see if your library path where FactoMineR is installed, is among the returned paths. If it is not, then you might need to add it manually, something like this might work:

REvaluate[".libPaths( c( .libPaths(), \"C:/Users/Claude/Documents/R/win-library/3.6\") )"]

This has to be run first, before you try to load the library. If my guess is right, then the call to library() should work after this.

Leonid

claudemante · October 21, 2019, 2:08pm

Thanks Leonid, it works now!

Claude

leonids · October 21, 2019, 2:40pm

Good to know, Claude. Was happy to help.

Leonid

vsubram6 · March 19, 2020, 11:37pm

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

rlinktest.nb (5.82 KB)

leonids · March 20, 2020, 8:40am

Hello Vijaya,

Apparently, you simply didn’t escape the string argument properly. This worked for me (on Mac OS X, R 3.6.2):

REvaluate[ 
   "morris(model=NULL,factors=4,r=2,design=list(type=\"oat\",levels=5, 
    grid.jump=3),binf=0,bsup=1,scale=TRUE)"
]

(note the “oat” argument).

murray · March 24, 2020, 4:08pm

Some obstacles (Mathematica 12.1 on macOS Catalina):

With current versions OpenJDK, there is no jre!
I cannot get rJava to install; ends up with a compile error.

leonids · March 25, 2020, 9:16pm

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.

hamoodrak · April 12, 2020, 1:58pm

Hi Leonid,

I have a similar problem here, although it is not about RLink or installing a package. I have been able to successfully do both of these. However, there is an optimization package called BB which has the function spg (Spectral Projection Gradient) for large scale nonlinear optimization. When I call the following code in R it runs perfectly fine. Following is the R Code.Here sc2.f is the objective function for optimization and p0 gives a vector of the initial guess for the optimization variables.

require("BB") 
sc2.f <- function(x){ sum((1:length(x)) * (exp(x) - x)) / 10}
p0 <- rnorm(50)
ans.spg1 <- spg(par=p0, fn=sc2.f)

when this code is run it gives prints the following. f-value is the value of the objective function and pgrad is the projected gradient.

iter:  0  f-value:  323.6774  pgrad:  52.38542 
iter:  10  f-value:  127.5661  pgrad:  0.1005832 
iter:  20  f-value:  127.5039  pgrad:  0.02815128 
iter:  30  f-value:  127.5001  pgrad:  0.01830088 
iter:  40  f-value:  127.5  pgrad:  0.0004423839 
iter:  50  f-value:  127.5  pgrad:  8.910206e-05 
iter:  60  f-value:  127.5  pgrad:  1.847411e-05

The point is, it does its job with ans.spg1 variable giving the values of the optimized variables

 ans.spg1
 $par
 [1]  1.843400e-04  4.004529e-07 -1.403083e-08 -5.314239e-08
 [5]  3.031558e-08 -4.387552e-08  3.866317e-08  4.334743e-08
 [9] -1.020669e-07  1.170379e-07  3.592466e-08  2.992959e-08
[13]  8.591248e-08 -2.758630e-07 -4.951071e-08 -4.020634e-08
[17]  8.010105e-08  6.033852e-08 -4.763555e-08  4.880627e-08
[21]  1.070940e-06  1.178099e-07  1.077314e-06  3.870496e-07
[25]  6.317214e-08 -3.753983e-08  3.771117e-07  3.925886e-07
[29]  3.955844e-07 -5.079168e-08  1.070812e-07  3.868255e-07
[33]  7.694439e-07  1.264478e-07  1.185176e-07 -4.721000e-08
[37]  7.853781e-07  7.736863e-07 -3.392351e-07  1.357027e-07
[41]  7.629153e-07  7.618032e-07 -4.939840e-08 -4.701460e-08
[45]  1.367395e-07  9.510446e-07  1.037346e-07 -5.175414e-07
[49] -4.894020e-08 -5.040282e-07

$value
[1] 127.5

$gradient
[1] 5.627498e-05

$fn.reduction
[1] 196.1774

$iter
[1] 62

$feval
[1] 63

$convergence
[1] 0

$message
[1] "Successful convergence"

Now the problem is the RLink is unable to handle this form of output, so when I run the following:

REvaluate["sc2.f <-function(x){sum(1:length(x))*(exp(x)-x)/10}"];
REvaluate["p0 <- rnorm(50)"];
REvaluate["library(\"BB\")"];
REvaluate["func <- spg(par = p0, fn = sc2.f, quiet=TRUE)"]

I get the following error

REvaluate::rerr: Failed to retrieve the value for variable or piece of code func <- spg(par = p0, fn = sc2.f, quiet=TRUE). The following R error was encountered: Error in spg(par = p0, fn = sc2.f, quiet = TRUE) : 
  function must return a scalar numeric value!

What can I do? Please advise. Since this is a thread for R in Mathematica I thought it would be best to post this question here so that it might catch your attention. I am attaching my notebook.

R spg call.nb (8.79 KB)

shenghuiy · April 12, 2020, 3:04pm

According to the doc spg function - RDocumentation 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
 }"]

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