I have a code snippet to reproduce the issue. For now you may use Chop as a workaround.

Thank very much Shenghui, I see now where the mistake was. I was grouping the parenthesis in the wrong way leading to an objective function that was returning a vector instead of scalar (how careless of me :D). spg requires an objective function that is scalar. Thank you very much for running the example for me.

First configuration step is impossible with current JDK, in my case 15.0.1, because there is no jre !

You know what, I worked around this by wrapping everything I do into a function like so

Cheers,

-Dmitry

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

Thanks a lot.

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

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

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.

Attachments:

R spg call.nb

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.

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 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

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

Leonid

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

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