I am having trouble assigning large matrices.

require 'rinruby'
R.m = Matrix.zero 5

produces

...
rm(.RINRUBY.PARSE.STRING)
d=matrix(c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0), 5, 5, TRUE)
print('RINRUBY.EVAL.FLAG')
...

which is fine but

require 'rinruby'
R.m = Matrix.zero 50

produces

...
rm(.RINRUBY.PARSE.STRING)
d=matrix(c(0,0,0,0,0 [snip] 0,0,0,0,0), 50, 50, TRUE)
print('RINRUBY.EVAL.FLAG')
Error: unexpected symbol in ",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0"
...

when using RinRuby 2.0.1, R 2.11.1, and Ruby 1.9.1p376 on Mac OS X 10.6.5.

I'm not very familiar with R and once I want to put a 600*600 Ruby matrix( each element is a float number)into R, like R.weight_matrix, I got the following error

In readBin(.RINRUBY.PULL.SOCKET, character(), 1, endian = "big") :
null terminator not found: breaking string at 10000 bytes

Any idea to solve the problem?

I noticed a weird issue with our test suite where sending SIGINT would sometimes cause my main test process to exit but my tests would keep going (sometimes it just keeps going and ignores any SIGINT)

We're using Rake::TestTask which will shell out a new Ruby process. The problem I found was that if we call rinruby's #eval function then it will setup SIGINT handlers and cause the test process not to exit. I feel like this behavior should be flaggable

I noticed this with rinruby 2.1.0 but get the same behavior on master

$ head /.../gems/rinruby-2.0.2/History.txt
=== 2.0.2 / 2011-02-03

while https://github.com/clbustos/rinruby/blob/master/History.txt#L1 says

=== 2.0.1 / 2010-05-01

Could you release a new Gem?

The purpose of this issue is to release a gem that actually works. The current gem does not work with the new R + Ruby.
(#53) is an issue about enhancements.

It would be nice to be able to assign and pull boolean and null variable between R and Ruby.
Both languages support boolean, so it is theoretically possible.
For R, since it has both Null an NA, we can map them both to nil in Ruby.

Like PR #38 test results in https://travis-ci.org/clbustos/rinruby/jobs/418977944, which do not include Travis-CI test related changes and was successfully built before the changes, jruby-head tests sometimes fail. This issue may be related to jruby/jruby#5280 . The current workaround seems to use older jruby.

Spec "RinRuby R interface on pull should pull a Matrix" fails on Ruby 2.1.1, but not on any other Ruby version. The problems lies on the comparison method. Maybe we should use "be_within" to allow some degree of error (e-10 or less) between ruby and R.

curious if you know how I could "pull" this list from R.. when I do I get the error from the title.. The data is coming from a SAS XPT file that I read into R using the SASxport library..

vars$VD$label
[1] "Study Identifier"
[2] "Unique Subject Identifier"
[3] "Site Name"
[4] "Site Number"
[5] "Subject ID"
[6] "System Visit Name"
[7] "Visit Name"
[8] "Page Name"
[9] "Page Sequence Number"
[10] "Line Number"
[11] "Did the visit occur - Decoded"
[12] "Did the visit occur"
[13] "Date of Visit - Numeric"
[14] "Date of Visit"
[15] "Visit occur at patient\x92s home - Decoded"
[16] "Visit occur at patient\x92s home"

If a string in R contains characters with diacritics, the pulled string in Ruby is shortened by number of these characters.

For instance, this code

require "rinruby"
R.eval "text <- 'zkouška'"
print R.pull "text"

prints zkoušk only. (Tested on Ruby 2.1.5, R 3.2.2, Ubuntu 15.10.)

Anyway - thanks for rinruby, it's really useful! (I use it in Jekyll plugin to generate a website from Rmd files.)

When I follow the example on the getting started page and type

>> R.eval "x <- rnorm(#{sample_size})"

the output is

  .RINRUBY.KEEPTRYING.VARIABLE <- TRUE
  while ( .RINRUBY.KEEPTRYING.VARIABLE ) {
    .RINRUBY.PULL.SOCKET <- try(suppressWarnings(socketConnection("127.0.0.1", 39014, blocking=TRUE, open="rb")),TRUE)
    if ( inherits(.RINRUBY.PULL.SOCKET,"try-error") ) {
      Sys.sleep(0.1)
    } else {
      .RINRUBY.KEEPTRYING.VARIABLE <- FALSE
    }
  }
  rm(.RINRUBY.KEEPTRYING.VARIABLE)
rinruby_get_value <-function() {
  value <- NULL
  type <- readBin(.RINRUBY.PULL.SOCKET, integer(), 1, endian="big")
  length <- readBin(.RINRUBY.PULL.SOCKET,integer(),1,endian="big")
  if ( type == 0 ) {
    value <- readBin(.RINRUBY.PULL.SOCKET,numeric(), length,endian="big")
    } else if ( type == 1 ) {
    value <- readBin(.RINRUBY.PULL.SOCKET,integer(), length, endian="big")
    } else if ( type == 2 ) {
    value <- readBin(.RINRUBY.PULL.SOCKET,character(),1,endian="big")
    } else {
      value <-NULL
    }
  value
  }
rinruby_pull <-function(var)
{
    if ( inherits(var ,"try-error") ) {
    writeBin(as.integer(-2),.RINRUBY.PULL.SOCKET,endian="big")
    } else {
      if (is.matrix(var)) {
        writeBin(as.integer(4),.RINRUBY.PULL.SOCKET,endian="big")
        writeBin(as.integer(dim(var)[1]),.RINRUBY.PULL.SOCKET,endian="big")
        writeBin(as.integer(dim(var)[2]),.RINRUBY.PULL.SOCKET,endian="big")

    }  else if ( is.double(var) ) {
      writeBin(as.integer(0),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(as.integer(length(var)),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(var,.RINRUBY.PULL.SOCKET,endian="big")
    } else if ( is.integer(var) ) {
      writeBin(as.integer(1),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(as.integer(length(var)),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(var,.RINRUBY.PULL.SOCKET,endian="big")
    } else if ( is.character(var) && ( length(var) == 1 ) ) {
      writeBin(as.integer(2),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(as.integer(nchar(var)),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(var,.RINRUBY.PULL.SOCKET,endian="big")
    } else if ( is.character(var) && ( length(var) > 1 ) ) {
      writeBin(as.integer(3),.RINRUBY.PULL.SOCKET,endian="big")
      writeBin(as.integer(length(var)),.RINRUBY.PULL.SOCKET,endian="big")
    } else {
      writeBin(as.integer(-1),.RINRUBY.PULL.SOCKET,endian="big")
    }
  }
}
rinruby_parseable<-function(var) {
  result=try(parse(text=var),TRUE)
  if(inherits(result, "try-error")) {
    writeBin(as.integer(-1),.RINRUBY.PULL.SOCKET, endian="big")
  } else {
    writeBin(as.integer(1),.RINRUBY.PULL.SOCKET, endian="big")
  }
}
.RINRUBY.PARSE.STRING <- rinruby_get_value()
rinruby_parseable(.RINRUBY.PARSE.STRING)
rm(.RINRUBY.PARSE.STRING)
x <- rnorm(10)
print('RINRUBY.EVAL.FLAG')
=> true

note brackets around cmd []
cmd is a string or an array as follows.

      @engine = IO.popen([cmd],"w+")

environment

java -version
java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02, mixed mode)

jruby -v
jruby 1.7.2 (1.9.3p327) 2013-01-04 302c706 on Java HotSpot(TM) 64-Bit Server VM 1.7.0_09-b05 [Windows 7-amd64]

trace

I've added a few puts() statements to trace ...

  puts "R cmd #{cmd}"
     begin
       @engine = IO.popen(cmd,"w+")
     rescue Exception => e  
        puts "e.message=#{e.message}"
        puts e.backtrace
        puts e.inspect  
        raise e.message
     end  
  puts "R @engine #{@engine}"

with the brackets ...

jruby -S irb
irb(main):001:0> require "rinruby"
R start
R require java
R platform windows-java
R executable "C:/Program Files/R/R-2.15.2/bin/i386/Rterm.exe"
R loaded readline
R cmd "C:/Program Files/R/R-2.15.2/bin/i386/Rterm.exe" --ess --slave
R @engine #IO:0x51a4f310

without the brackets ...

jruby -S irb
irb(main):001:0> require "rinruby"
R start
R require java
R platform windows-java
R executable "C:/Program Files/R/R-2.15.2/bin/i386/Rterm.exe"
R loaded readline
R cmd "C:/Program Files/R/R-2.15.2/bin/i386/Rterm.exe" --ess --slave
e.message=
java.lang.ProcessImpl.(ProcessImpl.java:181)
java.lang.ProcessImpl.start(ProcessImpl.java:133)
java.lang.ProcessBuilder.start(ProcessBuilder.java:1021)
jnr.posix.util.Java5ProcessMaker.start(Java5ProcessMaker.java:139)
org.jruby.util.ShellLauncher.buildProcess(ShellLauncher.java:492)
org.jruby.util.ShellLauncher.popenShared(ShellLauncher.java:734)
org.jruby.util.ShellLauncher.popen(ShellLauncher.java:693)
org.jruby.RubyIO.popen19(RubyIO.java:3931)
org.jruby.RubyIO$INVOKER$s$0$2$popen19.call(RubyIO$INVOKER$s$0$2$popen19.gen)
org.jruby.internal.runtime.methods.DynamicMethod.call(DynamicMethod.java:216)
org.jruby.internal.runtime.methods.DynamicMethod.call(DynamicMethod.java:212)
org.jruby.runtime.callsite.CachingCallSite.cacheAndCall(CachingCallSite.java:346)
org.jruby.runtime.callsite.CachingCallSite.call(CachingCallSite.java:204)
c_3a_.Users.bwalsh.jruby_minus_1_dot_7_dot_2.lib.ruby.gems.shared.gems.rinruby_minus_2_dot_0_dot_3.lib.rinruby.chained_6_rescue_4$RUBY$SYNTHETICinitialize(c:/Users/bwalsh/jruby-1.7.2/lib/ruby/gems/shared/gems/rinruby-2.0.3/lib/rinruby.rb:173)

Hi, I'm getting this error when I try to do a completely different command (rails generate active_admin:install).

Any idea why rinruby is trying to automatically start up R?

Thanks, Joel

 ./lib/ruby/gems/1.9.1/gems/rinruby-2.0.2/lib/rinruby.rb:164:in `popen': 
  No such file or directory - R --interactive --slave (Errno::ENOENT)
from /opt/ruby/ruby-1.9.2-p290/lib/ruby/gems/1.9.1/gems/rinruby-2.0.2/lib/rinruby.rb:164:in `initialize'
from /opt/ruby/ruby-1.9.2-p290/lib/ruby/gems/1.9.1/gems/rinruby-2.0.2/lib/rinruby.rb:789:in `new'
from /opt/ruby/ruby-1.9.2-p290/lib/ruby/gems/1.9.1/gems/rinruby-2.0.2/lib/rinruby.rb:789:in `<top (required)>'
from /opt/ruby/ruby-1.9.2-p290/lib/ruby/gems/1.9.1/gems/bundler-1.0.18/lib/bundler/runtime.rb:68:in `require'
   ...

I'm trying to integrate R into my Rails app with this library as a gem, but calls to R just hang. I'm on macOS. I've added the gem and bundled, and installed R from Homebrew. As a raw, baseline test, I've created a test file with the example from the top of the rinruby.rb file. But when I try to run the example, it just hangs. When I kill it, I get this stack trace, and I have no idea how to start trying to fix it:

tasks git:(statistics) ✗ ruby test.rb
^CTraceback (most recent call last):
	7: from test.rb:7:in `<main>'
	6: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:349:in `method_missing'
	5: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:394:in `assign'
	4: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:760:in `assignable?'
	3: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:742:in `complete?'
	2: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:630:in `socket_session'
	1: from /Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:744:in `block in complete?'
/Users/davidkrider/.rvm/gems/ruby-2.5.5/gems/rinruby-2.1.0/lib/rinruby.rb:744:in `read': Interrupt

using bundler, when calling my rackup script. /home/user/.rvm/rubies/ruby-2.2.3/bin/ruby -e at_exit{sleep(1)};$stdout.sync=true;$stderr.sync=true;load($0=ARGV.shift) /home/user/.rvm/gems/ruby-2.2.3/gems/ruby-debug-ide-0.4.24/bin/rdebug-ide --disable-int-handler --evaluation-timeout 10 --rubymine-protocol-extensions --port 33242 --dispatcher-port 43995 -- /home/user/.rvm/rubies/ruby-2.2.3/bin/rake test:drip RACK_ENV=test

the rinruby script will generate this cmd on debian:
R --interactive --slave
for some reason the shell does not have the right path to R and the execution fails. I find that calling
/usr/bin/R --interactive --slave will fix the issue but its a temporary fix.

any idea what to do to make sure the paths are correct?

His guys, this looks very interesting, I was wondering if this gem still being maintained?

in a controller's method, I have this (like a script in ruby):

@r = RinRuby.new(true,false)
@r.assign "name", name

begin
@r.eval "source("public/rscripts/e2_p1m1_Binaria_NN.R")"
@tatt = @r.pull "tatt"

rescue Exception => e

  LOGGER.debug "#{e.class}: #{e.message}"

end

@r.quit # free R

note:the script in R is obviously correct and it returns some variables and a barplot.

My problem is the @r.quit.

If I don't close conection between Ruby an R, I have a process called Rterm.exe, that seems never finish and is imposible open the pdf with the barplot. (In client,however, the html shows the numeric variables correctly).

If I close the conection with the method @r.quit. the process Rterm.exe seems finish correctly but my server throws a exception "Errno::ECONNRESET" and on screen appears a message like "We're sorry, but something went wrong."

I don't know if the method "quit" close another conection or thread and this is the reason of my problem...

I know this is not an issue with RinRuby but curious if there are any ways to get some added info. I can run summary or describe on the data and it displays just fine.. but trying to use the pull command to get the data into Ruby fails.. Hoping there is some way to tell what it doesn't like.. maybe if I knew what didn't fail I could process of elimination find the culprit.. Thanks! (I think I'll grab the source and start debugging)

Hi,

I included the gem in my Gemfile of a Rails 4.2.6 application.
After running bundle install i tried to execute some code in my rails console but unfortunately it is not starting anymore (it starts, but apparently some R script is blocking or delaying the execution, see the screenshot of my header bar of my terminal window)

Any ideas what could be causing this problem?

Thanks!

My versions are:

• R version 3.3.0 (2016-05-03)
• ruby 2.2.4p230
• Rails 4.2.6
• Working on a Mac
• R installed via homebrew

r.eval r_script appears to error suspiciously at the 10k character mark. Can this be increased?

I am receiving an error "Error in norm_val[i, ] <- dummy : replacement has length zero" with the following code:
R.eval <<-EOF

columns <- matrix(0, length(probes), count)

 for (i in c(1:count)) {
     if (i == 1) { columns <- cbind(get(paste0("col",i))) } 
     else { columns <- cbind(columns, get(paste0("col",i))) }    
     }

norm_val <- matrix(0, length(norm_probes), ncol(columns) - 1)

    for (i in 1:length(norm_probes)) {
    dummy <- columns[norm_probes[i] == columns[,1],]
    print(dummy)
    dummy <- dummy[-1]
    print(dummy)
    norm_val[i,] <- dummy
    }

EOF

 return R.pull "norm_val"

I dont know where to ask this question as its very particular with RinRuby. The code is working fine in R terminal.

Here it says:
print('RINRUBY.EVAL.FLAG')
Matrix[[0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0]]

this matrix is suppose to be filled with values but its coming empty??
Is there a limit in integer or character sizes which we pass to R from Ruby??

complete code is here, just incase you need it:
https://github.com/kumarsaurabh20/PlotApp/blob/master/app/controllers/uploads_controller.rb

Hi @clbustos and @fenrir-naru! First of all thanks for having developed this project. It seems to be the best approach to using R in Ruby at the moment. We're looking to add R Markdown support to gollum. This would turn gollum into a great open source tool for git-based reproducible reports. Being an open source maintainer myself, I fully understand how time consuming it can be. However, I'd like to ask if you could take the time to cut a new gem release of the current master branch at least, which seems to include some important bugfixes -- and preferably merge some of the improvements by @fenrir-naru (see e.g. #52).

Alternatively, if there are reasons why you think it would not be viable to keep using this gem, could you please let us know? Any tips about what a viable way would be to integrate R in a Ruby project in 2020 would be greatly appreciated!