rsruby install trouble

  • Thread starter Guybrush Threepwood
  • Start date
G

Guybrush Threepwood

Hello, trying for no particular reason to create a K constant calculator
for chemical equilibrium for a chemical reaction. The way the experiment
was done, I need to put a best fit line on some data. R, and therefore,
RSRuby, seems like the best to do this (if I'm wrong, please enlighten),
but I cannot get RSRuby working. I'm using R 2.8.1 (I found something
which said R 2.9.x doesn't work well with rsruby, not sure on the
validity of that, but, whatever), Mac OS X 10.4.11, and what happens is
the following.

I unpack the R package, and it goes into /Library/Frameworks/

I downloaded the rsruby distro, and try to run setup as ruby setup.rb
config -- -with-R-dir=$R_HOME (regardless of whether I set R_HOME to the
right directory (the installer thing says the right one is
/Library/Frameworks/r.something/Resources) or whether I put that in for
dir= it fails) and I get an error message, as it says it cannot find the
R directory. The README gives three solutions. The first, to put
something in the .bashrc file in ~ doesn't work as I don't have a
bashrc file (must say OSX isn't my forte, don't know if that is in an
earlier/later OSX distro). The second is to link a file in the
/Library/Frameworks/etcetera... to /usr/lib/, which when done, does
nothing. The last also deals with a file that I don't see anywhere.

Point is, anyone know a) what I'm doing wrong or (preferably) b) an
easier way to do this?

P.S. Here is the output

/rsruby-0.5 root# ruby setup.rb config -- --with-R-dir=$R_HOME
---> lib
---> lib/rsruby
<--- lib/rsruby
<--- lib
---> ext
/usr/bin/ruby /rsruby-0.5/ext/extconf.rb
--with-R-dir=/Library/Frameworks/R.framework/Resources/
checking for main() in -lR... no

ERROR: Cannot find the R library, aborting.
setup.rb:655:in `command': system("/usr/bin/ruby"
"/rsruby-0.5/ext/extconf.rb"
"--with-R-dir=/Library/Frameworks/R.framework/Resources/") failed
(RuntimeError)
from setup.rb:660:in `ruby'
from setup.rb:1238:in `extconf'
from setup.rb:1230:in `config_dir_ext'
from setup.rb:1532:in `__send__'
from setup.rb:1532:in `traverse'
from setup.rb:1530:in `dive_into'
from setup.rb:1530:in `traverse'
from setup.rb:1524:in `exec_task_traverse'
from setup.rb:1519:in `each'
from setup.rb:1519:in `exec_task_traverse'
from setup.rb:1223:in `exec_config'
from setup.rb:991:in `exec_config'
from setup.rb:826:in `__send__'
from setup.rb:826:in `invoke'
from setup.rb:773:in `invoke'
from setup.rb:1578
 
A

Alex Gutteridge

Hello, trying for no particular reason to create a K constant calculator
for chemical equilibrium for a chemical reaction. The way the experiment
was done, I need to put a best fit line on some data. R, and therefore,
RSRuby, seems like the best to do this (if I'm wrong, please enlighten),
but I cannot get RSRuby working. I'm using R 2.8.1 (I found something
which said R 2.9.x doesn't work well with rsruby, not sure on the
validity of that, but, whatever), Mac OS X 10.4.11, and what happens is
the following.

I unpack the R package, and it goes into /Library/Frameworks/

[snip]


Point is, anyone know a) what I'm doing wrong or (preferably) b) an
easier way to do this?
Click to expand...

Try the gem. This works for me with ruby 1.8.7, R 2.10.1 on OSX 10.6.4.
gem install rsruby --
Click to expand...
--with-R-dir=/Library/Frameworks/R.framework/Resources/
Building native extensions. This could take a while...
Successfully installed rsruby-0.5.1.1
1 gem installed
Installing ri documentation for rsruby-0.5.1.1...
Installing RDoc documentation for rsruby-0.5.1.1...
 
G

Guybrush Threepwood

Okay, now I'm trying to install rubygems, but am getting a weird error
message for that. Do I have to pass it anything, or should it just be
ruby setup.rb in the directory where the files are?

(the error)

/lib/rubygems.rb:723:in `set_paths': uninitialized constant Gem::Etc
(NameError)
from ./lib/rubygems.rb:719:in `each'
from ./lib/rubygems.rb:719:in `set_paths'
from ./lib/rubygems.rb:526:in `path'
from ./lib/rubygems/source_index.rb:66:in
`installed_spec_directories'
from ./lib/rubygems/source_index.rb:56:in `from_installed_gems'
from ./lib/rubygems.rb:736:in `source_index'
from ./lib/rubygems/gem_path_searcher.rb:86:in `init_gemspecs'
from ./lib/rubygems/gem_path_searcher.rb:21:in `initialize'
from ./lib/rubygems.rb:684:in `new'
from ./lib/rubygems.rb:684:in `searcher'
from ./lib/rubygems.rb:683:in `synchronize'
from ./lib/rubygems.rb:683:in `searcher'
from ./lib/rubygems/custom_require.rb:34:in `require'
from /usr/lib/ruby/1.8/tmpdir.rb:12
from ./lib/rubygems/custom_require.rb:31:in
`gem_original_require'
from ./lib/rubygems/custom_require.rb:31:in `require'
from setup.rb:95
 
A

Alex Gutteridge

Okay, now I'm trying to install rubygems, but am getting a weird error
message for that. Do I have to pass it anything, or should it just be
ruby setup.rb in the directory where the files are?

(the error)

./lib/rubygems.rb:723:in `set_paths': uninitialized constant Gem::Etc
(NameError)
from ./lib/rubygems.rb:719:in `each'
from ./lib/rubygems.rb:719:in `set_paths'
from ./lib/rubygems.rb:526:in `path'
from ./lib/rubygems/source_index.rb:66:in
`installed_spec_directories'
from ./lib/rubygems/source_index.rb:56:in `from_installed_gems'
from ./lib/rubygems.rb:736:in `source_index'
from ./lib/rubygems/gem_path_searcher.rb:86:in `init_gemspecs'
from ./lib/rubygems/gem_path_searcher.rb:21:in `initialize'
from ./lib/rubygems.rb:684:in `new'
from ./lib/rubygems.rb:684:in `searcher'
from ./lib/rubygems.rb:683:in `synchronize'
from ./lib/rubygems.rb:683:in `searcher'
from ./lib/rubygems/custom_require.rb:34:in `require'
from /usr/lib/ruby/1.8/tmpdir.rb:12
from ./lib/rubygems/custom_require.rb:31:in
`gem_original_require'
from ./lib/rubygems/custom_require.rb:31:in `require'
from setup.rb:95
Click to expand...

If you're on OSX you should already have rubygems (I think?). Your error
looks like it comes from having a <1.8.3 version of Ruby installed:

http://rubyforge.org/tracker/index.php?func=detail&aid=22313&group_id=126&atid=575
 
G

Guybrush Threepwood

Now I've gotten all this stuff working. The problem with getting the
right ruby and rubygems was I had an older version of xcode, but I got
the right one. So through macports I got ruby and rubygems, and through
rubygems I did the sudo install gem rsruby --
--with-R-dir=/Library/Frameworks/etcetera, and it installs correctly.
Problem is, when I type require 'rsruby' into irb (or put it into a
program), it doesn't know what it is. Do I have to hand it a path to
somewhere?
 
A

Alex Gutteridge

Now I've gotten all this stuff working. The problem with getting the
right ruby and rubygems was I had an older version of xcode, but I got
the right one. So through macports I got ruby and rubygems, and through
rubygems I did the sudo install gem rsruby --
--with-R-dir=/Library/Frameworks/etcetera, and it installs correctly.
Problem is, when I type require 'rsruby' into irb (or put it into a
program), it doesn't know what it is. Do I have to hand it a path to
somewhere?
Click to expand...

Have you required rubygems first (you will need to on older version of
ruby)? E.g.
=> true
 
G

Guybrush Threepwood

Sorry, actually, I'm having one more issue. When I get to the section of
the program that calls R, it says "Fatal Error: R home directory is not
defined." I thought I saw something to the effect that I stick a line of
code in some file, but I do not remember what. Do you know what that is?
 
R

Ryan Davis

Sorry, actually, I'm having one more issue. When I get to the section of
the program that calls R, it says "Fatal Error: R home directory is not
defined." I thought I saw something to the effect that I stick a line of
code in some file, but I do not remember what. Do you know what that is?
Click to expand...

IIRC, the readme will help with this and other issues that come up.
 
G

Guybrush Threepwood

As per the README, I stuck the line

"export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/Library/Frameworks/R.framework/Resources/bin"

into my .bashrc file, but no such luck. As for the other two options, I
cannot find the ldconfig file is says to run after doing what it says.
As noted, I'm a total newbie when it comes to this stuff, so I'm
probably just making a dumb mistake somewhere.
 
A

Alex Gutteridge

Sorry, actually, I'm having one more issue. When I get to the section of
Click to expand...
the program that calls R, it says "Fatal Error: R home directory is not
defined." I thought I saw something to the effect that I stick a line of
Click to expand...
code in some file, but I do not remember what. Do you know what that is?
Click to expand...

Assuming you are using Bash as your shell (I think it is the default in
OSX), to define R_HOME put

export R_HOME="/Library/Frameworks/R.Framework/Resources"

Into ~/.bashrc and source it / restart the terminal session. If you're
using a different shell then Google for how to set environment variables.
 
G

Guybrush Threepwood

Alex Gutteridge wrote in post #958443:
Assuming you are using Bash as your shell (I think it is the default in
OSX), to define R_HOME put

export R_HOME="/Library/Frameworks/R.Framework/Resources"

Into ~/.bashrc and source it / restart the terminal session. If you're
using a different shell then Google for how to set environment
variables.
Click to expand...

Unfortunately, that didn't work either, as it still spits out the same
error. I tried it with and without the quotes, but in both cases it just
doesn't see it. Any other possibilities?
 
A

Alex Gutteridge

Alex Gutteridge wrote in post #958443:

Unfortunately, that didn't work either, as it still spits out the same
error. I tried it with and without the quotes, but in both cases it just
Click to expand...
doesn't see it. Any other possibilities?
Click to expand...

Type the following and show me your terminal output.

export R_HOME="/Library/Frameworks/R.framework/Resources/"
$R_HOME
irb
require 'rsruby'
RSRuby.instance

This is what I get:

GUTTEA$ export R_HOME="/Library/Frameworks/R.framework/Resources/"
GUTTEA$ $R_HOME
-bash: /Library/Frameworks/R.framework/Resources/: is a directory
GUTTEA$ irb=> #<RSRuby:0x101176ce8 @class_table={}, @default_mode=-1, @caching=true,
@cache={"get"=>#<RObj:0x101176810>, "helpfun"=>#<RObj:0x101172f80>,
"help"=>#<RObj:0x101172f80>, "NaN"=>NaN, "FALSE"=>false, "TRUE"=>true,
"F"=>false, "NA"=>-2147483648, "eval"=>#<RObj:0x1011752a8>, "T"=>true,
"parse"=>#<RObj:0x101175820>}, @proc_table={}>
 
G

Guybrush Threepwood

Deadpool:~ Sam$ export
R_HOME="/Library/Frameworks/R.framework/Resources/"
Deadpool:~ Sam$ $R_HOME
-bash: /Library/Frameworks/R.framework/Resources/: is a directory
Deadpool:~ Sam$ irb
irb(main):001:0> require 'rubygems'
=> true
irb(main):002:0> require 'rsruby'
=> true
irb(main):003:0> RSRuby.instance
=> #<RSRuby:0x48c9e8 @caching=true, @cache={"get"=>#<RObj:0x48c948>,
"helpfun"=>#<RObj:0x48c060>, "help"=>#<RObj:0x48c060>, "NaN"=>NaN,
"FALSE"=>false, "TRUE"=>true, "F"=>false, "NA"=>-2147483648,
"eval"=>#<RObj:0x48c614>, "T"=>true, "parse"=>#<RObj:0x48c6f0>},
@proc_table={}, @class_table={}, @default_mode=-1>
 

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