alexgutteridge / rsruby

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1.

1 vote

dyld: NSLinkModule() error [Mac OS X]
1 comment Created 8 months ago by andruby

Title

Body
Hi, I have the Universal binary of R 2.9.0 for Mac OS X from http://www.freestatistics.org/cran/ installed and installed the rsruby gem: sudo gem install alexgutteridge-rsruby -- --with-R-dir=/Library/Frameworks/R.framework/Resources Whenever i require rsruby or run irb -r rsruby i get this error: irb -rrsruby dyld: NSLinkModule() error dyld: Symbol not found: _rb_complex_new Referenced from: /opt/local/lib/ruby/gems/1.8/gems/alexgutteridge-rsruby-0.5.1.1/lib/rsruby_c.bundle Expected in: flat namespace Is this a Mac only issue?
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Hi,

I have the Universal binary of R 2.9.0 for Mac OS X from http://www.freestatistics.org/cran/ installed and installed the rsruby gem:
```
sudo gem install alexgutteridge-rsruby -- --with-R-dir=/Library/Frameworks/R.framework/Resources
```
Whenever i require rsruby or run irb -r rsruby i get this error:
```
irb -rrsruby
dyld: NSLinkModule() error
dyld: Symbol not found: _rb_complex_new
  Referenced from: /opt/local/lib/ruby/gems/1.8/gems/alexgutteridge-rsruby-0.5.1.1/lib/rsruby_c.bundle
  Expected in: flat namespace
```
Is this a Mac only issue?
Comments

pityka Tue Aug 11 05:21:38 -0700 2009 | link

Use gem 0.5.1 or ruby1.9.

Comment
Use gem 0.5.1 or ruby1.9.
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2.

0 votes

Unpredictable "Segmentation Fault" when a variable is deleted and re-created several times (OS X)
1 comment Created 6 months ago by ozataman

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I am using RSRuby to perform a complex linear fit and consequent forecasting. The ruby wrapper is responsible for cycling through a very high number of data sets, each time dynamically generating the formula, wiping out old variables and creating new ones. At unpredictable intervals, I am encountering errors such as: "segmentation fault" "bus error" etc. I am not an expert in embedding C in Ruby, and therefore I am not quite sure what kind of traceback I can provide. I would be happy to provide any info if someone directs me in the right direction. Best, Oz
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I am using RSRuby to perform a complex linear fit and consequent forecasting. The ruby wrapper is responsible for cycling through a very high number of data sets, each time dynamically generating the formula, wiping out old variables and creating new ones.

At unpredictable intervals, I am encountering errors such as:

"segmentation fault" "bus error"

etc. I am not an expert in embedding C in Ruby, and therefore I am not quite sure what kind of traceback I can provide.

I would be happy to provide any info if someone directs me in the right direction.

Best,
Oz

Comments

ozataman Wed Jun 24 08:58:35 -0700 2009 | link

Here is an example trace I just received while using predict():

caught segfault

address 0xc0f5f4f7, cause 'memory not mapped'

Traceback:

1: makepredictcall(variables[[i]], vars[[i + 1]])

2: model.frame.default(formula = main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix, drop.unused.levels = TRUE)

3: model.frame(formula = main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix, drop.unused.levels = TRUE)

4: eval(expr, envir, enclos)

5: eval(mf, parent.frame())

6: lm(main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix)

7: eval(expr, envir, enclos)

8: function (expr, envir = parent.frame(), enclos = if (is.list(envir) || is.pairlist(envir)) parent.frame() else baseenv()) .Internal(eval(expr, envir, enclos))(expression(model.41 = lm(main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix)))

aborting ...

Segmentation fault

Comment
Here is an example trace I just received while using predict(): *** caught segfault *** address 0xc0f5f4f7, cause 'memory not mapped' Traceback: 1: makepredictcall(variables[[i]], vars[[i + 1]]) 2: model.frame.default(formula = main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix, drop.unused.levels = TRUE) 3: model.frame(formula = main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix, drop.unused.levels = TRUE) 4: eval(expr, envir, enclos) 5: eval(mf, parent.frame()) 6: lm(main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix) 7: eval(expr, envir, enclos) 8: function (expr, envir = parent.frame(), enclos = if (is.list(envir) || is.pairlist(envir)) parent.frame() else baseenv()) .Internal(eval(expr, envir, enclos))(expression(model.41 = lm(main ~ lag.41 + lag.42 + lag.52 + bihfeatures, data = feature.matrix))) aborting ... Segmentation fault
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3.

0 votes

Won't compile on Snow Leopard with ruby 1.9.1
2 comments Created 3 months ago by samwich

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Maybe mkmf changed in ruby 1.9? 'gem install rsruby' results in: lib/ruby/1.9.1/mkmf.rb:1221:in `dir_config': undefined method `split' for true:TrueClass (NoMethodError) from extconf.rb:3:in `<main>'
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Maybe mkmf changed in ruby 1.9?

'gem install rsruby' results in:

lib/ruby/1.9.1/mkmf.rb:1221:in dir_config': undefined methodsplit' for true:TrueClass (NoMethodError)
from extconf.rb:3:in `'

Comments

timrandg Fri Dec 04 17:00:17 -0800 2009 | link

for me it looks like a problem with:
rsruby_c.bundle: mach-o, but wrong architecture

Perhaps this file needs to be build on snow leopard. I will try installing from compiled code on my machine...
Tim

Comment
for me it looks like a problem with: rsruby_c.bundle: mach-o, but wrong architecture Perhaps this file needs to be build on snow leopard. I will try installing from compiled code on my machine... Tim
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timrandg Fri Dec 04 17:07:15 -0800 2009 | link

R must have been built with the '--enable-R-shlib'

This is a problem as snowleopard does not have a fortran compiler. installing gfortran works but for some reason R installation has a problem using it. So I cannot get R installed other than using the precompiled version. I don't think it is installing the necessary shared library. So I am stuck...until I either get the R compilation step to recognize the gfortran compiler or find a replacement fortran compiler for mac os x 10.6.

Comment
R must have been built with the '--enable-R-shlib' This is a problem as snowleopard does not have a fortran compiler. installing gfortran works but for some reason R installation has a problem using it. So I cannot get R installed other than using the precompiled version. I don't think it is installing the necessary shared library. So I am stuck...until I either get the R compilation step to recognize the gfortran compiler or find a replacement fortran compiler for mac os x 10.6.
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4.

0 votes

Snow leopard compilation problem with ruby 1.8.7 and OS X R version 2.9.2
1 comment Created 2 months ago by harleym

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I am following the documented installation procedures and the compilation fails as gcc compilation during the configuration check stage is using the -arch x86_64 option and the OS X version of R installed from R-2.9.2.dmg does not include the x86_64 headers although the Rconfig.h file does suggest that these headers are a supported architecture.
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I am following the documented installation procedures and the compilation fails as gcc compilation during the configuration check stage is using the -arch x86_64 option and the OS X version of R installed from R-2.9.2.dmg does not include the x86_64 headers although the Rconfig.h file does suggest that these headers are a supported architecture.

Comments

ananelson Mon Nov 16 12:48:19 -0800 2009 | link

I had the same issue and worked around it as follows. (I assume this issue only arises on 32-bit machines.)

1) Run "ruby setup.rb config -- --with-R-dir=/Library/Frameworks/R.framework/Resources" as per instructions.
2) Manually edit ext/Makefile and remove -arch x86_64 wherever it appears (it was in my Makefile in 3 places). This should just leave -arch i386.

It should then compile. Note if you run "ruby setup.rb config" again this re-generates the Makefile, and you will need to edit this again.

Comment
I had the same issue and worked around it as follows. (I assume this issue only arises on 32-bit machines.) 1) Run "ruby setup.rb config -- --with-R-dir=/Library/Frameworks/R.framework/Resources" as per instructions. 2) Manually edit ext/Makefile and remove -arch x86_64 wherever it appears (it was in my Makefile in 3 places). This should just leave -arch i386. It should then compile. Note if you run "ruby setup.rb config" again this re-generates the Makefile, and you will need to edit this again.
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