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How to disable R's crash prompt

10 messages · Wayne.Zhang at barclayscapital.com, Brian Ripley, Dirk Eddelbuettel +2 more

Original
Brian Ripley
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On Tue, 8 Mar 2011, Wayne.Zhang at barclayscapital.com wrote:

            

      
      
      
    

        
R does not do that in 'non-interactive mode'. Take a look at the 
code: that section is conditional on R_Interactive.

            

      
      
      
    

        
They do not control if R is interactive: the front-end (yours, I 
presume since you mention embedding but do not otherwise give any 
details) does.

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Wayne.Zhang at barclayscapital.com
    

    

      
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Thanks for your quick comment Mr. Ripley.  I'm a newbie in R so excuse me for not knowing the obvious.  Could you elaborate on what code I should look at, and what documentation I should go to?

This is my C++ code on calling embedded R (on redhat enterprise linux 4):

    char *localArgs[] = { "R", "--silent" };  // tried --slave, -f, --vanilla too
    Rf_initEmbeddedR(sizeof(localArgs)/sizeof(localArgs[0]), localArgs);

    PROTECT(load = lang2(install("source"), mkString(file.c_str())));	// file contains R code
    R_tryEval(load, R_GlobalEnv, &errorOccurred);

    PROTECT(call = lang2(install(entryPoint.c_str()), input));    // entry point is an R function defined in "file" above
    PROTECT(output = R_tryEval(call, R_GlobalEnv, &errorOccurred));

    UNPROTECT(3);


What should I do in C++ to make R non-interactive?

Thanks,
Wayne


-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Tuesday, March 08, 2011 9:51 AM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel at r-project.org
Subject: Re: [Rd] How to disable R's crash prompt

        
On Tue, 8 Mar 2011, Wayne.Zhang at barclayscapital.com wrote:

        

            

      
      
      
    

        
R does not do that in 'non-interactive mode'. Take a look at the 
code: that section is conditional on R_Interactive.

            

      
      
      
    

        
They do not control if R is interactive: the front-end (yours, I 
presume since you mention embedding but do not otherwise give any 
details) does.

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
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On 8 March 2011 at 09:24, Wayne.Zhang at barclayscapital.com wrote:

        
| Dear R devel,
| 
| I have a C++ app that calls into embedded R to perform some analytic calculations.  When my app encounters a segmentation fault, R always prints the following crash prompt and asks me to enter an action:
| 
| 
| *** caught segfault ***
| address 0x8, cause 'memory not mapped'
| 
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| 
| 
| 
| The problem is my app will be run in non-interactive mode, so there is no way for me to enter the action.  Is there a way to disable the crash prompt and have R simply crash the whole app?  I have tried using "-file=/dev/null", "-slave", "-vanilla", and pretty much all other start options, to no avail.

Are you using RInside?  You could try rebuilding it with the this (from
src/RInside.cpp) set to true

bool verbose = false;

as well as with possibly more debugging output added to the RInside
destructor (where I removed a few commented-out lines for brevity):

RInside::~RInside() {		// now empty as MemBuf is internal
    logTxt("RInside::dtor BEGIN", verbose);
    R_dot_Last();
    R_RunExitFinalizers();
    R_CleanTempDir();
    Rf_endEmbeddedR(0);
    logTxt("RInside::dtor END", verbose);
    instance_ = 0 ;
}

to at least confirm that you get here.  And if you really,really wanted to I
suppose you could try to do without some of these cleanup and finalizer
functions. But I think that would send you into somewhat uncharted territory,
so you probably want to do read Section 8.1 ("8.1 Embedding R under
Unix-alikes") of Writing R Extension carefully.  Best bet may still be to
avoid the segfault alltogether if you can.

Hope this helps, Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Wayne.Zhang at barclayscapital.com
    

    

      
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Hi Dirk,

My code on calling embedded R from C++ is attached in the other mail.

As you see, I'm not using RInside.  My app already works (except when it seg faults) so I prefer not to change it.  

Thanks,
Wayne


-----Original Message-----
From: Dirk Eddelbuettel [mailto:edd at debian.org] 
Sent: Tuesday, March 08, 2011 10:10 AM
To: Zhang, Wayne: IT (NYK)
Cc: r-devel at r-project.org
Subject: Re: [Rd] How to disable R's crash prompt

        
On 8 March 2011 at 09:24, Wayne.Zhang at barclayscapital.com wrote:

        
| Dear R devel,
| 
| I have a C++ app that calls into embedded R to perform some analytic calculations.  When my app encounters a segmentation fault, R always prints the following crash prompt and asks me to enter an action:
| 
| 
| *** caught segfault ***
| address 0x8, cause 'memory not mapped'
| 
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| 
| 
| 
| The problem is my app will be run in non-interactive mode, so there is no way for me to enter the action.  Is there a way to disable the crash prompt and have R simply crash the whole app?  I have tried using "-file=/dev/null", "-slave", "-vanilla", and pretty much all other start options, to no avail.

Are you using RInside?  You could try rebuilding it with the this (from
src/RInside.cpp) set to true

bool verbose = false;

as well as with possibly more debugging output added to the RInside
destructor (where I removed a few commented-out lines for brevity):

RInside::~RInside() {		// now empty as MemBuf is internal
    logTxt("RInside::dtor BEGIN", verbose);
    R_dot_Last();
    R_RunExitFinalizers();
    R_CleanTempDir();
    Rf_endEmbeddedR(0);
    logTxt("RInside::dtor END", verbose);
    instance_ = 0 ;
}

to at least confirm that you get here.  And if you really,really wanted to I
suppose you could try to do without some of these cleanup and finalizer
functions. But I think that would send you into somewhat uncharted territory,
so you probably want to do read Section 8.1 ("8.1 Embedding R under
Unix-alikes") of Writing R Extension carefully.  Best bet may still be to
avoid the segfault alltogether if you can.

Hope this helps, Dirk

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Barry Rowlingson
    

    

      
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On Tue, Mar 8, 2011 at 2:24 PM,  <Wayne.Zhang at barclayscapital.com> wrote:

            

      
      
      
    

        
If someone from Barclays Capital is writing programs that are being
allowed to seg fault and they want to *ignore* the seg fault then I'm
taking all my money away from Barclays Capital and keeping it away.
Barclays Capital, the bank that likes to say "seg fault".

 Your code can't possibly seg fault - our governments are always
telling us banks are too big to fail.

 That's enough banker bashing.

Barry

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Mar 8, 2011, at 10:01 AM, <Wayne.Zhang at barclayscapital.com> <Wayne.Zhang at barclayscapital.com> wrote:

        

            

      
      
      
    

        
R_Interactive = FALSE;

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Wayne.Zhang at barclayscapital.com
    

    

      
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That did the trick.  Thank you soooooo much Simon!

Wayne


-----Original Message-----
From: Simon Urbanek [mailto:simon.urbanek at r-project.org] 
Sent: Tuesday, March 08, 2011 5:28 PM
To: Zhang, Wayne: IT (NYK)
Cc: ripley at stats.ox.ac.uk; r-devel at r-project.org
Subject: Re: [Rd] How to disable R's crash prompt

        
On Mar 8, 2011, at 10:01 AM, <Wayne.Zhang at barclayscapital.com> <Wayne.Zhang at barclayscapital.com> wrote:

        

            

      
      
      
    

        
R_Interactive = FALSE;

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Barry Rowlingson
    

    

      
      #
    

  


  

      
On Tue, Mar 8, 2011 at 10:41 PM,  <Wayne.Zhang at barclayscapital.com> wrote:

            

      
      
      
    

        
But really you *should* fix the segfault. Either you know why it
happens, in which case you should spot it before it happens and do
something sensible, or you don't know why it happens, in which case it
could be a serious bug in your code.

 Even if you *do* know why it happens, there may be other bugs in your
code that cause segfaults that you *dont* know about, and you'll miss
them because you are stupidly ignoring all segfaults.

 Fix the bugs.

Barry

  
  


  


      

    

    

      
      

        


  

        

      Wayne.Zhang at barclayscapital.com
    

    

      
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I never said I wasn't going to fix the bug, and believe me big banks do want their apps to be of high quality, but until the bugs are fixed I want my app to die instead of becoming a zombie.  But thanks for your opinion and all others that offered help along the way.

Wayne


-----Original Message-----
From: b.rowlingson at googlemail.com [mailto:b.rowlingson at googlemail.com] On Behalf Of Barry Rowlingson
Sent: Wednesday, March 09, 2011 5:26 AM
To: Zhang, Wayne: IT (NYK)
Cc: simon.urbanek at r-project.org; ripley at stats.ox.ac.uk; r-devel at r-project.org
Subject: Re: [Rd] How to disable R's crash prompt

        
On Tue, Mar 8, 2011 at 10:41 PM,  <Wayne.Zhang at barclayscapital.com> wrote:

            

      
      
      
    

        
But really you *should* fix the segfault. Either you know why it
happens, in which case you should spot it before it happens and do
something sensible, or you don't know why it happens, in which case it
could be a serious bug in your code.

 Even if you *do* know why it happens, there may be other bugs in your
code that cause segfaults that you *dont* know about, and you'll miss
them because you are stupidly ignoring all segfaults.

 Fix the bugs.

Barry
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