R help - Oct 2012 - R crashing after successfully running compiled code

I'm running R 2.15.1x64, though the same problem persists for 2.13.0x32 and
2.13.0x64.

I am trying to run compiled C code using the .C convention. The
code compiles without problems, dynamically loads within the R
workspace with no problems, and even runs and gives correct results with
no problems.

However, R will randomly crash within a few minutes of successfully using
the compiled function.

For example, if I run my compiled function using:
dyn.load("mycfun.dll")
answer<-.C("mycfun", parameters...), I get a completely sensible
result that gets stored to "answer".
However, if I try to do too many things to "answer", the R exits
without warning.
I've tried dyn.unload in hopes that R would become stable afterwards, but
in this case using the function crashes R without fail.

Usually, I can either plot, or view, or save "answer" to a file - but
never
take more than a single action before R exits. This does not appear to
depend on how long R has been open. Initially, I thought it was a bug in
the "inline" function, but I'm finding the same problem now that
I'm using
the dynamically loaded file directly. I'm used to R being insanely stable,
and am somewhat mystified by this whole problem.

My next move is to learn the ".Call" convention, as I suspect that
my problem is related to my "C" function using memory that R
doesn't
know is used. But - before I invest a while lot more time on this, I'd
like to know whether anybody things this is likely to solve the problem.
If not, I may just want to run my code entirely in C, and forget the
R problem.

-- 
Adam Clark
University of Minnesota, EEB
100 Ecology Building
1987 Upper Buford Circle
St. Paul, MN 55108
(857)-544-6782

	[[alternative HTML version deleted]]

On Oct 31, 2012, at 3:13 AM, Adam Clark <atclark at umn.edu> wrote:
> I'm running R 2.15.1x64, though the same problem persists for 2.13.0x32
and
> 2.13.0x64.
> 
> I am trying to run compiled C code using the .C convention. The
> code compiles without problems, dynamically loads within the R
> workspace with no problems, and even runs and gives correct results with
> no problems.
> 
> However, R will randomly crash within a few minutes of successfully using
> the compiled function.
> 
> For example, if I run my compiled function using:
> dyn.load("mycfun.dll")
> answer<-.C("mycfun", parameters...), I get a completely
sensible
> result that gets stored to "answer".
> However, if I try to do too many things to "answer", the R exits
> without warning.
> I've tried dyn.unload in hopes that R would become stable afterwards,
but
> in this case using the function crashes R without fail.
> 
> Usually, I can either plot, or view, or save "answer" to a file -
but never
> take more than a single action before R exits. This does not appear to
> depend on how long R has been open. Initially, I thought it was a bug in
> the "inline" function, but I'm finding the same problem now
that I'm using
> the dynamically loaded file directly. I'm used to R being insanely
stable,
> and am somewhat mystified by this whole problem.
> 
> My next move is to learn the ".Call" convention, as I suspect
that
> my problem is related to my "C" function using memory that R
doesn't
> know is used. But - before I invest a while lot more time on this, I'd
> like to know whether anybody things this is likely to solve the problem.
> If not, I may just want to run my code entirely in C, and forget the
> R problem.
Hi Adam,

Can you make a minimal reproducible example of your C sources available? I'm
relatively certain that the problem is in the memory management therein, but I
obviously can't say more without seeing the code.

Michael
> 
> -- 
> Adam Clark
> University of Minnesota, EEB
> 100 Ecology Building
> 1987 Upper Buford Circle
> St. Paul, MN 55108
> (857)-544-6782
> 
>    [[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On 12-10-30 11:13 PM, Adam Clark wrote:
> I'm running R 2.15.1x64, though the same problem persists for 2.13.0x32
and
> 2.13.0x64.
>
> I am trying to run compiled C code using the .C convention. The
> code compiles without problems, dynamically loads within the R
> workspace with no problems, and even runs and gives correct results with
> no problems.
>
> However, R will randomly crash within a few minutes of successfully using
> the compiled function.
>
> For example, if I run my compiled function using:
> dyn.load("mycfun.dll")
> answer<-.C("mycfun", parameters...), I get a completely
sensible
> result that gets stored to "answer".
> However, if I try to do too many things to "answer", the R exits
> without warning.
> I've tried dyn.unload in hopes that R would become stable afterwards,
but
> in this case using the function crashes R without fail.
>
> Usually, I can either plot, or view, or save "answer" to a file -
but never
> take more than a single action before R exits. This does not appear to
> depend on how long R has been open. Initially, I thought it was a bug in
> the "inline" function, but I'm finding the same problem now
that I'm using
> the dynamically loaded file directly. I'm used to R being insanely
stable,
> and am somewhat mystified by this whole problem.
>
> My next move is to learn the ".Call" convention, as I suspect
that
> my problem is related to my "C" function using memory that R
doesn't
> know is used. But - before I invest a while lot more time on this, I'd
> like to know whether anybody things this is likely to solve the problem.
> If not, I may just want to run my code entirely in C, and forget the
> R problem.
I think your C code has a bug in it.  The bug might go away when you 
rewrite the function to work within the .Call convention, but it is 
probably easier to find the bug and fix it with the current code.

Things to look for:

Are you fully allocating all arrays in R before passing them to C?  The 
C code receives a pointer and will happily write to it, whether that 
makes sense or not.

Are you careful with your limits on vectors?  In R, a vector is indexed 
from 1 to n, but the same vector in C is indexed from 0 to n-1.  If the 
C code writes to entry n, that will eventually cause problems.

Are you allocating memory in your C code?  There are several ways to do 
that, depending on how you want it managed.  If you do it one way and 
expect it to be managed in a different way, you'll get problems.

Duncan Murdoch
>