Hi,
I'm seeing something that may be a bug in R's standalone math library,
which is packaged by Debian as r-mathlib. I reported it to the Debian BTS
as http://bugs.debian.org/657573
I'm using Debian squeeze, and the code was tested with r-mathlib 2.11.1-6
(default on stable) and 2.14.1-1 (from testing/unstable).
I summarize this report below. The following code with the R math library
hangs. Note that set_seed is defined as taking two unsigned int arguments,
so 0's are valid arguments. I'm guessing that since 0 is as low as an
unsigned integer can go, it represents some kind of edge case.
################################################
#define MATHLIB_STANDALONE
#include <Rmath.h>
int main(void)
{
set_seed(0, 0);
rgamma(1, 1);
}
################################################
If I add the definitions of `get_seed` and `set_seed` from
`src/nmath/standalone/sunif.c` to my code, then the hang disappears.
################################################
#define MATHLIB_STANDALONE
#include <Rmath.h>
/* A version of Marsaglia-MultiCarry */
static unsigned int I1=1234, I2=5678;
void set_seed(unsigned int i1, unsigned int i2)
{
I1 = i1; I2 = i2;
}
void get_seed(unsigned int *i1, unsigned int *i2)
{
*i1 = I1; *i2 = I2;
}
int main(void)
{
set_seed(0, 0);
rgamma(1, 1);
}
################################################
I assume sunif.c defines the `get_seed` and `set_seed` for the R
standalone random number generation facilities.
However, I wonder why
a) redefining them in my source file makes the hang go away
and
b) why doesn't redefining `get_seed` and `set_seed` (even with the same
definition) give a linker error, since the function has been defined in
the library already?
Dirk also pointed out (in the bug report) that you get the following
##########################################################
int main(void)
{
set_seed(0, 0);
cout << "one normal " << norm_rand() << endl;
}
##########################################################
edd at max:/tmp$ g++ -o faheem faheem.cpp -lRmath; ./faheem
one normal -inf
One would expect norm_rand to return finite values, even in edge cases.
If you want me to report this as a bug, let me know. Thanks.
Regards, Faheem
On 28 January 2012 at 02:33, Faheem Mitha wrote:
|
| Hi,
|
| I'm seeing something that may be a bug in R's standalone math library,
| which is packaged by Debian as r-mathlib. I reported it to the Debian BTS
| as http://bugs.debian.org/657573
|
| I'm using Debian squeeze, and the code was tested with r-mathlib 2.11.1-6
| (default on stable) and 2.14.1-1 (from testing/unstable).
|
| I summarize this report below. The following code with the R math library
| hangs. Note that set_seed is defined as taking two unsigned int arguments,
| so 0's are valid arguments. I'm guessing that since 0 is as low as an
| unsigned integer can go, it represents some kind of edge case.
|
| ################################################
| #define MATHLIB_STANDALONE
| #include <Rmath.h>
|
| int main(void)
| {
| set_seed(0, 0);
| rgamma(1, 1);
| }
| ################################################
|
| If I add the definitions of `get_seed` and `set_seed` from
| `src/nmath/standalone/sunif.c` to my code, then the hang disappears.
|
| ################################################
| #define MATHLIB_STANDALONE
| #include <Rmath.h>
|
| /* A version of Marsaglia-MultiCarry */
|
| static unsigned int I1=1234, I2=5678;
|
| void set_seed(unsigned int i1, unsigned int i2)
| {
| I1 = i1; I2 = i2;
| }
|
| void get_seed(unsigned int *i1, unsigned int *i2)
| {
| *i1 = I1; *i2 = I2;
| }
|
| int main(void)
| {
| set_seed(0, 0);
| rgamma(1, 1);
| }
| ################################################
|
| I assume sunif.c defines the `get_seed` and `set_seed` for the R
| standalone random number generation facilities.
|
| However, I wonder why
|
| a) redefining them in my source file makes the hang go away
|
| and
|
| b) why doesn't redefining `get_seed` and `set_seed` (even with the same
| definition) give a linker error, since the function has been defined in
| the library already?
|
| Dirk also pointed out (in the bug report) that you get the following
|
| ##########################################################
| int main(void)
| {
| set_seed(0, 0);
| cout << "one normal " << norm_rand() << endl;
| }
| ##########################################################
|
| edd at max:/tmp$ g++ -o faheem faheem.cpp -lRmath; ./faheem
| one normal -inf
Well I actually sent you a complete program of which you showed only an
incomplete part. A better quote would have shown all:
#define MATHLIB_STANDALONE
#include <Rmath.h>
#include <iostream>
using std::cout;
using std::endl;
int main(void) {
set_seed(0, 0);
cout << "one normal " << norm_rand() << endl;
}
That does indeed return -Inf on my Ubuntu server. It works with other seed
values as does the rgamma which hangs only for value 0 and 0.
Dirk
| One would expect norm_rand to return finite values, even in edge cases.
|
| If you want me to report this as a bug, let me know. Thanks.
|
| Regards, Faheem
|
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
"Outside of a dog, a book is a man's best friend. Inside of a dog, it
is too
dark to read." -- Groucho Marx
On Fri, 27 Jan 2012, Dirk Eddelbuettel wrote:> | Dirk also pointed out (in the bug report) that you get the following > | > | ########################################################## > | int main(void) > | { > | set_seed(0, 0); > | cout << "one normal " << norm_rand() << endl; > | } > | ########################################################## > | > | edd at max:/tmp$ g++ -o faheem faheem.cpp -lRmath; ./faheem > | one normal -inf > > Well I actually sent you a complete program of which you showed only an > incomplete part. A better quote would have shown all: > > #define MATHLIB_STANDALONE > #include <Rmath.h> > #include <iostream> > using std::cout; > using std::endl; > > int main(void) { > set_seed(0, 0); > cout << "one normal " << norm_rand() << endl; > } > > > That does indeed return -Inf on my Ubuntu server. It works with other seed > values as does the rgamma which hangs only for value 0 and 0.Yes, apologies for not including the complete code. Btw, adding the definitions of `get_seed` and `set_seed` from | `src/nmath/standalone/sunif.c` fixes the problem here as well. faheem at orwell[default branch:rev 12]:~/corrmodel/bug$ ./edd one normal -1.26974 where previously it was giving -inf. Regards, Faheem