R help - Jun 2011 - Arules: R Crashes when running eclat with tidLists=TRUE

Hello,

I'm using the eclat function of the arules package (1.0-6) for the
identification of frequent itemsets. I need the tidLists, but if I set
in the function tidLists=TRUE R crashes (Windows XP Professional SP3,
32 bit, R version 2.12.1 (2010-12-16), reproducible on two different
computers) with two different error messages or non at all. Minimum
examples are:

	library(arules)
	data("Adult")

	eclat(Adult, parameter=list(support=0.05, tidLists=FALSE)) # OK
	eclat(Adult, parameter=list(support=0.50, tidLists=TRUE))  # OK
	eclat(Adult, parameter=list(support=0.05, tidLists=TRUE))  # crashes

I started to search the cause of the problem and figured out that the
problem must be  located in the external function reclat called in
eclat.R using the source of the arules package:

    result <- .Call("reclat",
        ## transactions
        items at p,
        items at i,
        items at Dim,
        ## parameter
        parameter, control,
        data at itemInfo,
        PACKAGE = "arules")

Then I looked into the source code of reclat.c, trying to follow the
tidList=TRUE parameter, but I have no C programming experience. It
looks to me that the problem may be in the item set report function
"_report_R" where memory is allocated and or released (see code
fragments below).

My question are:

a) Does anyone else can confirm the problem?

b) Does anyone know, if this may be a problem of the binary package
(e.g. how it was compiled) or if it is a problem of the source code
for reclat?

c) Does anyone know how to fix the problem and how?

Thanks and regards,

Dirk


/*----------------------------------------------------------------------
  Item Set Report Function
----------------------------------------------------------------------*/

static void _report_R (int *ids, int cnt, int supp, int *tal, void *data)
{
(...)

	if (flags & OF_LIST) {
			  vec1 = (int*)realloc(ruleset->trnb, size1 *sizeof(int));
			  if (!vec1) {
				  if (vec) free(vec);
				  if (vec2) free(vec2);
				  _cleanup(); error(msg(E_NOMEM));}
			  ruleset->trnb = vec1;
		  }
(...)
	if (flags & OF_LIST) {        /* if to list the transactions, */
	  h = ruleset->trtotal;
	  if (supp < 0) {             /* if bit vector representation */
		  for (i = 0; i < tacnt; i++) {  /* traverse the bit vector */
			  if (h >= size2) {
				  size2 += (size2 > BLKSIZE) ? (size2 >> 1) : BLKSIZE;
				  vec1 = (int*)realloc(ruleset->trans, size2 *sizeof(int));
				  if (!vec1) {
					  if (vec) free(vec);
					  if (vec2) free(vec2);
					  _cleanup(); error(msg(E_NOMEM));}
				  ruleset->trans = vec1;
			  }
			  if (tal[i >> BM_SHIFT] & (1 << (i & BM_MASK))) {
				  /*Rprintf(" %d", i+1);*/
				  ruleset->trans[h] = i;
				  h++;
			  }
		  }
	  }                       /* print the indices of set bits */
	  else {                      /* if list of transaction ids */
		  if ((h + supp) >= size2) {
			  while ((h + supp) >= size2) {
				  size2 += (size2 > BLKSIZE) ? (size2 >> 1) : BLKSIZE;
			  }
			  vec1 = (int*)realloc(ruleset->trans, size2 *sizeof(int));
			  if (!vec1) {
				  if (vec) free(vec);
				  if (vec2) free(vec2);
				  _cleanup(); error(msg(E_NOMEM));}
			  ruleset->trans = vec1;
		  }
		  for (i = 0; i < supp; i++) {
			  /*Rprintf(" %d", tal[i]); */
			  ruleset->trans[h] = tal[i];
			  h++;
		  }                           /* traverse and print */
	  }
	  ruleset->trtotal = ruleset->trnb[ruleset->rnb] = h;
	}                             /* the transaction identifiers */
(...)

Hello,

This simple SVD calculation (commands are copied immediately below) crashes on
my Ubuntu machine (R 2.13.0). However it works fine on my Windows 7 machine, so
I suspect there's a problem with (my?) Ubuntu and / or R. Can anybody else
reproduce it (with Ubuntu 11.04)? Thanks in advance.

p <- 500
n <- 300
set.seed(1234)
x <- matrix(rnorm(n*p), n, p)
sih <- var(x)
b <- svd(sih)

produces:

?*** caught illegal operation ***
address 0x42b8c9, cause 'illegal operand'

Traceback:
?1: .Call("La_svd", jobu, jobv, x, double(min(n, p)), u, v,
"dgsedd",???? PACKAGE = "base")
?2: La.svd(x, nu, nv)
?3: svd(sih)

I'm using Ubuntu 11.04 and 
> version
?????????????? _??????????????????????????? 
platform?????? i686-pc-linux-gnu??????????? 
arch?????????? i686???????????????????????? 
os???????????? linux-gnu??????????????????? 
system???????? i686, linux-gnu????????????? 
status????????????????????????????????????? 
major????????? 2??????????????????????????? 
minor????????? 13.0???????????????????????? 
year?????????? 2011???????????????????????? 
month????????? 04?????????????????????????? 
day??????????? 13?????????????????????????? 
svn rev??????? 55427??????????????????????? 
language?????? R??????????????????????????? 
version.string R version 2.13.0 (2011-04-13)

Thanks,

Matias

Update

I had the chance to test the issue tonight using R version 2.12.2
on a Linux (Ubuntu 10.04.2, x86_64, kernel 2.6.32-32-generic) system:

It does also crash (with a support of 0.01 instead of 0.05 posted
earlier) running

	eclat(Adult, parameter=list(support=0.01, tidLists=TRUE))

but I got some more information, which supports my initial guess:

	 *** caught segfault ***
	address 0xa481b70, cause 'memory not mapped'

	Traceback:
	 1: .Call("reclat", items at p, items at i, items at Dim, parameter,
                   control, data at itemInfo, PACKAGE = "arules")
	 2: eclat(Adult, parameter = list(support = 0.01,
                   tidLists = TRUE))

It also crashes on a virtual x86_32 Windows XP Home SP3 running on the
same linux machine ...


Does anyone know how to fix the problem and how?


Thanks and regards,

Dirk

> Hello,
> 
> I'm using the eclat function of the arules package (1.0-6) for the
> identification of frequent itemsets. I need the tidLists, but if I set
> in the function tidLists=TRUE R crashes (Windows XP Professional SP3,
> 32 bit, R version 2.12.1 (2010-12-16), reproducible on two different
> computers) with two different error messages or non at all. Minimum
> examples are:
> 
> 	library(arules)
> 	data("Adult")
> 
> 	eclat(Adult, parameter=list(support=0.05, tidLists=FALSE)) # OK
> 	eclat(Adult, parameter=list(support=0.50, tidLists=TRUE))  # OK
> 	eclat(Adult, parameter=list(support=0.05, tidLists=TRUE))  # crashes
> 
> I started to search the cause of the problem and figured out that the
> problem must be  located in the external function reclat called in
> eclat.R using the source of the arules package:
> 
>     result <- .Call("reclat",
>         ## transactions
>         items at p,
>         items at i,
>         items at Dim,
>         ## parameter
>         parameter, control,
>         data at itemInfo,
>         PACKAGE = "arules")
> 
> Then I looked into the source code of reclat.c, trying to follow the
> tidList=TRUE parameter, but I have no C programming experience. It
> looks to me that the problem may be in the item set report function
> "_report_R" where memory is allocated and or released (see code
> fragments below).
> 
> My question are:
> 
> a) Does anyone else can confirm the problem?
> 
> b) Does anyone know, if this may be a problem of the binary package
> (e.g. how it was compiled) or if it is a problem of the source code
> for reclat?
> 
> c) Does anyone know how to fix the problem and how?
> 
> Thanks and regards,
> 
> Dirk
> 
> 
> /*----------------------------------------------------------------------
>   Item Set Report Function
> ----------------------------------------------------------------------*/
> 
> static void _report_R (int *ids, int cnt, int supp, int *tal, void *data)
> {
> (...)
> 
> 	if (flags & OF_LIST) {
> 			  vec1 = (int*)realloc(ruleset->trnb, size1 *sizeof(int));
> 			  if (!vec1) {
> 				  if (vec) free(vec);
> 				  if (vec2) free(vec2);
> 				  _cleanup(); error(msg(E_NOMEM));}
> 			  ruleset->trnb = vec1;
> 		  }
> (...)
> 	if (flags & OF_LIST) {        /* if to list the transactions, */
> 	  h = ruleset->trtotal;
> 	  if (supp < 0) {             /* if bit vector representation */
> 		  for (i = 0; i < tacnt; i++) {  /* traverse the bit vector */
> 			  if (h >= size2) {
> 				  size2 += (size2 > BLKSIZE) ? (size2 >> 1) : BLKSIZE;
> 				  vec1 = (int*)realloc(ruleset->trans, size2 *sizeof(int));
> 				  if (!vec1) {
> 					  if (vec) free(vec);
> 					  if (vec2) free(vec2);
> 					  _cleanup(); error(msg(E_NOMEM));}
> 				  ruleset->trans = vec1;
> 			  }
> 			  if (tal[i >> BM_SHIFT] & (1 << (i & BM_MASK))) {
> 				  /*Rprintf(" %d", i+1);*/
> 				  ruleset->trans[h] = i;
> 				  h++;
> 			  }
> 		  }
> 	  }                       /* print the indices of set bits */
> 	  else {                      /* if list of transaction ids */
> 		  if ((h + supp) >= size2) {
> 			  while ((h + supp) >= size2) {
> 				  size2 += (size2 > BLKSIZE) ? (size2 >> 1) : BLKSIZE;
> 			  }
> 			  vec1 = (int*)realloc(ruleset->trans, size2 *sizeof(int));
> 			  if (!vec1) {
> 				  if (vec) free(vec);
> 				  if (vec2) free(vec2);
> 				  _cleanup(); error(msg(E_NOMEM));}
> 			  ruleset->trans = vec1;
> 		  }
> 		  for (i = 0; i < supp; i++) {
> 			  /*Rprintf(" %d", tal[i]); */
> 			  ruleset->trans[h] = tal[i];
> 			  h++;
> 		  }                           /* traverse and print */
> 	  }
> 	  ruleset->trtotal = ruleset->trnb[ruleset->rnb] = h;
> 	}                             /* the transaction identifiers */
> (...)