Hi all,
I am a PhD student and I am working on a C project that involves some
statistical calculations. So, I tried to embed R into C, in order to
call R functions from a C program. My program seems to get the correct
results from R. However, it appears to have a lot of memory allocation
issues, in contrast to the small amounts of memory that my code
allocates. Some additional info that might be useful: I have build R
from source with shared libraries enabled and the compiler I use is gcc
version 4.61 in a Ubuntu 11.10 linux machine.
This is my function:
static int prediction(double *berHistory, int berValues, double *ber)
{
SEXP e;
SEXP bers;
SEXP mean;
int i;
int errorOccurred;
static int init = 0;
char *argv[] = {"REmbeddedPostgres", "--gui=none", "--silent"};
int argc = sizeof(argv)/sizeof(argv[0]);
// Initialize Embedded R
if (init == 0)
{
Rf_initEmbeddedR(argc, argv);
}
init = 1;
// Allocate bers and copy values
PROTECT(bers = allocVector(REALSXP, berValues));
for (i = 0; i < berValues; i++)
{
REAL(bers)[i] = berHistory[i];
}
PROTECT(mean = allocVector(REALSXP, 1));
PROTECT(e = lang2(install("mean"), bers));
mean = R_tryEval(e, R_GlobalEnv, &errorOccurred);
if (errorOccurred)
{
printf("error occurred in mean\n");
}
for (i = 0; i < berValues; i++)
{
REAL(bers)[i] = REAL(bers)[i] / REAL(mean)[0];
}
*ber = REAL(mean)[0];
Rf_endEmbeddedR(0);
UNPROTECT(3);
return 0;
}
And these are the errors from Valgrind output:
HEAP SUMMARY:
==2909== in use at exit: 18,832,260 bytes in 6,791 blocks
==2909== total heap usage: 21,758 allocs, 14,967 frees, 30,803,476
bytes allocated
==2909==
==2909== 160 (40 direct, 120 indirect) bytes in 1 blocks are definitely
lost in loss record 179 of 1,398
==2909== at 0x4028876: malloc (vg_replace_malloc.c:236)
==2909== by 0x41B364C: nss_parse_service_list (nsswitch.c:626)
==2909== by 0x41B3C59: __nss_database_lookup (nsswitch.c:167)
==2909== by 0x59272F8: ???
==2909== by 0x5928CCC: ???
==2909== by 0x416ABA6: getpwuid_r@@GLIBC_2.1.2 (getXXbyYY_r.c:256)
==2909== by 0x416A4ED: getpwuid (getXXbyYY.c:117)
==2909== by 0x439CCB9: do_fileinfo (platform.c:944)
==2909== by 0x43289ED: bcEval (eval.c:4430)
==2909== by 0x4332CA4: Rf_eval (eval.c:397)
==2909== by 0x43377E0: Rf_applyClosure (eval.c:855)
==2909== by 0x432F17E: bcEval (eval.c:4410)
==2909==
==2909== 160 (40 direct, 120 indirect) bytes in 1 blocks are definitely
lost in loss record 180 of 1,398
==2909== at 0x4028876: malloc (vg_replace_malloc.c:236)
==2909== by 0x41B364C: nss_parse_service_list (nsswitch.c:626)
==2909== by 0x41B3C59: __nss_database_lookup (nsswitch.c:167)
==2909== by 0x5926148: ???
==2909== by 0x5926F3C: ???
==2909== by 0x41694A6: getgrgid_r@@GLIBC_2.1.2 (getXXbyYY_r.c:256)
==2909== by 0x4168CAD: getgrgid (getXXbyYY.c:117)
==2909== by 0x439CCEB: do_fileinfo (platform.c:947)
==2909== by 0x43289ED: bcEval (eval.c:4430)
==2909== by 0x4332CA4: Rf_eval (eval.c:397)
==2909== by 0x43377E0: Rf_applyClosure (eval.c:855)
==2909== by 0x432F17E: bcEval (eval.c:4410)
==2909==
==2909== LEAK SUMMARY:
==2909== definitely lost: 80 bytes in 2 blocks
==2909== indirectly lost: 240 bytes in 20 blocks
==2909== possibly lost: 0 bytes in 0 blocks
==2909== still reachable: 18,831,940 bytes in 6,769 blocks
Reachable error summary is far too long to include in this mail. The
interesting thing is that reachable errors are all caused by this small
function.
Any ideas? I would also appreciate any suggestions on how to improve
the R-C integration in my code.
Thank you in advance,
Nikos
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