On 02/07/2012 04:08 PM, Hervé Pagès wrote:
Hi,
This is what I get with recent R devel on a 64-bit Ubuntu laptop:
> mydf <- data.frame(a=1:2080, b=1001:2040, c=letters, d=LETTERS,
e=1:1040)
> mydf_in_a_character_vector <- capture.output(mydf)
Error in print.default(m, ..., quote = quote, right = right) :
cannot allocate memory block of size 17179869182.6 Gb
The error is thrown inside src/main/printarray.c:425
Rprintf("%*s%s", R_print.gap, "",
EncodeString(x[i + j * r], w[j], quote, right));
where the array w is the result of an unPROTECTed allocation earlier in
the function, and a garbage collection triggered in MatrixRowLabel (in
this case; allocation also occurs in MatrixColLabel, Rprintf).
PROTECTion seems to have been implemented in the file assuming that the
only allocations are at the head of the function; the return in the
_PRINT_DEAL_c_eq_0 macro makes it difficult to balance the protection
stack, and R_alloc seems to be a better solution anyway. diff attached.
Martin Morgan
I get something similar with R 2.14.1.
Cheers,
H.
> sessionInfo()
R Under development (unstable) (2012-01-16 r58124)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
Index: src/main/printarray.c
===================================================================
--- src/main/printarray.c (revision 58290)
+++ src/main/printarray.c (working copy)
@@ -137,7 +137,6 @@
/* initialization; particularly of row labels, rl= dimnames(.)[[1]] and
* rn = names(dimnames(.))[1] : */
#define _PRINT_INIT_rl_rn \
- SEXP sw; \
int *w; \
int width, rlabw = -1, clabw = -1; /* -Wall */ \
int i, j, jmin = 0, jmax = 0, lbloff = 0; \
@@ -159,9 +158,8 @@
_PRINT_INIT_rl_rn;
- sw = allocVector(INTSXP, c);
x = LOGICAL(sx) + offset;
- w = INTEGER(sw);
+ w = (int *) R_alloc(c, sizeof(int));
/* compute w[j] = column-width of j(+1)-th column : */
for (j = 0; j < c; j++) {
formatLogical(&x[j * r], r, &w[j]);
@@ -234,9 +232,8 @@
_PRINT_INIT_rl_rn;
- sw = allocVector(INTSXP, c);
x = INTEGER(sx) + offset;
- w = INTEGER(sw);
+ w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatInteger(&x[j * r], r, &w[j]);
_PRINT_SET_clabw;
@@ -271,19 +268,14 @@
static void printRealMatrix(SEXP sx, int offset, int r_pr, int r, int c,
SEXP rl, SEXP cl, const char *rn, const char *cn)
{
- SEXP sd, se;
double *x;
int *d, *e;
_PRINT_INIT_rl_rn;
- PROTECT(sd = allocVector(INTSXP, c));
- PROTECT(se = allocVector(INTSXP, c));
- sw = allocVector(INTSXP, c);
- UNPROTECT(2);
x = REAL(sx) + offset;
- d = INTEGER(sd);
- e = INTEGER(se);
- w = INTEGER(sw);
+ d = (int *) R_alloc(c, sizeof(int));
+ e = (int *) R_alloc(c, sizeof(int));
+ w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatReal(&x[j * r], r, &w[j], &d[j], &e[j], 0);
@@ -319,27 +311,18 @@
static void printComplexMatrix(SEXP sx, int offset, int r_pr, int r, int c,
SEXP rl, SEXP cl, const char *rn, const char *cn)
{
- SEXP sdr, ser, swr, sdi, sei, swi;
Rcomplex *x;
int *dr, *er, *wr, *di, *ei, *wi;
_PRINT_INIT_rl_rn;
- PROTECT(sdr = allocVector(INTSXP, c));
- PROTECT(ser = allocVector(INTSXP, c));
- PROTECT(swr = allocVector(INTSXP, c));
- PROTECT(sdi = allocVector(INTSXP, c));
- PROTECT(sei = allocVector(INTSXP, c));
- PROTECT(swi = allocVector(INTSXP, c));
- PROTECT(sw = allocVector(INTSXP, c));
- UNPROTECT(7);
x = COMPLEX(sx) + offset;
- dr = INTEGER(sdr);
- er = INTEGER(ser);
- wr = INTEGER(swr);
- di = INTEGER(sdi);
- ei = INTEGER(sei);
- wi = INTEGER(swi);
- w = INTEGER(sw);
+ dr = (int *) R_alloc(c, sizeof(int));
+ er = (int *) R_alloc(c, sizeof(int));
+ wr = (int *) R_alloc(c, sizeof(int));
+ di = (int *) R_alloc(c, sizeof(int));
+ ei = (int *) R_alloc(c, sizeof(int));
+ wi = (int *) R_alloc(c, sizeof(int));
+ w = (int *) R_alloc(c, sizeof(int));
/* Determine the column widths */
@@ -391,9 +374,8 @@
SEXP *x;
_PRINT_INIT_rl_rn;
- sw = allocVector(INTSXP, c);
x = STRING_PTR(sx)+offset;
- w = INTEGER(sw);
+ w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatString(&x[j * r], r, &w[j], quote);
_PRINT_SET_clabw;
@@ -437,9 +419,8 @@
Rbyte *x;
_PRINT_INIT_rl_rn;
- sw = allocVector(INTSXP, c);
x = RAW(sx) + offset;
- w = INTEGER(sw);
+ w = (int *) R_alloc(c, sizeof(int));
for (j = 0; j < c; j++) {
formatRaw(&x[j * r], r, &w[j]);
_PRINT_SET_clabw;
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