Displaying 20 results from an estimated 24 matches for "size_needed".
2011 Oct 05
1
Moderating consequences of garbage collection when in C
...lloc(size_t, int);
char* S_alloc(long, int);
Index: src/main/memory.c
===================================================================
--- src/main/memory.c (revision 57169)
+++ src/main/memory.c (working copy)
@@ -2503,6 +2503,17 @@
R_gc_internal(0);
}
+void R_gc_needed(R_size_t size_needed)
+{
+ if (FORCE_GC || NO_FREE_NODES() || VHEAP_FREE() < size_needed) {
+ R_gc_internal(size_needed);
+ if (NO_FREE_NODES())
+ mem_err_cons();
+ if (VHEAP_FREE() < size_needed)
+ mem_err_heap(0);
+ }
+}
+
static void R_gc_full(R_size_t size_needed)...
2015 Apr 09
2
Trash Plugin bugs
...the lowest limit */
- if (size > bytes_limit) {
+ if (bytes_limit > 0 && size > bytes_limit) {
*too_large_r = TRUE;
break;
}
2. Trash plugin does not use bytes_ceil/count_ceil to calculate size_needed/count_needed to expunge.
Trash plugin may expunge more messages that nedeed.
+ if (ctx->bytes_ceil!=(uint64_t)-1 && ctx->bytes_ceil < size + ctx->bytes_over) {
+ size_needed = size + ctx->bytes_over - ctx->bytes_ceil;
+ }...
2001 Jul 02
0
ReleaseLargeFreeVectors SIGSEGV (?) (PR#1008)
...malloc.c:3111
3111 malloc.c: No such file or directory.
(gdb) bt
#0 0x40111109 in chunk_free (ar_ptr=0x401a5d40, p=0x94723a8) at malloc.c:3111
#1 0x40110f9a in __libc_free (mem=0x94727d0) at malloc.c:3023
#2 0x80a6b60 in ReleaseLargeFreeVectors () at memory.c:673
#3 0x80a82b2 in RunGenCollect (size_needed=2000) at memory.c:1079
#4 0x80a9365 in R_gc_internal (size_needed=2000) at memory.c:1669
#5 0x80a9027 in Rf_allocVector (type=14, length=2000) at memory.c:1541
#6 0x808cb58 in Rf_duplicate (s=0x9548498) at duplicate.c:140
#7 0x80660fa in do_makelist (call=0x8a3f7c0, op=0x81a7c00, args=0x8239258...
2008 Oct 03
1
Memory crash
...ng. Any suggestions?
Ubuntu 8.04, R-2.7.2.
G?ran
-------------------------------------------------------------------
> glmmboot(y ~ x, cluster = cluster, data = res$dat, family =
binomial, boot = 400)
Program received signal SIGSEGV, Segmentation fault.
0x000000000041a817 in R_gc_internal (size_needed=3000) at memory.c:1317
1317 PROCESS_NODES();
(gdb) where
#0 0x000000000041a817 in R_gc_internal (size_needed=3000) at memory.c:1317
#1 0x000000000041c31c in Rf_allocVector (type=14, length=3000)
at memory.c:1968
#2 0x000000000052a647 in duplicate1 (s=0x20cb4a0) at duplicate.c:214
#3 0x...
2002 Nov 11
2
R 1.6.1: help with debugging error in RunGenCollect(), R_gc_internal
...t various model parameters against a
spatial distribution of biological cells. At some point, varying from
run to run, it generates the Segmentation fault:
Program received signal SIGSEGV, Segmentation fault.
0xffffffdc in ?? ()
(gdb) where
#0 0xffffffdc in ?? ()
#1 0x080bcae7 in RunGenCollect (size_needed=6777) at memory.c:1286
#2 0x080bdaa0 in R_gc_internal (size_needed=6777) at memory.c:1859
#3 0x080bd729 in Rf_allocVector (type=13, length=13554) at memory.c:1722
#4 0x08090a71 in CPtrToRObj (p=0x98db958, arg=0x98b29f8, Fort=1, type=13)
at dotcode.c:209
#5 0x080933cb in do_dotCode (call=0x8...
2015 Jan 18
2
default min-v/nsize parameters
...atic double R_NGrowIncrFrac = 0.05, R_NShrinkIncrFrac = 0.2;
345 static int R_NGrowIncrMin = 40000, R_NShrinkIncrMin = 0;
346 static double R_VGrowIncrFrac = 0.05, R_VShrinkIncrFrac = 0.2;
347 static int R_VGrowIncrMin = 80000, R_VShrinkIncrMin = 0;
348#endif
static void AdjustHeapSize(R_size_t size_needed)
{
R_size_t R_MinNFree = (R_size_t)(orig_R_NSize * R_MinFreeFrac);
R_size_t R_MinVFree = (R_size_t)(orig_R_VSize * R_MinFreeFrac);
R_size_t NNeeded = R_NodesInUse + R_MinNFree;
R_size_t VNeeded = R_SmallVallocSize + R_LargeVallocSize +
size_needed + R_MinVFree;
double node_occup...
2009 Sep 03
1
Running an expression 1MN times using embedded R
...m evaluating this expression
expression({ for(x in 1:5){ .Call('rh_status','x') }})
a million times from a program with R embedded in it. I have attached
reproducible code that crashes with
Program received signal SIGSEGV, Segmentation fault.
0x00002b499ca40a6e in R_gc_internal (size_needed=0) at memory.c:1309
1309 FORWARD_NODE(R_PPStack[i]);
Current language: auto; currently c
(bt output below)
The code crashes with R-2.8 on both OS X (10.5) and Linux (Linux
2.6.18-128.4.1.el5 #1 SMP Thu Jul 23 19:59:19 EDT 2009 x86_64 x86_64
x86_64 GNU/Linux)
Most of the code has been taken...
2003 Apr 21
0
sweave provoked segfault (PR#2809)
...er interface to help.
Type `q()' to quit R.
library(tools)
> > library(tools)
> gctorture()
> checkVignettes(dir='/home/paul/dse/src/pac/monitor', workdir = 'cur',
keepfiles=TRUE)
Program received signal SIGSEGV, Segmentation fault.
0x080c1598 in RunGenCollect (size_needed=0) at memory.c:1210
1210 PROCESS_NODES();
(gdb) bt
#0 0x080c1598 in RunGenCollect (size_needed=0) at memory.c:1210
#1 0x080c3089 in R_gc_internal (size_needed=0) at memory.c:1865
#2 0x080c27fe in Rf_cons (car=0xbfffbf40, cdr=0x81f65a0) at
memory.c:1534
#3 0x08097e35 in Rf_duplicate (s=0x...
2001 Jan 23
0
1.2.1 segfault
...size changed.
0xef5b7400 in poll ()
(gdb)
Continuing.
> gctorture()
>
Program received signal SIGWINCH, Window size changed.
0xef5b7400 in poll ()
(gdb)
Continuing.
> tst <- spanSS.f <- span(SSmodel)
Program received signal SIGSEGV, Segmentation fault.
0x7111c in RunGenCollect (size_needed=2) at memory.c:1027
1027 FORWARD_CHILDREN(s);
(gdb) bt
#0 0x7111c in RunGenCollect (size_needed=2) at memory.c:1027
#1 0x731c8 in R_gc_internal (size_needed=2) at memory.c:1670
#2 0x72dbc in Rf_allocVector (type=13, length=4) at memory.c:1542
#3 0x48794 in CPtrToRObj (p=0xd9fb78, arg=0xd9f20...
2011 Aug 26
2
read.table segfaults
> fil2s <- read.table("../Data/fil2_s.txt", header = FALSE, sep = "\t")
Program received signal SIGSEGV, Segmentation fault.
0x000000000041c2e1 in RunGenCollect (size_needed=8192000) at memory.c:1514
1514 PROCESS_NODES();
(gdb)
> sessionInfo()
R version 2.13.1 Patched (2011-08-25 r56798)
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=C...
2002 Jun 12
3
help debugging segfaults
...gs = 0;
1854 for (pargs = args ; pargs != R_NilValue ; pargs =
CDR(pargs)) {
1855 if(argConverters[nargs]) {
1864 PROTECT(s = CPtrToRObj(cargs[nargs], CAR(pargs),
which));
Program received signal SIGSEGV, Segmentation fault.
0x080ddc6a in RunGenCollect (size_needed=1515400) at memory.c:1133
1133 SEXP next = NEXT_NODE(s);
This is obtained on Linux (Mandrake 8.2 w/enterprise kernel 2.4.8) running
on dual P3-866 Xeon with 2GB RAM, using R-1.5.0 compiled from source.
Any help/hints/comments are greatly appreciated!
Regards,
Andy
Andy I. Lia...
2002 Jun 12
3
help debugging segfaults
...gs = 0;
1854 for (pargs = args ; pargs != R_NilValue ; pargs =
CDR(pargs)) {
1855 if(argConverters[nargs]) {
1864 PROTECT(s = CPtrToRObj(cargs[nargs], CAR(pargs),
which));
Program received signal SIGSEGV, Segmentation fault.
0x080ddc6a in RunGenCollect (size_needed=1515400) at memory.c:1133
1133 SEXP next = NEXT_NODE(s);
This is obtained on Linux (Mandrake 8.2 w/enterprise kernel 2.4.8) running
on dual P3-866 Xeon with 2GB RAM, using R-1.5.0 compiled from source.
Any help/hints/comments are greatly appreciated!
Regards,
Andy
Andy I. Lia...
2015 Jan 20
1
default min-v/nsize parameters
...static int R_NGrowIncrMin = 40000, R_NShrinkIncrMin = 0;
>> 346 static double R_VGrowIncrFrac = 0.05, R_VShrinkIncrFrac = 0.2;
>> 347 static int R_VGrowIncrMin = 80000, R_VShrinkIncrMin = 0;
>> 348#endif
>>
>> static void AdjustHeapSize(R_size_t size_needed)
>> {
>> R_size_t R_MinNFree = (R_size_t)(orig_R_NSize * R_MinFreeFrac);
>> R_size_t R_MinVFree = (R_size_t)(orig_R_VSize * R_MinFreeFrac);
>> R_size_t NNeeded = R_NodesInUse + R_MinNFree;
>> R_size_t VNeeded = R_SmallVallocSize + R_LargeVallocSize...
2001 Feb 20
2
segfault
...39;ve managed to trap the following segfault with xxgdb and gctorture() set. The
segfault seems to move around if gctorture() is not set, but has now occurred twice
in the same spot with it set. xxgdb gives the message
Program received signal SIGSEGV, Segmentation fault.
0x71244 in RunGenCollect (size_needed=2) at memory.c:1027
and the source listing points to FORWARD_CHILDREN(s); in the following section from
src/main/memory.c
#ifndef EXPEL_OLD_TO_NEW
/* scan nodes in uncollected old generations with old-to-new pointers */
for (gen = num_old_gens_to_collect; gen < NUM_OLD_GENERATIONS; gen...
2015 Jan 19
0
default min-v/nsize parameters
...0.05, R_NShrinkIncrFrac = 0.2;
> 345 static int R_NGrowIncrMin = 40000, R_NShrinkIncrMin = 0;
> 346 static double R_VGrowIncrFrac = 0.05, R_VShrinkIncrFrac = 0.2;
> 347 static int R_VGrowIncrMin = 80000, R_VShrinkIncrMin = 0;
> 348#endif
>
> static void AdjustHeapSize(R_size_t size_needed)
> {
> R_size_t R_MinNFree = (R_size_t)(orig_R_NSize * R_MinFreeFrac);
> R_size_t R_MinVFree = (R_size_t)(orig_R_VSize * R_MinFreeFrac);
> R_size_t NNeeded = R_NodesInUse + R_MinNFree;
> R_size_t VNeeded = R_SmallVallocSize + R_LargeVallocSize +
> size_needed + R_M...
2002 Jun 18
1
can't find array overruns (was: help debugging segfaults)
...; pargs != R_NilValue ; pargs =
> CDR(pargs)) {
> 1855 if(argConverters[nargs]) {
> 1864 PROTECT(s = CPtrToRObj(cargs[nargs],
> CAR(pargs),
> which));
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x080ddc6a in RunGenCollect (size_needed=1515400) at memory.c:1133
> 1133 SEXP next = NEXT_NODE(s);
>
> This is obtained on Linux (Mandrake 8.2 w/enterprise kernel
> 2.4.8) running
> on dual P3-866 Xeon with 2GB RAM, using R-1.5.0 compiled from source.
>
> Any help/hints/comments are greatly appr...
2015 Jan 15
2
default min-v/nsize parameters
Just wanted to start a discussion on whether R could ship with more
appropriate GC parameters. Right now, loading the recommended package
Matrix leads to:
> library(Matrix)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1076796 57.6 1368491 73.1 1198505 64.1
Vcells 1671329 12.8 2685683 20.5 1932418 14.8
Results may vary, but here R needed 64MB of N cells and 15MB
2008 Sep 27
1
seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}
...umber of arguments to "<-"
Program received signal SIGABRT, Aborted.
0x0000003294e30155 in raise () from /lib64/libc.so.6
(gdb) bt
#0 0x0000003294e30155 in raise () from /lib64/libc.so.6
#1 0x0000003294e31bf0 in abort () from /lib64/libc.so.6
#2 0x00000000004184f5 in R_gc_internal (size_needed=0)
at ../../../R/src/main/memory.c:761
#3 0x000000000041b121 in Rf_cons (car=0x1b2ec088, cdr=0x1a3436d8)
at ../../../R/src/main/memory.c:1755
#4 0x0000000000578472 in applydefine (call=<value optimized out>,
op=0x1a3617a8, args=0x1ad47590, rho=0x1b2ea428)
at ../../../R/src/...
2008 Jul 14
0
RODBC Seg Fault
...ry.c:2445
#1 0x006b17cb in inRODBCClose (thisHandle=0x8c1f358) at RODBC.c:1250
#2 0x006b190d in chanFinalizer (ptr=0x9100380) at RODBC.c:1271
#3 0x0805b6eb in R_RunWeakRefFinalizer (w=0x90da4f8) at memory.c:1062
#4 0x0805b810 in RunFinalizers () at memory.c:1107
#5 0x0805cf17 in R_gc_internal (size_needed=1) at memory.c:2205
#6 0x0805da69 in Rf_allocVector (type=16, length=1) at memory.c:1968
#7 0x006b3955 in RODBCDriverConnect (connection=0x90b0208, id=0x90b0288,
useNRows=0x90b02c8) at RODBC.c:277
#8 0x08161a19 in do_dotcall (call=0x89b9ba8, op=0x85518dc, args=<value
optimized out>, en...
2009 Sep 30
2
R 2.9.2 crashes when sorting latin1-encoded strings
Hi everyone!
I think I stumbled over a bug in the latest R 2.9.2 patched for OS X:
> R version 2.9.2 Patched (2009-09-24 r49861)
> i386-apple-darwin9.8.0
When I try to sort latin1-encoded character vectors, R sometimes
crashes with a segmentation fault. I'm running OS X 10.5.8 and have
observed this behaviour both with the i386 and x86_64 builds, in the
R.app GUI as well as on