Displaying 20 results from an estimated 24 matches for "r_gc_internal".
2006 Oct 19
0
Memory leak
...(eval.c:1107)
==11423== Address 0x473D163 is 3 bytes inside a block of size 168
free'd
==11423== at 0x401B2A3: free (vg_replace_malloc.c:233)
==11423== by 0x80ED27C: ReleaseLargeFreeVectors (memory.c:759)
==11423== by 0x80EED30: RunGenCollect (memory.c:1351)
==11423== by 0x80F0635: R_gc_internal (memory.c:2141)
==11423== by 0x80F000C: Rf_allocVector (memory.c:1942)
==11423== by 0x814F67A: RestoreToEnv (saveload.c:2038)
==11423== by 0x8150465: do_loadFromConn2 (saveload.c:2358)
==11423== by 0x80F95FF: do_internal (names.c:1097)
==11423== by 0x80CB320: Rf_eval (eval.c:431)
==1...
2002 Nov 11
2
R 1.6.1: help with debugging error in RunGenCollect(), R_gc_internal
...tion 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=0x89f3880, op=0x8222154, args=0x833b380,
env=0x8346e9...
2019 Feb 26
8
Intermittent crashes with inset `[<-` command
The following code crashes after about 300 iterations on my?x86_64-w64-mingw32?machine on R 3.5.2 --vanilla.??
Others have duplicated this (see?https://github.com/tidyverse/magrittr/issues/190?if necessary), but I don't know how machine/OS-dependent it may be.??
If it doesn't crash for you, please try increasing the length of the x vector.
Substituting the commented-out line for the one
2019 Feb 27
2
Intermittent crashes with inset `[<-` command
...(Rmain.c:29)
==4711== Address 0x19b3ab90 is 0 bytes inside a block of size 160,048
free'd
==4711== at 0x4C2ACBD: free (vg_replace_malloc.c:530)
==4711== by 0x4FAFCB2: ReleaseLargeFreeVectors (memory.c:1055)
==4711== by 0x4FAFCB2: RunGenCollect (memory.c:1825)
==4711== by 0x4FAFCB2: R_gc_internal (memory.c:2998)
==4711== by 0x4FB166F: Rf_allocVector3 (memory.c:2682)
==4711== by 0x4FB2310: Rf_allocVector (Rinlinedfuns.h:577)
==4711== by 0x4FB2310: R_alloc (memory.c:2197)
==4711== by 0x5023F7A: logicalSubscript (subscript.c:575)
==4711== by 0x5026DA3: Rf_makeSubscript (subscrip...
2008 Oct 03
1
Memory crash
...am only guessing. 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...
2019 Feb 27
0
Intermittent crashes with inset `[<-` command
...dress 0x19b3ab90 is 0 bytes inside a block of size 160,048
> free'd
> ==4711== at 0x4C2ACBD: free (vg_replace_malloc.c:530)
> ==4711== by 0x4FAFCB2: ReleaseLargeFreeVectors (memory.c:1055)
> ==4711== by 0x4FAFCB2: RunGenCollect (memory.c:1825)
> ==4711== by 0x4FAFCB2: R_gc_internal (memory.c:2998)
> ==4711== by 0x4FB166F: Rf_allocVector3 (memory.c:2682)
> ==4711== by 0x4FB2310: Rf_allocVector (Rinlinedfuns.h:577)
> ==4711== by 0x4FB2310: R_alloc (memory.c:2197)
> ==4711== by 0x5023F7A: logicalSubscript (subscript.c:575)
> ==4711== by 0x5026DA3: R...
2009 Sep 03
1
Running an expression 1MN times using embedded R
Hello,
I'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 h...
2011 Oct 05
1
Moderating consequences of garbage collection when in C
...(void);
+void R_gc_needed(size_t);
char* R_alloc(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);
+ }
+}...
2007 Jun 21
2
segfault during cbind
...is 72,976 bytes inside a block of size 182,760 free'd
==25398== at 0x4C226DB: free (in /usr/lib64/valgrind/amd64-linux/vgpreload_memcheck.so)
==25398== by 0x4F2D848: ReleaseLargeFreeVectors (memory.c:760)
==25398== by 0x4F359E9: RunGenCollect (memory.c:1378)
==25398== by 0x4F38938: R_gc_internal (memory.c:2171)
==25398== by 0x4F38046: Rf_allocVector (memory.c:1961)
==25398== by 0x4EDE779: duplicate1 (duplicate.c:221)
==25398== by 0x4EDD698: Rf_duplicate (duplicate.c:115)
==25398== by 0x4E7BB34: cbind (bind.c:1258)
==25398== by 0x4E7B430: do_bind (bind.c:1113)
==25398== by...
2008 Sep 27
1
seg.fault from nlme::gnls() {was "[R-sig-ME] GNLS Crash"}
...incorrect number 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 .....
2001 Jul 02
0
ReleaseLargeFreeVectors SIGSEGV (?) (PR#1008)
...ory.
(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,
rho=0x824e510) at builtin.c:367
#8 0x809136f i...
2015 Feb 05
2
Invalid read of size 8
...76)
==954== by 0xBE8C0: do_set (eval.c:2028)
==954== by 0xB0404: Rf_eval (eval.c:629)
==954== by 0xE9012: Rf_ReplIteration (main.c:260)
==954== Address 0x107df7fb8 is 40 bytes inside a block of size 176 free'd
==954== at 0x4D8D: free (vg_replace_malloc.c:477)
==954== by 0xF0BCA: R_gc_internal (memory.c:1026)
==954== by 0xF2400: Rf_allocVector3 (memory.c:2578)
==954== by 0x2BBCE: Rf_allocMatrix (Rinlinedfuns.h:189)
==954== by 0xA92D449: NPHDPHMM (in /Users/NPHDPHMM.so)
==954== by 0x8632A: do_dotcall (dotcode.c:652)
==954== by 0xB036A: Rf_eval (eval.c:657)
==954== by 0xB...
2007 Mar 07
3
Garbage collector crashes after calling a C function
...= by 0x4BE9107: Rf_eval (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4BEBA3F: do_set (in /usr/lib64/R/lib/libR.so)
### This is the RunGenCollect memory error
==9370== Invalid write of size 8
==9370== at 0x4C1F73A: RunGenCollect (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4C23E55: R_gc_internal (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4C22DC3: Rf_cons (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4C23AE1: Rf_allocList (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4B6926B: installAttrib (in /usr/lib64/R/lib/libR.so)
==9370== by 0x4B69961: Rf_classgets (in /usr/lib64/R/lib/li...
2013 Jun 11
3
load/unload segfault puzzle
Dear r-devel readers,
I have a pretty deep problem with package loading and unloading in
the development version of the lme4 package
<https://github.com/lme4/lme4>; it's not boiled down to a properly
minimal example yet (this has been difficult), but I am posting anyway
in the hopes that someone has ideas about how to proceed farther,
since I'm nearly stumped. Apologies in advance
2008 Aug 07
1
dput function (PR#12112)
Full_Name: Juan Gea
Version: R version 2.6.2
OS: Fedora Core 6
Submission from: (NULL) (79.153.48.49)
Abort:
objeS <- matrix("AAA",1000000)
class(objeS)
outTxt <- textConnection("vaClob", open = "w", local = FALSE)
dput(objeS,outTxt)
close(outTxt)
R version 2.6.2 (2008-02-08)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN
2008 Jul 14
0
RODBC Seg Fault
...(s=0x0) at memory.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
optimize...
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
2003 Apr 21
0
sweave provoked segfault (PR#2809)
...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=0x8324ff0) at duplicate.c:108
#4 0x080c9abf in GetObject (cptr=0xbfffc2d0) at objects.c:40
#5 0x080ca663 in do_usemethod (call=0x82c5d28, op=0x8209874,
arg...
2001 Jan 23
0
1.2.1 segfault
...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=0xd9f208, Fort=1) at dotcode.c:180
#4 0x511d0 in do_dotCode (call=0x8ad148, op=0xd9f668, args=0xda163c,
env=0xd9da48) at dotcode.c:1778
#5 0x56c44 in...
2008 Apr 29
2
reproducible segmentation fault caused by textConnection()
Dear all,
It seems that textConnection() can trigger a segmentation fault. The
following script (using two large loops) makes this bug reproducible:
for (i in 1:10000) {
z=textConnection(NULL,open='w')
for (j in 1:100) {
write(runif(1)*1e6,file=z)
write('\n',file=z)
}
close(z)
}
The bug could be reproduced on R-2.6.1, R-2.7.0 and on the latest
R-devel