search for: rungencollect

...Rf_eval (eval.c:455) ==11423== by 0x80CCAC1: do_begin (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:...

...he garbage collector executes, giving a segmentation fault. As some of you suggested, I have executed my function with valgrind, and I get no memory errors, but some memory leaks (which I am not able to locate although compiling my program with the -c flag), and I also get the memory error from RunGenCollect: (which I suppose is causes the segmentation fault). You can see a small piece of the valgrind output below Using gctorture to make the garbage collector crash inside the execution of my program didn't work (my program finished). The question is: what are the typical programming errors that...

...big loop to fit 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_dotC...

...n_Rmainloop (main.c:1082) ==4711== by 0x40075A: main (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:5...

...==4711== by 0x40075A: main (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: logica...

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

...ct output from the following lines in reg-tests-2.R: x <- c("a", NA, "b") factor(x) factor(x, exclude="") The solution (kludgy, but the whole concept is kludgy) is to forward R_print.na_string and R_print.na_string_noquote with the other "roots" in RunGenCollect (after the comment /* forward all roots */). Radford Neal

> 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] L...

...nargs = 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...

...nargs = 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...

...EF988D: Rf_eval (eval.c:507) ==25398== Address 0x8F46010 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...

I'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_GEN...

...p=0x94723a8) at 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, a...

...or a HTML browser 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_du...

...IGWINCH, Window 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...

...r (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...

...2.R: > x <- c("a", NA, "b") > factor(x) > factor(x, exclude="") > The solution (kludgy, but the whole concept is kludgy) is > to forward R_print.na_string and R_print.na_string_noquote > with the other "roots" in RunGenCollect (after the comment > /* forward all roots */). > Radford Neal "Interesting" ... .. more serioulsy: Thank you, Radford! As this about garbage collection, I found I can pretty well reproduce the problem via something like x <- c("a", NA, "b"...

...lue ; 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. > > &gt...

If anyone has a few extra CPU cycles to spare, I'd appreciate it if you could verify a problem that I have encountered. Run the code below and tell me if it crashes your R before completion. library(lme4) data(bdf) dump<-sapply( 1:50000, function(i) { fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf, random = ~ IQ.ver.cen | schoolNR); cat("