[Bioc-devel] Segfault/Valgrind/bgx
Ernest Turro
ernest.turro at ic.ac.uk
Sat May 5 17:39:49 CEST 2007
Dear all,
my package ( svn co https://hedgehog.fhcrc.org/bioconductor/trunk/
madman/Rpacks/bgx ) segfaults sometimes. I say sometimes because, for
instance, on lamb1 it doesn't, and on wellington it does, on my own
machine it doesn't - except if I run it through valgrind...). When I
run the code as a standalone binary, there are no segfaults. Anyway,
the problem according to valgrind's stack trace appears to be in
libR.so - not directly in my own C code. I think it occurs when calling:
# bgx/R/mcmc.R:36
# free allocated memory on user interrupt/end of simulation
on.exit(.C("freeBGXMemory", as.integer(out.ind), as.integer
(numberGenesToWatch), PACKAGE = "bgx"))
Specifically, when calling as.integer(numberGenesToWatch).
The relevant part of valgrind's stack trace is below. The full trace
is below that. Does anyone have any ideas? I've been debugging for
quite a while and I really don't know what more to do..
Many thanks!
#######
==15885== Conditional jump or move depends on uninitialised value(s)
==15885== at 0x4105D34: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Use of uninitialised value of size 4
==15885== at 0x4105D44: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4105D44: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x8 is not stack'd, malloc'd or (recently) free'd
*** caught segfault ***
address 0x8, cause 'memory not mapped'
Traceback:
1: as.integer(numberGenesToWatch)
2: mcmc.bgx(pm, mm, samplesets, probesets, numberOfCategories,
categories, unknownProbeSeqs, numberOfUnknownProbeSeqs,
numberOfGenesToWatch, genesToWatch, firstProbeInEachGeneToWatch,
iter, burnin, adaptive, output = output, samplenames = sampleNames
(aData), basepath = basepath)
3: bgx(Dilution, samplesets = c(2, 2), probeAff = FALSE, burnin =
1024, iter = 1024, genes = c(12500:12549), output = "all")
aborting ...
==15885==
==15885== ERROR SUMMARY: 21 errors from 14 contexts (suppressed: 197
from 1)
==15885== malloc/free: in use at exit: 54,925,394 bytes in 20,541
blocks.
==15885== malloc/free: 241,570 allocs, 221,029 frees, 133,688,648
bytes allocated.
==15885== For counts of detected errors, rerun with: -v
==15885== searching for pointers to 20,541 not-freed blocks.
==15885== checked 52,933,860 bytes.
#################
######
###### Full trace below
######
#################
et04 at fh-et04:~/Desktop$ R -d "valgrind --tool=memcheck --leak-
check=full" --vanilla < /usr/local/lib/R/site-library/bgx/R-ex/bgx.R
==15885== Memcheck, a memory error detector.
==15885== Copyright (C) 2002-2006, and GNU GPL'd, by Julian Seward et
al.
==15885== Using LibVEX rev 1658, a library for dynamic binary
translation.
==15885== Copyright (C) 2004-2006, and GNU GPL'd, by OpenWorks LLP.
==15885== Using valgrind-3.2.1-Debian, a dynamic binary
instrumentation framework.
==15885== Copyright (C) 2000-2006, and GNU GPL'd, by Julian Seward et
al.
==15885== For more details, rerun with: -v
==15885==
==15885== Syscall param socketcall.send(msg) points to uninitialised
byte(s)
==15885== at 0x40007F2: (within /lib/ld-2.5.so)
==15885== by 0x440FF66: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x440DE43: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x440E157: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x439CF24: getpwuid_r (in /lib/tls/i686/cmov/
libc-2.5.so)
==15885== by 0x439C867: getpwuid (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4137B13: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== Address 0xBEA56143 is on thread 1's stack
==15885==
==15885== Syscall param socketcall.send(msg) points to uninitialised
byte(s)
==15885== at 0x40007F2: (within /lib/ld-2.5.so)
==15885== by 0x440FF66: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x440E206: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x440E6D7: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x439BA14: getgrgid_r (in /lib/tls/i686/cmov/
libc-2.5.so)
==15885== by 0x439B167: getgrgid (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4137B74: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== Address 0xBEA56112 is on thread 1's stack
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014770: (within /lib/ld-2.5.so)
==15885== by 0x4005B69: (within /lib/ld-2.5.so)
==15885== by 0x4007995: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x5488678 is 40 bytes inside a block of size 43
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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==15885==
==15885== Invalid read of size 4
==15885== at 0x4014787: (within /lib/ld-2.5.so)
==15885== by 0x4005B69: (within /lib/ld-2.5.so)
==15885== by 0x4007995: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x4EBB90C is 44 bytes inside a block of size 47
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014759: (within /lib/ld-2.5.so)
==15885== by 0x4005B69: (within /lib/ld-2.5.so)
==15885== by 0x4007995: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x4A87224 is 36 bytes inside a block of size 39
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
> ### Name: bgx
> ### Title: Fully Bayesian integrated approach to the analysis of
Affymetrix
> ### GeneChip data
> ### Aliases: bgx standalone.bgx
> ### Keywords: manip
>
> ### ** Examples
> library(bgx)
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affy
Loading required package: affyio
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014787: (within /lib/ld-2.5.so)
==15885== by 0x44133D2: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4413639: _dl_sym (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x45EFDE7: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFD72: dlsym (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x42114D6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x404503B: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== Address 0x518DE7C is 12 bytes inside a block of size 14
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4044FFA: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
Loading required package: gcrma
Loading required package: matchprobes
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014743: (within /lib/ld-2.5.so)
==15885== by 0x44133D2: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4413639: _dl_sym (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x45EFDE7: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFD72: dlsym (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x42114D6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x404503B: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== Address 0x4C62ED8 is 16 bytes inside a block of size 19
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4044FFA: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014787: (within /lib/ld-2.5.so)
==15885== by 0x400D2A9: (within /lib/ld-2.5.so)
==15885== by 0x4009812: (within /lib/ld-2.5.so)
==15885== by 0x44133D2: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4413639: _dl_sym (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x45EFDE7: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFD72: dlsym (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x42114D6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x404503B: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x4BF67C4 is 60 bytes inside a block of size 62
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
Loading required package: splines
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014743: (within /lib/ld-2.5.so)
==15885== by 0x4005B69: (within /lib/ld-2.5.so)
==15885== by 0x4007995: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x52573E0 is 48 bytes inside a block of size 50
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014743: (within /lib/ld-2.5.so)
==15885== by 0x400D2A9: (within /lib/ld-2.5.so)
==15885== by 0x4009812: (within /lib/ld-2.5.so)
==15885== by 0x44133D2: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4413639: _dl_sym (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x45EFDE7: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFD72: dlsym (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x42114D6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x404503B: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x52573E0 is 48 bytes inside a block of size 50
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4006EB4: (within /lib/ld-2.5.so)
==15885== by 0x40078D9: (within /lib/ld-2.5.so)
==15885== by 0x4010D94: (within /lib/ld-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x40108ED: (within /lib/ld-2.5.so)
==15885== by 0x45EFC2C: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFB63: dlopen (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x4211515: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4044EB8: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4014770: (within /lib/ld-2.5.so)
==15885== by 0x44133D2: (within /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x4413639: _dl_sym (in /lib/tls/i686/cmov/libc-2.5.so)
==15885== by 0x45EFDE7: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x400CFA5: (within /lib/ld-2.5.so)
==15885== by 0x45F02AB: (within /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x45EFD72: dlsym (in /lib/tls/i686/cmov/libdl-2.5.so)
==15885== by 0x42114D6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x404503B: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== Address 0x4FBD070 is 8 bytes inside a block of size 11
alloc'd
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x4044FFA: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4045517: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
> if(require(affydata) && require(hgu95av2cdf)) {
+ data(Dilution)
+ eset <- bgx(Dilution, samplesets=c(2,2), probeAff=FALSE,
burnin=1024, iter=1024,
+ genes=c(12500:12549), output="all")
+ }
Loading required package: affydata
Loading required package: hgu95av2cdf
Analysing 4 array(s) in 2 condition(s):
- condition 1: 2 array(s)
- condition 2: 2 array(s)
Analysing genes 12500:12549
Starting MCMC simulation...
1024 burnin sweeps completed.
1024 post burn-in sweeps completed.
MCMC duration: 0h 36m 7s
==15885==
==15885== Conditional jump or move depends on uninitialised value(s)
==15885== at 0x4105D34: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Use of uninitialised value of size 4
==15885== at 0x4105D44: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885==
==15885== Invalid read of size 4
==15885== at 0x4105D44: Rf_allocVector (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113194: Rf_usemethod (in /usr/lib/R/lib/libR.so)
==15885== by 0x4113668: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DA74E: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9A1D: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x408C17D: Rf_endcontext (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCEDF: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== Address 0x8 is not stack'd, malloc'd or (recently) free'd
*** caught segfault ***
address 0x8, cause 'memory not mapped'
Traceback:
1: as.integer(numberGenesToWatch)
2: mcmc.bgx(pm, mm, samplesets, probesets, numberOfCategories,
categories, unknownProbeSeqs, numberOfUnknownProbeSeqs,
numberOfGenesToWatch, genesToWatch, firstProbeInEachGeneToWatch,
iter, burnin, adaptive, output = output, samplenames = sampleNames
(aData), basepath = basepath)
3: bgx(Dilution, samplesets = c(2, 2), probeAff = FALSE, burnin =
1024, iter = 1024, genes = c(12500:12549), output = "all")
aborting ...
==15885==
==15885== ERROR SUMMARY: 21 errors from 14 contexts (suppressed: 197
from 1)
==15885== malloc/free: in use at exit: 54,925,394 bytes in 20,541
blocks.
==15885== malloc/free: 241,570 allocs, 221,029 frees, 133,688,648
bytes allocated.
==15885== For counts of detected errors, rerun with: -v
==15885== searching for pointers to 20,541 not-freed blocks.
==15885== checked 52,933,860 bytes.
==15885==
==15885==
==15885== 88 bytes in 22 blocks are definitely lost in loss record 27
of 64
==15885== at 0x4021620: malloc (vg_replace_malloc.c:149)
==15885== by 0x40216AA: realloc (vg_replace_malloc.c:306)
==15885== by 0x417F049: (within /usr/lib/R/lib/libR.so)
==15885== by 0x417F1B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4180C62: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4180DE1: (within /usr/lib/R/lib/libR.so)
==15885== by 0x4181716: (within /usr/lib/R/lib/libR.so)
==15885== by 0x406A73F: (within /usr/lib/R/lib/libR.so)
==15885== by 0x411030D: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DB986: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885==
==15885==
==15885== 556 bytes in 1 blocks are possibly lost in loss record 32
of 64
==15885== at 0x4021A55: operator new[](unsigned)
(vg_replace_malloc.c:195)
==15885== by 0x637A121: bgx (bgx.cc:263)
==15885== by 0x40AD099: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9BBA: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885==
==15885==
==15885== 572 bytes in 1 blocks are possibly lost in loss record 33
of 64
==15885== at 0x4021A55: operator new[](unsigned)
(vg_replace_malloc.c:195)
==15885== by 0x6379CDF: bgx (bgx.cc:249)
==15885== by 0x40AD099: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9BBA: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885==
==15885==
==15885== 1,108 bytes in 1 blocks are possibly lost in loss record 40
of 64
==15885== at 0x4021A55: operator new[](unsigned)
(vg_replace_malloc.c:195)
==15885== by 0x637A3C4: bgx (bgx.cc:270)
==15885== by 0x40AD099: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9BBA: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DAEE6: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DCF36: Rf_applyClosure (in /usr/lib/R/lib/libR.so)
==15885== by 0x40D97A7: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885== by 0x40DC5B7: (within /usr/lib/R/lib/libR.so)
==15885== by 0x40D9941: Rf_eval (in /usr/lib/R/lib/libR.so)
==15885==
==15885== LEAK SUMMARY:
==15885== definitely lost: 88 bytes in 22 blocks.
==15885== possibly lost: 2,236 bytes in 3 blocks.
==15885== still reachable: 54,923,070 bytes in 20,516 blocks.
==15885== suppressed: 0 bytes in 0 blocks.
==15885== Reachable blocks (those to which a pointer was found) are
not shown.
==15885== To see them, rerun with: --show-reachable=yes
Segmentation fault (core dumped)
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