Hi Ben, Thanks for the bug report.
On 20 August 2007 at 01:48, Ben Goodrich wrote: | -----BEGIN PGP SIGNED MESSAGE----- | Hash: SHA1 | | Package: r-base-core | Version: 2.5.1-2 | Severity: important | | Hi Dirk, | | To replicate this problem on a amd64 machine, do | | cd /tmp | echo "log(1)" > crash.R | R -d "valgrind --verbose --db-attach=yes" --vanilla < crash.R IIRC the last time I used valgrind I also didn't always get it to terminate cleanly. I am not sure if this is necessarily R's fault. So let me CC Peter on this so that I can borrow from his expertise on R, amd64 and valgrind: Pete, any thoughts as this how ? | The last line is adapted from | | http://cran.r-project.org/doc/manuals/R-exts.html#Using-valgrind | | I do not experience the following problem on a 32bit machine with Debian | unstable, nor on a RHEL 64bit server (R 2.5.1 in both cases). But it | happens on this amd64 machine whether I use r-base from unstable or | build the source from CRAN. Anyway, it prevents using R with valgrind to | investigate memory problems with contributed packages. I could of course also be a valgrind bug on Debian. Your RHEL success is a counter example suggesting that it may not be R's fault. Dirk | | ==16581== Memcheck, a memory error detector. | ==16581== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al. | ==16581== Using LibVEX rev 1732, a library for dynamic binary translation. | ==16581== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP. | ==16581== Using valgrind-3.2.3-Debian, a dynamic binary instrumentation | framework. | ==16581== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al. | ==16581== | - --16581-- Command line | - --16581-- /usr/lib/R/bin/exec/R | - --16581-- --vanilla | - --16581-- Startup, with flags: | - --16581-- --suppressions=/usr/lib/valgrind/debian-libc6-dbg.supp | - --16581-- --verbose | - --16581-- --db-attach=yes | - --16581-- Contents of /proc/version: | - --16581-- Linux version 2.6.22.2-slh64-smp-1 ([EMAIL PROTECTED]) (gcc | version 4.1.3 20070718 | (prerelease) (Debian 4.1.2-14)) #1 SMP PREEMPT Fri Aug 10 17:19:56 CEST 2007 | - --16581-- Arch and hwcaps: AMD64, amd64-sse2 | - --16581-- Page sizes: currently 4096, max supported 4096 | - --16581-- Valgrind library directory: /usr/lib/valgrind | - --16581-- Reading syms from /usr/lib/R/bin/exec/R (0x400000) | - --16581-- object doesn't have a symbol table | - --16581-- Reading syms from /lib/ld-2.6.1.so (0x4000000) | - --16581-- Reading debug info from /lib/ld-2.6.1.so... | - --16581-- ... CRC mismatch (computed 635CD41D wanted 1F3B7BF3) | - --16581-- Reading debug info from /usr/lib/debug/lib/ld-2.6.1.so... | - --16581-- Reading syms from /usr/lib/valgrind/amd64-linux/memcheck | (0x38000000) | - --16581-- object doesn't have a dynamic symbol table | - --16581-- Reading suppressions file: | /usr/lib/valgrind/debian-libc6-dbg.supp | - --16581-- Reading suppressions file: /usr/lib/valgrind/default.supp | vex amd64->IR: unhandled instruction bytes: 0x66 0x66 0x66 0x66 | ==16581== valgrind: Unrecognised instruction at address 0x4016321. | ==16581== Your program just tried to execute an instruction that Valgrind | ==16581== did not recognise. There are two possible reasons for this. | ==16581== 1. Your program has a bug and erroneously jumped to a non-code | ==16581== location. If you are running Memcheck and you just saw a | ==16581== warning about a bad jump, it's probably your program's fault. | ==16581== 2. The instruction is legitimate but Valgrind doesn't handle it, | ==16581== i.e. it's Valgrind's fault. If you think this is the case or | ==16581== you are not sure, please let us know and we'll try to fix it. | ==16581== Either way, Valgrind will now raise a SIGILL signal which will | ==16581== probably kill your program. | ==16581== | ==16581== Process terminating with default action of signal 4 (SIGILL): | dumping core | ==16581== Illegal opcode at address 0x4016321 | ==16581== at 0x4016321: memcpy (in /lib/ld-2.6.1.so) | ==16581== by 0x400466E: dl_main (in /lib/ld-2.6.1.so) | ==16581== by 0x4014457: _dl_sysdep_start (in /lib/ld-2.6.1.so) | ==16581== by 0x400230A: _dl_start (in /lib/ld-2.6.1.so) | ==16581== by 0x4000A67: (within /lib/ld-2.6.1.so) | ==16581== | ==16581== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- | ==16581== ---- Attach to | debugger ? --- [Return/N/n/Y/y/C/c] ---- ==16581== ---- Attach to | debugger ? --- | [Return/N/n/Y/y/C/c] ---- ==16581== ---- Attach to debugger ? --- | [Return/N/n/Y/y/C/c] ---- | ==16581== ---- Attach to debugger ? --- [Return/N/n/Y/y/C/c] ---- | ==16581== ---- Attach to | debugger ? --- [Return/N/n/Y/y/C/c] ---- ==16581== ---- Attach to | debugger ? --- | [Return/N/n/Y/y/C/c] ---- ==16581== | ==16581== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 1 from 1) | - --16581-- | - --16581-- supp: 1 strlen-not-intercepted-early-enough-HACK-5 | ==16581== malloc/free: in use at exit: 0 bytes in 0 blocks. | ==16581== malloc/free: 0 allocs, 0 frees, 0 bytes allocated. | ==16581== | ==16581== All heap blocks were freed -- no leaks are possible. | - --16581-- memcheck: sanity checks: 0 cheap, 1 expensive | - --16581-- memcheck: auxmaps: 0 auxmap entries (0k, 0M) in use | - --16581-- memcheck: auxmaps: 0 searches, 0 comparisons | - --16581-- memcheck: SMs: n_issued = 7 (112k, 0M) | - --16581-- memcheck: SMs: n_deissued = 0 (0k, 0M) | - --16581-- memcheck: SMs: max_noaccess = 524287 (8388592k, 8191M) | - --16581-- memcheck: SMs: max_undefined = 0 (0k, 0M) | - --16581-- memcheck: SMs: max_defined = 1 (16k, 0M) | - --16581-- memcheck: SMs: max_non_DSM = 7 (112k, 0M) | - --16581-- memcheck: max sec V bit nodes: 0 (0k, 0M) | - --16581-- memcheck: set_sec_vbits8 calls: 0 (new: 0, updates: 0) | - --16581-- memcheck: max shadow mem size: 4256k, 4M | - --16581-- translate: fast SP updates identified: 149 ( 88.6%) | - --16581-- translate: generic_known SP updates identified: 10 ( 5.9%) | - --16581-- translate: generic_unknown SP updates identified: 9 ( 5.3%) | - --16581-- tt/tc: 774 tt lookups requiring 773 probes | - --16581-- tt/tc: 774 fast-cache updates, 2 flushes | - --16581-- transtab: new 387 (8,365 -> 144,072; ratio 172:10) | [0 scs] | - --16581-- transtab: dumped 0 (0 -> ??) | - --16581-- transtab: discarded 0 (0 -> ??) | - --16581-- scheduler: 1,142 jumps (bb entries). | - --16581-- scheduler: 0/393 major/minor sched events. | - --16581-- sanity: 1 cheap, 1 expensive checks. | - --16581-- exectx: 30,011 lists, 1 contexts (avg 0 per list) | - --16581-- exectx: 1 searches, 0 full compares (0 per 1000) | - --16581-- exectx: 0 cmp2, 0 cmp4, 0 cmpAll | Illegal instruction | | | - -- System Information: | Debian Release: lenny/sid | APT prefers unstable | APT policy: (500, 'unstable') | Architecture: amd64 (x86_64) | | Kernel: Linux 2.6.22.2-slh64-smp-1 (SMP w/2 CPU cores; PREEMPT) | Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) | Shell: /bin/sh linked to /bin/bash | | Versions of packages r-base-core depends on: | ii libbz2-1.0 1.0.3-7 high-quality block-sorting | file co | ii libc6 2.6.1-1 GNU C Library: Shared libraries | ii libgcc1 1:4.2.1-2 GCC support library | ii libgfortran2 4.2.1-2 Runtime library for GNU | Fortran ap | ii libice6 2:1.0.3-3 X11 Inter-Client Exchange | library | ii libjpeg62 6b-13 The Independent JPEG | Group's JPEG | ii libpaper-utils 1.1.22 library for handling paper | charact | ii libpcre3 7.2-1 Perl 5 Compatible Regular | Expressi | ii libpng12-0 1.2.15~beta5-2 PNG library - runtime | ii libreadline5 5.2-3 GNU readline and history | libraries | ii libsm6 2:1.0.3-1+b1 X11 Session Management library | ii libx11-6 2:1.0.3-7 X11 client-side library | ii libxt6 1:1.0.5-3 X11 toolkit intrinsics library | ii perl 5.8.8-7 Larry Wall's Practical | Extraction | ii tcl8.4 8.4.15-1 Tcl (the Tool Command | Language) v8 | ii tk8.4 8.4.15-1 Tk toolkit for Tcl and X11, | v8.4 - | ii unzip 5.52-10 De-archiver for .zip files | ii zip 2.32-1 Archiver for .zip files | ii zlib1g 1:1.2.3.3.dfsg-5 compression library - runtime | | Versions of packages r-base-core recommends: | ii r-base-dev 2.5.1-2 GNU R installation of | auxiliary GN | ii r-recommended 2.5.1-2 GNU R collection of | recommended pa | | - -- no debconf information | -----BEGIN PGP SIGNATURE----- | Version: GnuPG v1.4.6 (GNU/Linux) | | iD8DBQFGySsezQDSXIcN85kRAmIUAJ9lpklhtIKrR6p6wdWfCLNCKw9W0gCfenR6 | 532nilxJ7FsLJa16xiU9H4Y= | =NypY | -----END PGP SIGNATURE----- | -- Three out of two people have difficulties with fractions. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". 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