Re: [Rd] View() segfaulting ...
On Wed, 24 Apr 2024 19:35:42 -0400 Ben Bolker wrote: > I'm using bleeding-edge R-devel, so maybe my build is weird. Can > anyone else reproduce this? > >View() seems to crash on just about anything. Not for me, sorry. If you have a sufficiently new processor, you can use `rr` [*] to capture the crash, set a breakpoint in in_R_X11_dataviewer and rewind, then set a watchpoint on the stack canary and run the program forward again: https://www.redhat.com/en/blog/debugging-stack-protector-failures If you can't locate the canary, try setting watchpoints on large local variables. Without `rr`, the procedure is probably the same, but without rewinding: set a breakpoint in in_R_X11_dataviewer, set some watchpoints, see if they fire when they shouldn't, start from scratch if you get past the watchpoints and the process crashes. I think that that either an object file didn't get rebuilt when it should have, or a shared library used by something downstream from View() got an ABI-breaking update. If this still reproduces with a clean rebuild of R, it's definitely worth investigating further, perhaps using AddressSanitizer. Valgrind may be lacking the information about the stack canary and thus failing to distinguish between overwriting the canary and normal access to a stack variable via a pointer. -- Best regards, Ivan [*] https://rr-project.org/ Edit distance of one from the domain name of the R project! Use rr replay -g $EVENT_NUMBER to debug past the initial execve() from the shell wrapper: https://github.com/rr-debugger/rr/wiki/FAQ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] View() segfaulting ...
As suggested by Josh Ulrich, here's what I get when running under valgrind. $ R -d valgrind ==218120== Memcheck, a memory error detector ==218120== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==218120== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==218120== Command: /usr/local/lib/R/bin/exec/R ==218120== R Under development (unstable) (2024-04-24 r86483) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. gcoto> gctorture(TRUE) > View(1:3) *** stack smashing detected ***: terminated ==218120== ==218120== Process terminating with default action of signal 6 (SIGABRT) ==218120==at 0x4D619FC: __pthread_kill_implementation (pthread_kill.c:44) ==218120==by 0x4D619FC: __pthread_kill_internal (pthread_kill.c:78) ==218120==by 0x4D619FC: pthread_kill@@GLIBC_2.34 (pthread_kill.c:89) ==218120==by 0x4D0D475: raise (raise.c:26) ==218120==by 0x4CF37F2: abort (abort.c:79) ==218120==by 0x4D54675: __libc_message (libc_fatal.c:155) ==218120==by 0x4E01599: __fortify_fail (fortify_fail.c:26) ==218120==by 0x4E01565: __stack_chk_fail (stack_chk_fail.c:24) ==218120==by 0x27B686AD: in_R_X11_dataviewer (dataentry.c:540) ==218120==by 0x495C7C7: do_External (dotcode.c:573) ==218120==by 0x499A07F: bcEval_loop (eval.c:8141) ==218120==by 0x49B501C: bcEval (eval.c:7524) ==218120==by 0x49B501C: bcEval (eval.c:7509) ==218120==by 0x49B538A: Rf_eval (eval.c:1167) ==218120==by 0x49B755E: R_execClosure (eval.c:2398) ==218120== ==218120== HEAP SUMMARY: ==218120== in use at exit: 42,061,827 bytes in 9,305 blocks ==218120== total heap usage: 23,905 allocs, 14,600 frees, 66,039,858 bytes allocated ==218120== ==218120== LEAK SUMMARY: ==218120==definitely lost: 0 bytes in 0 blocks ==218120==indirectly lost: 0 bytes in 0 blocks ==218120== possibly lost: 5,868 bytes in 14 blocks ==218120==still reachable: 42,055,959 bytes in 9,291 blocks ==218120== of which reachable via heuristic: ==218120== newarray : 4,264 bytes in 1 blocks ==218120== suppressed: 0 bytes in 0 blocks ==218120== Rerun with --leak-check=full to see details of leaked memory ==218120== ==218120== For lists of detected and suppressed errors, rerun with: -s ==218120== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0) Aborted (core dumped) bolker:~/R$ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] View() segfaulting ...
I'm using bleeding-edge R-devel, so maybe my build is weird. Can anyone else reproduce this? View() seems to crash on just about anything. View(1:3) *** stack smashing detected ***: terminated Aborted (core dumped) If I debug(View) I get to the last line of code with nothing obviously looking pathological: Browse[1]> debug: invisible(.External2(C_dataviewer, x, title)) Browse[1]> x $x [1] "1" "2" "3" Browse[1]> title [1] "Data: 1:3" Browse[1]> *** stack smashing detected ***: terminated Aborted (core dumped) R Under development (unstable) (2024-04-24 r86483) Platform: x86_64-pc-linux-gnu Running under: Pop!_OS 22.04 LTS Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0 locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=en_CA.UTF-8LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C time zone: America/Toronto tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.5.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
