sudden-onset R-related 3dMVM crash

AFNI Message Board
1

Gentlefolk:

I'm generating a null-hypothesis distribution using random permutations of group labels for a project I'm working on with Gang. The approach invokes 3dMVM. Disturbingly, several iterations of permutation go nicely and then all heck breaks loose rendering the following message:

*** caught segfault ***
address 0x0, cause 'invalid permissions'

Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch({ ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return && !quietly) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(data.table)
9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
10: suppressPackageStartupMessages(library(data.table))
11: eval(ei, envir)
12: eval(ei, envir)
13: withVisible(eval(ei, envir))
14: source(find.in.path("lib_dataTable.R"))
15: eval(ei, envir)
16: eval(ei, envir)
17: withVisible(eval(ei, envir))
18: source(first.in.path("AFNIio.R"))
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault

This has happened twice now. I did a full AFNI and R re-installation the first time and it worked for three permutation iterations. Suspiciously, each crash happened around 11:30 p.m. central european time. I suspect some tricksy remote management issues from my university.

Appending output (see below) from running afni_system_check.py -check_all.

Any advice appreciated!!

Paul

-------------------------------- general ---------------------------------
architecture:         64bit Mach-O
cpu type:             arm64
system:               Darwin
release:              25.5.0
version:              Darwin Kernel Version 25.5.0: Tue Jun  9 22:18:58 PDT 2026; root:xnu-12377.121.10~1/RELEASE_ARM64_T6000
distribution:         26.5.2
number of CPUs:       10
user:                 paulhamilton
apparent login shell: zsh
shell RC file:        .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/paulhamilton/abin/afni
afni version         : Precompiled binary macos_13_ARM: Jul  7 2026 
                     : AFNI_26.2.01 'Gordian III'
AFNI_version.txt     : AFNI_26.2.01, macos_13_ARM, Jul 07 2026, build
afnipy version       : AFNI_26.2.01
which python         : /opt/homebrew/opt/python/libexec/bin/python
python version       : 3.14.6
which R              : /usr/local/bin/R
R version            : R version 4.6.1 (aarch64-apple-darwin23)

instances of various programs found in PATH:
    afni    : 1   (/Users/paulhamilton/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/4.6/Resources/bin/R)
    python  : 1   (/opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/bin/python3.14)
    python2 : 0 
    python3 : 2 
      /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/bin/python3.14
      /usr/bin/python3

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    build_afni.py        : success
    uber_subject.py      : success
    3dMVM                : FAILURE
        
         *** caught segfault ***
        address 0x0, cause 'invalid permissions'
        
        Traceback:
         1: dyn.load(file, DLLpath = DLLpath, ...)
         2: library.dynam(lib, package, package.lib)
         3: loadNamespace(package, lib.loc)
         4: doTryCatch(return(expr), name, parentenv, handler)
         5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
         6: tryCatchList(expr, classes, parentenv, handlers)
         7: tryCatch({    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return && !quietly)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
         8: library(data.table)
         9: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
        10: suppressPackageStartupMessages(library(data.table))
        11: eval(ei, envir)
        12: eval(ei, envir)
        13: withVisible(eval(ei, envir))
        14: source(find.in.path("lib_dataTable.R"))
        15: eval(ei, envir)
        16: eval(ei, envir)
        17: withVisible(eval(ei, envir))
        18: source(first.in.path("AFNIio.R"))
        An irrecoverable exception occurred. R is aborting now ...
        Segmentation fault
    rPkgsInstall         : FAILURE
        
         *** caught segfault ***
        address 0x0, cause 'invalid permissions'
        
        Traceback:
         1: .Call("R_SUMA_HistString", ExecName, args, ohist)
         2: AFNI.command.history(ExecName, args, NULL)
         3: read.rPkgsInstall.opts.batch(args, verb = 0)
        An irrecoverable exception occurred. R is aborting now ...
        Segmentation fault

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh           : /bin/tcsh
tcsh version         : 6.21.00
which Xvfb           : /opt/X11/bin/Xvfb

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE
        
         *** caught segfault ***
        address 0x0, cause 'invalid permissions'
        
        Traceback:
         1: .Call("R_SUMA_HistString", ExecName, args, ohist)
         2: AFNI.command.history(ExecName, args, NULL)
         3: read.rPkgsInstall.opts.batch(args, verb = 0)
        An irrecoverable exception occurred. R is aborting now ...
        Segmentation fault

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
   module file : /opt/homebrew/lib/python3.14/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.10.7

** failed to load module flask
-- flask is required

** failed to load module flask_cors
-- flask_cors is required

-------------------------------- env vars --------------------------------
PATH                       = /opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/pkg/env/global/bin:/opt/X11/bin:/usr/local/munki:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/paulhamilton/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/usr/local/gfortran/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH                 = 
R_LIBS                     = /Users/paulhamilton/sw/R-4.3.1
LD_LIBRARY_PATH            = 
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = 
CONDA_SHLVL                = 
CONDA_DEFAULT_ENV          = 
CC                         = 
HOMEBREW_PREFIX            = /opt/homebrew

----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------

    .afnirc                   : found
    .sumarc                   : found
    .afni/help/all_progs.COMP : found

--------- shell startup files ----------

   -- considered operations: path, apsearch
   
   -- note: followers should not need edits, so edit flags should be 0
      (have 0 follower(s), which can be ignored)
   
   no modifications needed across 1 dot files
   
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_data7
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas    : found TT_N27+tlrc  under /Users/paulhamilton/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.5

which brew           : /opt/homebrew/bin/brew
brew version         : Homebrew 6.0.8

which git            : /usr/bin/git
git version          : git version 2.50.1 (Apple Git-155)
which gcc            : /usr/bin/gcc
gcc version          : Apple clang version 21.0.0 (clang-2100.1.1.101)

brew gcc(s)          : /opt/homebrew/bin/gcc-13
                       /opt/homebrew/bin/gcc-16
CommandLineTools SDK : MacOSX26.5.sdk

=========================  summary, please fix:  =========================
*  AFNI programs show FAILURE
*  missing R packages (see rPkgsInstall)
*  python library flask is required
*  python library flask_cors is required
*  insufficient data for AFNI bootcamp
   (see "Prepare for Bootcamp" on install pages)
2

Paul,

I ran into the same compatibility issue on my Mac: R version 4.6.x isn't playing nice with the current version of AFNI.

To fix this, I suggest pointing your environment back to an older, compatible R version (e.g. 4.5.3). You can update your symbolic link by running the following commands (you may need sudo for the /Library directory):

cd /Library/Frameworks/R.framework/Versions/
sudo rm Current
sudo ln -s 4.5xxx Current

In case 4.5xxx isn't already installed on your machine, you will need to download and install that version first.

Once the R path is reverted, go ahead and rebuild AFNI:

build_afni.py -build_root ~/afni_build
afni_system_check.py -check_all

Hopefully, this resolves the issue for you as well. Let me know how it goes.

Gang Chen

3

Thanks much, Gang.

Your fix worked just fine. My actual battle was with my version of R which insists on auto-updating itself and assigning Current to the most recent version of R every night around midnight. Got that fixed, too. Now just letting the permutations pile up. :star_struck:

Paul

4

Ha, the automatic R upgrade explains the mysterious midnight breakdown! Glad to hear the issue is fully resolved now.

Gang Chen

5

Argh. I got cocky and spoke too soon. I assumed that Homebrew auto-updates were the culprit so I added

HOMEBREW_NO_AUTO_UPDATE=1

to my .zshrc file but time went by and version 4.6 showed back up in /Library/Frameworks/R.framework/Versions linked to Current.

I don't have auto-updates turned on for R, either. I'll keep trying to find the culprit but let me know if I'm missing any obvious alternatives? Looking at activity logs on my machine, I see some suspicious looking stuff involving libxpc.dylib happening exactly when the unwanted update to R 4.6 occurs. Will dig more.

Take care,

Paul