AFNI build failure on macOS 14.7.4 with M2 chip (glib/gts errors)

Installation Issues
1

Hi AFNI team,

I'm trying to install AFNI on my Mac with the following specs:

  • Chip: Apple M2
  • OS: macOS 14.7.4

I followed the installation instructions, but ran into issues during this step:
tcsh OS_notes.macos_12_ARM_b_user.tcsh

The build failed and AFNI was not installed into ~/abin, so many program tests show as FAILURE.

Main issue:

AFNI programs remain in afni_build and did not move into abin.
The hist_messages.txt in afni_build shows the following error:

** error: failed run_cmd: make AFNI_WHOMADEIT=build LOCAL_CC_PATH=/usr/bin/gcc itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/clementinekung/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:

*** GLIB 1.2.8 or better is required. The latest version of GLIB
*** is always available from ftp://ftp.gtk.org/.
make[2]: *** No rule to make target `clean'. Stop.
make[2]: *** No targets specified and no makefile found. Stop.
error: /Library/Developer/CommandLineTools/usr/bin/ranlib: can't open file: src/.libs/libgts.a (No such file or directory)
cp: src/.libs/libgts.a: No such file or directory
make[1]: *** [libgts.a] Error 1
cp: SUMA/libgts.a: No such file or directory
cp: SUMA/libgts.a: No such file or directory
make: *** [libgts.a] Error 1

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

below are the message with anfi_check_installation.py

-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Thu Dec 19 20:55:26 PST 2024; root:xnu-10063.141.1.703.2~1/RELEASE_ARM64_T8112
distribution: 14.7.4
number of CPUs: 8
user: clementinekung
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.1.13, anyos_text_atlas, Jun 12 2025, local
which python : /Users/clementinekung/miniconda3/bin/python
python version : 3.12.2
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)

instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 2
/Users/clementinekung/miniconda3/bin/python3.12
/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/bin/python3.13
python2 : 0
python3 : 3
/Users/clementinekung/miniconda3/bin/python3.12
/opt/homebrew/Cellar/python@3.13/3.13.5/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/usr/bin/python3

testing ability to start various programs...
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
build_afni.py : success
uber_subject.py : success
3dMVM : FAILURE

rPkgsInstall         : FAILURE

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

which tcsh : /opt/homebrew/bin/tcsh
tcsh version : 6.24.15
which Xvfb : /opt/X11/bin/Xvfb

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

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

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

++ module loaded: matplotlib.pyplot
module file : /Users/clementinekung/miniconda3/lib/python3.12/site-packages/matplotlib/pyplot.py
matplotlib version : 3.9.2

** failed to load module flask
-- flask is not required, but is desirable

** failed to load module flask_cors
-- flask_cors is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /Users/clementinekung/fsl/share/fsl/bin:/Users/clementinekung/fsl/share/fsl/bin:/Users/clementinekung/miniconda3/bin:/Users/clementinekung/miniconda3/condabin:/opt/ants/bin:/Library/Frameworks/GStreamer.framework/Versions/1.0/bin:/Users/clementinekung/Library/Python/3.11/bin:/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:/opt/X11/bin:/opt/homebrew/opt/python/libexec/bin:/Users/clementinekung/abin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/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

PYTHONPATH =
R_LIBS = /Users/clementinekung/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 = 1
CONDA_DEFAULT_ENV = base
CC =
HOMEBREW_PREFIX = /opt/homebrew

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

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

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

-- good: .cshrc seems to contain 'source .tcshrc'
-- considered operations: path, apsearch

-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

no modifications needed across 3 dot files

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc

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

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.5.6

which git : /usr/bin/git
git version : git version 2.39.5 (Apple Git-154)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 16.0.0 (clang-1600.0.26.6)

brew gcc(s) : /opt/homebrew/bin/gcc-13
/opt/homebrew/bin/gcc-15
CommandLineTools SDK : MacOSX15.2.sdk

========================= summary, please fix: =========================

  • just be aware: login shell 'zsh', but our code examples use 'tcsh'
  • missing program: afni
  • failure under initial "AFNI and related program tests"
  • AFNI programs show FAILURE
  • missing R packages (see rPkgsInstall)
  • insufficient data for AFNI bootcamp
    (see "Prepare for Bootcamp" on install pages)
  • possibly missing atlases
2

Hello,

To be sure, do you have glib and pkg-config installed? I would expect so after running the OS_notes commands.

brew install glib pkg-config

And are you initializing the shell for homebrew?

cd
grep -d skip shellenv .??*

Thanks,
-rick