Hi there,
I am trying to install AFNI on a mac mini with macOS Sonoma (14.7.2) with an M2 chip. It may/may not be relevant that this is an NIH machine.
I was able to install AFNI correctly on an admin account but not my regular account. After granting admin privileges to my regular account for the duration of this installation, deleting the older AFNI files on my regular account, and running all the steps for the installation (as given on 1.1.8. macOS 12+ (Apple Silicon/ARM processor/chip: M1, M2, …) — AFNI, SUMA and FATCAT: v25.0.06), the user-level install script is failing.
Here's the content of "out.mac_12_b_user.txt":
set os = `uname -s`
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = `uname -m`
uname -m
if ( 0 ) then
set rver = `R --version | head -n 1 | cut -d ' ' -f 3`
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : arm64
CPU : arm64
echo R ver : 4.3.1
R ver : 4.3.1
echo
defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
if ( ! -f /Users/chholakp2/abin/init_user_dotfiles.py ) then
echo -- skipping install of AFNI anyos_text_atlas
-- skipping install of AFNI anyos_text_atlas
endif
echo ++ setting up user dotfiles
++ setting up user dotfiles
/Users/chholakp2/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/chholakp2/abin
-- good: .tcshrc seems to contain 'source .cshrc'
-- 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 4 dot files
which init_user_dotfiles.py
/Users/chholakp2/abin/init_user_dotfiles.py
if ( 0 ) then
if ( arm64 == x86_64 ) then
set package = macos_13_ARM
endif
echo ++ compiling AFNI package macos_13_ARM
++ compiling AFNI package macos_13_ARM
echo ++ running: build_afni.py -build_root ~/afni_build -package macos_13_ARM
++ running: build_afni.py -build_root ~/afni_build -package macos_13_ARM
build_afni.py -build_root /Users/chholakp2/afni_build -package macos_13_ARM
-- build_afni.py, version 0.14, November 17, 2024
-- current AFNI: AFNI_25.0.06, anyos_text_atlas, Feb 12 2025
-- cleaning old build root dir, /Users/chholakp2/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/chholakp2/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_25.0.06
-- checking out git tag AFNI_25.0.06
-- using repo branch (detached), tag AFNI_25.0.06
-- removing old atlas dir, prev/afni_atlases_dist
-- moving old atlas dir afni_atlases_dist to prev/afni_atlases_dist
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- removing old NiiVue backup, prev/niivue_afni.umd.js
-- moving old niivue niivue_afni.umd.js to prev/niivue_afni.umd.js
-- downloading NiiVue, niivue_afni.umd.js
-- preparing to run 'make' build of package macos_13_ARM
-- copying README files
-- copying Makefile.macos_13_ARM to Makefile
-- building make target 'itall'
-- consider monitoring the build in a separate window with:
cd /Users/chholakp2
tail -f /Users/chholakp2/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
** error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/chholakp2/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 = 1, CONDA_DEFAULT_ENV = base
-- shell/system command history is in:
/Users/chholakp2/afni_build/hist_commands.txt
++ screen text history is in:
/Users/chholakp2/afni_build/hist_messages.txt
rehash
if ( ! 1 ) then
echo -- already have R_LIBS=/Users/chholakp2/sw/R-4.3.1
-- already have R_LIBS=/Users/chholakp2/sw/R-4.3.1
endif
if ( ! -d /Users/chholakp2/sw/R-4.3.1/data.table ) then
echo ++ building R libraries: rPkgsInstall -pkgs ALL
++ building R libraries: rPkgsInstall -pkgs ALL
mkdir -p /Users/chholakp2/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt
** ERROR: Failed to load R_io.so
And, here's the output of afni_system_check:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Fri Nov 15 15:11:49 PST 2024; root:xnu-10063.141.1.702.7~1/RELEASE_ARM64_T6020
distribution: 10.16 (sw_vers 14.7.2)
number of CPUs: 12
user: chholakp2
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.0.06, anyos_text_atlas, Feb 12 2025, local
which python : /Users/chholakp2/anaconda3/bin/python
python version : 3.9.12
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 : 1 (/Users/chholakp2/anaconda3/bin/python3.9)
python2 : 0
python3 : 3
/Users/chholakp2/anaconda3/bin/python3.9
/usr/local/Cellar/python@3.13/3.13.2/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
Warning message:
package ‘data.table’ was built under R version 4.3.3
rPkgsInstall : FAILURE
------------------------ 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
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
_++ module loaded: matplotlib.pyplot
module file : /Users/chholakp2/anaconda3/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.1
++ module loaded: flask
module file : /Users/chholakp2/anaconda3/lib/python3.9/site-packages/flask/__init__.py
flask version : 1.1.2
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.13/3.13.2/Frameworks/Python.framework/Versions/3.13/bin/python3.13)
-------------------------------- env vars --------------------------------
PATH = /Users/chholakp2/anaconda3/bin:/Users/chholakp2/anaconda3/condabin:/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:/Users/chholakp2/abin
PYTHONPATH (sub-shell) =
R_LIBS (sub-shell) = /Users/chholakp2/sw/R-4.3.1
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
CC (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- 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 : /usr/local/bin/brew
brew version : Homebrew 4.4.21
which git : /usr/bin/git
git version : git version 2.39.3 (Apple Git-146)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 15.0.0 (clang-1500.3.9.4)
brew gcc(s) : /usr/local/bin/gcc-14
CommandLineTools SDK : MacOSX14.4.sdk
** consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.82.4/lib/libglib-2.0.dylib
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* 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
* consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
Could you please help me figure out how to proceed with this installation?
Thanks,
Parth
