Dear AFNI developers,
I tried installing AFNI on my MacBook Air M3 chip (macOS 15.2) following the guideline here: 1.1.8. macOS 12+ (Apple Silicon/ARM processor/chip: M1, M2, …) — AFNI, SUMA and FATCAT: v25.0.07
I got an error when running the following command:
tcsh OS_notes.macos_12_ARM_b_user.tcsh
which logged the following message:
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/ll/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/ll/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/ll/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/ll/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/ll/afni_build -package macos_13_ARM
-- build_afni.py, version 0.14, November 17, 2024
-- current AFNI: AFNI_25.0.07, anyos_text_atlas, Feb 25 2025
-- cleaning old build root dir, /Users/ll/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/ll/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_25.0.07
-- checking out git tag AFNI_25.0.07
-- using repo branch (detached), tag AFNI_25.0.07
-- 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/ll
tail -f /Users/ll/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/ll/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
--------------------------------------------------
from niml.h:5,
from niml_private.h:4,
from niml_b64.c:1:
/opt/homebrew/Cellar/gcc/14.2.0_1/lib/gcc/current/gcc/aarch64-apple-darwin24/14/include-fixed/_stdio.h:78:10: fatal error: sys/cdefs.h: No such file or directory
78 | #include <sys/cdefs.h>
| ^~~~~~~~~~~~~
compilation terminated.
make[1]: *** [niml_b64.o] Error 1
mv: rename *.o to ../*.o: No such file or directory
make: *** [niml_b64.o] Error 1
--------------------------------------------------
** warning: in conda environment
CONDA_SHLVL = 1, CONDA_DEFAULT_ENV = base
-- shell/system command history is in:
/Users/ll/afni_build/hist_commands.txt
++ screen text history is in:
/Users/ll/afni_build/hist_messages.txt
rehash
if ( ! 1 ) then
echo -- already have R_LIBS=/Users/ll/sw/R-4.3.1
-- already have R_LIBS=/Users/ll/sw/R-4.3.1
endif
if ( ! -d /Users/ll/sw/R-4.3.1/data.table ) then
echo ++ building R libraries: rPkgsInstall -pkgs ALL
++ building R libraries: rPkgsInstall -pkgs ALL
mkdir -p /Users/ll/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt
** ERROR: Failed to load R_io.so
I've tried the suggestions from other threads such as installing gcc@13, but the same error still occurred.
Can you provide some insights on it?
Thank you for the assistance.
Best regards,
Lee Lin