Hello,
I need some help with installation. This did not happen when I tried to install on M2 laptop. It also seems like my device is macOS 14? I checked others' post on this installation issue and have updated commandlinetools and install again accordingly, but I still have error messages when I run
tcsh OS_notes.macos_12_ARM_b_user.tcsh
% tcsh OS_notes.macos_12_ARM_b_user.tcsh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 5083 100 5083 0 0 10307 0 --:--:-- --:--:-- --:--:-- 10289
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/ssuhan/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/ssuhan/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/ssuhan/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/ssuhan/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/ssuhan/afni_build -package macos_13_ARM
-- build_afni.py, version 0.14, November 17, 2024
-- current AFNI: AFNI_25.1.11, anyos_text_atlas, May 23 2025
-- preparing build_root dir, /Users/ssuhan/afni_build
-- creating build_root dir, /Users/ssuhan/afni_build
-- running 'git clone' on afni repo ...
(please be patient)
-- have default git tag LAST_TAG, will checkout AFNI_25.1.11
-- checking out git tag AFNI_25.1.11
-- using repo branch (detached), tag AFNI_25.1.11
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- 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/ssuhan
tail -f /Users/ssuhan/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
++ need alternate compiler, trying /opt/homebrew/bin/gcc-15
(if this fails, try passing one via -cc_path)
** error: failed run_cmd: make AFNI_WHOMADEIT=build LOCAL_CC_PATH=/opt/homebrew/bin/gcc-15 itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/ssuhan/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
--------------------------------------------------
vecmat.h:67:18: warning: 'tempA_ivec3' defined but not used [-Wunused-variable]
67 | static THD_ivec3 tempA_ivec3 , tempB_ivec3 ; /* temps for macros below */
| ^~~~~~~~~~~
/bin/rm -f mcw_glob.o
/opt/homebrew/bin/gcc-15 -arch arm64 -DDARWIN -DARM_M1 -O1 -m64 -Wall -Wno-deprecated-declarations -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -c mcw_glob.c -I. -I/opt/homebrew/include -I/opt/X11/include -I/usr/include -Icoxplot -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -Ileej3 -DHAVE_ZLIB -DHAVE_GIFTI -If2c
mcw_glob.c: In function 'afni_glob':
mcw_glob.c:342:23: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(char *, int)' [-Wincompatible-pointer-types]
342 | pglob->gl_errfunc = errfunc;
| ^
make: *** [mcw_glob.o] Error 1
--------------------------------------------------
** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base
-- shell/system command history is in:
/Users/ssuhan/afni_build/hist_commands.txt
++ screen text history is in:
/Users/ssuhan/afni_build/hist_messages.txt
rehash
if ( ! 0 ) then
echo ++ setting R_LIBS=/Users/ssuhan/sw/R-4.3.1
++ setting R_LIBS=/Users/ssuhan/sw/R-4.3.1
setenv R_LIBS /Users/ssuhan/sw/R-4.3.1
echo export R_LIBS=/Users/ssuhan/sw/R-4.3.1
echo export R_LIBS=/Users/ssuhan/sw/R-4.3.1
echo setenv R_LIBS /Users/ssuhan/sw/R-4.3.1
else
if ( ! -d /Users/ssuhan/sw/R-4.3.1/data.table ) then
echo ++ building R libraries: rPkgsInstall -pkgs ALL
++ building R libraries: rPkgsInstall -pkgs ALL
mkdir -p /Users/ssuhan/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt
** ERROR: Failed to load R_io.so
Thank you!