Hi AFNI team,
I am trying to install AFNI on an M1 Macbook Air. I followed all of the instructions here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_macOS_12_Silicon.html. Here is the terminal output from the final step:
(base) ian@Ians-MacBook-Air-2 ~ % 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 3324 100 3324 0 0 12928 0 --:--:-- --:--:-- --:--:-- 13035
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
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 50203 100 50203 0 0 107k 0 --:--:-- --:--:-- --:--:-- 107k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/ian/abin
-- running @update.afni.binaries version 3.22, May 5, 2023
-- no current AFNI package found in path...
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f
-- attempting to install package anyos_text_atlas under
install dir: /Users/ian/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 139 0 --:--:-- --:--:-- --:--:-- 140
++ update needed, installing...
++ downloading full package: curl -O -f anyos_text_atlas.tgz ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 89.9M 100 89.9M 0 0 8340k 0 0:00:11 0:00:11 --:--:-- 8526k
++ extracting package anyos_text_atlas.tgz...
++ syncing new binaries...
done, yay (binaries are under /Users/ian/abin)
/Users/ian/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/ian/abin
-- no .cshrc, will create one as a follower of .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)
dot file mods : want 6 modifications across 4 files:
file path flatdir apsearch follower
.bashrc 1 0 1 0
.zshrc 1 0 1 0
.cshrc 0 0 0 1
.tcshrc 1 0 1 0
-- file .bashrc does not yet exist to back up
-- updated dot file .bashrc
-- backing up .zshrc to .zshrc.adot.bak
-- updated dot file .zshrc
-- file .cshrc does not yet exist to back up
-- updated dot file .cshrc
-- backing up .tcshrc to .tcshrc.adot.bak
-- updated dot file .tcshrc
source ~/.cshrc
source /Users/ian/.tcshrc
if ( -f /Users/ian/anaconda3/etc/profile.d/conda.csh ) then
source /Users/ian/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/ian/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/ian/anaconda3
setenv _CONDA_EXE /Users/ian/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/ian/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/ian/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/ian/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/ian/anaconda3/bin
alias conda source /Users/ian/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/ian/anaconda3/bin:/Users/ian/anaconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/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:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/ian/abin
if ( 1 ) then
if ( != ) then
endif
if ( arm64 == x86_64 ) then
set package = macos_13_ARM_clang
endif
build_afni.py -build_root /Users/ian/afni_build -package macos_13_ARM_clang
-- current AFNI: AFNI_23.2.12, anyos_text, Sep 29 2023
-- preparing build_root dir, /Users/ian/afni_build
-- creating build_root dir, /Users/ian/afni_build
-- running 'git clone' on afni repo ...
(please be patient)
-- have default git tag LAST_TAG, will checkout AFNI_23.2.12
-- checking out git tag AFNI_23.2.12
-- using repo branch (detached), tag AFNI_23.2.12
-- 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_clang
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'
++ building ...
consider monitoring the build in a separate window with:
cd /Users/ian
tail -f /Users/ian/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
** error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
** error:
-- status: building FAILURE
see 'make' log file /Users/ian/afni_build/build_src/log_make.txt
-- shell/system command history is in:
/Users/ian/afni_build/hist_commands.txt
++ screen text history is in:
/Users/ian/afni_build/hist_messages.txt
rsync -av /Users/ian/afni_build/build_src/macos_13_ARM_clang/ /Users/ian/abin/
building file list ... rsync: link_stat "/Users/ian/afni_build/build_src/macos_13_ARM_clang/." failed: No such file or directory (2)
done
sent 29 bytes received 20 bytes 98.00 bytes/sec
total size is 0 speedup is 0.00
rsync error: some files could not be transferred (code 23) at /AppleInternal/Library/BuildRoots/d9889869-120b-11ee-b796-7a03568b17ac/Library/Caches/com.apple.xbs/Sources/rsync/rsync/main.c(996) [sender=2.6.9]
I can also send the 'make' log file but it seems too big to post here.
Sincerely,
Ian
