Hi AFNI Gurus, I am struggling with afni installation on my new Mac Pro M2 air - Sonoma 14.4.1 (23E224). I used 'macos_13_ARM_clang' for the build. This is the output of afni_system_check:
(base) laego@laegodeMacBook-Air ~ % build_afni.py -build_root $HOME/afni_build -package macos_13_ARM_clang
-- current AFNI: AFNI_24.1.11, anyos_text, May 10 2024
-- cleaning old build root dir, /Users/laego/afni_build
-- preparing build_root dir, /Users/laego/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.10
-- checking out git tag AFNI_24.1.10
-- using repo branch (detached), tag AFNI_24.1.10
-- 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_clang
-- copying README files
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'
-- consider monitoring the build in a separate window with:
cd /Users/laego
tail -f /Users/laego/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/laego/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
--------------------------------------------------
>> AFNI_version.h ; \
echo "#undef AFNI_VERSION_PLATFORM" >> AFNI_version.h ; \
echo '#define AFNI_VERSION_PLATFORM "'macos_13_ARM_clang'"' \
>> AFNI_version.h ;
( cd niml/ ; make all 'CC=/opt/homebrew/bin/gcc-13 -arch arm64 -DDARWIN -DARM_M1 -O1 -m64 -Wall -Wno-deprecated-declarations -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC ' ; /bin/mv -f *.o .. ; )
/opt/homebrew/bin/gcc-13 -arch arm64 -DDARWIN -DARM_M1 -O1 -m64 -Wall -Wno-deprecated-declarations -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -I../f2c -c niml_b64.c
make[1]: /opt/homebrew/bin/gcc-13: No such file or directory
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/laego/afni_build/hist_commands.txt
++ screen text history is in:
/Users/laego/afni_build/hist_messages.txt
(base) laego@laegodeMacBook-Air ~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.4.0
version: Darwin Kernel Version 23.4.0: Fri Mar 15 00:19:22 PDT 2024; root:xnu-10063.101.17~1/RELEASE_ARM64_T8112
distribution: 14.4.1
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.1.11, anyos_text, May 10 2024, local
which python : /Users/laego/anaconda3/bin/python
python version : 3.11.5
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/laego/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/bin/python3.12
python2 : 0
python3 : 3
/Users/laego/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.12/3.12.3/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/usr/bin/python3
** have python3 but not python2
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
uber_subject.py : success
3dMVM : FAILURE
Error in dyn.load(ll) :
无法载入共享目标对象‘/Users/laego/abin/R_io.so’：:
dlopen(/Users/laego/abin/R_io.so, 0x0006): tried: '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/laego/abin/R_io.so' (no such file), '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
停止执行
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
tcsh version : 6.21.00
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
无法载入共享目标对象‘/Users/laego/abin/R_io.so’：:
dlopen(/Users/laego/abin/R_io.so, 0x0006): tried: '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/laego/abin/R_io.so' (no such file), '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
停止执行
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /Users/laego/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.4
++ module loaded: flask
module file : /Users/laego/anaconda3/lib/python3.11/site-packages/flask/__init__.py
flask version : 2.2.5
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /Users/laego/anaconda3/bin:/Users/laego/anaconda3/condabin:/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:/Library/Apple/usr/bin:/opt/homebrew/opt/python/libexec/bin:/Users/laego/abin:/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/laego/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- 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 -------------------------------
** failed to parse X version string, ''
** for macos install instructions, see:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html
XQuartz version :
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.0
========================= 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 program: Xvfb
* missing R packages (see rPkgsInstall)
* please run: cp /Users/laego/abin/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* possibly missing atlases
* strange XQuartz version:
* consider installing gcc under homebrew
* consider installing glib under homebrew
Ps： I also have install issues with R-4.3.1: incompatible architecture
The error referred to (R_io.so) in my computer
Error in dyn.load(ll) :
无法载入共享目标对象‘/Users/laego/abin/R_io.so’：:
dlopen(/Users/laego/abin/R_io.so, 0x0006): tried: '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/laego/abin/R_io.so' (no such file), '/Users/laego/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64e' or 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
停止执行
Thanks a lot for your help!