I tried to install on a new Mac mini with M2 chip. I run into errors when running the commend "tcsh OS_notes.macos_12_ARM_b_user.tcsh". I run into error at here:
build_afni.py -build_root /Users/li.14492/afni_build -package macos_13_ARM_clang
-- current AFNI: AFNI_24.1.03, anyos_text, Apr 18 2024
-- cleaning old build root dir, /Users/li.14492/afni_build
-- preparing build_root dir, /Users/li.14492/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.03
-- checking out git tag AFNI_24.1.03
-- using repo branch (detached), tag AFNI_24.1.03
-- 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/li.14492/Documents
tail -f /Users/li.14492/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/li.14492/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
--------------------------------------------------
| ~~~~~~^~~
/bin/rm -f pbar_color_defs.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 -c pbar_color_defs.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
In file included from afni.h:11,
from pbar_color_defs.c:1:
imseq.h:20:10: fatal error: Xm/Xm.h: No such file or directory
20 | #include <Xm/Xm.h>
| ^~~~~~~~~
compilation terminated.
make: *** [pbar_color_defs.o] Error 1
--------------------------------------------------
** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base
-- shell/system command history is in:
/Users/li.14492/afni_build/hist_commands.txt
++ screen text history is in:
/Users/li.14492/afni_build/hist_messages.txt
rehash
setenv R_LIBS /Users/li.14492/sw/R-4.3.1
echo export R_LIBS=/Users/li.14492/sw/R-4.3.1
echo export R_LIBS=/Users/li.14492/sw/R-4.3.1
echo setenv R_LIBS /Users/li.14492/sw/R-4.3.1
mkdir -p /Users/li.14492/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt
I also run afni_system_check.py -check_all and have the outputs below:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.3.0
version: Darwin Kernel Version 23.3.0: Wed Dec 20 21:33:31 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T8112
distribution: 14.3.1
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.1.03, anyos_text, Apr 18 2024, local
which python : /opt/anaconda3/bin/python
python version : 3.11.7
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 (/opt/anaconda3/bin/python3.11)
python2 : 0
python3 : 3
/opt/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
setenv: Too many arguments.
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
setenv: Too many arguments.
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /opt/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.0
++ module loaded: flask
module file : /opt/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 = /opt/anaconda3/bin:/opt/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:/opt/X11/bin:/Library/Apple/usr/bin:/Applications/Privileges.app/Contents/Resources:/usr/local/laps:/Users/li.14492/abin
PYTHONPATH =
R_LIBS = /Users/li.14492/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.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 -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.19
========================= 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 R packages (see rPkgsInstall)
* 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
* consider installing gcc under homebrew
* consider installing glib under homebrew
Not sure why it says "consider installing gcc under homebrew" and "consider installing glib under homebrew". I already have them installed with homebrew.
It will be extremely helpful if you can give any advice. Thanks.
I have made some progress and moved the installation forward by a bit, but still fail at installing afni. The current error messages are at below. Will share the entire log files if needed :
I end up installing afni successfully. There are several rounds of error messages / debugs, and they are solved by installing these packages by homebrew: openmotif, libomp and gsl.
The only glitch now is that when I use afni commend in the terminal to open the afni GUI, it shows an error saying
Initializing: X11Error: Can't open display: :0.0.
This can not be solved by setting different display variables in the startup script. I found that for me to open afni GUI, I have to manually open XQuartz first, and then run the afni commend. I didn't have to in the other of my older Mac.
You might want to reboot once, and see if that behavior continues. Sometimes a /tmp/.x11... file needs to be created, but that usually happens when running the afni GUI.
Can you try a reboot, just this one time (and after any XQuartz upgrade/install)?
Then let us know if it persists.
(1) I reboot the Mac, and also made sure that the XQuartz is updated. The issue persist. I can open afni GUI only if I first open XQuartz myself; otherwise, I am not able to open the GUI, with an error message "Initializing: X11Error: Can't open display: :0.0."
(2) I also run into error when trying to open SUMA GUI. I am not able to open suma GUI even if already opened XQuartz. I received error message
suma:
No input specified, loading some toy surfaces...
Use '.' and ',' to cycle between them.
See suma -help for assistance.
trying lame single buffer visual
++ Notice SUMA_XtWarn_handler (SUMA_display.c:4152 @15:04:30):
X11 Warning 1:trying lame single buffer visual
Have 1 X11 warnings so far, see Help-->Message Log if curious.
This notice is shown once for each additional 10 warnings.
Error: no good visual
My current folder doesn't have any surface files. However, in the other of my old Mac, suma gui will still open with a toy surface, but now the GUI does not open at all.
% otool -L ~/abin/afni
/Users/li.14492/abin/afni:
/opt/homebrew/opt/openmotif/lib/libXm.4.dylib (compatibility version 5.0.0, current version 5.4.0)
/opt/homebrew/opt/libxt/lib/libXt.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/homebrew/opt/libxft/lib/libXft.2.dylib (compatibility version 6.0.0, current version 6.8.0)
/opt/homebrew/opt/fontconfig/lib/libfontconfig.1.dylib (compatibility version 14.0.0, current version 14.1.0)
/opt/homebrew/opt/libpng/lib/libpng16.16.dylib (compatibility version 60.0.0, current version 60.0.0)
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/homebrew/opt/libxmu/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/homebrew/opt/libxp/lib/libXp.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current version 16.0.0)
/opt/homebrew/opt/libxext/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/opt/homebrew/opt/libx11/lib/libX11.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 8.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1345.100.2)
To add, I am not able to open suma even after I open XQuartz. I received error messages like this:
bash-3.2$ suma
suma:
No input specified, loading some toy surfaces...
Use '.' and ',' to cycle between them.
See suma -help for assistance.
trying lame single buffer visual
++ Notice SUMA_XtWarn_handler (SUMA_display.c:4152 @16:02:35):
X11 Warning 1:trying lame single buffer visual
Have 1 X11 warnings so far, see Help-->Message Log if curious.
This notice is shown once for each additional 10 warnings.
Error: no good visual
Those directories and permissions under /tmp/.X11-unix seem right. The problem with suma may or may not be related.
Focusing on suma for a moment, what does 'otool -L' show for it?
Also, just to be sure, would you try running suma after completely deactivating conda? I haven't seen a problem like that, but want to be sure.
Were you in a conda environment when you compiled the AFNI package?
regarding suma, if I do 'otool -L' on suma, it shows this:
(base) li.14492@ascpsy-nc304484 analysis_fmri % otool -L /Users/li.14492/abin/suma
/Users/li.14492/abin/suma:
/opt/homebrew/opt/openmotif/lib/libXm.4.dylib (compatibility version 5.0.0, current version 5.4.0)
/opt/homebrew/opt/jpeg-turbo/lib/libjpeg.8.dylib (compatibility version 8.0.0, current version 8.3.2)
/opt/homebrew/opt/libxt/lib/libXt.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/homebrew/opt/libxft/lib/libXft.2.dylib (compatibility version 6.0.0, current version 6.8.0)
/opt/homebrew/opt/fontconfig/lib/libfontconfig.1.dylib (compatibility version 14.0.0, current version 14.1.0)
/opt/homebrew/opt/libpng/lib/libpng16.16.dylib (compatibility version 60.0.0, current version 60.0.0)
/usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
/opt/homebrew/opt/libxmu/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/homebrew/opt/libxp/lib/libXp.6.dylib (compatibility version 9.0.0, current version 9.0.0)
/opt/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current version 16.0.0)
/opt/homebrew/opt/libxext/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/opt/homebrew/opt/libx11/lib/libX11.6.dylib (compatibility version 11.0.0, current version 11.0.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 8.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1345.100.2)
/opt/X11/lib/libGLU.1.dylib (compatibility version 5.0.0, current version 5.1.0)
/opt/X11/lib/libGL.1.dylib (compatibility version 4.0.0, current version 4.0.0)
/opt/homebrew/opt/glib/lib/libglib-2.0.0.dylib (compatibility version 8001.0.0, current version 8001.0.0)
I'm not under conda environment when compiled the AFNI package. But the python version I current use is the one in conda
(base) % which python
/opt/anaconda3/bin/python
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.