AFNI version info (afni -ver): AFNI_23.2.04
Hello!
I'm running into some issues using 3dMVM. I tried updating my binaries (@update.afni.binaries -d), but it still says "FAILURE" for 3dMVM. For reference, I'm running this on macOS Monterey Version 12.6.5.
This is the output when I run afni_system_check.py -check_all :
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 21.6.0
version: Darwin Kernel Version 21.6.0: Thu Mar 9 20:08:59 PST 2023; root:xnu-8020.240.18.700.8~1/RELEASE_X86_64
distribution: 12.6.5
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macos_10.12_local: Aug 9 2023
: AFNI_23.2.04 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.04, macos_10.12_local, Aug 09 2023, official
which python : /usr/local/bin/python
python version : 3.9.13
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
instances of various programs found in PATH:
afni : 1 (/Users/liuj10/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
python2 : 0
python3 : 2
/usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/liuj10/abin/R_io.so':
dlopen(/Users/liuj10/abin/R_io.so, 0x0006): Symbol not found: (_FcCharSetCopy)
Referenced from: '/opt/X11/lib/libXft.2.dylib'
Expected in: '/opt/X11/lib/libfontconfig.1.dylib'
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
------------------------ 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 : success
R RHOME : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
/usr/local/bin/python3.9 (sym link to /usr/local/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/bin/python3.9)
-------------------------------- env vars --------------------------------
PATH = /usr/local/ANTs/bin/:/Users/liuj10/fsl/share/fsl/bin:/Users/liuj10/fsl/share/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin/:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin/:/opt/X11/bin:/Users/liuj10/abin:/Users/liuj10/abin:/Users/liuj10/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, 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 : found TT_N27+tlrc under /Users/liuj10/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.0_beta4
which brew : /usr/local/bin/brew
brew version : Homebrew 4.0.4
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.72.3/lib/libglib-2.0.dylib
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* python library matplotlib is required
(see AFNI install docs for details)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* consider installing gcc under homebrew
Any ideas for how I can troubleshoot?
Thanks!
Janelle