Hi,
Yes, here is the full output. Additional information that may be helpful is that we just updated our software to Catalina on our Mac.
Thank you!!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64
distribution: 10.15.7
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/DSNLab/abin/afni
afni version : Precompiled binary macos_10.12_local: Oct 2 2020
: AFNI_20.3.00 'Vespasian'
AFNI_version.txt : AFNI_20.3.00, macos_10.12_local, Oct 02 2020
which python : /usr/local/bin/python
python version : 2.7.3
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) -- "Taking Off Again"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/DSNLab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python2 : 2
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python3 : 1 (/usr/bin/python3)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/DSNLab/abin/R_io.so':
dlopen(/Users/DSNLab/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/DSNLab/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /Library/Frameworks/R.framework/Resources
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** have PyQt4, but cannot load QtCore, QtGui; error is:
**************************************************
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: dlopen(/usr/local/lib/python2.7/site-packages/PyQt4/QtCore.so, 2): Library not loaded: /usr/local/opt/qt@4/lib/QtCore.framework/Versions/4/QtCore
Referenced from: /usr/local/Cellar/pyqt@4/4.12.1_1/lib/python2.7/site-packages/PyQt4/QtCore.so
Reason: image not found
**************************************************
RuntimeError: module compiled against API version 9 but this version of numpy is 7
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python2 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python2.7 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /usr/local/opt/php@7.2/sbin:/usr/local/opt/php@7.2/bin:/usr/local/opt/openssl@1.1/bin:/usr/local/ants/Scripts:/usr/local/ants/bin:/usr/local/fsl/bin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Apple/usr/bin:/opt/ImageMagick/bin:/Users/DSNLab/abin:/Applications/MATLAB_R2016a.app/bin:/Applications/Sublime Text.app/Contents/SharedSupport/bin
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ 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/DSNLab/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.4
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** consider linking /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.66.1/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:/opt/X11/lib/flat_namespace:/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'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* AFNI programs show FAILURE
* check for partial install of PyQt4
* insufficient data for AFNI bootcamp
* consider linking /usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
