thanks Peter and TIA
well if i re-run "xcode-select --install" i just get:
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
and then if i type
softwareupdate --list
it says "No new software available."
the output of afni_system_check.py is clearly a mess:
[MacBook-Pro:~] torrisi% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
:
AFNI_version.txt : AFNI_20.1.18, macos_10.12_local, Jun 30 2020
which python : /usr/bin/python
python version : 2.7.16
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/torrisi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)
testing ability to start various programs...
afni : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/afni
Reason: image not found
suma : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dAllineate
Reason: image not found
3dRSFC : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dRSFC
Reason: image not found
SurfMesh : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/SurfMesh
Reason: image not found
3dClustSim : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dClustSim
Reason: image not found
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/Users/torrisi/abin/R_io.so':
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/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 : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/torrisi/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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/torrisi/abin
------------------------------ OS specific -------------------------------
XQuartz version :
which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* OS X version might be old
