Hi RIck
okay i've rebooted and adjusted some .bashrc and .cshrc text and now both afni and suma open. yay. however when i open afni, and as it opens (during splash screens etc), i get this large printout to the terminal:
[MacBook-Pro:~] torrisi% afni
Precompiled binary macos_10.12_local: Jun 30 2020 (Version AFNI_20.1.18 'Otho')
** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to SM Laconte for great efforts
Initializing: X11[The X.Org Foundation v 11804000].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++
. Widgets...... Input files:
** Searching subdirectories of './' for data+./AFNI_data5/
session # 1 = ./AFNI_data5/ ==> 3 datasets+./abin/
session # 2 = ./abin/ ==> 54 datasets
dataset count = 57
Time series = 0 files readfind: .//Library/Application Support/CallHistoryTransactions: Operation not permitted
find: .//Library/Application Support/com.apple.sharedfilelist: Operation not permitted
find: .//Library/Application Support/com.apple.TCC: Operation not permitted
find: .//Library/Application Support/FileProvider: Operation not permitted
find: .//Library/Application Support/AddressBook: Operation not permitted
find: .//Library/Application Support/CallHistoryDB: Operation not permitted
find: .//Library/Autosave Information: Operation not permitted
find: .//Library/IdentityServices: Operation not permitted
find: .//Library/Calendars: Operation not permitted
find: .//Library/Messages: Operation not permitted
find: .//Library/HomeKit: Operation not permitted
find: .//Library/Sharing: Operation not permitted
find: .//Library/Mail: Operation not permitted
find: .//Library/Safari: Operation not permitted
find: .//Library/Suggestions: Operation not permitted
find: .//Library/Containers/com.apple.VoiceMemos: Operation not permitted
find: .//Library/Containers/com.apple.archiveutility: Operation not permitted
find: .//Library/Containers/com.apple.Home: Operation not permitted
find: .//Library/Containers/com.apple.Safari: Operation not permitted
find: .//Library/Containers/com.apple.iChat: Operation not permitted
find: .//Library/Containers/com.apple.CloudDocs.MobileDocumentsFileProvider: Operation not permitted
find: .//Library/Containers/com.apple.mail: Operation not permitted
find: .//Library/Containers/com.apple.news: Operation not permitted
find: .//Library/Containers/com.apple.stocks: Operation not permitted
find: .//Library/PersonalizationPortrait: Operation not permitted
find: .//Library/Metadata/CoreSpotlight: Operation not permitted
find: .//Library/Reminders: Operation not permitted
find: .//Library/Cookies: Operation not permitted
find: .//Library/Caches/com.apple.HomeKit.configurations: Operation not permitted
find: .//Library/Caches/CloudKit: Operation not permitted
find: .//Library/Caches/com.apple.ap.adprivacyd: Operation not permitted
find: .//.Trash: Operation not permitted
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
** ERROR: Table: can't open file
find: ./Library//Application Support/CallHistoryTransactions: Operation not permitted
find: ./Library//Application Support/com.apple.sharedfilelist: Operation not permitted
find: ./Library//Application Support/com.apple.TCC: Operation not permitted
find: ./Library//Application Support/FileProvider: Operation not permitted
find: ./Library//Application Support/AddressBook: Operation not permitted
find: ./Library//Application Support/CallHistoryDB: Operation not permitted
find: ./Library//Autosave Information: Operation not permitted
find: ./Library//IdentityServices: Operation not permitted
find: ./Library//Calendars: Operation not permitted
find: ./Library//Messages: Operation not permitted
find: ./Library//HomeKit: Operation not permitted
find: ./Library//Sharing: Operation not permitted
find: ./Library//Mail: Operation not permitted
find: ./Library//Safari: Operation not permitted
find: ./Library//Suggestions: Operation not permitted
find: ./Library//Containers/com.apple.VoiceMemos: Operation not permitted
find: ./Library//Containers/com.apple.archiveutility: Operation not permitted
find: ./Library//Containers/com.apple.Home: Operation not permitted
find: ./Library//Containers/com.apple.Safari: Operation not permitted
find: ./Library//Containers/com.apple.iChat: Operation not permitted
find: ./Library//Containers/com.apple.CloudDocs.MobileDocumentsFileProvider: Operation not permitted
find: ./Library//Containers/com.apple.mail: Operation not permitted
find: ./Library//Containers/com.apple.news: Operation not permitted
find: ./Library//Containers/com.apple.stocks: Operation not permitted
find: ./Library//PersonalizationPortrait: Operation not permitted
find: ./Library//Metadata/CoreSpotlight: Operation not permitted
find: ./Library//Reminders: Operation not permitted
find: ./Library//Cookies: Operation not permitted
find: ./Library//Caches/com.apple.HomeKit.configurations: Operation not permitted
find: ./Library//Caches/CloudKit: Operation not permitted
find: ./Library//Caches/com.apple.ap.adprivacyd: Operation not permitted
.[tc]sv data = 28 files read
Path(s) to be searched for plugins:
/Users/torrisi/abin /Users/torrisi/abin/../lib
NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEX
NLfit & NLerr= Found 30 models
Plugins = 51 libraries read
reading s620_rest_r1+orig(193 million bytes)....++ AFNI is detached from terminal.
[MacBook-Pro:~] torrisi% ...........done
if it's not the reason unto itself, there seems to also be an issue with my R installs. here's my system check output now:
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 (current shell is csh)
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 30 2020
: AFNI_20.1.18 'Otho'
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 : 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/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 : found
.afni/help/all_progs.COMP : found
------------------------------ 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 = /Users/torrisi/anaconda/bin:/Users/torrisi/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/torrisi/abin:/Users/torrisi/abin:/Users/torrisi/abin:/sw/bin:/Users/torrisi/abin:/sw/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/torrisi/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under '/opt/X11/lib/flat_namespace'
-- found 'libXt' dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
