AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
November 09, 2022 09:26AM
Here is the output:

(base) annamynick@Annas-MBP-10 ~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 22.1.0
version: Darwin Kernel Version 22.1.0: Sun Oct 9 20:14:54 PDT 2022; root:xnu-8792.41.9~2/RELEASE_X86_64
distribution: 10.16
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/annamynick/abin/afni
afni version : Precompiled binary macos_10.12_local: Oct 12 2022
: AFNI_22.3.02 'Lucius Verus'
AFNI_version.txt : AFNI_22.3.02, macos_10.12_local, Oct 12 2022
which python : /Users/annamynick/opt/anaconda3/bin/python
python version : 3.7.4
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/annamynick/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/Users/annamynick/opt/anaconda3/bin/python3.7)
python2 : 0
python3 : 3
/Users/annamynick/opt/anaconda3/bin/python3.7
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/usr/bin/python3

** have python3 but not python2

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 : success

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 : /Users/annamynick/opt/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py
matplotlib version : 3.1.1

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /Users/annamynick/opt/anaconda3/bin:/Users/annamynick/opt/anaconda3/condabin:/Users/annamynick/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/annamynick/Library/Python/2.7/bin:/usr/local/share/dotnet:/opt/X11/bin:~/.dotnet/tools:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Users/annamynick/abin:/Users/annamynick/abin:/Users/annamynick/android-sdk-macosx/platform-tools/:/Users/annamynick/android-sdk-macosx/platform-tools/

PYTHONPATH =
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 : found AFNI_data6 under $HOME (1908108M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_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/annamynick/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : /usr/local/Homebrew/Library/Homebrew/os/mac/version.rb:32:in `block in from_symbol': unknown or unsupported macOS version: :dunno (MacOSVersionError)

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
** 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/2.66.2_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 'zsh'...
++ 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

========================= summary, please fix: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
Subject Author Posted

AFNI GUI fails to open following macOS 13 update

annamynick November 08, 2022 02:08PM

Re: AFNI GUI fails to open following macOS 13 update

Peter Molfese November 08, 2022 02:57PM

Re: AFNI GUI fails to open following macOS 13 update

annamynick November 09, 2022 09:26AM

Re: AFNI GUI fails to open following macOS 13 update

Daniel Glen November 09, 2022 10:00AM

Re: AFNI GUI fails to open following macOS 13 update

Peter Molfese November 09, 2022 10:01AM

Re: AFNI GUI fails to open following macOS 13 update

annamynick November 09, 2022 12:05PM