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June 07, 2021 08:49PM
Thank you. Please see below for the output.
Michael

[Michaels-MacBook-Pro-6:~] michaelspilka% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribution: 10.14.5
number of CPUs: 4
apparent login shell: bash (current shell is csh)
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/michaelspilka/abin/afni
afni version : Precompiled binary macos_10.12_local: Apr 16 2021
: AFNI_21.1.02 'Domitian'
AFNI_version.txt : AFNI_21.1.02, macos_10.12_local, Apr 16 2021
which python : /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python
python version : 3.8.8
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/michaelspilka/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/usr/bin/python
python2 : 0
python3 : 2
/Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin/python3.8
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6

** 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/michaelspilka/miniconda3/envs/py38_afni_tiny/lib/python3.8/site-packages/matplotlib/pyplot.py

-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

-------------------------------- env vars --------------------------------
PATH = /Users/michaelspilka/miniconda3/envs/py38_afni_tiny/bin:/Users/michaelspilka/miniconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/workbench/bin_macosx64:/Users/michaelspilka/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace:/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/michaelspilka/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.0_beta4

which brew : /usr/local/bin/brew
brew version : Homebrew 3.1.7

-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
** consider linking /usr/local/Cellar/gcc/10.2.0_4/lib/gcc/10/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.68.1/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 'csh'...
++ 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'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* insufficient data for AFNI bootcamp
Subject Author Posted

APQC output issues Attachments

mjss June 07, 2021 05:35PM

Re: APQC output issues

ptaylor June 07, 2021 05:56PM

Re: APQC output issues

mjss June 07, 2021 08:49PM

Re: APQC output issues

ptaylor June 07, 2021 09:53PM

Re: APQC output issues

mjss June 08, 2021 10:10AM

Re: APQC output issues

mjss June 08, 2021 10:11AM

Re: APQC output issues

mjss June 08, 2021 06:01PM

Re: APQC output issues

ptaylor June 09, 2021 05:02PM

Re: APQC output issues

mjss June 10, 2021 11:49AM

Re: APQC output issues

ptaylor June 10, 2021 06:23PM



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