Thank you. Using the -curl option got me further. Here is the output for the MacOS now with -checkall. There are still several failures it seems.
One thing I am especially confused about is "consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace" as I have confirmed with echo $DYLD_LIBRARY_PATH that it is set to that (and there is an export line in my .bashrc that is already there exporting that same path).
Thanks!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.4.0
version: Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 20
apparent login shell: sh
shell RC file: .profile (does not exist)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/jamie/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 3 2020
: AFNI_20.1.13 'Otho'
AFNI_version.txt : AFNI_20.1.13, macos_10.12_local, Jun 03 2020
which python : /Users/tlab/miniconda3/bin/python
python version : 3.7.6
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/jamie/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 4
/Users/tlab/miniconda3/bin/python3.7
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/Users/jamie/anaconda3/bin/python3.6
/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 : 4
/Users/tlab/miniconda3/bin/python3.7
/Users/jamie/anaconda3/bin/python3.6
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6
/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/jamie/abin/R_io.so':
dlopen(/Users/jamie/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/jamie/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 3.6.0 or later, but libR.dylib provides version 3.5.0
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
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- 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/python2 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python2.7 (sym link to /Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /Users/tlab/miniconda3/bin:/Users/tlab/miniconda3/condabin:/Users/jamie/mrtrix3/bin:/usr/local/opt/qt/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/Users/jamie/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/Users/jamie/dinifti:/Volumes/Documents/DTI Portfolio/shell-scripts:/Users/jamie/antsbin/bin:/usr/local/spharm:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MRIcron:/Library/TeX/texbin:/opt/X11/bin:/Users/jamie/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under /Users/tlab
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under /Users/tlab
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under /Users/tlab
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under /Users/tlab
atlas : found TT_N27+tlrc under /Users/jamie/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Error: Running Homebrew as root is extremely dangerous and no longer supported.
-- 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: =========================
* login shell 'sh', trusting user to translate code examples from 'tcsh'
* shell sh : MISSING login shell setup file .profile
* have python version 3.7.6, some programs need 2.7.x
* AFNI programs show FAILURE
* OS X version might be old
* consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
