AFNI does not work on Mac OS 10.15 - SOLVED

EXP.2086 · October 8, 2019, 3:38am

Hi,
AFNI is prevented to start on Mac OS 10.15.

Thanks,
2086

EDIT (rick): solved - see Justin’s post and follow-ups

pmolfese · October 8, 2019, 1:14pm

You need to relax the GateKeeper settings. You can read about it here.

Searching towards the bottom is: “How to open an app that hasn’t been notarized or is from an unidentified developer”.

Generally it takes us a little bit of time to verify everything on a new OS. For production scientific computers, I would recommend waiting some time before upgrading to a new OS release. Other softwares, such as Freesurfer, have been shown to be susceptible to changes in OS version due to dependency changes and will give you different numbers.

EXP.2086 · October 8, 2019, 2:22pm

Hi Peter,

Thanks for your reply and your suggestions.
And the result is that each lib called by AFNI needs to be allowed to run every time starting AFNI, and I haven’t start AFNI successfully yet. Fortunately, it’s not a computer for production.

2086

pmolfese · October 8, 2019, 2:56pm

You can disable gatekeeper entirely.

Run the following command in your terminal: sudo spctl --master-disable

In System Preferences > Security & Privacy > “Allow apps from” > Anywhere.

That should get you the rest of the way. I suppose we could figure out how to sign AFNI apps, but I suspect the communities will offer other workarounds as the install base of 10.15 gets larger.

discoraj · October 18, 2019, 5:52pm

Hi,
A few questions:
What procedure did you use to install afni?
Did you upgrade from 10.14 to 10.15 or is it a clean install?
What shell are you using? get the output from:


echo $0

thanks, Justin

Naveed · October 18, 2019, 8:02pm

I tried a clean install and its failed.
output from echo $0 = -bash

rickr · October 18, 2019, 9:42pm

To be sure, exactly what did you do for a clean install? Did you end up using @update.afni.binaries, for example? What command? Did you use Justin’s app, or follow instructions from a particular web page?

Thanks,

rick

Naveed · October 21, 2019, 1:52pm

This is a new Mac on OS 10.15 and it never had any AFNI installed.
yes update command also failed.
I tried both the app and the instruction, but both failed unfortunately.

jwaltz · October 22, 2019, 6:00pm

Hi-

Now, when I try to run AFNI, I get:

MacBook-Pro-86:BinaryPE jameswaltz$ dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib
Referenced from: /Applications/AFNI/afni
Reason: image not found

When I type “which libfontconfig.1.dylib”, it tells me:

/Applications/AFNI/libfontconfig.1.dylib

How do I tell AFNI to look for that library in the AFNI directory, instead of the X11 directory?

Thanks,

Jim Waltz

ptaylor · October 22, 2019, 9:11pm

Hi, Jim-

There are a couple of possibilities for that. To be able to target more precisely, what is the output of:


afni_system_check.py -check_all

?

–pt

rickr · October 22, 2019, 10:10pm

What is the text output as you run these commands from a terminal window?

cd
curl -O [https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries](https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries)
tcsh @update.afni.binaries -defaults -package macos_10.12_local

Thanks,

rick

Naveed · October 23, 2019, 1:36pm

Hi Rick,

Following is the output.

rt5212m-paed:~ naveed qureshi$ curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 45323 100 45323 0 0 283k 0 --:–:-- --:–:-- --:–:-- 281k
rt5212m-paed:~ naveed qureshi$ tcsh @update.afni.binaries -defaults -package macos_10.12_local
– running @update.afni.binaries version 3.13, September 24, 2019
– no current AFNI package found in path…
– install dir: using default ~/abin
– any downloads will be from https://afni.nimh.nih.gov via curl -O -f

– attempting to install package macos_10.12_local under
install dir: /Users/naveed qureshi/abin…
if: Expression Syntax.
rt5212m-paed:~ naveed qureshi$

rickr · October 23, 2019, 2:01pm

That looks like you are hitting some problem in the script that I am not seeing.

If you do not mind, would you please remove the newly created ‘abin’ directory and re-run the script using the -x option?

tcsh -x @update.afni.binaries -defaults -package macos_10.12_local

If you would prefer, it would be okay to even grab all of the text output and send it to me via email. Either way is good.

Thanks,

rick

Naveed · October 23, 2019, 2:15pm

Hi Rick,
I was able to install using this command
rt5212m-paed:~ naveed qureshi$ tcsh @update.afni.binaries -bindir ABIN -no_recur -defaults -package macos_10.12_local
However R installation in not working now.

rickr · October 23, 2019, 2:23pm

Oh, maybe the recur action pulled an old version. I will see what is under 10.7.

If you don’t mind, would you please move any R issues to a new thread?

If possible, please post the system check output with that post (or mail it).

afni_system_check.py -check_all

Thanks,

rick

Naveed · October 24, 2019, 6:57pm

Hi Rick,
Even It was installed, I still could not run AFNI, neither could I use the system check command.

Naveed

rickr · October 24, 2019, 8:48pm

Hi Naveed,

Open a new terminal window and try again.

Either way, assuming AFNI is under your ~/abin directory, you could try running:

~/abin/afni_system_check.py -check_all

Thanks,

rick

EXP.2086 · October 28, 2019, 3:34pm

Hi Rick,

Here the installation and afni_check log:

Last login: Mon Oct 28 23:24:06 on ttys000
z@Z tmp % tcsh -x ./@update.afni.binaries -local_package macos_10.12_local.tgz -do_extras
set prog = basename $0
basename ./@update.afni.binaries
set hostname = afni.nimh.nih.gov
set hostproto = https://
set hostsite = https://afni.nimh.nih.gov
set sysname = uname -s
uname -s
if ( 0 ) then
goto POST_HIST
set aub_version = 3.7, January 22, 2019
set obsolete_list = ( linux_gcc32 linux_gcc33_64 linux_glibc22 NIH.openSUSE.11.4_64 linux_fedora_21_64 linux_fedora_25_64 solaris29_suncc solaris29_suncc_64 macosx_10.5_Intel_64 macosx_10.6_Intel_64 macosx_10.7_Intel_64 macosx_10.7_local macosx_10.8_gcc macosx_10.8_icc )
set abin =
set package =
set local_package =
set prog_list = ( )
set tmp_dir = .tmp.install
set make_backup = 1
set sys_ok = 0
set system_progs = ( apt-get at cc cpp cmp diff du gcc less man md5sum od passwd perl python scp srm sudo vi vim wc xterm yum )
set show_system_progs = 0
set show_obsoletes = 0
set show_obsoletes_grep = 0
if ( 3 == 0 ) then
set help = 0
endif
set testing = 0
set test_protos = 0
set use_curl = 0
set do_extras = 0
set do_apsearch = 0
set do_dotfiles = 0
set do_recur = 1
set quick = 0
set revert = 0
set cert_verify = 1
set use_curl = 0
set bad_opt =
set ac = 1
while ( 1 < = 3 )
if ( -local_package == -apsearch ) then
if ( -local_package == -bindir ) then
if ( -local_package == -curl ) then
if ( -local_package == -d || -local_package == -defaults ) then
if ( -local_package == -do_dotfiles ) then
if ( -local_package == -do_extras ) then
if ( -local_package == -help ) then
if ( -local_package == -help_sys_progs ) then
if ( -local_package == -hist ) then
if ( -local_package == -local_package ) then
@ ac ++
if ( 2 > 3 ) then
set local_package = macos_10.12_local.tgz
if ( ! -f macos_10.12_local.tgz && -f macos_10.12_local.tgz.tgz ) then
if ( ! -f macos_10.12_local.tgz ) then
else if ( macos_10.12_local.tgz == -package ) then
@ ac ++
end
while ( 3 < = 3 )
if ( -do_extras == -apsearch ) then
if ( -do_extras == -bindir ) then
if ( -do_extras == -curl ) then
if ( -do_extras == -d || -do_extras == -defaults ) then
if ( -do_extras == -do_dotfiles ) then
if ( -do_extras == -do_extras ) then
set do_apsearch = 1
set do_dotfiles = 1
else if ( -do_extras == -help ) then
@ ac ++
end
while ( 4 < = 3 )
set tmpsite = https://afni.nimh.nih.gov
if ( https://afni.nimh.nih.gov != https://afni.nimh.nih.gov ) then
if ( 0 ) then
if ( != && 1 ) then
if ( 0 ) then
echo – running @update.afni.binaries version 3.7, January 22, 2019
– running @update.afni.binaries version 3.7, January 22, 2019
which afni
if ( 1 ) then
echo – no current AFNI package found in path…
– no current AFNI package found in path…
set cur_afni =
else
if ( == ) then
if ( == ) then
echo – install dir: using default ~/abin
– install dir: using default ~/abin
set abin = ~/abin
else
endif
if ( macos_10.12_local.tgz != ) then
if ( != ) then
if ( ! -f macos_10.12_local.tgz ) then
if ( macos_10.12_local.tgz == macos_10.12_local.tgz ) then
set local_package_dir = pwd
pwd
else if ( -d macos_10.12_local.tgz ) then
set package = macos_10.12_local
echo – will install from local package file: macos_10.12_local.tgz
– will install from local package file: macos_10.12_local.tgz
endif
if ( macos_10.12_local == ) then
which wget
set missing_wget = 0
which curl
set missing_curl = 0
if ( 0 ) echo – wget, curl status = 0, 0
if ( 0 && 0 ) then
set get_prog = ( wget )
if ( 0 || 0 ) set get_prog = ( curl -O -f )
if ( ! 1 ) then
echo – any downloads will be from https://afni.nimh.nih.gov via wget
– any downloads will be from https://afni.nimh.nih.gov via wget
echo

if ( macos_10.12_local =~ *.tgz ) set package = macos_10
echo – attempting to install package macos_10.12_local under
– attempting to install package macos_10.12_local under
if ( 0 > 0 ) echo (including only 0 programs)
echo install dir: /Users/z/abin…
install dir: /Users/z/abin…
if ( -d /Users/z/abin ) then
if ( 0 == 1 ) then
echo ++ creating install dir
++ creating install dir
mkdir -pv /Users/z/abin
if ( 0 ) then
echo

sleep 1
endif
set date = date +%Y_%m_%d
date +%Y_%m_%d
set backup_dir = auto_backup.macos_10.12_local
cd /Users/z/abin
if ( ! -w . ) then
set nerr = 0
foreach cprog ( apt-get at cc cpp cmp diff du gcc less man md5sum od passwd perl python scp srm sudo vi vim wc xterm yum )
if ( -e apt-get ) then
end
if ( -e at ) then
end
if ( -e cc ) then
end
if ( -e cpp ) then
end
if ( -e cmp ) then
end
if ( -e diff ) then
end
if ( -e du ) then
end
if ( -e gcc ) then
end
if ( -e less ) then
end
if ( -e man ) then
end
if ( -e md5sum ) then
end
if ( -e od ) then
end
if ( -e passwd ) then
end
if ( -e perl ) then
end
if ( -e python ) then
end
if ( -e scp ) then
end
if ( -e srm ) then
end
if ( -e sudo ) then
end
if ( -e vi ) then
end
if ( -e vim ) then
end
if ( -e wc ) then
end
if ( -e xterm ) then
end
if ( -e yum ) then
end
if ( 0 > 0 && ! 0 ) then
if ( ! 0 && ( -f macos_10.12_local.tgz || -d macos_10.12_local ) ) then
if ( -d .tmp.install ) then
echo ++ working in new temp dir, .tmp.install
++ working in new temp dir, .tmp.install
mkdir .tmp.install
if ( 0 ) then
cd .tmp.install
if ( 1 ) then
set temp_prog = tmp.@update.afni.binaries
set retry = 0
set bin_root = https://afni.nimh.nih.gov/pub/dist/bin
set get_package = https://afni.nimh.nih.gov/pub/dist/bin/macos_10.12_local/@update.afni.binaries
echo ++ getting install prog: wget macos_10.12_local/@update.afni.binaries …
++ getting install prog: wget macos_10.12_local/@update.afni.binaries …
echo wget https://afni.nimh.nih.gov/pub/dist/bin/macos_10.12_local/@update.afni.binaries
wget https://afni.nimh.nih.gov/pub/dist/bin/macos_10.12_local/@update.afni.binaries
wget https://afni.nimh.nih.gov/pub/dist/bin/macos_10.12_local/@update.afni.binaries
–2019-10-28 23:26:51-- https://afni.nimh.nih.gov/pub/dist/bin/macos_10.12_local/@update.afni.binaries
Resolving afni.nimh.nih.gov (afni.nimh.nih.gov)… 156.40.187.114
Connecting to afni.nimh.nih.gov (afni.nimh.nih.gov)|156.40.187.114|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: 45323 (44K) [text/plain]
Saving to: ‘@update.afni.binaries’

@update.afni.binari 100%[===================>] 44.26K 80.1KB/s in 0.6s

2019-10-28 23:26:53 (80.1 KB/s) - ‘@update.afni.binaries’ saved [45323/45323]

if ( 0 ) then
grep upgrade the AFNI binaries @update.afni.binaries
if ( 0 ) then
endif
if ( 0 ) then
if ( ! -x @update.afni.binaries ) then
echo – fixing lost permissions on @update.afni.binaries
– fixing lost permissions on @update.afni.binaries
chmod +x @update.afni.binaries
endif
cmp -s @update.afni.binaries …/@update.afni.binaries
if ( 2 ) then
echo ++ using updated @update.afni.binaries, instead…
++ using updated @update.afni.binaries, instead…
echo

if ( -f …/tmp.@update.afni.binaries ) rm -f …/tmp.@update.afni.binaries
mv @update.afni.binaries …/tmp.@update.afni.binaries
cd …
set args = ( -local_package macos_10.12_local.tgz -do_extras )
if ( macos_10.12_local.tgz != ) then
set ind = 1
while ( 1 < 3 )
if ( -local_package == -local_package ) then
@ ind += 1
set args[2] = /Users/z/Downloads/tmp/macos_10.12_local.tgz
break
endif
echo ++ running: tcsh tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
++ running: tcsh tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
tcsh tmp.@update.afni.binaries -no_recur -local_package /Users/z/Downloads/tmp/macos_10.12_local.tgz -do_extras
– running tmp.@update.afni.binaries version 3.13, September 24, 2019
– no current AFNI package found in path…
– install dir: using default ~/abin
– will install from local package file: macos_10.12_local.tgz
– any downloads will be from https://afni.nimh.nih.gov via wget

– attempting to install package macos_10.12_local under
install dir: /Users/z/abin…
– have install dir
deleting old temporary directory…
++ working in new temp dir, .tmp.install
– skipping update of tmp.@update.afni.binaries

++ update needed, installing…

++ extracting local package macos_10.12_local from /Users/z/Downloads/tmp/macos_10.12_local.tgz…
++ backing up current binaries to auto_backup.macos_10.12_local
++ installing new binaries…
++ adding /Users/z/abin to path in /Users/z/.cshrc …
++ adding /Users/z/abin to PATH in /Users/z/.bashrc …
– seem be be sourcing .bashrc from /Users/z/.bash_profile
– seem be be sourcing .bashrc from /Users/z/.profile
++ running apsearch -update_all_afni_help …
Killed
done, yay (binaries are under /Users/z/abin)
set ss = 0
if ( ! 0 ) then
echo …finished, removing temp version, tmp.@update.afni.binaries
…finished, removing temp version, tmp.@update.afni.binaries
rm -f tmp.@update.afni.binaries
endif
exit 0
z@Z tmp % cd ~/abin
z@Z abin % ./afni
zsh: killed ./afni
z@Z abin % ./afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.0.0
version: Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64
distribution: 10.15 x86_64
number of CPUs: 12
apparent login shell: zsh
shell RC file: .zshenv (does not exist)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_19.3.09, macos_10.12_local, Oct 25 2019
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/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 : 2
/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/usr/bin/python3

testing ability to start various programs…
afni : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
uber_subject.py : FAILURE
/bin/sh: uber_subject.py: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
3dMVM : FAILURE
/bin/sh: 3dMVM: command not found

none working, testing programs under implied /Users/z/abin…
afni : FAILURE

suma                 : FAILURE
    
3dSkullStrip         : FAILURE
    
uber_subject.py      : success
3dAllineate          : FAILURE
    
3dRSFC               : FAILURE
    
SurfMesh             : FAILURE
    
3dClustSim           : FAILURE
    
3dMVM                : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
/bin/sh: rPkgsInstall: command not found

R RHOME : /Library/Frameworks/R.framework/Resources

checking for $HOME files…
.afnirc : missing
.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

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /usr/local/ants/bin/:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/Library/Apple/bin:/Library/TeX/texbin:/opt/X11/bin:/Users/z/Documents/OneDrive/Sync/Scripts

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 : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : did not find TT_N27+tlrc

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

which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.15

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.62.2/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

========================= summary, please fix: =========================

login shell ‘zsh’, trusting user to translate code examples from ‘tcsh’
shell zsh : MISSING env shell setup file .zshenv
failure under initial “AFNI and related program tests”
AFNI programs show FAILURE
consider adding /Users/z/abin to your PATH
missing R packages (see rPkgsInstall)
please run: cp /Users/z/abin/AFNI.afnirc ~/.afnirc
please run: “suma -update_env” for .sumarc
please run: apsearch -update_all_afni_help
insufficient data for AFNI bootcamp
possibly missing atlases
consider installing gcc under homebrew

z@Z abin %

During instalationl the system showed

“apsearch” cannot be opened because the developer cannot be verified.
window with “move to trash” or “cancel” options, so “cancel” selected. When open afni in the abin dir after installation, or when run afni_system_check, the
“AFNI/SUMA/3dSkullStrip/…” cannot be opened because the developer cannot be verified.
window showed, with “move to trash” or “cancel” options, so “cancel” selected each time.

Thanks,
2086

discoraj · October 29, 2019, 6:53pm

Hi,
Let’s see if macOS has given you some extended attributes.
Can you run in the terminal?:


xattr ~/abin/afni

Can you post what you get (if you get something)?

If you do get something, you can remove the extended attributes with:


xattr -cr ~/abin

Thanks, Justin

EXP.2086 · October 30, 2019, 1:56am

Hi Justin,

All afni programs worked again, thank you very much.

The attribute was:

com.apple.quarantine

But there is still a small problem as with the zsh(default terminal in 10.15), when I open new terminal, it shows:

Last login: Wed Oct 30 10:04:10 on ttys001
/Users/z/.afni/help/all_progs.COMP.bash:1: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:2: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:3: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:4: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:5: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:6: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:7: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:8: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:9: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:10: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:11: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:12: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:13: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:14: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:15: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:16: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:17: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:18: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:19: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:20: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:21: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:22: command not found: complete
/Users/z/.afni/help/all_progs.COMP.bash:23: command not found: complete
…

My .bashrc env for afni:

afni

export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/opt/X11/lib/flat_namespace
export PATH=$PATH:/usr/local/afni
ahdir=apsearch -afni_help_dir
if [ -f “$ahdir/all_progs.COMP.bash” ]
then
. $ahdir/all_progs.COMP.bash
fi

My .zshrc:

if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi

afni_check in zsh:

z@Z ~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.0.0
version: Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64
distribution: 10.15 x86_64
number of CPUs: 12
apparent login shell: zsh
shell RC file: .zshenv (does not exist)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/afni
afni version : Precompiled binary macos_10.12_local: Oct 28 2019
: AFNI_19.3.10 ‘Nero’
AFNI_version.txt : AFNI_19.3.10, macos_10.12_local, Oct 28 2019
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/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 : 2
/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/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 : 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 : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

-------------------------------- env vars --------------------------------
PATH = /usr/local/ants/bin/:/usr/local/fsl/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/Apple/usr/bin:/Library/Apple/bin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/afni:/Users/z/Documents/OneDrive/Sync/Scripts:/Users/z/abin

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 : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /usr/local/afni

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

which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.15

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.62.2/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

========================= summary, please fix: =========================

login shell ‘zsh’, trusting user to translate code examples from ‘tcsh’
shell zsh : MISSING env shell setup file .zshenv
insufficient data for AFNI bootcamp

Best,
2086