afni.nimh.nih.gov

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com.apple.quarantine

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Last login: Wed Oct 30 10:04:10 on ttys001
/Users/z/.afni/help/all_progs.COMP.bash:1: command not found: complete
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# 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

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

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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