Hi all,
I am trying to install AFNI on a new MacBook Pro running Catalina. I followed the instructions except that I avoided homebrew (I use macports) and kept R 4 instead of R 3.6. I know that AFNI is not compatible with the newer version of R and that’s fine for the moment (I haven’t yet decided whether to roll back R to the previous version, because of other constraint). On this laptop, I mainly will use AFNI for visualization and a few terminal scripts that probably won’t involve R.
My issues (at the moment) are two:
- I am using zsh, and every time I open a terminal, I get a very long list of messages of the following type:
…
Users/gp/.afni/help/all_progs.COMP.bash:589: command not found: complete
/Users/gp/.afni/help/all_progs.COMP.bash:590: command not found: complete
/Users/gp/.afni/help/all_progs.COMP.bash:591: command not found: complete
/Users/gp/.afni/help/all_progs.COMP.bash:592: command not found: complete
From the message board I saw that the “complete” command is not part of the zsh set. Is there a way to solve this without changing the default shell to zsh?
- I am not able to launch AFNI from the terminal because, even though I get no error, XQuartz is not launched. I have installed the latest version of XQuartz and followed Justin’s instructions for giving Full Disk Access to launchd_startx, Terminal, and XQuartz (I even threw zsh in there for good measure). Still, it doesn’t work.
In the following is the output of afni_system_check.py -check_all. Note also the error about DYLD_LIBRARY_PATH, although I have the line:
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace
in both my .bashrc and .zshenv files.
Any help much appreciated!
thanks
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: zsh
shell RC file: .zshenv (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/gp/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 1 2020
: AFNI_20.2.16 ‘Aulus Vitellius’
AFNI_version.txt : AFNI_20.2.16, macos_10.12_local, Sep 01 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /opt/local/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/gp/abin/afni)
R : 1 (/opt/local/Library/Frameworks/R.framework/Versions/4.0/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 : 1 (/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 : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /opt/local/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
-------------------------------- env vars --------------------------------
PATH = /opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/gp/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ 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/gp/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which port : /opt/local/bin/port
port version : Version: 2.6.3
++ 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: =========================
- just be aware: login shell ‘zsh’, but our code examples use ‘tcsh’
- shell zsh : good: found env shell setup file .zshenv
- missing R packages (see rPkgsInstall)
- insufficient data for AFNI bootcamp
- OS X version might be old
- consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace