Problems with installation

Hello AFNI experts,

I am trying to install AFNI on my Mac Monterey with the M1 chip, and got stuck on fixing errors returned from the check command. Especially for the “missing R packages,” since I am pretty true that I have R installed.

Here are the results:

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 21.2.0
version: Darwin Kernel Version 21.2.0: Sun Nov 28 20:28:41 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T6000
distribution: 12.1
number of CPUs: 10
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/amyqi/abin/afni
afni version : Precompiled binary macos_10.12_local: Jan 12 2022
: AFNI_22.0.02 ‘Hadrian’
AFNI_version.txt : AFNI_22.0.02, macos_10.12_local, Jan 12 2022
which python : /Users/amyqi/miniconda3/bin/python
python version : 3.8.11
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/amyqi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/
python3 : 3

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : 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!

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/amyqi/.local/lib/python3.8/site-packages/matplotlib/
matplotlib version : 3.5.1

-------------------------------- env vars --------------------------------
PATH = /opt/homebrew/bin:/opt/homebrew/sbin:/Users/amyqi/miniconda3/bin:/Users/amyqi/miniconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/amyqi/abin


------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (948584M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/amyqi/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.1

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 3.3.11

– 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:
** 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 ‘bash’, but our code examples use ‘tcsh’
  • missing R packages (see rPkgsInstall)
  • OS X version might be old
  • consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

Thanks a lot!

Hi Amy,

This looks very good, particularly for an M1 setup, which is more difficult.

When you run “suma”, does it open a graphical interface?

For R, it is only complaining about a missing afex library. We can try to work through that, but if you don’t run into a group analysis program which complains about afex being missing, then it might not be worth fighting with.

  • rick

Hi Rick,

Yes, it does give a graphic interface when I run ‘suma.’

There is a huge possibility that I will be doing group analysis, so it is better if I can work this through. It would be great if you could help me with that.

Thanks a lot!