Hi,
It is my first time installing afni on M2 pro and I'm completely confused about how the path works. Before this, I have installed R and R studio on my Mac,
(1) Is it possible to link the afni setup to the R packages (e.g., afex, brms, car, etx.) that I have installed through R studio?
(2) Is it possible to use different version for Rstudio and afni? Currently, I am using v 4.3.1. But after I have installed afni, I'm using v. 3.6.3.
When I ran the afni_system_check.py -check-all, I received the following message.
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.5.0
version: Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:23 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T6020
distribution: 13.4.1
number of CPUs: 10
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/meilingsoh/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 29 2023
: AFNI_23.1.10 'Publius Helvius Pertinax'
AFNI_version.txt : AFNI_23.1.10, macos_10.12_local, Jun 29 2023, official
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.11.4
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
instances of various programs found in PATH:
afni : 1 (/Users/meilingsoh/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.11/3.11.4_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/bin/python3
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
which Xvfb : /opt/X11/bin/Xvfb
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: paran!
These packages are not installed on the computer: psych!
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 : /Library/Frameworks/R.framework/Resources
------------------------------ python libs -------------------------------
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-------------------------------- env vars --------------------------------
PATH = /Users/meilingsoh/anaconda3/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/meilingsoh/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- no .cshrc, will create one as a follower of .tcshrc
-- considered operations: path, flatdir, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 0 1
.tcshrc 0 0 1 0
.zshrc 0 0 0 0
------------------------------ 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/meilingsoh/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.0.26
-- consider installing gcc under homebrew
-- consider installing glib under homebrew
++ 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: =========================
* just be aware: login shell 'zsh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* python library matplotlib is required
(see AFNI install docs for details)
* dot file test : want 1 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)