Hello! I am currently in the process of installing AFNI on my computer (MacOS
14.6.1, M3). I am running into some errors when installing the R packages. I
have been using this tutorial:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_macOS_12_Silicon_old.html
When running the command to install R Libraries, I am met with this message:
ERROR: dependency ‘MatrixModels’ is not available for package
‘quantreg’
- removing ‘/Users/ganeshramsr/Library/R/3.6/library/quantreg’
ERROR: dependencies ‘pbkrtest’, ‘quantreg’ are not available for
package ‘car’ - removing ‘/Users/ganeshramsr/Library/R/3.6/library/car’
ERROR: dependencies ‘pbkrtest’, ‘car’ are not available for package
‘afex’ - removing ‘/Users/ganeshramsr/Library/R/3.6/library/afex’
ERROR: dependency ‘car’ is not available for package ‘phia’ - removing ‘/Users/ganeshramsr/Library/R/3.6/library/phia’
The downloaded source packages are in
‘/private/var/folders/2j/p_56lnvd7t99k3q0mm0ly5l8_6s8mt/T/RtmpLjLJlQ/downloaded_packages’
Warning messages:
1: In install.packages(c("afex", "phia", "snow", "nlme", "lmerTest"), :
installation of package ‘MatrixModels’ had non-zero exit status
2: In install.packages(c("afex", "phia", "snow", "nlme", "lmerTest"), :
installation of package ‘quantreg’ had non-zero exit status
3: In install.packages(c("afex", "phia", "snow", "nlme", "lmerTest"), :
installation of package ‘car’ had non-zero exit status
4: In install.packages(c("afex", "phia", "snow", "nlme", "lmerTest"), :
installation of package ‘afex’ had non-zero exit status
5: In install.packages(c("afex", "phia", "snow", "nlme", "lmerTest"), :
installation of package ‘phia’ had non-zero exit status
When I run afni_system_check.py -check_all I am given this:
-------------------------------- general ---------------------------------
architecture: 64bit Mach-O
cpu type: arm64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Mon Jul 29 21:14:04 PDT
2024; root:xnu-10063.141.2~1/RELEASE_ARM64_T8122
distribution: 14.6.1
number of CPUs: 8
apparent login shell: bash (current shell is zsh)
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/ganeshramsr/abin/afni
afni version : Precompiled binary macos_10.12_local: Oct 10 2024
: AFNI_24.3.02 'Elagabalus'
AFNI_version.txt : AFNI_24.3.02, macos_10.12_local, Oct 10 2024, official
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.13.0
which R : /usr/local/bin/R
R version : R version 3.6.3 (x86_64-apple-darwin15.6.0)
instances of various programs found in PATH:
afni : 1 (/Users/ganeshramsr/abin/afni)
R : 1
(/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1
(/opt/homebrew/Cellar/python@3.13/3.13.0_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.13/3.13.0_1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/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 : FAILURE
Error in library(data.table) : there is no package called
‘data.table’
Calls: source ... suppressPackageStartupMessages ->
withCallingHandlers -> library
Execution halted
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /bin/tcsh
tcsh version : 6.21.00
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: gamm4!
These packages are not installed on the computer: data.table!
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
** failed to load module flask
-- flask is not required, but is desirable
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH =
/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/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/X11/bin:/usr/local/laps:/Users/ganeshramsr/abin:/Users/ganeshramsr/abin:/Users/ganeshramsr/abin:/Users/ganeshramsr/abin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/ganeshramsr/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
CC =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- 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 4 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.zshrc 0 0 0 0
.bashrc 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/ganeshramsr/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.4.1
++ 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 'bash', but our code examples use 'tcsh'
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- python library matplotlib is required
(see AFNI install docs for details) - dot file test : want 1 modifications across 4 files:
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - consider installing gcc under homebrew
- consider installing glib under homebrew
Do I need these packages to continue with installation or are these missing
packages under MacOS? Is there another issue with installation I need to fix
before proceeding?