I am almost done with the AFNI installation on a mac OS, but I still get the following "please fix" messages
========================= summary, please fix: =========================
- have both .cshrc and .tcshrc, with former not applied
(consider adding 'source $HOME/.cshrc' to $HOME/.tcshrc) - missing R packages (see rPkgsInstall)
- python library matplotlib is required
(see AFNI install docs for details) - please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in csh
I think I can ignore the first and last message (Unsure how to set DYLD_LIBRARY_PATH - #3 by witherscp). However, I have tried installing again the rPkgsInstall and matplotlib and the "please fix" messages still appear. When checking the R --version, I receive the following output R version 3.6.3 (2020-02-29). I am wondering if perhaps this is due to the incompatible versions mentioned here: Xvfb and matplotlib missing - #2 by dglen
Here is the afni_check_system.py output:
-------------------------------- general ---------------------------------
architecture: 64bit Mach-O
cpu type: arm64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Thu Sep 12 23:35:29 PDT 2024; root:xnu-10063.141.1.701.1~1/RELEASE_ARM64_T6000
distribution: 14.7.1
number of CPUs: 8
apparent login shell: tcsh (current shell is csh)
** have both .cshrc and .tcshrc, with former not applied
(consider adding 'source $HOME/.cshrc' to $HOME/.tcshrc)
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/add8/abin/afni
afni version : Precompiled binary macos_10.12_local: Dec 6 2024
: AFNI_24.3.08 'Elagabalus'
AFNI_version.txt : AFNI_24.3.08, macos_10.12_local, Dec 06 2024, official
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.13.1
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/add8/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
/usr/bin/python3
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 : /opt/homebrew/bin/tcsh
tcsh version : 6.24.14
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: lme4!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: gamm4!
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: 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 = /Applications/NEURON/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Applications/NEURON/bin:/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:/Library/TeX/texbin:/opt/homebrew/opt/python/libexec/bin:/Users/add8/abin:/opt/homebrew/opt/python/libexec/bin:/Users/add8/abin/
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 0
CONDA_DEFAULT_ENV =
CC =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .cshrc seems to contain 'source .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)
no modifications needed across 2 dot files
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (471482M Avail)
top history: 08 Nov 2024 [rickr/ptaylor]: add afni/bad_scripts
data dir : found AFNI_demos under $HOME
top history: 07 Nov 2024 [rickr]: shrank AFNI_pamenc tree
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/add8/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.4.11
++ 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 'csh'...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
- have both .cshrc and .tcshrc, with former not applied
(consider adding 'source $HOME/.cshrc' to $HOME/.tcshrc) - missing R packages (see rPkgsInstall)
- python library matplotlib is required
(see AFNI install docs for details) - please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in csh