Hello,
I am having issues with my AFNI installation on Mac 14.6 with Intel processor and OS Sonoma 14.6.1.
I searched the forum for possible solutions but other cases appear to be slightly different and also I am not familiar with Mac terminal or AFNI installations. If anyone has any suggestions on what I could try I greatly appreciate it.
I am performing the steps as described here
1.1.9. macOS 12+ (Intel processor/chip) — AFNI, SUMA and FATCAT: v25.0.02.
I do not have any errors for the first two steps
B. zsh OS_notes.macos_12_intel_a_admin_pt1.zsh
C. zsh OS_notes.macos_12_intel_a_admin_pt2.zsh
However, after restarting and running the last command
tcsh OS_notes.macos_12_intel_b_user.tcsh
I get several errors.
----ERROR 1-----
++ building (please be patient)...
++ need alternate compiler, trying /usr/local/bin/gcc-14
(if this fails, try passing one via -cc_path)
** error: failed run_cmd: make AFNI_WHOMADEIT=build LOCAL_CC_PATH=/usr/local/bin/gcc-14 itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/laptop1/afni_build/build_src/log_make.txt
** error: tail from log_make.txt:
----ERROR 2-----
mv: rename dcm2niix_afni to macos_12_x86_64/dcm2niix_afni: No such file or directory
make: *** [install] Error 1
Here is the output from the
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Darwin
release: 23.6.0
version: Darwin Kernel Version 23.6.0: Mon Jul 29 21:13:00 PDT 2024; root:xnu-10063.141.2~1/RELEASE_X86_64
distribution: 10.16 (sw_vers 14.6.1)
number of CPUs: 8
user: laptop1
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_25.0.01, anyos_text, Jan 29 2025, local
which python : /Users/laptop1/miniconda3/bin/python
python version : 3.12.8
which R : /usr/local/bin/R
R version : R version 4.3.1 (x86_64-apple-darwin20)
instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/bin/R)
python : 2
/Users/laptop1/miniconda3/bin/python3.12
/usr/local/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13
python2 : 0
python3 : 3
/Users/laptop1/miniconda3/bin/python3.12
/usr/local/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 : FAILURE
/bin/sh: afni: command not found
suma : FAILURE
/bin/sh: suma: command not found
3dSkullStrip : FAILURE
/bin/sh: 3dSkullStrip: command not found
3dAllineate : FAILURE
/bin/sh: 3dAllineate: command not found
3dRSFC : FAILURE
/bin/sh: 3dRSFC: command not found
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found
3dClustSim : FAILURE
/bin/sh: 3dClustSim: command not found
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
rPkgsInstall : FAILURE
------------------------ 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
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
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.13/3.13.1/Frameworks/Python.framework/Versions/3.13/bin/python3.13)
-------------------------------- env vars --------------------------------
PATH = /Users/laptop1/miniconda3/bin:/Users/laptop1/miniconda3/condabin:/usr/local/bin:/usr/local/sbin:/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/opt/python/libexec/bin:/Users/laptop1/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin
PYTHONPATH (sub-shell) =
R_LIBS = /Users/laptop1/sw/R-4.3.1
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base
CC (sub-shell) =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, 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 3 dot files
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : found afni_handouts under $HOME/OneDrive/NOS
atlas : did not find TT_N27+tlrc
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /usr/local/bin/brew
brew version : Homebrew 4.4.20
which git : /usr/bin/git
git version : git version 2.39.5 (Apple Git-154)
which gcc : /usr/bin/gcc
gcc version : Apple clang version 16.0.0 (clang-1600.0.26.4)
brew gcc(s) : /usr/local/bin/gcc-14
CommandLineTools SDK : MacOSX15.1.sdk
** consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.82.4/lib/libglib-2.0.dylib
========================= summary, please fix: =========================
- just be aware: login shell 'zsh', but our code examples use 'tcsh'
- missing program: afni
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- python library matplotlib is required
(see AFNI install docs for details) - please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages) - possibly missing atlases
- consider linking /usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
laptop1@laptop1-MacBook-Pro-3 ~ % afni
zsh: command not found: afni
laptop1@laptop1-MacBook-Pro-3 ~ %