we get the following error while running this command:
tcsh OS_notes.macos_12_ARM_b_user.tcsh
the error:
error: the current package was made by build_afni.py
refusing to overwrite it without -overwrite_build
note: the typical update method in this case would be:
build_afni.py -build_root ~/afni_build
the outcome is that afni commands are not recognized while working in tcsh.
Thank you,
Meytal
Hi Meytal,
That suggests that what is in your abin was made via build_afni.py, and that @update.afni.binaries does not want to overwrite it.
What is the system check output?
afni_system_check.py -check_all
Dear Rick,
I was following the installation instructions on the webpage (for macOS12+), and when I got to section (E), it gave me the error I pasted previously.
Now I tried to also run
build_afni.py -build_root ~/afni_build
And afterwards I get the following output of afni_system_check (any idea why the following the instructions didn't work smoothly for me?):
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.6.0
version: Darwin Kernel Version 22.6.0: Sun Dec 17 22:12:45 PST 2023; root:xnu-8796.141.3.703.2~2/RELEASE_ARM64_T6000
distribution: 13.6.4
number of CPUs: 20
apparent login shell: zsh
shell RC file: .zshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/ramotlab/abin/afni
afni version : Precompiled binary macos_13_ARM_clang: Mar 3 2024
: AFNI_24.0.09 'Caracalla'
AFNI_version.txt : AFNI_24.0.09, macos_13_ARM_clang, Mar 03 2024, build
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.12.2
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)
instances of various programs found in PATH:
afni : 1 (/Users/ramotlab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.12/3.12.2_1/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.12/3.12.2_1/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/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
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: gamm4!
These packages are not installed on the computer: data.table!
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:/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/bin:/opt/homebrew/opt/python/libexec/bin:/Library/Frameworks/R.framework/Resources:/usr/local/gfortran/bin:/Users/ramotlab/abin:/usr/local/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin
PYTHONPATH =
R_LIBS = /Users/ramotlab/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- 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, 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 : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/ramotlab/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5
which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.10
========================= summary, please fix: =========================
* just be aware: login shell 'zsh', 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)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* consider installing gcc under homebrew
* consider installing glib under homebrew
Dear Rick,
The problem was resolved. Thank you!
Great, thanks for the update!
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