AFNI installation failure - MacBook Air M2

hkimneurology · June 25, 2024, 3:41pm

Hello I got error message as below after the installations as instructed.
Thanks in advance

-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 22.5.0
version: Darwin Kernel Version 22.5.0: Mon Apr 24 20:40:17 PDT 2023; root:xnu-8796.121.2~3/RELEASE_ARM64_T8112
distribution: 13.4
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.1.22, anyos_text, Jun 21 2024, local
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.12.4
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)

instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/usr/bin/python3

** have python3 but not python2

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
library(data.table)에서 다음과 같은 에러가 발생했습니다:
‘data.table’이라고 불리는 패키지가 없습니다
호출: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
실행이 정지되었습니다

------------------------ 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

-------------------------------- 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:/Users/hyeonjinkim/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =

----------------------------- 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 2 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 : did not find TT_N27+tlrc

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.7

========================= summary, please fix: =========================

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 installing gcc under homebrew
consider installing glib under homebrew

ptaylor · June 25, 2024, 8:56pm

Hi-

Your path includes the "abin" somewhere (specifically, /Users/hyeonjinkim/abin for your computer), so that is good, but it appears that no AFNI programs are actually being found---even the which afni line entry is blank.

To make sure that the binaries got copied there, could you copy+paste this into a terminal, and then copy+paste the output in a reply:

ls /Users/hyeonjinkim/abin/afni
ls -d /Users/hyeonjinkim/abin/* | wc -l

? (The first line checks to see if the "afni" program is present there, and the second counts how many files are in that directory).

Also, could you open a new terminal and run the system check again:

afni_system_check.py -check_all

? Opening a new terminal is just to source the shell files again, to see if that is simply what is needed after putting information there from setup.

--pt

hkimneurology · June 26, 2024, 1:32am

Thanks for your quick help.
I'm attaching the result that I got.

Last login: Wed Jun 26 10:28:22 on ttys000
[Hyeonjinui-MacBookAir:~] hyeonjinkim% ls /Users/hyeonjinkim/abin/afni
ls: /Users/hyeonjinkim/abin/afni: No such file or directory
ls -d /Users/hyeonjinkim/abin/* | wc -l
[Hyeonjinui-MacBookAir:~] hyeonjinkim% ls -d /Users/hyeonjinkim/abin/* | wc -l
425
[Hyeonjinui-MacBookAir:~] hyeonjinkim% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.5.0
version: Darwin Kernel Version 23.5.0: Wed May 1 20:19:05 PDT 2024; root:xnu-10063.121.3~5/RELEASE_ARM64_T8112
distribution: 14.5
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.1.22, anyos_text, Jun 21 2024, local
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.12.4
which R : /usr/local/bin/R
R version : R version 4.3.1 (aarch64-apple-darwin20)

instances of various programs found in PATH:
afni : 0
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/usr/bin/python3

** have python3 but not python2

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
library(data.table)에서 다음과 같은 에러가 발생했습니다:
‘data.table’이라고 불리는 패키지가 없습니다
호출: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
실행이 정지되었습니다

------------------------ 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

-------------------------------- 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:/Users/hyeonjinkim/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =

----------------------------- 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 2 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 : did not find TT_N27+tlrc

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.7

========================= summary, please fix: =========================

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 installing gcc under homebrew
consider installing glib under homebrew

[Hyeonjinui-MacBookAir:~] hyeonjinkim%

ptaylor · June 26, 2024, 9:06am

Hmmm. afni isn't found in that directory. Somehow, there appear to still be 425 files there, but none of the ones tested for. That is weird. I will send you a Message about sending the output text file of building locally.

--pt

hkimneurology · June 27, 2024, 4:31am

Thank you for your kind help.
I think everything was wrong with the start - I started the downloads in the other sheet type (-zsh).
I re-started the instructions in the home-brew shell (-tsch),
and checked the errors in new -tsch terminal.
I got message as below.
Please review it.
Thank you in advance.

best, HJ

-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.5.0
version: Darwin Kernel Version 23.5.0: Wed May 1 20:19:05 PDT 2024; root:xnu-10063.121.3~5/RELEASE_ARM64_T8112
distribution: 14.5
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/hyeonjinkim/abin/afni
afni version : Precompiled binary macos_13_ARM_clang: Jun 27 2024
: AFNI_24.1.22 'Publius Septimius Geta'
AFNI_version.txt : AFNI_24.1.22, macos_13_ARM_clang, 6 27 2024, build
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.12.4
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/hyeonjinkim/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 1 (/opt/homebrew/Cellar/python@3.12/3.12.4/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.12/3.12.4/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 : success

------------------------ 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 : success

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:/Users/hyeonjinkim/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS = /Users/hyeonjinkim/sw/R-4.3.1
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
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 2 dot files

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1902788M Avail)
top history: ... 2024 [rickr]: 3drefit -newid FT/SUMA/FT_SurfVol.nii
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
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/hyeonjinkim/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.8.5

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.3.7

-- consider installing gcc under homebrew
-- consider installing glib under homebrew

========================= summary, please fix: =========================

python library matplotlib is required
(see AFNI install docs for details)

ptaylor · July 1, 2024, 12:33am

Hi, HJ-

I think things are mostly looking good there.

One thing to consider is getting the additional Python libraries: Matplotlib, Flask and Flask-Cors. To do this on macOS, probably the easiest thing is to use Anaconda or Miniconda for using conda to make an environment with those. (On macOS, this seems to be the easiest way to get Python libraries nowadays.) A description of how to do this, and recipes for getting the set of necessary libraries for current AFNI usage, are provided here.

--pt