M2 mac installation issues- R packages and AFNI program shows failure

tfink7 · January 11, 2024, 3:29pm

Need some help troubleshooting this install issue have tried redownloading newest version of R and have followed all instructions from https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_macOS_12_Silicon.html#quick-setup-general-users

~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 23.1.0
version: Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:45 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6020
distribution: 14.1
number of CPUs: 10
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/tfink7/abin/afni
afni version : Precompiled binary macos_10.12_local: Dec 8 2023
: AFNI_23.3.13 'Septimius Severus'
AFNI_version.txt : AFNI_24.0.00, anyos_text, Jan 07 2024, local
which python : /opt/salt/bin/python
python version : 3.7.12
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/tfink7/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/bin/R)
python : 2
/opt/salt/.pyenv/versions/3.7.12/bin/python3.7
/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/bin/python3.11
python2 : 0
python3 : 3
/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/bin/python3
/opt/salt/.pyenv/versions/3.7.12/bin/python3.7

** 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
Error in dyn.load(ll) :
unable to load shared object '/Users/tfink7/abin/R_io.so':
dlopen(/Users/tfink7/abin/R_io.so, 0x0006): tried: '/Users/tfink7/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/tfink7/abin/R_io.so' (no such file), '/Users/tfink7/abin/R_io.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
module file : /Users/tfink7/.local/lib/python3.7/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.3

** 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:/Applications/Privileges.app/Contents/Resources:/opt/salt/bin:/usr/local/sbin:/opt/homebrew/opt/python/libexec/bin:/Users/tfink7/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS = /Users/tfink7/sw/R-4.3.1

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

----------------------------- 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/tfink7/abin

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

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.3

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

just be aware: login shell 'zsh', but our code examples use 'tcsh'
AFNI programs show FAILURE
missing R packages (see rPkgsInstall)
insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
consider installing gcc under homebrew
consider installing glib under homebrew

rickr · January 11, 2024, 5:25pm

It seems like the installation build did not succeed, since you are still using the macos_10.12_local binaries. What is the output from:

cat ~/afni_build/hist_messages.txt

Thanks,

rick

tfink7 · January 11, 2024, 6:00pm

~ % cat ~/afni_build/hist_messages.txt

-- current AFNI: AFNI_24.0.00, anyos_text, Jan 07 2024
-- cleaning old build root dir, /Users/tfink7/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/tfink7/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.0.00
-- checking out git tag AFNI_24.0.00
-- using repo branch (detached), tag AFNI_24.0.00
-- removing old atlas dir, prev/afni_atlases_dist
-- moving old atlas dir afni_atlases_dist to prev/afni_atlases_dist
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- removing old NiiVue backup, prev/niivue_afni.umd.js
-- moving old niivue niivue_afni.umd.js to prev/niivue_afni.umd.js
-- downloading NiiVue, niivue_afni.umd.js

-- preparing to run 'make' build of package macos_13_ARM_clang
-- copying README files
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/tfink7
tail -f /Users/tfink7/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/tfink7/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

In file included from niml.h:5,
from niml_private.h:4,
from niml_b64.c:1:
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/include-fixed/stdio.h:78:10: fatal error: _stdio.h: No such file or directory
78 | #include <_stdio.h>
| ^~~~~~~~~~
compilation terminated.
make[1]: *** [niml_b64.o] Error 1
mv: rename .o to ../.o: No such file or directory
make: *** [niml_b64.o] Error 1

-- shell/system command history is in:
/Users/tfink7/afni_build/hist_commands.txt

++ screen text history is in:
/Users/tfink7/afni_build/hist_messages.txt

diazjm · January 17, 2024, 1:24am

I seem to be having a similar issue with R packages not being installed. But I am additionally having trouble with AFNI being built/installed at all. The output from my log is: -------------------------------- general ---------------------------------
architecture: 64bit
cpu type: arm
system: Darwin
release: 23.1.0
version: Darwin Kernel Version 23.1.0: Mon Oct 9 21:28:45 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6020
distribution: 14.1.2
number of CPUs: 10
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.0.01, anyos_text, Jan 11 2024, local
which python : /opt/homebrew/opt/python/libexec/bin/python
python version : 3.11.7
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@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
python2 : 0
python3 : 2
/opt/homebrew/Cellar/python@3.11/3.11.7/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/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
setenv: Too many arguments.

------------------------ 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
setenv: Too many arguments.

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
module file : /opt/homebrew/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.2

** 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:/opt/homebrew/opt/python/libexec/bin:/Users/jazmindiaz/abin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH =
R_LIBS = /Users/jazmindiaz/sw/R-4.3.2

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (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 : found AFNI_data6 under $HOME (471482M Avail)
top history: ... [gangc]: redo 0.BGA as 1.bga and update run.MSS.txt
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 : did not find TT_N27+tlrc

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

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.4

========================= 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)
please run: "suma -update_env" for .sumarc
please run: apsearch -update_all_afni_help
possibly missing atlases
consider installing gcc under homebrew
consider installing glib under homebrew

tfink7 · January 17, 2024, 1:37am

I haven't found a solution yet, let me know if you figure something out!

rickr · January 17, 2024, 3:27pm

Hi @tfink7,

The problem of a missing header file like that is something that a few others have run into, but one that we have not yet figured out (short of a full operating system wipe and reinstall).

I assume your system has been upgraded into its current state. It seems that when going the upgrade route, confusion may arise between the homebrew compilers and the paths to system dependencies. Surprisingly, wiping and reinstalling either homebrew or the CommandLineTools has not resolved it.

But there are one or two things you might try. First, what is the output from:

ls /Library/Developer/CommandLineTools/Packages

rick

rickr · January 17, 2024, 3:36pm

Hi @diazjm,

I suspect you are in the same boat as @tfink7, but we should be sure.
What is the output from:

cat ~/afni_build/hist_messages.txt

Thanks,

rick

diazjm · January 17, 2024, 7:25pm

Hi Rick, I appreciate your response. Here is the output of that txt file:

-- current AFNI: AFNI_24.0.01, anyos_text, Jan 11 2024
-- preparing build_root dir, /Users/jazmindiaz/afni_build
-- creating build_root dir, /Users/jazmindiaz/afni_build
-- running 'git clone' on afni repo ...
(please be patient)
-- have default git tag LAST_TAG, will checkout AFNI_24.0.01
-- checking out git tag AFNI_24.0.01
-- using repo branch (detached), tag AFNI_24.0.01
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- downloading NiiVue, niivue_afni.umd.js

-- preparing to run 'make' build of package macos_13_ARM_clang
-- copying README files
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/jazmindiaz
tail -f /Users/jazmindiaz/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/jazmindiaz/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

In file included from niml.h:5,
from niml_private.h:4,
from niml_b64.c:1:
/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/13/include-fixed/stdio.h:78:10: fatal error: _stdio.h: No such file or directory
78 | #include <_stdio.h>
| ^~~~~~~~~~
compilation terminated.
make[1]: *** [niml_b64.o] Error 1
mv: rename .o to ../.o: No such file or directory
make: *** [niml_b64.o] Error 1

rickr · January 17, 2024, 9:38pm

Yes @diazjm, it looks like the same issue. What do you show for this?

ls -l /Library/Developer/CommandLineTools/Packages

Thanks,

rick

diazjm · January 18, 2024, 3:41am

Hi Rick, I don't seem to have the Packages folder in that directory. Here's what that command shows:
% ls -l /Library/Developer/CommandLineTools/Packages
ls: /Library/Developer/CommandLineTools/Packages: No such file or directory

And this is what shows in one directory above:
% ls -l /Library/Developer/CommandLineTools/
total 0
drwxr-xr-x 5 root wheel 160 Nov 16 2022 Library
drwxr-xr-x 10 root wheel 320 Jan 17 20:16 SDKs
drwxr-xr-x 7 root wheel 224 Nov 16 2022 usr

rickr · January 18, 2024, 2:35pm

Cool, what does the long listing under SDKs show?
Apparently the 13.3 SDK might be broken, so if that is your version, it might be good to change.

rick

diazjm · January 18, 2024, 7:01pm

This is what's in SDKs:

ls -l SDKs
total 0
lrwxr-xr-x 1 root wheel 14 Jan 17 20:16 MacOSX.sdk -> MacOSX14.2.sdk
drwxr-xr-x 7 root wheel 224 Sep 18 17:29 MacOSX12.3.sdk
lrwxr-xr-x 1 root wheel 14 Sep 18 17:28 MacOSX12.sdk -> MacOSX12.3.sdk
drwxr-xr-x 7 root wheel 224 Nov 12 2022 MacOSX13.1.sdk
drwxr-xr-x 7 root wheel 224 Jan 17 20:16 MacOSX13.3.sdk
lrwxr-xr-x 1 root wheel 14 Jan 17 20:16 MacOSX13.sdk -> MacOSX13.3.sdk
drwxr-xr-x 7 root wheel 224 Nov 13 11:25 MacOSX14.2.sdk
lrwxr-xr-x 1 root wheel 14 Jan 17 20:15 MacOSX14.sdk -> MacOSX14.2.sdk

How should I go about updating the version?

rickr · January 18, 2024, 7:19pm

Hmmm, did you just update those yesterday? Did you reboot after that? Did you try running build_afni.py (or the user install script) after rebooting?

Thanks,

rick

diazjm · January 18, 2024, 9:32pm

Restarting and re-running the install script seems to have resolved the issues. Thank you so much for your help! Would you say that updating the SDK might have been the solution?

tfink7 · January 18, 2024, 9:46pm

This is the output I get
~ % ls /Library/Developer/CommandLineTools/Packages

ls: /Library/Developer/CommandLineTools/Packages: No such file or directory

rickr · January 18, 2024, 10:39pm

If you initially ran the user install without either a reboot, or if you updated the SDK afterwards, either of those might have made a difference. It is great that this is working!

rick

rickr · January 18, 2024, 10:43pm

Hi @tfink7,

Can you check the /Library/Developer/CommandLineTools/SDKs directory, instead?
Showing the long format:

ls -l /Library/Developer/CommandLineTools/SDKs

Thanks,

rick

tfink7 · January 18, 2024, 10:51pm

ls -l /Library/Developer/CommandLineTools/SDKs
total 0
lrwxr-xr-x 1 root wheel 14 Oct 19 23:07 MacOSX.sdk -> MacOSX13.3.sdk
drwxr-xr-x 7 root wheel 224 Dec 1 2022 MacOSX12.3.sdk
lrwxr-xr-x 1 root wheel 14 Oct 19 23:07 MacOSX12.sdk -> MacOSX12.3.sdk
drwxr-xr-x 7 root wheel 224 Mar 9 2023 MacOSX13.3.sdk
lrwxr-xr-x 1 root wheel 14 Oct 19 23:06 MacOSX13.sdk -> MacOSX13.3.sdk

rickr · January 18, 2024, 11:03pm

That is what I was looking for, that you are using the 13.3 SDK. I think you could either change that to use 12.3, or possibly try another "xcode-select --install" to get the 14 package.
If you want to try something for now (edit: added 'sudo' for ln):

cd /Library/Developer/CommandLineTools/SDKs
sudo rm MacOSX.sdk
sudo ln -s MacOSX12.3.sdk MacOSX.sdk

Then go back to your afni_build/build_src directory and just try "make".
That should either go far, or fail immediately with the stdio.h error.

rick

rroy4 · February 14, 2024, 6:14pm

Hi Rick,

I believe I may be having the same issue discussed in this thread. Has a solution to this issue been found?

In case you find it helpful I am putting some outputs below.

rroy4$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 23.3.0
version: Darwin Kernel Version 23.3.0: Wed Dec 20 21:33:31 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T8112
distribution: 10.16
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni :
:
AFNI_version.txt : AFNI_24.0.06, anyos_text, Feb 08 2024, local
which python : /Users/rroy4/anaconda3/bin/python
python version : 3.11.5
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 : 2
/Users/rroy4/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.11/3.11.7_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11
python2 : 0
python3 : 3
/Users/rroy4/anaconda3/bin/python3.11
/opt/homebrew/Cellar/python@3.11/3.11.7_1/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/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
setenv: Too many arguments.

------------------------ 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
setenv: Too many arguments.

R RHOME : /Library/Frameworks/R.framework/Resources

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
module file : /Users/rroy4/anaconda3/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.2

++ module loaded: flask
module file : /Users/rroy4/anaconda3/lib/python3.11/site-packages/flask/init.py
flask version : 2.2.2

** failed to load module flask_cors
-- flask_cors is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /Users/rroy4/anaconda3/bin:/Users/rroy4/anaconda3/condabin:/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:/opt/homebrew/opt/python/libexec/bin:/Users/rroy4/abin:/opt/homebrew/opt/python/libexec/bin

PYTHONPATH (sub-shell) =
R_LIBS = /Users/rroy4/sw/R-4.3.1

LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

.afnirc                   : found
.sumarc                   : missing
.afni/help/all_progs.COMP : missing

--------- shell startup files ----------

-- good: .cshrc seems to contain 'source .tcshrc'
-- 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 : did not find TT_N27+tlrc

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

which brew : /opt/homebrew/bin/brew
brew version : Homebrew 4.2.8

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

just be aware: login shell 'bash', but our code examples use 'tcsh'
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
missing program: afni
failure under initial "AFNI and related program tests"
AFNI programs show FAILURE
missing R packages (see rPkgsInstall)
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

(base) LRSCB-KQ2XKTW5L:~ rroy4$ cat ~/afni_build/hist_messages.txt

-- current AFNI: AFNI_24.0.06, anyos_text, Feb 08 2024
-- cleaning old build root dir, /Users/rroy4/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/rroy4/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.0.06
-- checking out git tag AFNI_24.0.06
-- using repo branch (detached), tag AFNI_24.0.06
-- removing old atlas dir, prev/afni_atlases_dist
-- moving old atlas dir afni_atlases_dist to prev/afni_atlases_dist
-- downloading AFNI atlas package, afni_atlases_dist.tgz
-- unpacking atlas package, afni_atlases_dist
-- removing old NiiVue backup, prev/niivue_afni.umd.js
-- moving old niivue niivue_afni.umd.js to prev/niivue_afni.umd.js
-- downloading NiiVue, niivue_afni.umd.js

-- preparing to run 'make' build of package macos_13_ARM_clang
-- copying README files
-- copying other_builds/Makefile.macos_13_ARM_clang to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/rroy4
tail -f /Users/rroy4/afni_build/build_src/log_make.txt
# use ctrl-c to terminate 'tail' command (not the build)
++ building (please be patient)...
error: failed run_cmd: make AFNI_WHOMADEIT=build itall >& log_make.txt
-- status: building FAILURE
see 'make' log file /Users/rroy4/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

| ^~~~~~~~~~~
(cd leej3;
/opt/homebrew/bin/gcc-13 -arch arm64 -DDARWIN -DARM_M1 -O1 -m64 -Wall -Wno-deprecated-declarations -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -c whats_my_exepath.c;
/bin/cp -f whats_my_exepath.o ..;
cd ..)
/bin/rm -f afni
/opt/homebrew/bin/gcc-13 -arch arm64 -DDARWIN -DARM_M1 -O1 -m64 -Wall -Wno-deprecated-declarations -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -DWHATS_MY_EXEPATH -o afni afni.o afni_func.o afni_widg.o afni_warp.o afni_fimmer.o afni_slice_short.o afni_slice_float.o afni_filer.o afni_slice_byte.o afni_slice_complex.o afni_pcor.o afni_pcor_float.o afni_transforms.o pbar.o afni_graph.o afni_plugin.o afni_cluster.o parser.o parser_int.o afni_plugout.o afni_fimfunc.o afni_setup.o afni_receive.o mcw_graf.o afni_splash.o afni_pplug_env.o afni_pplug_2dfunc.o afni_friends.o afni_ttren.o afni_pplug_1dfunc.o afni_driver.o afni_niml.o afni_sumafunc.o afni_slice_rgbyte.o afni_version.o afni_lock.o afni_vol2surf.o afni_pplug_instacorr.o afni_pplug_instacalc.o afni_pplug_tstat.o afni_whelp.o whats_my_exepath.o -m64 -dynamic -L. -L/opt/homebrew/lib -L/opt/X11/lib -L/usr/lib -lmrix -lcoxplot -lmri libXmHTML.a libjpeg.a -lmri -lf2c -lXm -ljpeg -lXt -lXft -lfontconfig -lpng16 -liconv -lXmu -lXp -lXpm -lXext -lX11 -lz -lexpat -lm -lc -lm -lc
ld: file not found: libjpeg.a
collect2: error: ld returned 1 exit status
make: *** [afni] Error 1

-- shell/system command history is in:
/Users/rroy4/afni_build/hist_commands.txt

++ screen text history is in:
/Users/rroy4/afni_build/hist_messages.txt