AFNI Installzation failure

Emmy · June 20, 2024, 2:47pm

Hello,

I used a macOS(Intel processor), and I tried to follow the instruction to download, but when I continue to Step E "tcsh OS_notes.macos_12_intel_b_user.tcsh", it gave me an error with:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 10939 0 --:--:-- --:--:-- --:--:-- 10968
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.4.1
R ver : 4.4.1
echo

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 121k 0 --:--:-- --:--:-- --:--:-- 121k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- no current AFNI package found in path...
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 156 0 --:--:-- --:--:-- --:--:-- 157
++ no update needed
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.20, anyos_text, Jun 20 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.20
-- checking out git tag AFNI_24.1.20
-- using repo branch (detached), tag AFNI_24.1.20
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

| ^
dfe.c:67:1: error: return type defaults to 'int' [-Wimplicit-int]
67 | y_newrec(Void)
| ^~
dfe.c:83:1: error: return type defaults to 'int' [-Wimplicit-int]
83 | c_dfe(cilist a)
| ^~~
make[1]: [dfe.o] Error 1
mv: rename libf2c.a to ../libf2c.a: No such file or directory
make: * [libf2c.a] Error 1

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.4.1
echo export R_LIBS=/Users/syja/sw/R-4.4.1
echo export R_LIBS=/Users/syja/sw/R-4.4.1
echo setenv R_LIBS /Users/syja/sw/R-4.4.1
mkdir -p /Users/syja/sw/R-4.4.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

** ERROR: Failed to load R_io.so

I wonder could anyone help me on that? Thank you so much!

discoraj · June 20, 2024, 7:46pm

Hi,

At the terminal can you let me know the output of?:

gcc --version

and

R --version

I haven't yet tested our intel install with R 4.4.1, but that may not be the problem.

Did the first two steps give any errors?
These:

zsh OS_notes.macos_12_intel_a_admin_pt1.zsh
zsh OS_notes.macos_12_intel_a_admin_pt2.zsh

Thanks, Justin

Emmy · June 20, 2024, 8:08pm

Hi,

the output of the first command is :
Apple clang version 15.0.0 (clang-1500.3.9.4)

Target: x86_64-apple-darwin23.4.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin
And the output of the second command is:
R version 4.4.1 (2024-06-14) -- "Race for Your Life"

Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under the terms of the

GNU General Public License versions 2 or 3.

For more information about these matters see

Licenses - GNU Project - Free Software Foundation.

For the first two steps, they did not five me any errors.

Thank you for your help!

Emmy

rickr · June 21, 2024, 3:10pm

Hi Emmy,

What is the output of:

echo CC is $CC
ls -l /usr/local/bin/gcc*

Thanks,

rick

Emmy · June 21, 2024, 3:22pm

Hi Rickr,

the out put is
ls -l /usr/local/bin/gcc*
CC is
lrwxr-xr-x 1 root admin 21 Jun 18 16:53 /usr/local/bin/gcc-13 -> /usr/local/bin/gcc-14
lrwxr-xr-x 1 syja admin 33 Jun 18 16:50 /usr/local/bin/gcc-14 -> ../Cellar/gcc/14.1.0_1/bin/gcc-14
lrwxr-xr-x 1 syja admin 36 Jun 18 16:50 /usr/local/bin/gcc-ar-14 -> ../Cellar/gcc/14.1.0_1/bin/gcc-ar-14
lrwxr-xr-x 1 syja admin 36 Jun 18 16:50 /usr/local/bin/gcc-nm-14 -> ../Cellar/gcc/14.1.0_1/bin/gcc-nm-14
lrwxr-xr-x 1 syja admin 40 Jun 18 16:50 /usr/local/bin/gcc-ranlib-14 -> ../Cellar/gcc/14.1.0_1/bin/gcc-ranlib-14

rickr · June 21, 2024, 3:42pm

Oh, we never put the install of gcc 13 into the intel notes. Please do:

brew install gcc@13

And then repeat the user install steps:

tcsh OS_notes.macos_12_intel_b_user.tcsh

Please let us know how it goes, thanks!

rick

Emmy · June 21, 2024, 5:57pm

Thank you for your advice!

When I do the first command, it gave me this error:
==> Downloading https://ghcr.io/v2/homebrew/core/gcc/13/manifests/13.3.0

###################################################################################################################### 100.0%

==> Fetching gcc@13

==> Downloading https://ghcr.io/v2/homebrew/core/gcc/13/blobs/sha256:4c479e51e3e4dc9eefacd32a8fce5f8f0f707311df3e06e2f6b470dd

###################################################################################################################### 100.0%

==> Pouring gcc@13--13.3.0.sonoma.bottle.tar.gz

Error: The brew link step did not complete successfully

The formula built, but is not symlinked into /usr/local

Could not symlink bin/gcc-13

Target /usr/local/bin/gcc-13

is a symlink belonging to gcc. You can unlink it:

brew unlink gcc

To force the link and overwrite all conflicting files:

brew link --overwrite gcc@13

To list all files that would be deleted:

brew link --overwrite gcc@13 --dry-run

Possible conflicting files are:

/usr/local/bin/gcc-13 -> /usr/local/bin/gcc-14

Error: Could not symlink include/c++/14/algorithm

Target /usr/local/include/c++/14/algorithm

is a symlink belonging to gcc. You can unlink it:

brew unlink gcc

To force the link and overwrite all conflicting files:

brew link --overwrite gcc

To list all files that would be deleted:

brew link --overwrite gcc --dry-run

discoraj · June 21, 2024, 6:59pm

Try the afni install anyway.
afni should find the gcc 13.
If not, we can do the linking.

Emmy · June 21, 2024, 7:13pm

Hi Rick,
I tried to install command and the terminal gave me the below feedback:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 10376 0 --:--:-- --:--:-- --:--:-- 10386
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.3.1
R ver : 4.3.1
echo

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 160k 0 --:--:-- --:--:-- --:--:-- 160k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/syja/abin
-- have current build label local
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 156 0 --:--:-- --:--:-- --:--:-- 157

++ update needed, installing...

++ downloading full package: curl -O -f anyos_text_atlas.tgz ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 65.9M 100 65.9M 0 0 15.3M 0 0:00:04 0:00:04 --:--:-- 15.3M
++ extracting package anyos_text_atlas.tgz...
++ syncing new binaries...
done, yay (binaries are under /Users/syja/abin)
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

| ^
dfe.c:67:1: error: return type defaults to 'int' [-Wimplicit-int]
67 | y_newrec(Void)
| ^~
dfe.c:83:1: error: return type defaults to 'int' [-Wimplicit-int]
83 | c_dfe(cilist a)
| ^~~
make[1]: [dfe.o] Error 1
mv: rename libf2c.a to ../libf2c.a: No such file or directory
make: * [libf2c.a] Error 1

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo setenv R_LIBS /Users/syja/sw/R-4.3.1
mkdir -p /Users/syja/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

oo Warning:
Failed to load R_io.so with this error message:

dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다

This is just weird since I dont speak Korean but the terminal gave me feedback in that way.

And when I enter the evaluation command: afni_system_check.py -check_all
The terminal gave me this:
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 23.4.0
version: Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:31 PST 2024; root:xnu-10063.101.15~2/RELEASE_X86_64
distribution: 10.16
number of CPUs: 16
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/syja/abin/afni
afni version : dyld[41664]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
:
AFNI_version.txt : AFNI_24.1.22, anyos_text, Jun 21 2024, local
which python : /Users/syja/anaconda3/bin/python
python version : 3.10.9
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 : 1 (/Users/syja/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/bin/R)
python : 1 (/Users/syja/anaconda3/bin/python3.10)
python2 : 0
python3 : 4
/Users/syja/anaconda3/bin/python3.10
/Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3

** have python3 but not python2

testing ability to start various programs...
afni : FAILURE
dyld[41669]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: /Users/syja/abin/afni
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
suma : FAILURE
dyld[41670]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <8F919DA1-00FC-3379-94DA-FACFBD8BDC69> /Users/syja/abin/suma
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dSkullStrip : FAILURE
dyld[41671]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <34F670FE-2B1A-3C99-8CF1-AC4CAFE92039> /Users/syja/abin/3dSkullStrip
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dAllineate : FAILURE
dyld[41672]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <12452873-CB4C-3448-AE54-72DFEED6E7B0> /Users/syja/abin/3dAllineate
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dRSFC : FAILURE
dyld[41673]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <2EE7B084-F085-38E5-BEF7-87C8AA7FAAB2> /Users/syja/abin/3dRSFC
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
SurfMesh : FAILURE
dyld[41674]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <6A26E5D3-00D9-344D-B342-155A44A8D3BC> /Users/syja/abin/SurfMesh
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dClustSim : FAILURE
dyld[41675]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: /Users/syja/abin/3dClustSim
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
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
dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다

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

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

++ module loaded: matplotlib.pyplot
module file : /Users/syja/anaconda3/lib/python3.10/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.0

++ module loaded: flask
module file : /Users/syja/anaconda3/lib/python3.10/site-packages/flask/init.py
flask version : 2.2.2

** 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 /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
/usr/local/bin/python3.9 (sym link to /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9)

-------------------------------- env vars --------------------------------
PATH = /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin

PYTHONPATH (sub-shell) =
R_LIBS = /Users/syja/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

----------------------------- 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 : found TT_N27+tlrc under /Users/syja/abin

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

which brew : /usr/local/bin/brew
brew version : Homebrew 4.3.6

** consider linking /usr/local/Cellar/gcc/14.1.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.80.3/lib/libglib-2.0.dylib

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

just be aware: login shell 'zsh', but our code examples use 'tcsh'
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)
consider linking /usr/local/Cellar/gcc/14.1.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib

Thank you,
Emmy

discoraj · June 21, 2024, 7:26pm

OK. Yes weird for the Korean text.
Maybe we do have to link gcc.
Rick will have to give us a hint for that.

Emmy · June 21, 2024, 7:38pm

Thank you!

rickr · June 21, 2024, 8:02pm

Hi Emma,

Did you possibly make the link from gcc-13 to gcc-14 yourself? I have never heard of that, and it would seem very weird for homebrew to do, but more likely for you.

In any case, we definitely do not want to use gcc-14 at this point (we will deal with that soon, but not yet). If you made the link yourself, just do:

sudo rm /usr/local/bin/gcc-13

Otherwise, try the suggested commands (not sure which might work):

brew unlink gcc
brew link --overwrite gcc@13

Thanks,

rick

Emmy · June 21, 2024, 8:14pm

Hi Rick,

No, I don't think I do that (I dont even sure what does that mean). But I would try both of the commands to see.

So should I apply the command tcsh OS_notes.macos_12_intel_b_user.tcsh after I apply above mentioned commands?

Thank you!

rickr · June 21, 2024, 8:52pm

Sure, go ahead and try again, it would be good to see results of that build_afni.py command. But the basic thing you might check first is the state of /usr/local/bin/gcc-13. If that still points to 14, we can think more of how to fix it first.

ls -l /usr/local/bin/gcc*

Thanks,

rick

Emmy · June 24, 2024, 6:01pm

Hi Rick,

Thank you!
Now the state shows it points to 13:
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % ls -l /usr/local/bin/gcc*
lrwxr-xr-x 1 syja admin 34 Jun 21 16:16 /usr/local/bin/gcc-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-13
lrwxr-xr-x 1 syja admin 37 Jun 21 16:16 /usr/local/bin/gcc-ar-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-ar-13
lrwxr-xr-x 1 syja admin 37 Jun 21 16:16 /usr/local/bin/gcc-nm-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-nm-13
lrwxr-xr-x 1 syja admin 41 Jun 21 16:16 /usr/local/bin/gcc-ranlib-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-ranlib-13
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ %

However, after I try these: brew unlink gcc
brew link --overwrite gcc@13, and thenapply tcsh OS_notes.macos_12_intel_b_user.tcsh, it gave me the same error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 11316 0 --:--:-- --:--:-- --:--:-- 11285
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.3.1
R ver : 4.3.1
echo

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 169k 0 --:--:-- --:--:-- --:--:-- 169k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/syja/abin
-- have current build label local
-- any downloads will be from

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 156 0 --:--:-- --:--:-- --:--:-- 156
++ no update needed
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

AFNI_version.h ;
echo "#undef AFNI_VERSION_PLATFORM" >> AFNI_version.h ;
echo '#define AFNI_VERSION_PLATFORM "'macos_12_x86_64'"'
AFNI_version.h ;
( cd niml/ ; make all 'CC=/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC ' ; /bin/mv -f *.o .. ; )
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -I../f2c -c niml_b64.c
make[1]: /usr/local/bin/gcc-13: No such file or directory
make[1]: *** [niml_b64.o] Error 1
mv: rename .o to ../.o: No such file or directory
make: *** [niml_b64.o] Error 1

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo setenv R_LIBS /Users/syja/sw/R-4.3.1
mkdir -p /Users/syja/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

oo Warning:
Failed to load R_io.so with this error message:

dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % brew unlink gcc
Unlinking /usr/local/Cellar/gcc/14.1.0_1... 34 symlinks removed.
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % brew link --overwrite gcc@13
Linking /usr/local/Cellar/gcc@13/13.3.0... 33 symlinks created.
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % tcsh OS_notes.macos_12_intel_b_user.tcsh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 14744 0 --:--:-- --:--:-- --:--:-- 14732
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.3.1
R ver : 4.3.1
echo

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 173k 0 --:--:-- --:--:-- --:--:-- 173k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/syja/abin
-- have current build label local
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 156 0 --:--:-- --:--:-- --:--:-- 156
++ no update needed
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -c afni_whelp.c -I. -I/usr/local/include -I/opt/X11/include -I/usr/local/include/netpbm -I/usr/include -Icoxplot -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -Ileej3 -DHAVE_ZLIB -DHAVE_GIFTI -If2c
(cd leej3;
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load -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

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo setenv R_LIBS /Users/syja/sw/R-4.3.1
mkdir -p /Users/syja/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

oo Warning:
Failed to load R_io.so with this error message:

dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % ls -l /usr/local/bin/gcc*
lrwxr-xr-x 1 syja admin 34 Jun 21 16:16 /usr/local/bin/gcc-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-13
lrwxr-xr-x 1 syja admin 37 Jun 21 16:16 /usr/local/bin/gcc-ar-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-ar-13
lrwxr-xr-x 1 syja admin 37 Jun 21 16:16 /usr/local/bin/gcc-nm-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-nm-13
lrwxr-xr-x 1 syja admin 41 Jun 21 16:16 /usr/local/bin/gcc-ranlib-13 -> ../Cellar/gcc@13/13.3.0/bin/gcc-ranlib-13
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % brew unlink gcc
brew link --overwrite gcc@13
Unlinking /usr/local/Cellar/gcc/14.1.0_1... 0 symlinks removed.
Warning: Already linked: /usr/local/Cellar/gcc@13/13.3.0
To relink, run:
brew unlink gcc@13 && brew link gcc@13
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % brew link --overwrite gcc@13
Warning: Already linked: /usr/local/Cellar/gcc@13/13.3.0
To relink, run:
brew unlink gcc@13 && brew link gcc@13
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % tcsh OS_notes.macos_12_intel_b_user.tcsh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 11599 0 --:--:-- --:--:-- --:--:-- 11620
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.3.1
R ver : 4.3.1
echo

Emmy · June 24, 2024, 6:10pm

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 172k 0 --:--:-- --:--:-- --:--:-- 172k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/syja/abin
-- have current build label local
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 155 0 --:--:-- --:--:-- --:--:-- 156
++ no update needed
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -c afni_whelp.c -I. -I/usr/local/include -I/opt/X11/include -I/usr/local/include/netpbm -I/usr/include -Icoxplot -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -Ileej3 -DHAVE_ZLIB -DHAVE_GIFTI -If2c
(cd leej3;
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load -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

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo setenv R_LIBS /Users/syja/sw/R-4.3.1
mkdir -p /Users/syja/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

oo Warning:
Failed to load R_io.so with this error message:

dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다

discoraj · June 24, 2024, 7:16pm

try:

brew install jpeg

and rerun the installation

Emmy · June 25, 2024, 3:09pm

thank you for you advice, I tried this and rerun the installation and gave me this output:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3521 100 3521 0 0 10732 0 --:--:-- --:--:-- --:--:-- 10767
set os = uname -s
uname -s
if ( 0 ) then
if ( Darwin != Darwin ) then
set cpu = uname -m
uname -m
if ( 0 ) then
set rver = R --version | head -n 1 | cut -d ' ' -f 3
R --version
cut -d -f 3
head -n 1
if ( 0 ) then
echo OS : Darwin
OS : Darwin
echo CPU : x86_64
CPU : x86_64
echo R ver : 4.3.1
R ver : 4.3.1
echo

defaults write org.macosforge.xquartz.X11 wm_ffm -bool true
defaults write org.x.X11 wm_ffm -bool true
defaults write com.apple.Terminal FocusFollowsMouse -string YES
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 53097 100 53097 0 0 158k 0 --:--:-- --:--:-- --:--:-- 158k
tcsh @update.afni.binaries -no_recur -package anyos_text_atlas -bindir /Users/syja/abin
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /Users/syja/abin
-- have current build label local
-- any downloads will be from https://afni.nimh.nih.gov via curl -O -f

-- attempting to install package anyos_text_atlas under
install dir: /Users/syja/abin...
-- have install dir
++ working in new temp dir, .tmp.install
-- skipping update of @update.afni.binaries
++ downloading test file: curl -O -f anyos_text_atlas/AFNI_version.txt ...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 42 100 42 0 0 156 0 --:--:-- --:--:-- --:--:-- 156
++ no update needed
/Users/syja/abin/init_user_dotfiles.py -shell_list bash zsh tcsh -do_updates path apsearch -dir_bin /Users/syja/abin
-- 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 4 dot files

source ~/.cshrc
source /Users/syja/.tcshrc
if ( -f /Users/syja/anaconda3/etc/profile.d/conda.csh ) then
source /Users/syja/anaconda3/etc/profile.d/conda.csh
setenv CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv _CONDA_ROOT /Users/syja/anaconda3
setenv _CONDA_EXE /Users/syja/anaconda3/bin/conda
setenv CONDA_PYTHON_EXE /Users/syja/anaconda3/bin/python
if ( ! 1 ) then
if ( /Users/syja/anaconda3/bin/conda == ) then
endif
if ( alias conda == ) then
alias conda
if ( 1 ) then
set _CONDA_PFX=dirname "${_CONDA_EXE}"
dirname /Users/syja/anaconda3/bin/conda
set _CONDA_PFX=dirname "${_CONDA_PFX}"
dirname /Users/syja/anaconda3/bin
alias conda source /Users/syja/anaconda3/etc/profile.d/conda.csh
unset _CONDA_PFX
else
setenv CONDA_SHLVL 0
if ( ! 0 ) then
set prompt=
endif
else
else
setenv PATH /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/Users/syja/abin
if ( 1 ) then
if ( != ) then
endif
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.4.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
setenv R_LIBS /Users/syja/sw/R-4.3.1
if ( x86_64 == x86_64 ) then
set package = macos_12_x86_64
else
build_afni.py -build_root /Users/syja/afni_build -package macos_12_x86_64

-- current AFNI: AFNI_24.1.22, anyos_text, Jun 21 2024
-- cleaning old build root dir, /Users/syja/afni_build
-- backing up dir build_src
-- preparing build_root dir, /Users/syja/afni_build
-- have default git tag LAST_TAG, will checkout AFNI_24.1.22
-- checking out git tag AFNI_24.1.22
-- using repo branch (detached), tag AFNI_24.1.22
-- 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_12_x86_64
-- copying README files
-- copying Makefile.macos_12_x86_64 to Makefile
-- building make target 'itall'

-- consider monitoring the build in a separate window with:
cd /Users/syja
tail -f /Users/syja/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/syja/afni_build/build_src/log_make.txt
error: tail from log_make.txt:

/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -Wcomment -Wformat -DUSE_TRACING -DHAVE_XDBE -DDONT_USE_MCW_MALLOC -c afni_whelp.c -I. -I/usr/local/include -I/opt/X11/include -I/usr/local/include/netpbm -I/usr/include -Icoxplot -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -Ileej3 -DHAVE_ZLIB -DHAVE_GIFTI -If2c
(cd leej3;
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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
/usr/local/bin/gcc-13 -O2 -DDARWIN -m64 -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/usr/local/lib -L/opt/X11/lib -L/usr/local/lib -Wl,-x -Wl,-multiply_defined -Wl,warning -Wl,-bind_at_load -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

** warning: in conda environment
CONDA_SHLVL = 0, CONDA_DEFAULT_ENV = base

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

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

rehash
setenv R_LIBS /Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo export R_LIBS=/Users/syja/sw/R-4.3.1
echo setenv R_LIBS /Users/syja/sw/R-4.3.1
mkdir -p /Users/syja/sw/R-4.3.1
rPkgsInstall -pkgs ALL
tee out.rPkgsInstall.txt

oo Warning:
Failed to load R_io.so with this error message:

dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다

Emmy · June 25, 2024, 3:10pm

then i run the evaluation command:
(base) syja@dynamic-oit-ip4-wifirestricted01-10-17-75-223 ~ % afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 23.4.0
version: Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:31 PST 2024; root:xnu-10063.101.15~2/RELEASE_X86_64
distribution: 10.16
number of CPUs: 16
apparent login shell: zsh
shell RC file: .zshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/syja/abin/afni
afni version : dyld[89914]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
:
AFNI_version.txt : AFNI_24.1.22, anyos_text, Jun 21 2024, local
which python : /Users/syja/anaconda3/bin/python
python version : 3.10.9
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 : 1 (/Users/syja/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/bin/R)
python : 1 (/Users/syja/anaconda3/bin/python3.10)
python2 : 0
python3 : 4
/Users/syja/anaconda3/bin/python3.10
/Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9
/usr/bin/python3

** have python3 but not python2

testing ability to start various programs...
afni : FAILURE
dyld[89919]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: /Users/syja/abin/afni
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
suma : FAILURE
dyld[89920]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <8F919DA1-00FC-3379-94DA-FACFBD8BDC69> /Users/syja/abin/suma
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dSkullStrip : FAILURE
dyld[89921]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <34F670FE-2B1A-3C99-8CF1-AC4CAFE92039> /Users/syja/abin/3dSkullStrip
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dAllineate : FAILURE
dyld[89922]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <12452873-CB4C-3448-AE54-72DFEED6E7B0> /Users/syja/abin/3dAllineate
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dRSFC : FAILURE
dyld[89923]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <2EE7B084-F085-38E5-BEF7-87C8AA7FAAB2> /Users/syja/abin/3dRSFC
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
SurfMesh : FAILURE
dyld[89924]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <6A26E5D3-00D9-344D-B342-155A44A8D3BC> /Users/syja/abin/SurfMesh
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
3dClustSim : FAILURE
dyld[89925]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: /Users/syja/abin/3dClustSim
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
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
dyn.load(ll)에서 다음과 같은 에러가 발생했습니다:
공유된 객체 '/Users/syja/abin/R_io.so'를 로드 할 수 없습니다:
dlopen(/Users/syja/abin/R_io.so, 0x0006): Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python
Referenced from: <86730901-707D-3DEC-8FA9-5CD4BF68BD81> /Users/syja/abin/R_io.so
Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file)
호출: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
실행이 정지되었습니다

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

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

++ module loaded: matplotlib.pyplot
module file : /Users/syja/anaconda3/lib/python3.10/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.0

++ module loaded: flask
module file : /Users/syja/anaconda3/lib/python3.10/site-packages/flask/init.py
flask version : 2.2.2

** 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 /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12)
/usr/local/bin/python3.9 (sym link to /Library/Frameworks/Python.framework/Versions/3.9/bin/python3.9)

-------------------------------- env vars --------------------------------
PATH = /Users/syja/anaconda3/bin:/Users/syja/anaconda3/condabin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.12/bin:/usr/local/bin:/usr/local/sbin:/Library/Frameworks/Python.framework/Versions/3.9/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/Apple/usr/bin:/usr/local/opt/python/libexec/bin:/Users/syja/abin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin:/usr/local/opt/python/libexec/bin

PYTHONPATH (sub-shell) =
R_LIBS = /Users/syja/sw/R-4.4.1
LD_LIBRARY_PATH (sub-shell) =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
CONDA_SHLVL = 1
CONDA_DEFAULT_ENV = base

----------------------------- 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 : found TT_N27+tlrc under /Users/syja/abin

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

which brew : /usr/local/bin/brew
brew version : Homebrew 4.3.7

** consider linking /usr/local/Cellar/gcc/14.1.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.80.3/lib/libglib-2.0.dylib

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

just be aware: login shell 'zsh', but our code examples use 'tcsh'
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)
consider linking /usr/local/Cellar/gcc/14.1.0_1/lib/gcc/current/libgomp.1.dylib under /usr/local/lib

discoraj · June 26, 2024, 2:47pm

Hmm.
It still didn't find libjpg.
and it is looking for python 2.7 for some reason.
Not sure about the many versions of python 3 with conda.
Maybe @rickr can help a little better than I...