another Catalina issue: install troubles

AFNI Message Board
1

Hi guys-

I see some Catalina threads on here but they didn’t quite solve my issue.
I have a new macbook running 10.15.5.
I’m installing according to the AFNI instructions and get to this line and see:

[MacBook-Pro:~] torrisi% suma -update_env
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/suma
Reason: image not found
Abort

i’ve changed my default shell to tcsh and i was able to download most of AFNI and have ~/abin/ directory, although if type
afni -ver
i get the same error “dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib”

thoughts? sorry about this, and for choosing mac over linux

-sam

2

Hi Sam-

What’s the output of:


afni_system_check.py -check_all

And have you tried reinstalling XQuartz after you did the upgrade?

3

thanks Peter and TIA

well if i re-run “xcode-select --install” i just get:
xcode-select: error: command line tools are already installed, use “Software Update” to install updates

and then if i type
softwareupdate --list
it says “No new software available.”

the output of afni_system_check.py is clearly a mess:

[MacBook-Pro:~] torrisi% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
:
AFNI_version.txt : AFNI_20.1.18, macos_10.12_local, Jun 30 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/torrisi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)

testing ability to start various programs…
afni : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/afni
Reason: image not found
suma : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dAllineate
Reason: image not found
3dRSFC : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dRSFC
Reason: image not found
SurfMesh : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/SurfMesh
Reason: image not found
3dClustSim : FAILURE
dyld: Library not loaded: /opt/X11/lib/libXt.6.dylib
Referenced from: /Users/torrisi/abin/3dClustSim
Reason: image not found
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/Users/torrisi/abin/R_io.so’:
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

checking for $HOME files…
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/torrisi/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ 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/torrisi/abin

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

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt

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

  • AFNI programs show FAILURE
  • please run: “suma -update_env” for .sumarc
  • please run: apsearch -update_all_afni_help
  • insufficient data for AFNI bootcamp
  • OS X version might be old
4

Hi Sam,

To be sure, what is the output from:

ls -l /opt/X11/lib/libXt*

Thanks,

  • rick
5

hi again guys

omg i’m an idiot. i hadn’t fully installed xquartz, sorry. i may have also messed up some path stuff last night as i tried to troubleshoot, so i’m still getting an error about DYLD_LIBRARY_PATH but overall it’s looking better. first i’ll paste my current output of afni_system_check, and then at the bottom of this message i’ll respond to rick’s newest inquiry:

[MacBook-Pro:~] torrisi% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 30 2020
: AFNI_20.1.18 ‘Otho’
AFNI_version.txt : AFNI_20.1.18, macos_10.12_local, Jun 30 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/torrisi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/Users/torrisi/abin/R_io.so’:
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/torrisi/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ 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/torrisi/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

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

  • AFNI programs show FAILURE
  • insufficient data for AFNI bootcamp
  • OS X version might be old
  • consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace

and:

[MacBook-Pro:~] torrisi% ls -l /opt/X11/lib/libXt*
-rwxr-xr-x 1 root wheel 698896 Oct 29 2016 /opt/X11/lib/libXt.6.dylib
-rwxr-xr-x 1 root wheel 34224 Oct 29 2016 /opt/X11/lib/libXt.7.dylib
lrwxr-xr-x 1 torrisi wheel 13 Jul 1 10:46 /opt/X11/lib/libXt.dylib → libXt.6.dylib
-rwxr-xr-x 1 root wheel 71104 Oct 29 2016 /opt/X11/lib/libXtst.6.dylib
lrwxr-xr-x 1 torrisi wheel 15 Jul 1 10:46 /opt/X11/lib/libXtst.dylib → libXtst.6.dylib

6

That does not look too bad. There are some updates that need to be made to afni_system_check.py for 10.15, but I have not looked into it yet.

A more simple test might be to try to start suma. Does it open the GUI?

Though you may need to reboot first, having just installed XQuartz.

  • rick
7

Hi RIck

okay i’ve rebooted and adjusted some .bashrc and .cshrc text and now both afni and suma open. yay. however when i open afni, and as it opens (during splash screens etc), i get this large printout to the terminal:

[MacBook-Pro:~] torrisi% afni
Precompiled binary macos_10.12_local: Jun 30 2020 (Version AFNI_20.1.18 ‘Otho’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to SM Laconte for great efforts

Initializing: X11[The X.Org Foundation v 11804000].
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can’t find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to ‘NO’.
+++++++++++++++++++++++++++++++++++++++++++
. Widgets… Input files:
** Searching subdirectories of ‘./’ for data+./AFNI_data5/
session # 1 = ./AFNI_data5/ ==> 3 datasets+./abin/
session # 2 = ./abin/ ==> 54 datasets
dataset count = 57
Time series = 0 files readfind: .//Library/Application Support/CallHistoryTransactions: Operation not permitted
find: .//Library/Application Support/com.apple.sharedfilelist: Operation not permitted
find: .//Library/Application Support/com.apple.TCC: Operation not permitted
find: .//Library/Application Support/FileProvider: Operation not permitted
find: .//Library/Application Support/AddressBook: Operation not permitted
find: .//Library/Application Support/CallHistoryDB: Operation not permitted
find: .//Library/Autosave Information: Operation not permitted
find: .//Library/IdentityServices: Operation not permitted
find: .//Library/Calendars: Operation not permitted
find: .//Library/Messages: Operation not permitted
find: .//Library/HomeKit: Operation not permitted
find: .//Library/Sharing: Operation not permitted
find: .//Library/Mail: Operation not permitted
find: .//Library/Safari: Operation not permitted
find: .//Library/Suggestions: Operation not permitted
find: .//Library/Containers/com.apple.VoiceMemos: Operation not permitted
find: .//Library/Containers/com.apple.archiveutility: Operation not permitted
find: .//Library/Containers/com.apple.Home: Operation not permitted
find: .//Library/Containers/com.apple.Safari: Operation not permitted
find: .//Library/Containers/com.apple.iChat: Operation not permitted
find: .//Library/Containers/com.apple.CloudDocs.MobileDocumentsFileProvider: Operation not permitted
find: .//Library/Containers/com.apple.mail: Operation not permitted
find: .//Library/Containers/com.apple.news: Operation not permitted
find: .//Library/Containers/com.apple.stocks: Operation not permitted
find: .//Library/PersonalizationPortrait: Operation not permitted
find: .//Library/Metadata/CoreSpotlight: Operation not permitted
find: .//Library/Reminders: Operation not permitted
find: .//Library/Cookies: Operation not permitted
find: .//Library/Caches/com.apple.HomeKit.configurations: Operation not permitted
find: .//Library/Caches/CloudKit: Operation not permitted
find: .//Library/Caches/com.apple.ap.adprivacyd: Operation not permitted
find: .//.Trash: Operation not permitted
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
** ERROR: Table: can’t open file
find: ./Library//Application Support/CallHistoryTransactions: Operation not permitted
find: ./Library//Application Support/com.apple.sharedfilelist: Operation not permitted
find: ./Library//Application Support/com.apple.TCC: Operation not permitted
find: ./Library//Application Support/FileProvider: Operation not permitted
find: ./Library//Application Support/AddressBook: Operation not permitted
find: ./Library//Application Support/CallHistoryDB: Operation not permitted
find: ./Library//Autosave Information: Operation not permitted
find: ./Library//IdentityServices: Operation not permitted
find: ./Library//Calendars: Operation not permitted
find: ./Library//Messages: Operation not permitted
find: ./Library//HomeKit: Operation not permitted
find: ./Library//Sharing: Operation not permitted
find: ./Library//Mail: Operation not permitted
find: ./Library//Safari: Operation not permitted
find: ./Library//Suggestions: Operation not permitted
find: ./Library//Containers/com.apple.VoiceMemos: Operation not permitted
find: ./Library//Containers/com.apple.archiveutility: Operation not permitted
find: ./Library//Containers/com.apple.Home: Operation not permitted
find: ./Library//Containers/com.apple.Safari: Operation not permitted
find: ./Library//Containers/com.apple.iChat: Operation not permitted
find: ./Library//Containers/com.apple.CloudDocs.MobileDocumentsFileProvider: Operation not permitted
find: ./Library//Containers/com.apple.mail: Operation not permitted
find: ./Library//Containers/com.apple.news: Operation not permitted
find: ./Library//Containers/com.apple.stocks: Operation not permitted
find: ./Library//PersonalizationPortrait: Operation not permitted
find: ./Library//Metadata/CoreSpotlight: Operation not permitted
find: ./Library//Reminders: Operation not permitted
find: ./Library//Cookies: Operation not permitted
find: ./Library//Caches/com.apple.HomeKit.configurations: Operation not permitted
find: ./Library//Caches/CloudKit: Operation not permitted
find: ./Library//Caches/com.apple.ap.adprivacyd: Operation not permitted

.[tc]sv data = 28 files read
Path(s) to be searched for plugins:
/Users/torrisi/abin /Users/torrisi/abin/…/lib

NLfit & NLerr= Optimizer (AFNI_NLFIM_METHOD) is SIMPLEX
NLfit & NLerr= Found 30 models

Plugins = 51 libraries read
reading s620_rest_r1+orig(193 million bytes)…++ AFNI is detached from terminal.
[MacBook-Pro:~] torrisi% …done

if it’s not the reason unto itself, there seems to also be an issue with my R installs. here’s my system check output now:

afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.5.0
version: Darwin Kernel Version 19.5.0: Tue May 26 20:41:44 PDT 2020; root:xnu-6153.121.2~2/RELEASE_X86_64
distribution: unknown Darwin
number of CPUs: 8
apparent login shell: tcsh (current shell is csh)
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/torrisi/abin/afni
afni version : Precompiled binary macos_10.12_local: Jun 30 2020
: AFNI_20.1.18 ‘Otho’
AFNI_version.txt : AFNI_20.1.18, macos_10.12_local, Jun 30 2020
which python : /usr/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 4.0.2 (2020-06-22) – “Taking Off Again”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/torrisi/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/bin/python3)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/Users/torrisi/abin/R_io.so’:
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

-------------------------------- env vars --------------------------------
PATH = /Users/torrisi/anaconda/bin:/Users/torrisi/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/torrisi/abin:/Users/torrisi/abin:/Users/torrisi/abin:/sw/bin:/Users/torrisi/abin:/sw/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer Demo
data dir : found suma_demo under $HOME
top history: …s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/torrisi/abin

------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11

which brew : /usr/local/bin/brew
brew version : Homebrew 2.4.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
** env var DYLD_LIBRARY_PATH is not set to contain /opt/X11/lib/flat_namespace
(so afni and suma may fail)

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

  • AFNI programs show FAILURE
  • OS X version might be old
  • consider setting DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace
8

Hi,
For “Operation not permitted” errors:
Try going to the System Preferences, then Security & Privacy, then Full Disk Access.
Then make sure that launchd_startx, Terminal, and XQuartz are there and checked.
See attached.
You will need admin access.
Thanks, Justin

Screen Shot 2020-07-02 at 10.12.04 AM.jpg
Screen Shot 2020-07-02 at 10.12.04 AM.jpg1296×1124 137 KB

9

thanks Justin, that worked! no more Operation not permitted errors on launch.

now what about the system check’s evaluation of 3dMVM and R installs… despite having R installed and a working Rstudio, I’m still getting:

3dMVM : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/Users/torrisi/abin/R_io.so’:
dlopen(/Users/torrisi/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/torrisi/abin/R_io.so
Reason: image not found
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

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

10

Hi, Sam-

I will jump in for Justin here-- I think it is the R-4.* version.

At present on Macs, I think you have to have R-3.6.*.

–pt

11

ok got it… thanks everyone!