AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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xiyuezh
March 01, 2022 06:15PM
Hi experts,

I have some issue when trying to run 3dMVM.
It says:
Quote
updating R_LD_LIBRARY_PATH ...

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

Error in dyn.load(ll) :
unable to load shared object '/Users/xiyuezh/abin/R_io.so':
dlopen(/Users/xiyuezh/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/xiyuezh/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
Unmatched '.

File /Users/xiyuezh/abin/R_io.so exists in this folder. Then I checked 
afni_system_check.py -check_all

Quote
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/xiyuezh/abin/R_io.so':
dlopen(/Users/xiyuezh/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/xiyuezh/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

For the summary part, it says:
Quote
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* check for partial install of PyQt4
* consider installing gcc under homebrew
* consider installing glib under homebrew
* please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh

The computer is Mac Mojave 10.14.6.
AFNI version is Precompiled binary macos_10.12_local: Jan 31 2022 (Version AFNI_22.0.04 'Hadrian')
The R version is 4.1.1 (2021-08-10) -- "Kick Things". Platform: x86_64-apple-darwin17.0 (64-bit).

Could you please help to have a look? Thank you so much!!


Best,
Xiyue
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Subject Author Posted

3dMVM : FAILURE

xiyuezh March 01, 2022 06:15PM

Re: 3dMVM : FAILURE

gang March 02, 2022 10:41AM

Re: 3dMVM : FAILURE

xiyuezh March 02, 2022 04:42PM