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

History of AFNI updates  

|
July 16, 2021 02:01PM
I am not sure how to resolve the fixes that I need to make. How do I set the DYLD_LIBRARY_PATH? Also, how can I resolve the issue involved with 3dMVM? Thanks for the help!


-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              19.6.0
version:              Darwin Kernel Version 19.6.0: Thu May  6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64
distribution:         10.15.7
number of CPUs:       8
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/witherscp/abin/afni
afni version         : Precompiled binary macos_10.12_local: Jul 14 2021 
                     : AFNI_21.2.01 'Nerva'
AFNI_version.txt     : AFNI_21.2.01, macos_10.12_local, Jul 14 2021
which python         : /usr/bin/python
python version       : 2.7.16
which R              : /usr/local/bin/R
R version            : R version 3.4.1 (2017-06-30) -- "Single Candle"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/witherscp/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.4/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 : 2 
      /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
      /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/witherscp/abin/R_io.so':
          dlopen(/Users/witherscp/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
          Referenced from: /Users/witherscp/abin/R_io.so
          Reason: Incompatible library version: R_io.so requires version 3.6.0 or later, but libR.dylib provides version 3.4.0
        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

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
    /usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)

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

PYTHONPATH = 
R_LIBS = 
LD_LIBRARY_PATH = 
DYLD_LIBRARY_PATH (sub-shell) = ...completed.
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = ...completed.

------------------------------ 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: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo    under $HOME
           top history: ...s_New/data/Build_tmp on Mon Mar  4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas    : found TT_N27+tlrc  under /Users/witherscp/abin

------------------------------ OS specific -------------------------------
XQuartz version      : 2.8.1

which brew           : /usr/local/bin/brew
brew version         : Homebrew 3.2.2

-- 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
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in cur shell 'bash'...
** env var DYLD_LIBRARY_PATH is set, but without /opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  just be aware: login shell 'bash', but our code examples use 'tcsh'
*  AFNI programs show FAILURE
*  consider installing gcc under homebrew
*  consider installing glib under homebrew
*  please set DYLD_LIBRARY_PATH to include /opt/X11/lib/flat_namespace
*  please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh
Subject Author Posted

Unsure how to set DYLD_LIBRARY_PATH

witherscp July 16, 2021 02:01PM

Re: Unsure how to set DYLD_LIBRARY_PATH

gang July 18, 2021 11:59AM

Re: Unsure how to set DYLD_LIBRARY_PATH

witherscp July 19, 2021 09:01AM

Re: Unsure how to set DYLD_LIBRARY_PATH

witherscp July 19, 2021 10:48AM

Re: Unsure how to set DYLD_LIBRARY_PATH

rick reynolds July 19, 2021 10:51AM