Hello,
I’ve been trying to install AFNI unsuccessfully for a while in a 10.11.6 Mac OS X El Captain. The error seems to be the following:
Error in dyn.load(ll) :
unable to load shared object ‘/Users/fernanda/abin/R_io.so’:
dlopen(/Users/fernanda/abin/R_io.so, 6): Symbol not found: _getentropy
When running the afni_system_check.py, I got:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.6.0
version: Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64
distribution: 10.11.6
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/fernanda/abin/afni
afni version : Precompiled binary macos_10.12_local: Feb 10 2021
: AFNI_21.0.08 ‘Titus’
AFNI_version.txt : AFNI_21.0.08, macos_10.12_local, Feb 10 2021
which python : /Users/fernanda/anaconda3/bin/python
python version : 3.7.3
which R : /usr/local/bin/R
R version : R version 3.6.3 (2020-02-29) – “Holding the Windsock”
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/fernanda/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python : 2
/Users/fernanda/anaconda3/bin/python3.7
/usr/bin/python
python2 : 0
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/Users/fernanda/anaconda3/bin/python3.7
** have python3 but not python2
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/fernanda/abin/R_io.so’:
dlopen(/Users/fernanda/abin/R_io.so, 6): Symbol not found: _getentropy
Referenced from: /Users/fernanda/abin/libpython2.7.dylib (which was built for Mac OS X 10.12)
Expected in: /usr/lib/libSystem.B.dylib
in /Users/fernanda/abin/libpython2.7.dylib
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 : /Users/fernanda/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py
– 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 = /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/fernanda/anaconda3/bin:/Users/fernanda/anaconda3/condabin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/fernanda/abin:/Users/fernanda/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
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 : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/fernanda/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 3.0.1-10-g0d36d54
– 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’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
– recent OS X, cheating to check DYLD_LIBRARY_PATH in shell ‘tcsh’…
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
- just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
- AFNI programs show FAILURE
- insufficient data for AFNI bootcamp
- consider installing gcc under homebrew
- consider installing glib under homebrew
Any help on how to resolve this issue would be very appreciated!
Thanks in advance,
Fernanda