Hi, no worries - totally understand how things pile up quickly on the MB!
I believe I do have Xcode already installed ("which g++" returns "/usr/bin/g++").
I did the copy/pasting for the bash stuff, and also restarted my computer. After this, the output of "afni_system_check.py -check_all" is:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution: 10.15.6
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 27 2020
: AFNI_20.2.19 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.19, macos_10.12_local, Sep 27 2020
which python : /Users/liuj10/opt/anaconda2/bin/python
python version : 2.7.16
which R : /Users/liuj10/opt/anaconda2/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/liuj10/abin/afni)
R : 2
/Users/liuj10/opt/anaconda2/bin/R
/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R
python : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
python2 : 2
/Users/liuj10/opt/anaconda2/bin/python2.7
/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/liuj10/abin/R_io.so':
dlopen(/Users/liuj10/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/liuj10/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 : /Users/liuj10/opt/anaconda2/lib/R
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/liuj10/opt/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.pyc
-------------------------------- env vars --------------------------------
PATH = /usr/local/ANTs/bin/:/Users/liuj10/opt/anaconda2/bin:/Users/liuj10/opt/anaconda2/condabin:/usr/local/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin:/opt/X11/bin:/Users/liuj10/abin:/Users/liuj10/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/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 : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/liuj10/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.1
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.64.3/lib/libglib-2.0.dylib
++ 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
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /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
And when I try to run my 3dMVM script it throws this error:
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/liuj10/abin/R_io.so':
dlopen(/Users/liuj10/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/liuj10/abin/R_io.so
Reason: image not found
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
However, a colleague recommended trying "conda deactivate" so if I enter that and then check output of "afni_system_check.py -check_all" I get:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distribution: 10.15.6
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/liuj10/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 27 2020
: AFNI_20.2.19 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.19, macos_10.12_local, Sep 27 2020
which python : /usr/bin/python
python version : 2.7.16
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/liuj10/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.6/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 : success
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/ANTs/bin:/Users/liuj10/opt/anaconda2/condabin:/usr/local/fsl/bin:/usr/local/DTIPrepTools-0.1.1-Linux/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/MATLAB_R2019a.app/bin:/opt/X11/bin:/Users/liuj10/abin:/Users/liuj10/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/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 : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /Users/liuj10/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.5.1
-- for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
-- consider installing gcc under homebrew
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.64.3/lib/libglib-2.0.dylib
++ 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
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* insufficient data for AFNI bootcamp
Then when I try running the 3dMVM script, it seems to start working (calling on the correct R), but still throws an error:
updating R_LD_LIBRARY_PATH ...
Read 299 items
Loading required package: lme4
Loading required package: Matrix
Error: package or namespace load failed for ‘afex’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘data.table’
Execution halted
And I've tried doing install.packages("afex") but even if that works, it still throws the same error so something still seems to be wrong with how AFNI and R are communicating. Also, any time I open a new terminal window I have to re-enter conda deactivate otherwise AFNI still defaults to pointing to anaconda's R. Is there a more permanent solution I could implement?
Thanks!
Janelle
