Last login: Mon Nov 21 19:02:29 on ttys000
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
[Michaels-MacBook-Pro-2:~] amlung% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/amlung/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 9 2022
: AFNI_22.3.05 'Lucius Verus'
AFNI_version.txt : AFNI_22.3.05, macos_10.12_local, Nov 09 2022
which python : /usr/local/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/amlung/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 2
/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
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/amlung/abin/R_io.so':
dlopen(/Users/amlung/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/amlung/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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** have PyQt4, but cannot load QtCore, QtGui; error is:
**************************************************
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named sip
**************************************************
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
/usr/local/bin/python2 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python2.7 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/amlung/abin:/Applications/workbench/bin_macosx64/
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = /Users/amlung/abin
------------------------------ 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/amlung/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.2
which brew : /usr/local/bin/brew
brew version : Homebrew >=1.7.1 (shallow or no git repository)
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
++ 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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* check for partial install of PyQt4
* python library matplotlib is required
(see AFNI install docs for details)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* consider installing gcc under homebrew
* consider installing glib under homebrew
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung% python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.py
import site # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py
import os # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.pyc
import errno # builtin
import posix # builtin
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.py
import posixpath # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/posixpath.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/stat.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/stat.py
import stat # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/stat.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/genericpath.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/genericpath.py
import genericpath # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/genericpath.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/warnings.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/warnings.py
import warnings # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/warnings.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/linecache.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/linecache.py
import linecache # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/linecache.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/types.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/types.py
import types # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/types.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/UserDict.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/UserDict.py
import UserDict # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/UserDict.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_abcoll.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_abcoll.py
import _abcoll # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_abcoll.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/abc.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/abc.py
import abc # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/abc.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_weakrefset.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_weakrefset.py
import _weakrefset # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_weakrefset.pyc
import _weakref # builtin
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/copy_reg.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/copy_reg.py
import copy_reg # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/copy_reg.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/traceback.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/traceback.py
import traceback # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/traceback.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.py
import sysconfig # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sysconfig.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py
import re # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_compile.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_compile.py
import sre_compile # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_compile.pyc
import _sre # builtin
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_parse.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_parse.py
import sre_parse # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_parse.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_constants.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_constants.py
import sre_constants # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/sre_constants.pyc
dlopen("/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so", 2);
import _locale # dynamically loaded from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/_locale.so
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_sysconfigdata.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_sysconfigdata.py
import _sysconfigdata # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_sysconfigdata.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.py
import _osx_support # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/_osx_support.pyc
# /usr/local/lib/python2.7/site-packages/sitecustomize.pyc matches /usr/local/lib/python2.7/site-packages/sitecustomize.py
import sitecustomize # precompiled from /usr/local/lib/python2.7/site-packages/sitecustomize.pyc
import encodings # directory /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/__init__.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/__init__.py
import encodings # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/__init__.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/codecs.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/codecs.py
import codecs # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/codecs.pyc
import _codecs # builtin
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/aliases.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/aliases.py
import encodings.aliases # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/aliases.pyc
# /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/utf_8.pyc matches /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/utf_8.py
import encodings.utf_8 # precompiled from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/encodings/utf_8.pyc
Python 2.7.16 (default, Sep 2 2019, 12:01:16)
[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.39.2)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
dlopen("/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so", 2);
import readline # dynamically loaded from /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so
>>>
>>>
>>>
KeyboardInterrupt
>>>
>>>
KeyboardInterrupt
>>>
KeyboardInterrupt
>>>
KeyboardInterrupt
>>> exit
Use exit() or Ctrl-D (i.e. EOF) to exit
>>> exit()
# clear __builtin__._
# clear sys.path
# clear sys.argv
# clear sys.ps1
# clear sys.ps2
# clear sys.exitfunc
# clear sys.exc_type
# clear sys.exc_value
# clear sys.exc_traceback
# clear sys.last_type
# clear sys.last_value
# clear sys.last_traceback
# clear sys.path_hooks
# clear sys.path_importer_cache
# clear sys.meta_path
# clear sys.flags
# clear sys.float_info
# restore sys.stdin
# restore sys.stdout
# restore sys.stderr
# cleanup __main__
# cleanup[1] encodings
# cleanup[1] site
# cleanup[1] sysconfig
# cleanup[1] abc
# cleanup[1] _weakrefset
# cleanup[1] sre_constants
# cleanup[1] _codecs
# cleanup[1] _warnings
# cleanup[1] zipimport
# cleanup[1] _sysconfigdata
# cleanup[1] mpl_toolkits
# cleanup[1] encodings.utf_8
# cleanup[1] _osx_support
# cleanup[1] codecs
# cleanup[1] readline
# cleanup[1] sitecustomize
# cleanup[1] signal
# cleanup[1] traceback
# cleanup[1] posix
# cleanup[1] encodings.aliases
# cleanup[1] exceptions
# cleanup[1] _weakref
# cleanup[1] re
# cleanup[1] _locale
# cleanup[1] sre_compile
# cleanup[1] _sre
# cleanup[1] sre_parse
# cleanup[2] copy_reg
# cleanup[2] posixpath
# cleanup[2] errno
# cleanup[2] _abcoll
# cleanup[2] types
# cleanup[2] genericpath
# cleanup[2] stat
# cleanup[2] warnings
# cleanup[2] UserDict
# cleanup[2] os.path
# cleanup[2] linecache
# cleanup[2] os
# cleanup sys
# cleanup __builtin__
# cleanup ints: 20 unfreed ints
# cleanup floats
[Michaels-MacBook-Pro-2:~] amlung% python -V
Python 2.7.16
[Michaels-MacBook-Pro-2:~] amlung% python3 -version
Unknown option: -e
usage: /Library/Frameworks/Python.framework/Versions/3.11/Resources/Python.app/Contents/MacOS/Python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Try `python -h' for more information.
[Michaels-MacBook-Pro-2:~] amlung% python3 --version
Python 3.11.0
[Michaels-MacBook-Pro-2:~] amlung% pip install matplotlib
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at [
pip.pypa.io] pip 21.0 will remove support for this functionality.
Requirement already satisfied: matplotlib in /usr/local/lib/python2.7/site-packages (2.2.5)
Requirement already satisfied: subprocess32 in /usr/local/lib/python2.7/site-packages (from matplotlib) (3.5.4)
Requirement already satisfied: pytz in /usr/local/lib/python2.7/site-packages (from matplotlib) (2022.6)
Requirement already satisfied: backports.functools-lru-cache in /usr/local/lib/python2.7/site-packages (from matplotlib) (1.6.4)
Requirement already satisfied: six>=1.10 in /usr/local/lib/python2.7/site-packages (from matplotlib) (1.16.0)
Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python2.7/site-packages (from matplotlib) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python2.7/site-packages (from matplotlib) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python2.7/site-packages (from matplotlib) (0.10.0)
Requirement already satisfied: numpy>=1.7.1 in /usr/local/lib/python2.7/site-packages (from matplotlib) (1.16.6)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python2.7/site-packages (from matplotlib) (2.4.7)
Requirement already satisfied: setuptools in /usr/local/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib) (41.0.1)
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung%
[Michaels-MacBook-Pro-2:~] amlung% afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: i386
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
distribution: 10.14.6
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/amlung/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 9 2022
: AFNI_22.3.05 'Lucius Verus'
AFNI_version.txt : AFNI_22.3.05, macos_10.12_local, Nov 09 2022
which python : /usr/local/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/amlung/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R)
python : 2
/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/usr/bin/python
python2 : 1 (/usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
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/amlung/abin/R_io.so':
dlopen(/Users/amlung/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/amlung/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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** have PyQt4, but cannot load QtCore, QtGui; error is:
**************************************************
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named sip
**************************************************
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is required
-- python binaries under /usr/local/bin:
/usr/local/bin/python (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11)
/usr/local/bin/python2 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python2.7 (sym link to /usr/local/Cellar/python@2/2.7.16_1/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/Library/Frameworks/Python.framework/Versions/3.11/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/amlung/abin:/Applications/workbench/bin_macosx64/
PYTHONPATH = /usr/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = /Users/amlung/abin
------------------------------ 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/amlung/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.8.2
which brew : /usr/local/bin/brew
brew version : Homebrew >=1.7.1 (shallow or no git repository)
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
++ 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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* check for partial install of PyQt4
* python library matplotlib is required
(see AFNI install docs for details)
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
* consider installing gcc under homebrew
* consider installing glib under homebrew
