Hello,
I have been having issues getting uber_subject.py to work on my laptop (MacOSMojave, version 10.14.5). I would appreciate any insight on how to fix this issue. I do have to admit that I am VERY new to using AFNI and it can simply be an error on my part but I just can figure out what the error is.
When I initial run uber_subject.py I get this initial error:
PyQt4 must be installed to run the uber_subject.py GUI
--> see the output of: uber_subject.py -help_install
When running afni_system_check.py -check_all this is the output:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.6.0
version: Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64
distribution: 10.14.5 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/hectorarciniega/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 13 2019
: AFNI_19.2.24 'Claudius'
AFNI_version.txt : AFNI_19.2.24, macos_10.12_local, Sep 13 2019
which python : /usr/local/bin/python
python version : 2.7.16
which R : /usr/local/bin/R
R version : R version 3.5.3 (2019-03-11) -- "Great Truth"
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/hectorarciniega/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/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/3.7/bin/python3.7)
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 : FAILURE
oo Warning:
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
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 not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/hectorarciniega/abin:/Applications/abin:/usr/bin:/Users/hectorarciniega/bin:/usr/local/lib
PYTHONPATH = /sw/bin/local/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) = /Applications/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/hectorarciniega/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.13
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** consider linking /usr/local/Cellar/gcc/9.2.0_1/lib/gcc/9/libgomp.1.dylib under /usr/local/lib
++ found valid link /usr/local/lib/libglib-2.0.dylib
to ../Cellar/glib/2.62.0_1/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 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
* check for partial install of PyQt4
* insufficient data for AFNI bootcamp
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
