Dear afni experts
I have tried many times to launch my uber_subject.py
Following is my output of afni_system_check.py -check_all
==========================================
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.7.0
version: Darwin Kernel Version 18.7.0: Sun Dec 1 18:59:03 PST 2019; root:xnu-4903.278.19~1/RELEASE_X86_64
distribution: 10.14.6 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/lsj/abin/afni
afni version : Precompiled binary macos_10.12_local: Jan 17 2020
: AFNI_20.0.00 'Galba'
AFNI_version.txt : AFNI_20.0.00, macos_10.12_local, Jan 17 2020
which python : /sw/bin/python
python version : 2.7.17
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/lsj/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/sw/bin/python2.7
/usr/bin/python
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/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 : 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 -------------------------------
++ module loaded: PyQt4
module file : /usr/local/lib/python2.7/site-packages/PyQt4/__init__.pyc
** have PyQt4, but cannot load QtCore, QtGui; error is:
**************************************************
**************************************************
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-- python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7
-- python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /usr/local/Cellar/python/3.7.6_1/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/lsj/abin
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) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: 22 Oct 2019 [discoraj]: added Cluster Explorer 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/lsj/abin
------------------------------ OS specific -------------------------------
XQuartz version : 2.7.11
which fink : /sw/bin/fink
fink version : Package manager version: 0.45.0
which brew : /usr/local/bin/brew
brew version : Homebrew 2.2.3
++ found 'brew' at /usr/local/bin/brew
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
** warning: have brew? PyQt4, but non-brew python /sw/bin/python
++ 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: =========================
* check for partial install of PyQt4
===================================================================
I have already install fink 0.45.0
After I run the sudo fink install pyqt4-mac-py27
I found this error: Failed: phase installing: phonon-mac-shlibs-4.5.0-39 failed
I further try fink selfupdate, but it didn’t solve the problem
following system information:
Package manager version: 0.45.0
Distribution version: selfupdate-rsync Thu Jan 23 00:01:03 2020, 10.14.5, x86_64
Trees: local/main stable/main
Xcode.app: 11.3.1
Xcode command-line tools: 11.3.1.0.1.1576735732
Max. Fink build jobs: 4
================================================================
I also post my .cshrc file for anyone can help me to set
setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace
set path = ( $path /Users/lsj/abin )
if ( -f $HOME/.afni/help/all_progs.COMP ) then
source $HOME/.afni/help/all_progs.COMP
endif
source /sw/bin/init.csh
set filec
set autolist
set nobeep
alias ls ls -G
alias ll ls -lG
setenv PYTHONPATH /usr/local/lib/python2.7/site-packages
================================================================
Did anyone can help me to fix this problem?
I really need to run uber_subject.py for my data.
I would very appreciate anyone who can give me some suggestion on it.
Thanks