afni.nimh.nih.gov

Hi experts,
I used the app to install the AFNI on Mac but the uber_subject does not work even after I used fink and brew to install the pyqt. Could you please help me on that? And I also install the python following the instructions but it did not show python2 in the output of checking file.

Thanks!


-------------------------------- general ---------------------------------
architecture: 64bit
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 x86_64
number of CPUs: 8
apparent login shell: csh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/xc363/abin/afni
afni version : Precompiled binary macos_10.12_local: Sep 6 2019
: AFNI_19.2.23 'Claudius'
AFNI_version.txt : AFNI_19.2.23, macos_10.12_local, Sep 06 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/xc363/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 2
/usr/bin/python
/sw/bin/python2.7
python2 : 0
python3 : 1 (/usr/local/Cellar/python/3.7.4_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)

-------------------------------- env vars --------------------------------
PATH = /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/laps:/opt/X11/bin:/sw/bin:/Users/xc363/abin

PYTHONPATH = /usr/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) =

------------------------------ 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: ...ay 2019 [rickr]: AFNI_pamenc updates to global_*.txt
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/xc363/aglobal

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.45.0
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.11

++ 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 /usr/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 'csh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/lib/gcc/lib:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

========================= summary, please fix: =========================
* check for partial install of PyQt4
* consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
* have brew? PyQt4, but non-brew python /usr/bin/python