Hello members,
I am a neurologist and new to AFNI and f-MRI analysis. I have installed AFNI on my MAC(Mojave). I am however unable to install Uber_subject.py. I have fink already installed but it is showing error message while populating python resources. I have brew installed pyqt4 but I am not sure if I have set up the python path correctly for fink to access that directory. I am attaching the error messages here. Any help on this matter would be greatly appreciated.
Thanks
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.2.0
version: Darwin Kernel Version 18.2.0: Mon Nov 12 20:24:46 PST 2018; root:xnu-4903.231.4~2/RELEASE_X86_64
distribution: 10.14.2 x86_64
number of CPUs: 4
apparent login shell: bash (current shell is csh)
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /Users/devavrat/abin/afni
afni version : Precompiled binary macos_10.12_local: Nov 22 2019
: AFNI_19.3.14 ‘Nero’
AFNI_version.txt : AFNI_19.3.14, macos_10.12_local, Nov 22 2019
which python : /Users/devavrat/anaconda3/bin/python
python version : 3.7.1
which R : /Users/devavrat/anaconda3/bin/R
R version : R version 3.5.1 (2018-07-02) – “Feather Spray”
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/Users/devavrat/abin/afni)
R : 2
/Users/devavrat/anaconda3/bin/R
/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R
python : 3
/sw/bin/python2.7
/Users/devavrat/anaconda3/bin/python3.7
/usr/bin/python
python2 : 0
python3 : 2
/Users/devavrat/anaconda3/bin/python3.7
/Library/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 : FAILURE
oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lme4!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: brms!
R RHOME : /Users/devavrat/anaconda3/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/devavrat/anaconda3/lib/python3.7/site-packages/matplotlib/pyplot.py
– python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
/usr/local/bin/python3.7 (sym link to /Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7)
-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/sbin:/usr/local/opt/qt/bin:/usr/local/fsl/bin:/Users/devavrat/anaconda3/bin:/Users/devavrat/anaconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Users/devavrat/abin:/Users/devavrat/abin:/Users/devavrat/abin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME/CD
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: …����������������������������������������������������
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /Users/devavrat/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 2.2.0
++ 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 /Users/devavrat/anaconda3/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’…
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
========================= summary, please fix: =========================
- login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
- have python version 3.7.1, some programs need 2.7.x
- missing R packages (see rPkgsInstall)
- please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in csh