Failed to determine the layout of your Qt installation. (installing

Dear AFNI users,

Hi, I have a trouble opening ‘’. I followed the instruction from It seems that PyQt4 was not fully installed as the message on installation, and finally reached “Install PyQt4, via JDK and fink (optional)”.
‘Fink’ was well installed (fink –version returns ‘0.45.0’).

The problem lies on the next part. When I run 3-iii. ‘sudo fink install pyqt4-mac-py27’, I encountered the message as below.

Warning: Package index cache disabled because cannot access indexer lockfile:
Read-only file system
Scanning package description files…
Information about 322 packages read in 2 seconds.
Failed: no package found for specification ‘pyqt4-mac-py27’!

It seems that everything was well installed as the output ‘ -check_all’ shows.

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.3.0
version: Darwin Kernel Version 19.3.0: Thu Jan 9 20:58:23 PST 2020; root:xnu-6153.81.5~1/RELEASE_X86_64
distribution: 10.15.3 x86_64
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/coglab/abin/afni
afni version : Precompiled binary macos_10.12_local: Feb 26 2020
: AFNI_20.0.18 ‘Galba’
AFNI_version.txt : AFNI_20.0.18, macos_10.12_local, Feb 26 2020
which python : /usr/bin/python
python version : 2.7.16
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/coglab/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.5/Resources/bin/R)
python : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 : 1 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 2

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : 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 -------------------------------
** failed to load module PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
module file : /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/matplotlib/pyplot.pyc

– python binaries under /usr/local/bin:
/usr/local/bin/python3 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)
/usr/local/bin/python3.6 (sym link to /Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

-------------------------------- env vars --------------------------------
PATH = /sw/bin:/sw/bin:/sw/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Users/coglab/abin:/Users/coglab/abin

PYTHONPATH = /sw/lib/qt4-mac/lib/python2.7/site-packages

DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace


------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
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/coglab/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 2.2.6

++ 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:
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace

========================= nothing to fix, yay! =========================

When I type “

python -c 'from PyQt4 import QtCore, QtGui'

”, I see the message as below.

Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named PyQt4

Here are additional outputs that might help you figure out what the problem is…

brew install pyqt

Warning: pyqt 5.14.0 is already installed and up-to-date
To reinstall 5.14.0, run brew reinstall pyqt

As I failed to install pyqt4 with fink, I tried it with python, which I failed again…
I downloaded SIP and PyQt4, and installed SIP with python. Then when I tried to install PyQt4, I received message below.

python -q /usr/local/bin/qmake --verbose

Determining the layout of your Qt installation…
/usr/local/bin/qmake -spec macx-g++ -o
make -f
g++ -c -pipe -O2 -arch x86_64 -Xarch_x86_64 -mmacosx-version-min=10.5 -Wall -W -DQT_NO_DEBUG -DQT_CORE_LIB -DQT_SHARED -I/usr/local/etc/qt4/mkspecs/macx-g++ -I. -I/usr/local/Cellar/qt@4/4.8.7_5/lib/QtCore.framework/Versions/4/Headers -I/usr/local/Cellar/qt@4/4.8.7_5/lib/QtCore.framework/Versions/4/Headers -I/usr/local/include -I. -F/usr/local/lib -o qtdirs.o qtdirs.cpp
warning: include path for stdlibc++ headers not found; pass ‘-stdlib=libc++’ on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from qtdirs.cpp:1:
In file included from /usr/local/Cellar/qt@4/4.8.7_5/lib/QtCore.framework/Versions/4/Headers/QCoreApplication:1:
In file included from /usr/local/Cellar/qt@4/4.8.7_5/lib/QtCore.framework/Versions/4/Headers/qcoreapplication.h:45:
In file included from /usr/local/include/QtCore/qobject.h:47:
In file included from /usr/local/include/QtCore/qobjectdefs.h:45:
In file included from /usr/local/include/QtCore/qnamespace.h:45:
/usr/local/include/QtCore/qglobal.h:68:10: fatal error: ‘algorithm’ file not found
1 warning and 1 error generated.
make: *** [qtdirs.o] Error 1
Error: Failed to determine the layout of your Qt installation. Try again using
the --verbose flag to see more detail about the problem.

I tried everything I can, I changed system integrity protection status (disabled) and so on…

Can you help me opening


I think this might be a Python 2.7 / Python 3.* version mismatch, since you have multiple versions of Python on your computer.

However, I’d like to step back and doublecheck about the need for using We really don’t recommend using it anymore-- it doesn’t have all the options that can use, and in general we find it muuuuch simpler/faster to start with one of the examples and adjust it to your own processing needs.

Do any of the examples here–
– particularly any of the “modern” ones-- seem like a good start for your processing?