AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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annschoe
January 18, 2021 11:59PM
Hello pt,

Not Wheeeeeee :(

I have followed your instruction and conda now runs in tcsh (good). I am now getting error messages in both bash and tcsh (not so good). One thing of note is that in addition to following your instructions, I've also updated afni to the AFNI_21.0.04 'Titus'.

Here is the result of the newly failed afni_system_check, ran using bash 

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              19.6.0
version:              Darwin Kernel Version 19.6.0: Tue Nov 10 00:10:30 PST 2020; root:xnu-6153.141.10~1/RELEASE_X86_64
distribution:         10.15.7
number of CPUs:       8
apparent login shell: tcsh  (current shell is bash)
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/achoe2/abin/afni
afni version         : Precompiled binary macos_10.12_local: Jan 18 2021 
                     : AFNI_21.0.04 'Titus'
AFNI_version.txt     : AFNI_21.0.04, macos_10.12_local, Jan 18 2021
which python         : /Users/achoe2/miniconda3/bin/python
python version       : 3.8.5
which R              : /usr/local/bin/R
R version            : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/achoe2/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 4 
      /Users/achoe2/miniconda3/bin/python3.8
      /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python2.7
      /opt/sw/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python2 : 2 
      /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python3 : 3 
      /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8
      /Users/achoe2/miniconda3/bin/python3.8
      /usr/bin/python3


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__.py

** have PyQt4, but cannot load QtCore, QtGui; error is:

   **************************************************
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: dlopen(/usr/local/lib/python2.7/site-packages/PyQt4/QtCore.so, 2): Symbol not found: _PyInt_Type
  Referenced from: /usr/local/lib/python2.7/site-packages/PyQt4/QtCore.so
  Expected in: flat namespace
 in /usr/local/lib/python2.7/site-packages/PyQt4/QtCore.so
   **************************************************


** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)
    /usr/local/bin/python3.8 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/Users/achoe2/miniconda3/bin:/Users/achoe2/miniconda3/envs/py27_afni_tiny/bin:/Users/achoe2/miniconda3/condabin:/opt/sw/bin:/opt/sw/sbin:/Applications/freesurfer/7.1.1/bin:/Applications/freesurfer/7.1.1/fsfast/bin:/Applications/freesurfer/7.1.1/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/achoe2/abin:/Users/achoe2/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) = /Users/achoe2/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 .

------------------------------ OS specific -------------------------------
XQuartz version      : 2.7.11

which fink           : /opt/sw/bin/fink
fink version         : Package manager version: 0.45.2
which brew           : /usr/local/bin/brew
brew version         : Homebrew 2.7.4

++ 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/achoe2/miniconda3/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 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /Applications/freesurfer/7.1.1/lib/gcc/lib:/opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  check for partial install of PyQt4
*  insufficient data for AFNI bootcamp

And here is the previously successful output of afni_system_check, ran on bash, before the miniconda-on-tcsh change. 

-------------------------------- general ---------------------------------
architecture:         64bit 
system:               Darwin
release:              19.6.0
version:              Darwin Kernel Version 19.6.0: Tue Nov 10 00:10:30 PST 2020; root:xnu-6153.141.10~1/RELEASE_X86_64
distribution:         10.15.7
number of CPUs:       8
apparent login shell: tcsh  (current shell is bash)
shell RC file:        .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /Users/achoe2/abin/afni
afni version         : Precompiled binary macos_10.12_local: Jan 14 2021 
                     : AFNI_21.0.03 'Titus'
AFNI_version.txt     : AFNI_21.0.03, macos_10.12_local, Jan 14 2021
which python         : /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python
python version       : 2.7.18
which R              : /usr/local/bin/R
R version            : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh           : /bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/Users/achoe2/abin/afni)
    R       : 1   (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
    python  : 3 
      /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python2.7
      /opt/sw/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python2 : 2 
      /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin/python2.7
      /System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
    python3 : 2 
      /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8
      /usr/bin/python3


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

++ module loaded: matplotlib.pyplot
   module file : /Users/achoe2/miniconda3/envs/py27_afni_tiny/lib/python2.7/site-packages/matplotlib/pyplot.pyc

-- python binaries under /usr/local/bin:
    /usr/local/bin/python3 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)
    /usr/local/bin/python3.8 (sym link to /usr/local/Cellar/python@3.8/3.8.5/Frameworks/Python.framework/Versions/3.8/bin/python3.8)

-------------------------------- env vars --------------------------------
PATH = /Users/achoe2/miniconda3/envs/py27_afni_tiny/bin:/Users/achoe2/miniconda3/condabin:/usr/local/bin:/opt/sw/bin:/opt/sw/sbin:/Applications/freesurfer/7.1.1/bin:/Applications/freesurfer/7.1.1/fsfast/bin:/Applications/freesurfer/7.1.1/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/Library/Apple/usr/bin:/Users/achoe2/abin:/Users/achoe2/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) = /Users/achoe2/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 .

------------------------------ OS specific -------------------------------
XQuartz version      : 2.7.11

which fink           : /opt/sw/bin/fink
fink version         : Package manager version: 0.45.2
which brew           : /usr/local/bin/brew
brew version         : Homebrew 2.7.4

++ found 'brew' at /usr/local/bin/brew
++ 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 'bash'...
++ found evar DYLD_LIBRARY_PATH = :/opt/X11/lib/flat_namespace
-- recent OS X, cheating to check DYLD_LIBRARY_PATH in shell 'tcsh'...
++ found evar DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace:/opt/X11/lib/flat_namespace

=========================  summary, please fix:  =========================
*  insufficient data for AFNI bootcamp

In both cases, the python 2.7 is activated via conda, but I see that the failed afni_system_check seems to be picking the base(?) regardless. Could this be the issue? I am also noticing that there are suddenly more instances of python, python2, and python3 after the change. Finally, I am also noticing something about non-brewed pyqt4...



help?


Sincerely,
Ann
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Subject Author Posted

tcsh vs. Miniconda

annschoe January 18, 2021 04:33PM

Re: tcsh vs. Miniconda

ptaylor January 18, 2021 08:25PM

Re: tcsh vs. Miniconda

annschoe January 18, 2021 11:59PM

Re: tcsh vs. Miniconda

ptaylor January 19, 2021 09:09AM

Re: tcsh vs. Miniconda

annschoe January 19, 2021 11:33AM

Re: tcsh vs. Miniconda

ptaylor January 19, 2021 04:25PM