AFNI programs disappeared - How to re-install?

Hello Experts,

Missing File problem. What is the best way to reinstall without affecting projects.

1. AFNI worked yesterday.
2. Today I am missing files: apsearch and SurfMesh. Maybe more. Unsure
3. @update.afni.binaries did not fixed.
I would like to make sure there will be no problems later on projects and not erase any work done previously.

Is there a way to reinstall or restore missing files?


**** output of ***

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 15.6.0
version: Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.
distribution: 10.11.6 x86_64
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/qjpham/abin/afni
afni version : Precompiled binary macosx_10.7_local: Jul 10 2017
: AFNI_17.2.02
AFNI_version.txt : AFNI_17.2.02, macosx_10.7_local, Jul 10 2017
which python : /sw/bin/python
python version : 2.7.13
which R : /usr/local/bin/R
R version : R version 3.4.0 (2017-04-21) – “You Stupid Darkness”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/qjpham/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 2
python2 : 1 (/sw/bin/python2.7)
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /sw/lib/qt4-mac/lib/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2 (sym link to /sw/bin/python2.7)

-------------------------------- env vars --------------------------------
PATH = /Users/qjpham/mybin:/Users/qjpham/abin:/sw/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Applications:/Users/qjpham/DicomBrowser-1.5.2/bin

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

DYLD_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME/Afni Bootcamp
top history: … [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME/Afni Bootcamp
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME/Afni Bootcamp
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME/Afni Bootcamp
atlas : found TT_N27+tlrc under /Users/qjpham/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.41.1
which brew : /usr/local/bin/brew
brew version : Homebrew 1.2.4

++ found ‘brew’ at /usr/local/bin/brew
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
– recent OS X, cannot check DYLD_LIBRARY_PATH in cur shell, cheating …
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
– recent OS X, cannot check DYLD_LIBRARY_PATH in shell ‘tcsh’, cheating …
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace
++ found without flat_namespace: /opt/X11/lib/libXt.7.dylib
link libXt.dylib points to /opt/X11/lib/libXt.6.dylib (good!)

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate from ‘tcsh’
  • AFNI programs show FAILURE
  • please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in bash
  • please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh

Hi Joseph,

Missing SurfMesh I can see (and you probably do not care), but
it is surprising that you might be missing apsearch. Are you sure
about missing apsearch? And do you actually use SurfMesh?

You should be able to restore the previous version by running:

@update.afni.binaries -revert

But I expect that is not really needed.

  • rick