Hello Experts,
Missing File problem. What is the best way to reinstall without affecting projects.
Summery:
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?
Joseph
**** output of afni_system_check.py ***
-------------------------------- 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-3248.60.11.5.3~1/RELEASE_X86_64
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
/sw/bin/python2.7
/usr/bin/python
python2 : 1 (/sw/bin/python2.7)
python3 : 0
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : 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)
/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
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/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:
/opt/X11/lib/flat_namespace/libXt.6.dylib
-- 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
