Problem changing directories

nstuart · May 21, 2019, 2:01pm

Hi all,

I recently installed AFNI, and there are no errors when I check. However, whenever I put any directory change in, I get the following message “No such file or directory”. Is this a problem anyone else has had? Is there a way I can fix this problem, because I know that the directories I am inputting exist.

Thank you!!

ptaylor · May 21, 2019, 2:17pm

Hi-

I think we’ll need some more specifics to know what might be happening. What system are you on (linux, mac, windows-linux)?

What does this mean: “whenever I put any directory change in”? Can you please copy+paste an example of:

a command you are using,
the output given
and the directory run from (output of typing “pwd” in a terminal)

What is the output of “afni_system_check.py -check_all”?

–pt

nstuart · May 21, 2019, 2:36pm

Thank you so much for your help, I am using a mac.

Here is one example of a command and output (fMRIdata is an external hard drive plugged into my laptop at the moment, but I get the same output when I try to change directories into “Documents” or something else that is on my physical laptop):
cd fMRIdata
-bash: cd: fMRIdata: No such file or directory

Here is the output of “pwd”
/Users/nikkistuart

Here is the output for “afni_system_check.py -check_all”
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 18.5.0
version: Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64
distribution: 10.14.4 x86_64
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/nikkistuart/abin/afni
afni version : Precompiled binary macos_10.12_local: May 10 2019
: AFNI_19.1.08 ‘Caligula’
AFNI_version.txt : AFNI_19.1.08, macos_10.12_local, May 10 2019
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/nikkistuart/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 0
python3 : 2
/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7
/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6

** 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

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 -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/3.7/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/nikkistuart/abin:/Users/nikkistuart/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) = :/opt/X11/lib/flat_namespace
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …9 [ptaylor]: added FT_analysis/results.QC_FT.05 tree
data dir : found AFNI_demos under $HOME
top history: 22 Apr 2019 [rickr]: added AFNI_pamenc
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/nikkistuart/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 2.1.2

– for PyQt4 under brew, consider running:
brew install cartr/qt4/pyqt
– consider installing gcc under homebrew
– consider installing glib under homebrew
++ 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

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

login shell ‘bash’, trusting user to translate code examples from ‘tcsh’

ptaylor · May 21, 2019, 3:55pm

Hm, I wonder if some variable got set incorrectly in a ~/.*rc during the setup.

Can you please run the following:


afni_system_check.py -dot_file_pack DOT_FILES.tgz

and then send the created DOT_FILES.tgz file to me? (I will PM you instructions for that.)

–pt