Trouble Downloading Old Versions of AFNI

AFNI Message Board
1

Hi,

We’ve been trying to download an older version of afni and we are running into some issues. Following these commands:
cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -local_package PATH_TO_FILE/linux_ubuntu_16_64.tgz -do_extras

from the afni download page:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu20.html#slow-setup-install-afni-binaries

We ran the command tcsh -x -v @update.afni.binaries -local_package afni_tars/AFNI_20.3.05.tgz -do_extras and get the following echo command and verbose outputs in an output file:

– running @update.afni.binaries version 3.21, July 22, 2022
– no current AFNI package found in path…
– install dir: using default ~/abin
– will install from local package file: AFNI_20.3.05.tgz
– any downloads will be from https://afni.nimh.nih.gov via wget

– attempting to install package AFNI_20.3.05 under
install dir: /home/hughes/abin…
– have install dir
deleting old temporary directory…
++ working in new temp dir, .tmp.install
++ getting install prog: wget bin/misc/@update.afni.binaries …
wget https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
– fixing lost permissions on @update.afni.binaries
++ using updated @update.afni.binaries, instead…

++ running: tcsh tmp.@update.afni.binaries -no_recur -local_package /home/hughes/afni_tars/AFNI_20.3.05.tgz -do_extras
– running tmp.@update.afni.binaries version 3.21, July 22, 2022
– no current AFNI package found in path…
– install dir: using default ~/abin
– will install from local package file: AFNI_20.3.05.tgz
– any downloads will be from https://afni.nimh.nih.gov via wget

– attempting to install package AFNI_20.3.05 under
install dir: /home/hughes/abin…
– have install dir
deleting old temporary directory…
++ working in new temp dir, .tmp.install
– skipping update of tmp.@update.afni.binaries

++ update needed, installing…

++ extracting local package AFNI_20.3.05 from /home/hughes/afni_tars/AFNI_20.3.05.tgz…
++ backing up current binaries to auto_backup.AFNI_20.3.05
deleting previous backup directory, auto_backup.AFNI_20.3.05 …
++ installing new binaries…

If anyone can help us resolve this, we would really appreciate your help!

Thanks!

2

Hello,

I am not actually sure what the problem is, or in what way you see one.
What does “afni -ver” show after that?

  • rick
3

When we put afni -ver, we get the following:

Command ‘afni’ not found, did you mean:
command ‘pfni’ from deb adacontrol (1.21r6b-7)
Try: sudo apt install

Best,
Dominique Hughes

4

You might have to open a new terminal or something, to source the startup file, depending on your shell.
Well, how about getting more details. What is the output from this?

~/abin/afni_system_check.py -check_all

Thanks,

  • rick
5

(base) hughes@pascal:~/abin$ python afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.15.0-41-generic
version: #44-Ubuntu SMP Wed Jun 22 14:20:53 UTC 2022
distribution: Ubuntu 22.04.1 LTS
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/hughes/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 18 2022
: AFNI_22.2.12 ‘Marcus Aurelius’
AFNI_version.txt : AFNI_22.2.12, linux_ubuntu_16_64, Sep 18 2022
which python : /home/hughes/anaconda3/bin/python
python version : 3.9.7
which R : /usr/bin/R
R version : R version 4.2.1 (2022-06-23) – “Funny-Looking Kid”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/hughes/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/home/hughes/anaconda3/bin/python3.9)
python2 : 0
python3 : 2
/home/hughes/anaconda3/bin/python3.9
/usr/bin/python3.10

** 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
3dMVM : success

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

R RHOME : /usr/lib/R

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 : /home/hughes/anaconda3/lib/python3.9/site-packages/matplotlib/pyplot.py
matplotlib version : 3.4.3

-------------------------------- env vars --------------------------------
PATH = /usr/local/go/bin:/usr/local/go/bin:/home/hughes/anaconda3/bin:/home/hughes/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/local/matlab/bin:/usr/local/maple/bin:/usr/local/mathematica/Executables:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11:/usr/games:/snap/bin:/home/hughes/go/bin:/home/hughes/go/bin:/home/hughes/abin:/home/hughes/abin/afni:/home/hughes/abin/suma

PYTHONPATH =
R_LIBS = /home/hughes/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1269877M Avail)
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
data dir : found AFNI_demos under $HOME
top history: …ct 2020 [taylorp]: updated scripts under FATCAT_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 .

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.8 (amd64)

have Ubuntu system: Ubuntu 22.04.1 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 18 2022

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

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
6

Great, so when you open a new terminal at this point, does afni work?
Does “afni -ver” show the version that you are hoping it shows?

  • rick
7

It’s AFNI version 22.2.12, still, but we need an earlier AFNI version, preferably 20.3.05.

Best,
Dominique Hughes

8

This is a little strange, since it works for me and it shows the version during install.
I will send you direct email, and maybe we can do a quick zoom chat or something.

  • rick