ubuntu 22 install?

AFNI Message Board
1

Hey AFNI folks,
I see installation instructions for Ubuntu 20, but the latest version is 22. I just bought some new Linux workstations for my lab and figured it made sense to start from a clean install of the latest version of Ubuntu. I was hoping the AFNI installation instructions for version 20 would work, but I’m running into errors. Following these instructions: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu20.html
all was well until I got to this line:


sudo apt-get install -y tcsh xfonts-base libssl-dev       \
                        python-is-python3                 \
                        python3-matplotlib python3-numpy  \
                        gsl-bin netpbm gnome-tweak-tool   \
                        libjpeg62 xvfb xterm vim curl     \
                        gedit evince eog                  \
                        libglu1-mesa-dev libglw1-mesa     \
                        libxm4 build-essential            \
                        libcurl4-openssl-dev libxml2-dev  \
                        libgfortran-8-dev libgomp1        \
                        gnome-terminal nautilus           \
                        gnome-icon-theme-symbolic         \
                        firefox xfonts-100dpi             \
                        r-base-dev cmake                  \
                        libgdal-dev libopenblas-dev       \
                        libnode-dev libudunits2-dev       \
                        libgfortran4

Here is the corresponding output:
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
Note, selecting ‘adwaita-icon-theme-full’ instead of ‘gnome-icon-theme-symbolic’
Package gnome-tweak-tool is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
gnome-tweaks

E: Package ‘gnome-tweak-tool’ has no installation candidate
E: Unable to locate package libgfortran-8-dev
E: Unable to locate package libgfortran4

I’d appreciate any suggestions/pointers.

2

To briefly clarify, I tried the “Quick setup” steps first, but when I run:
afni_system_check.py -check_all

this is what I get:
-------------------------------- 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 Jammy Jellyfish
number of CPUs: 32
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/oem/abin/afni
afni version : afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_22.1.14, linux_ubuntu_16_64, Jun 24 2022
which python : /usr/bin/python
python version : 3.10.4
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/oem/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.10)
python2 : 0
python3 : 1 (/usr/bin/python3.10)

** have python3 but not python2

testing ability to start various programs…
afni : FAILURE
afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
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 : missing
.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 : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.5.1

-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/afni/bin:/home/oem/abin

PYTHONPATH =
R_LIBS = /home/oem/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (937292M 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 /home/oem/abin

------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.5 (amd64)

have Ubuntu system: ubuntu 22.04 Jammy Jellyfish

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

  • AFNI programs show FAILURE
  • please run: “suma -update_env” for .sumarc
3

Hi Will,

You can probably check the libgsl version via:

ls -l /usr/lib/x86_64-linux-gnu/libgsl.so.*

Then link to the existing file.

For openmotif and libGLw, maybe try:

sudo apt-get install -y libmotif-dev libglw1-mesa-dev
  • rick
4

Done. The output of:
afni_system_check.py -check_all

Now says: nothing to fix, yay!

So yay, thank you Rick!

5

Great, thanks for the update!

  • rick