Hello!
I ran into some difficulty while installing AFNI on Windows 11 via Ubuntu 22.04, specifically with missing binary libraries.
After following the installation steps online, I entered the command:
afni_system_check.py -check_all
and I received the following output:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 4.4.0-22621-Microsoft
version: #2506-Microsoft Fri Jan 01 08:00:00 PST 2016
distribution: ubuntu 22.04 Jammy Jellyfish
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/waterssj/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_24.0.14, linux_ubuntu_16_64, Mar 18 2024, official
which python : /usr/bin/python
python version : 3.10.12
which R : /usr/bin/R
R version : R version 4.3.3 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/waterssj/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
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
uber_subject.py : success
3dMVM : success
** missing 5 binary libraries across 5 programs
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /home/waterssj/.local/lib/python3.10/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.3
** failed to load module flask
-- flask is not required, but is desirable
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/waterssj/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/Python38/Scripts/:/mnt/c/Program Files/Python38/:/mnt/c/Program Files/Python37/Scripts/:/mnt/c/Program Files/Python37/:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program Files/MATLAB/R2022b/bin:/mnt/c/Program Files/MATLAB/R2021b/bin:/mnt/c/Program Files/Git/cmd:/mnt/c/Program Files/dotnet/:/mnt/c/Program Files/PowerShell/7/:/mnt/c/Users/water/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/water/AppData/Local/GitHubDesktop/bin:/snap/bin:/home/waterssj/abin
PYTHONPATH =
R_LIBS = /home/waterssj/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL =
CONDA_DEFAULT_ENV =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (975485M Avail)
top history: ... [gangc]: redo 0.BGA as 1.bga and update run.MSS.txt
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/waterssj/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.8 (amd64)
have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing binary library: libXm.so.4
* missing binary library: libGLw.so.1
* missing binary library: libGLU.so.1
* missing binary library: libgsl.so.19
* missing binary library: libgslcblas.so.0
* missing program: Xvfb
* please run: "suma -update_env" for .sumarc
* dot file test : want 1 modifications across 3 files:
I tried fixing the error by running the command:
suma -update_env
but I received the following output:
suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
I also tried updating the binaries by entering the command:
@update.afni.binaries -d
but I received the following output:
-- running @update.afni.binaries version 3.24, December 7, 2023
-- have AFNI binaries under /home/waterssj/abin
-- have current build label official
-- install dir: using existing /home/waterssj/abin
afni: error while loading shared libraries: libXm.so.4: cannot open shared object file: No such file or directory
** failed setting package from 'afni -ver'
checking AFNI_version.txt instead...
** failed setting package from 'AFNI_version.txt', failing
It appears that the issue has something to do with missing binary libraries, but updating the binaries doesn't work.
I'd greatly appreciate any help with fixing the issue!