Hi,
I have tried referring to the methods posted on the forum, but I still can't solve it. I would appreciate your help.
Here's the output of afni_system_check.
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 5.4.0-174-generic
version: #193-Ubuntu SMP Thu Mar 7 14:29:28 UTC 2024
distribution: ubuntu 20.04 Focal Fossa
number of CPUs: 44
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/dl2/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_24.1.19, linux_ubuntu_16_64, Jun 14 2024, official
which python : /usr/local/fsl/bin/python
python version : 3.11.8
which R :
instances of various programs found in PATH:
afni : 1 (/home/dl2/abin/afni)
R : 0
python : 2
/usr/local/fsl/bin/python3.11
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/usr/local/fsl/bin/python3.11
/usr/bin/python3.8
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 : FAILURE
R: Command not found.
** missing 4 binary libraries across 5 programs
** missing binary library 'libR.so' in program R_io.so
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.21.00
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.
R RHOME : R: Command not found.
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/local/fsl/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.3
++ module loaded: flask
module file : /usr/local/fsl/lib/python3.11/site-packages/flask/init.py
flask version : 3.0.2
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/dl2/.poetry/bin:/home/dl2/.local/share/umake/bin:/usr/local/fsl/share/fsl/bin:/usr/local/fsl/share/fsl/bin:/home/dl2/bin:/home/dl2/.local/bin:/home/dl2/anaconda3/condabin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/fsl/share/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/cuda-8.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/dl2/.poetry/bin:/home/dl2/abin
PYTHONPATH =
R_LIBS = /home/dl2/R
LD_LIBRARY_PATH = /usr/local/cuda-8.0/lib64
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
CONDA_SHLVL = 0
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 (416106M Avail)
top history: ... 2024 [rickr]: 3drefit -newid FT/SUMA/FT_SurfVol.nii
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/dl2/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.10 (amd64)
have Ubuntu system: ubuntu 20.04 Focal Fossa
========================= summary, please fix: =========================
- just be aware: login shell 'bash', but our code examples use 'tcsh'
- missing program: R
- failure under initial "AFNI and related program tests"
- AFNI programs show FAILURE
- missing binary library: libR.so
- missing binary library: libXm.so.4
- missing binary library: libGLw.so.1
- missing binary library: libgsl.so.19
- missing binary library: libgslcblas.so.0
- missing program: Xvfb
- missing R packages (see rPkgsInstall)
- please run: "suma -update_env" for .sumarc
- dot file test : want 1 modifications across 3 files: