Hi,
Following the standard quick install instructions on Fedora 39 (with a tcsh shell), I ended up with various errors. The commands in the "please run" section are throwing errors themselves.
The output of afni_system_check.py -check_all was:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type:
system: Linux
release: 6.8.4-200.fc39.x86_64
version: #1 SMP PREEMPT_DYNAMIC Thu Apr 4 20:45:21 UTC 2024
distribution: fedora 39 Workstation Edition
number of CPUs: 16
apparent login shell: tcsh
shell RC file: .tcshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/chholak/abin/afni
afni version : afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_24.1.17, linux_openmp_64, Jun 07 2024, official
which python : /usr/bin/python
python version : 3.12.3
which R : /usr/bin/R
R version : R version 4.3.3 (x86_64-redhat-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/chholak/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.12)
python2 : 0
python3 : 1 (/usr/bin/python3.12)
** have python3 but not python2
testing ability to start various programs...
afni : FAILURE
afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
3dAllineate : FAILURE
3dAllineate: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
3dClustSim : FAILURE
3dClustSim: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called ‘data.table’
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
** missing 4 binary libraries across 7 programs
** missing 2 binary libraries in program R_io.so
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
tcsh version : 6.24.10
which Xvfb :
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
unable to load shared object '/home/chholak/abin/R_io.so':
libXp.so.6: cannot open shared object file: No such file or directory
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted
R RHOME : /usr/lib64/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /home/chholak/.local/lib/python3.12/site-packages/matplotlib/pyplot.py
matplotlib version : 3.9.0
** 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/chholak/.local/bin:/home/chholak/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/chholak/abin
PYTHONPATH =
R_LIBS = /home/chholak/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 : missing
--------- 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 2 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (1906104M 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/chholak/abin
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.19.2
which yum : /usr/bin/yum
yum version : 4.19.2
========================= summary, please fix: =========================
- AFNI programs show FAILURE
- missing binary library: libXp.so.6
- missing binary library: libpng12.so.0
- missing binary library: libgsl.so.0
- missing binary library: libgslcblas.so.0
- missing program: Xvfb
- missing R packages (see rPkgsInstall)
- please run: "suma -update_env" for .sumarc
- please run: apsearch -update_all_afni_help
- dot file test : want 1 modifications across 2 files:
====================================================================
What should I do? Is there any other information that I can provide?
Thanks,
Parth