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April 28, 2022 05:50PM
I have solved most of the missing library problems with my AFNI installation on a new machine running Fedora 35, but I have a persistent error about libgsl.so.0 when I try to run 3DSkullStrip and 3DRSFC. Also persistent error about missing R packages despite installing the packages twice. Details follow:


architecture: 64bit ELF
system: Linux
release: 5.17.4-200.fc35.x86_64
version: #1 SMP PREEMPT Wed Apr 20 15:37:53 UTC 2022
distribution: fedora 35
number of CPUs: 12
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/billhoffman/abin/afni
afni version : Precompiled binary linux_openmp_64: Apr 24 2022
: AFNI_22.1.06 'Antoninus Pius'
AFNI_version.txt : AFNI_22.1.06, linux_openmp_64, Apr 24 2022
which python : /usr/bin/python
python version : 3.10.4
which R : /usr/bin/R
R version : R version 4.1.3 (2022-03-10) -- "One Push-Up"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/billhoffman/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python3.10)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.10)


testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.0: 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.0: cannot open shared object file: No such file or directory
SurfMesh : success
3dClustSim : success
3dMVM : success

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

oo Warning:
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: lmerTest!


R RHOME : /usr/lib64/R

checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : None

** have PyQt4, but cannot load QtCore, QtGui; error is:

**************************************************
**************************************************


++ module loaded: matplotlib.pyplot
module file : /usr/lib64/python3.10/site-packages/matplotlib/pyplot.py
matplotlib version : 3.5.1

-------------------------------- env vars --------------------------------
PATH = /home/billhoffman/.local/bin:/home/billhoffman/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/home/billhoffman/abin:/home/billhoffman/abin

PYTHONPATH =
R_LIBS = /home/billhoffman/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (2192271M 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 : did not find TT_N27+tlrc

------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.11.1
which yum : /usr/bin/yum
yum version : 4.11.1


========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* check for partial install of PyQt4
* possibly missing atlases
Subject Author Posted

Ongoing problemsgetting AFNI to work on Fedora

hoffmanwil April 28, 2022 05:50PM

Re: Ongoing problemsgetting AFNI to work on Fedora

rick reynolds April 28, 2022 09:24PM

Re: Ongoing problemsgetting AFNI to work on Fedora

hoffmanwil April 29, 2022 06:44PM

Re: Ongoing problemsgetting AFNI to work on Fedora

rick reynolds April 29, 2022 07:19PM

Re: Ongoing problemsgetting AFNI to work on Fedora

hoffmanwil May 03, 2022 12:40PM

Re: Ongoing problemsgetting AFNI to work on Fedora

rick reynolds May 03, 2022 03:07PM

Re: Ongoing problemsgetting AFNI to work on Fedora

hoffmanwil May 03, 2022 06:00PM

Re: Ongoing problemsgetting AFNI to work on Fedora

rick reynolds May 03, 2022 06:24PM



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