I faced the error 3dRSFC: error while loading shared libraries: libgsl.so.19:
i can't run the 3dReHo command for this error
my afni version - (Version AFNI_23.2.02)
Howdy-
It would be great to see the full afni -ver output, so we can see the OS you are using, but actually the most useful thing might just be to see the full output of:
afni_system_check.py -check_all
.... if you could please copy+paste that here.
--pt
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 4.4.0-19041-Microsoft
version: #2311-Microsoft Tue Nov 08 17:09:00 PST 2022
distribution: ubuntu 22.04 Jammy Jellyfish
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/badol/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Jul 28 2023
: AFNI_23.2.02 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.02, linux_ubuntu_16_64, Jul 28 2023, official
which python : /usr/bin/python
python version : 3.10.6
which R : /usr/bin/R
R version : R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
instances of various programs found in PATH:
afni : 1 (/home/badol/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 : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: Error 40
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: Error 40
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
** missing binary library 'libgsl.so.19' across 2 programs
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /usr/lib/python3/dist-packages/matplotlib/pyplot.py
matplotlib version : 3.5.1
-------------------------------- env vars --------------------------------
PATH = /home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:/mnt/c/Users/User/install/bin/:/Users/User/ANTs/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files (x86)/VMware/VMware Player/bin/:/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/nodejs/:/mnt/c/Program Files/Git/cmd:/mnt/c/Program Files/PostgreSQL/10/lib:/mnt/c/Program Files/PostgreSQL/10/bin:/mnt/c/Program Files/dotnet/:/mnt/c/Users/User/anaconda3:/mnt/c/Users/User/anaconda3/Library/mingw-w64/bin:/mnt/c/Users/User/anaconda3/Library/usr/bin:/mnt/c/Users/User/anaconda3/Library/bin:/mnt/c/Users/User/anaconda3/Scripts:/mnt/c/Users/User/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/User/AppData/Roaming/npm:/mnt/c/Users/User/AppData/Local/Programs/Microsoft VS Code/bin:/snap/bin:/home/badol/abin
PYTHONPATH =
R_LIBS = /home/badol/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, apsearch
(not on a mac, should skip flatdir)
-- 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 (121874M Avail)
top history: ...3 [rickr]: renamed GroupAna_cases scripts and output
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/badol/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.9 (amd64)
have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Jul 28 2023
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing binary library: libgsl.so.19
* dot file test : want 1 modifications across 3 files:
Cool, thanks.
You are using Ubuntu 22.04, and the setup notes for that are here.
The specific message is about libgsl not being linked; that could be because either the package isn't installed or the link isn't created, or both. To make sure that that dependency is present, and then while we're at it to make sure no other dependencies are missing, could you please copy+paste the few commands in this section of the notes, "Install prerequisite packages"? Importantly, the third step there includes making the link for GSL.
After you run that, could you open up a new terminal, and see if afni_system_check.py -check_all still reports those program errors?
--pt
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19
i already ran the command but after that when i ran the afni_system_check.py -check_all it give me same results
Hmmm, OK. What is the output of:
ls -l /usr/lib/x86_64-linux-gnu/libgsl*
on your system?
--pt
-rw-r--r-- 1 root root 5727436 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.a
lrwxrwxrwx 1 root root 16 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.so -> libgsl.so.27.0.0
lrwxrwxrwx 1 root root 38 Aug 8 13:00 /usr/lib/x86_64-linux-gnu/libgsl.so.19 -> /usr/lib/x86_64-linux-gnu/libgsl.so.23
lrwxrwxrwx 1 root root 38 Aug 8 09:38 /usr/lib/x86_64-linux-gnu/libgsl.so.23 -> /usr/lib/x86_64-linux-gnu/libgsl.so.19
lrwxrwxrwx 1 root root 16 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.so.27 -> libgsl.so.27.0.0
-rw-r--r-- 1 root root 2873384 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.so.27.0.0
-rw-r--r-- 1 root root 474946 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgslcblas.a
lrwxrwxrwx 1 root root 20 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgslcblas.so -> libgslcblas.so.0.0.0
lrwxrwxrwx 1 root root 20 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgslcblas.so.0 -> libgslcblas.so.0.0.0
-rw-r--r-- 1 root root 264320 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0
OK, these seem a bit tangled, because there are some circular links:
lrwxrwxrwx 1 root root 16 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.so -> libgsl.so.27.0.0
lrwxrwxrwx 1 root root 38 Aug 8 13:00 /usr/lib/x86_64-linux-gnu/libgsl.so.19 -> /usr/lib/x86_64-linux-gnu/libgsl.so.23
lrwxrwxrwx 1 root root 38 Aug 8 09:38 /usr/lib/x86_64-linux-gnu/libgsl.so.23 -> /usr/lib/x86_64-linux-gnu/libgsl.so.19
lrwxrwxrwx 1 root root 16 Dec 6 2021 /usr/lib/x86_64-linux-gnu/libgsl.so.27 -> libgsl.so.27.0.0
I think the important ones to have are:
/usr/lib/x86_64-linux-gnu/libgsl.so.27 -> libgsl.so.27.0.0- and we have to create
/usr/lib/x86_64-linux-gnu/libgsl.so.19pointing to/usr/lib/x86_64-linux-gnu/libgsl.so.27
On Ubuntu 22.04, I don't think there should be one with version number ending in 23, so let's unlink that:
sudo unlink /usr/lib/x86_64-linux-gnu/libgsl.so.23
Then, run this command to create the link specified in the install instructions:
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19
What do the outputs of:
ls -l /usr/lib/x86_64-linux-gnu/libgsl*
afni_system_check.py -check_all
look like after that?
--pt