Good morning,
I’m receiving this error message when using 3dSkullStrip on Ubuntu 18.04.1 LTS 64 bit. 3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
I’ve been working the whole day on this, and I saw that also other users reported the same problem, so I tried to follow previous posts in the community and to fix it by myself. In the begining rPkgsInstall -pkgs ALL -check showed me that I had problems with brms and some other packages, or whatever they are, I’m not very expert abaut it. I got to the point where rPkgsInstall -pkgs ALL -check
prints
This package has been verified on the computer: afex
This package has been verified on the computer: phia
This package has been verified on the computer: snow
This package has been verified on the computer: nlme
This package has been verified on the computer: lme4
This package has been verified on the computer: paran
This package has been verified on the computer: psych
This package has been verified on the computer: brms
No problem with python-qt4, when I type uber_subject.py a GUI starts.
I hope I gave all needed informetion.
Can you help me?
Can you please send the output of “afni_system_check.py -check_all”, for example posting it to the Message Board? We will need more details to try to help fix the install/dependency issues.
I assume that you have performed the large “sudo apt-get install …” command in the install instructions, but can you please try this again:
sudo apt-get install -y gsl-bin
(3dSkullstrip is complaining about a GSL dependency that it can’t sort out.)
I installed AFNI on my pc, following the instructions on the website, more than a year ago, and everything was going well. Today it was the first time that I tried 3dSkullStrip, so I don’t know if the problem has always been present or if it new. Yesterday I installed ANTs, I don’t know if this may have messed up something. Anyway, if I perform sudo apt-get install -y gsl-bin, it just says that everything is already installed
Reading package lists... Done
Building dependency tree
Reading state information... Done
gsl-bin is already the newest version (2.4+dfsg-6).
The following packages were automatically installed and are no longer required:
linux-headers-4.15.0-32 linux-headers-4.15.0-32-generic
linux-image-4.15.0-32-generic linux-modules-4.15.0-32-generic
linux-modules-extra-4.15.0-32-generic
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
here’s the output of “afni_system_check.py -check_all”
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.15.0-36-generic
version: #39-Ubuntu SMP Mon Sep 24 16:19:09 UTC 2018
distribution: Ubuntu 18.04 bionic
number of CPUs: 4
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/cauzzo_s/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Apr 28 2018
: AFNI_18.1.08
AFNI_version.txt : AFNI_18.1.08, linux_ubuntu_16_64, Apr 28 2018
which python : /usr/bin/python
python version : 2.7.15rc1
which R : /usr/bin/R
R version : R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/cauzzo_s/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)
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: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
SurfMesh : success
3dClustSim : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /home/cauzzo_s/bin:/home/cauzzo_s/.local/bin:/home/cauzzo_s/code/antsbin/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cauzzo_s/abin
PYTHONPATH =
R_LIBS = /home/cauzzo_s/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/cauzzo_s/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.3ubuntu0.1 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Apr 28 2018
========================= summary, please fix: =========================
* AFNI programs show FAILURE
* insufficient data for AFNI bootcamp
Note that your binaries are ~minorly old now-- who remembers all the way back to April??-- so you might also want to consider running
@update.afni.binaries -d
as a final bit of AFNI hygiene.
-pt
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.