When trying to install afni on a new Linux computer, afni system check gives me three errors, one each for SUMA, 3dSkullStrip and SurfMesh, however libGLU.so.1 is found in /usr/lib as a link to libGLU.so.1.3.1 as shown here:
cd /usr/lib
ls -l libGLU*
lrwxrwxrwx. 1 root 15 Nov 6 10:34 libGLU.so.1 → libGLU.so.1.3.1
-rwxr-xr-x. 1 root 560272 Jun 10 2014 libGLU.so.1.3.1
so it’s not clear what is causing the problem.
afni system check Results:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1127.19.1.el7.x86_64
version: #1 SMP Tue Aug 25 17:23:54 UTC 2020
distribution: CentOS Linux 7.8.2003 Core
number of CPUs: 4
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/knutsonk/abin/afni
afni version : Precompiled binary linux_openmp_64: Oct 19 2020
: AFNI_20.3.01 ‘Vespasian’
AFNI_version.txt : AFNI_20.3.01, linux_openmp_64, Oct 19 2020
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/bin/R
R version : R version 3.6.0 (2019-04-26) – “Planting of a Tree”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/knutsonk/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 0
testing ability to start various programs…
afni : success
suma : FAILURE
suma: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
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: snow!
These packages are not installed on the computer: lmerTest!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: brms!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
R RHOME : /usr/lib64/R
checking for $HOME files…
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.7/site-packages/PyQt4/init.pyc
** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/knutsonk/abin:/home/knutsonk/.local/bin:/home/knutsonk/bin:/home/knutsonk/abin:/home/knutsonk/abin:/home/knutsonk/abin
PYTHONPATH =
R_LIBS =
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/knutsonk/abin
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
========================= summary, please fix: =========================
- just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- please run: “suma -update_env” for .sumarc
- insufficient data for AFNI bootcamp