Hi,
My lab just transferred our data to a new server and reinstalled AFNI on that server. When running afni_system_check.py -check_all it seems that all of the AFNI functions successfully installed:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.18.0-240.1.1.el8_3.x86_64
version: #1 SMP Thu Nov 19 17:20:08 UTC 2020
distribution: CentOS Linux 8.3.2011
number of CPUs: 2
apparent login shell: sh
shell RC file: .profile (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /export/home/fs01/ngc26/abin/afni
afni version : Precompiled binary linux_centos_7_64: Feb 8 2021
: AFNI_21.0.07 'Titus'
AFNI_version.txt : AFNI_21.0.07, linux_centos_7_64, Feb 08 2021
which python : /usr/bin/python
python version : 2.7.17
which R : /usr/bin/R
R version : R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/export/home/fs01/ngc26/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/libexec/platform-python3.6)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
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!
These packages are not installed on the computer: brms!
R RHOME : /usr/lib64/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /export/home/fs01/ngc26/abin/:/opt/ohpc/pub/mpi/libfabric/1.10.1/bin:/opt/ohpc/pub/mpi/ucx-ohpc/1.8.0/bin:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/bin:/opt/ohpc/pub/compiler/gcc/9.3.0/bin:/opt/ohpc/pub/utils/prun/2.0:/opt/ohpc/pub/utils/autotools/bin:/opt/ohpc/pub/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
PYTHONPATH =
R_LIBS = /home/fs01/ngc26/R
LD_LIBRARY_PATH = /opt/ohpc/pub/mpi/libfabric/1.10.1/lib:/opt/ohpc/pub/mpi/ucx-ohpc/1.8.0/lib:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib:/opt/ohpc/pub/compiler/gcc/9.3.0/lib64:/usr/local/lib
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 /export/home/fs01/ngc26/abin/
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.2.23
which yum : /usr/bin/yum
yum version : 4.2.23
========================= summary, please fix: =========================
* just be aware: login shell 'sh', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
However, there are some AFNI functions that keep giving this error (this example is with 3dMatch, but the same happens with 3dNetCorr)
3dMatch: symbol lookup error: 3dMatch: undefined symbol: gsl_stats_correlation
After digging around for possible answers it seems like a GSL installation problem and potentially an issue with symbolic links; however, I do not know too much about these symbolic links and I don't want to mess up any important directories for the AFNI installation. Any suggestions on what might be going on with this gsl_stats_correlation error?
Here is my afni -ver
Precompiled binary linux_centos_7_64: Feb 8 2021 (Version AFNI_21.0.07 'Titus')
