Hi,
I have the exact same issue as in Cant Install R on Ubuntu 16.04 - except that I am trying to install R for AFNI on Centos 6.9. When I try to run the code:
rPkgsInstall -pkgs ALL
I get the following error:
oo Warning:
Failed to load R_io.so with this error message:
Error in dyn.load(ll) :
unable to load shared object ‘/home/riz/abin/R_io.so’:
libXp.so.4: cannot open shared object file: No such file or directory
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted
When, I ran the following command:
afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-696.13.2.el6.x86_64
version: #1 SMP Thu Oct 5 21:22:16 UTC 2017
distribution: CentOS 6.9 Final
number of CPUs: 12
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/riz/abin/afni
afni version : afni: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
:
AFNI_version.txt : AFNI_17.3.00, linux_openmp_64, Oct 12 2017
which python : /usr/bin/python
python version : 2.6.6
which R : /usr/bin/R
R version : R version 3.4.1 (2017-06-30) – “Single Candle”
which tcsh : /bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/riz/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python)
python2 : 1 (/usr/bin/python)
python3 : 0
testing ability to start various programs…
afni : FAILURE
afni: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
suma : FAILURE
suma: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : FAILURE
3dAllineate: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
3dClustSim : FAILURE
3dClustSim: error while loading shared libraries: libXpm.so.4: cannot open shared object file: No such file or directory
checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
Error in dyn.load(ll) :
unable to load shared object ‘/home/riz/abin/R_io.so’:
libXpm.so.4: cannot open shared object file: No such file or directory
Calls: source … withVisible → eval → eval → set_R_io → dyn.load
Execution halted
checking for $HOME files…
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.6/site-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/home/riz/abin:/home/riz/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/riz/abin
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.2.29
========================= summary, please fix: =========================
- AFNI programs show FAILURE
- missing R packages (see rPkgsInstall)
- consider running: cp /home/riz/abin/AFNI.afnirc ~/.afnirc
- consider running “suma -update_env” for .sumarc
- consider running: apsearch -update_all_afni_help
- insufficient data for AFNI bootcamp
Any help would be appreciated. Thanks!