Thank you very much. I have these remaining errors when I attempt to install the R packages for AFNI (see below last parts of the output).
Apologies for the novice questions, but are these errors specific to R or is there something within the AFNI installations I can do? I tried to uninstall and re-installed R, but I am still getting this problem. I have also included the output for the afni_check all below.
Thank you,
Tamara
Terminal output from R installation (rPkgsInstall)
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/home/ttavare/R/sf’
ERROR: dependency ‘RcppParallel’ is not available for package ‘StanHeaders’
* removing ‘/home/ttavare/R/StanHeaders’
ERROR: dependency ‘igraph’ is not available for package ‘threejs’
* removing ‘/home/ttavare/R/threejs’
ERROR: dependency ‘RcppParallel’ is not available for package ‘rstantools’
* removing ‘/home/ttavare/R/rstantools’
ERROR: dependency ‘gsl’ is not available for package ‘rtdists’
* removing ‘/home/ttavare/R/rtdists’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/home/ttavare/R/spdep’
ERROR: dependencies ‘StanHeaders’, ‘RcppParallel’ are not available for package ‘rstan’
* removing ‘/home/ttavare/R/rstan’
ERROR: dependency ‘rstantools’ is not available for package ‘projpred’
* removing ‘/home/ttavare/R/projpred’
ERROR: dependencies ‘rstan’, ‘threejs’ are not available for package ‘shinystan’
* removing ‘/home/ttavare/R/shinystan’
ERROR: dependencies ‘rstan’, ‘rstantools’, ‘shinystan’, ‘projpred’ are not available for package ‘brms’
* removing ‘/home/ttavare/R/brms’
The downloaded source packages are in
‘/tmp/RtmpUgR1of/downloaded_packages’
++ Note: @ 15:05:29
This package has been installed on the computer: brms
ttavare@MitchellLabImage2:/usr/lib/R$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 5.4.0-80-generic
version: #90-Ubuntu SMP Fri Jul 9 22:49:44 UTC 2021
distribution: Ubuntu 20.04.3 LTS
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/ttavare/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 1 2021
: AFNI_21.2.06 'Nerva'
AFNI_version.txt : AFNI_21.2.06, linux_ubuntu_16_64, Sep 01 2021
which python : /software/anaconda3/bin/python
python version : 3.8.3
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/ttavare/abin/afni)
R : 1 (/usr/bin/R)
python : 2
/software/anaconda3/bin/python3.8
/usr/bin/python2.7
python2 : 1 (/usr/bin/python2.7)
python3 : 2
/software/anaconda3/bin/python3.8
/usr/bin/python3.8
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: brms!
R RHOME : /usr/lib/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
++ module loaded: matplotlib.pyplot
module file : /software/anaconda3/lib/python3.8/site-packages/matplotlib/pyplot.py
-------------------------------- env vars --------------------------------
PATH = /software/anaconda3/bin:/software/anaconda3/condabin:/software/BrainSuite/BrainSuite19b/bin:/software/itksnap/3.8.0/bin:/software/ANTs/2.1.0/bin:/software/3D-Slicer/4.11.2:/software/MeVisLab/MeVisLab3.4GCC-7/bin:/software/workbench/1.4.2/bin_linux64:/software/MRIcroGL:/software/mricron:/software/MRIConvert-2.0.7/usr/bin:/software/Mango:/software/nifty_reg-1.3.9/bin:/software/matlab/R2020a/bin:/software/palm:/software/freesurfer/6.0.0/bin:/software/fsl/6.0.4/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/ttavare/abin
PYTHONPATH =
R_LIBS = /home/ttavare/R
LD_LIBRARY_PATH = /software/freesurfer/6.0.0/lib
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 20 Feb 2020 [rickr]: updated FT_analysis examples
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 $HOME
atlas : found TT_N27+tlrc under /home/ttavare/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.6 (amd64)
have Ubuntu system: Ubuntu 20.04.3 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 1 2021
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
ttavare@MitchellLabImage2:/usr/lib/R$
