Hi everyone,

I am trying to run 3dMVM on a computing cluster, and I am running into the following error:

Error: package or namespace load failed for ‘lsmeans’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘multcomp’
Error: package ‘lsmeans’ could not be loaded
Execution halted

However, when I run the following command, I get no error:

rPkgsInstall -pkgs "lsmeans"

I have also tried installing lsmeans in R, and I get a write error for the default directory, which prompts me to install it locally. The local install works, but 3dMVM still cant load the package.


This has all led me to run the afni system check, which gives me:

[nbald@cubic-login3 logs]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture:         64bit
system:               Linux
release:              3.10.0-862.el7.x86_64
version:              #1 SMP Fri Apr 20 16:44:24 UTC 2018
distribution:         CentOS Linux 7.6.1810 Core
number of CPUs:       40
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /cbica/home/nbald/software/afni/inuse/afni
afni version         : Precompiled binary linux_openmp_64: Apr 14 2020
                     : AFNI_20.1.01 'Otho'
AFNI_version.txt     : AFNI_20.1.01, linux_openmp_64, Apr 14 2020
which python         : /cbica/software/external/python/anaconda/3/bin/python
python version       : 3.6.5
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   (/gpfs/fs001/cbica/home/nbald/software/afni/inuse/afni)
    R       : 1   (/usr/bin/R)
    python  : 2
      /gpfs/fs001/cbica/software/external/python/anaconda/3/bin/python3.6
      /usr/bin/python2.7
    python2 : 1   (/usr/bin/python2.7)
    python3 : 2
      /gpfs/fs001/cbica/software/external/python/anaconda/3/bin/python3.6
      /usr/bin/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: brms!


R RHOME : /usr/lib64/R

checking for $HOME files...
    .afnirc                   : found
    .sumarc                   : missing
    .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 : /cbica/software/external/python/anaconda/3/lib/python3.6/site-packages/matplotlib/pyplot.py

-------------------------------- env vars --------------------------------
PATH = /cbica/home/nbald/software/afni/inuse:/cbica/software/external/freesurfer/centos7/5.3.0/bin:/cbica/software/external/freesurfer/centos7/5.3.0/fsfast/bin:/cbica/software/external/freesurfer/centos7/5.3.0/tktools:/cbica/software/external/fsl/centos7/5.0.11/bin:/cbica/software/external/freesurfer/centos7/5.3.0/mni/bin:/cbica/home/nbald/abin:/cbica/software/external/freesurfer/centos7/5.3.0/bin:/cbica/software/external/freesurfer/centos7/5.3.0/fsfast/bin:/cbica/software/external/freesurfer/centos7/5.3.0/tktools:/cbica/software/external/fsl/centos7/5.0.11/bin:/cbica/software/external/freesurfer/centos7/5.3.0/mni/bin:/cbica/software/external/gcc/centos7/5.2.0/bin:/usr/lib64/qt-3.3/bin:/cbica/home/nbald/perl5/bin:/usr/lib64/ccache:/cbica/software/lab/bin:/cbica/software/external/bin:/usr/lib64/openmpi/bin:/cbica/software/lab/captk/centos7/1.7.2/bin:/cbica/software/external/python/anaconda/3/bin:/cbica/software/lab/MUSE/centos7/3.0.5/bin:/cbica/software/lab/MARS/centos7/2.2.2/bin:/cbica/software/external/imagej:/cbica/software/external/dcmtk/centos7/3.6.3/bin:/cbica/software/external/gdcm/centos7/2.6.1/bin:/cbica/software/lab/SCPLearn/centos7/1.0.0:/cbica/software/external/swig/centos7/3.0.5/bin:/cbica/software/lab/dramms/centos7/1.4.2/bin:/cbica/software/lab/odvba/centos7/3.0/bin:/cbica/software/external/mricron/7.7.12:/cbica/software/external/freesurfer/centos7/5.3.0/bin:/cbica/software/external/nifticlib/2.0.0/bin:/cbica/software/lab/sbiaDti/253/bin:/cbica/software/lab/sbiaUtilities/0.3.3/centos7/bin:/cbica/software/external/fsl/centos7/5.0.11/bin:/cbica/software/external/mosek/7/tools/platform/linux64x86/bin:/cbica/software/external/matlab/R2018A/bin:/cbica/software/external/camino/1176/bin:/cbica/software/external/mipav/7.2.0:/cbica/software/external/minc/2.0.13/bin:/cbica/software/lab/mass/1.1.1/bin:/cbica/software/external/dtk/0.6:/cbica/software/external/dicom3tools/1.00.snapshot.20110207/bin:/cbica/software/lab/libra/centos7/1.0.4:/cbica/software/external/dependency_bundle/centos7/3817/bin:/cbica/software/external/ANTs/centos7/2.3.1/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtInstallerFramework/3.0/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtInstallerFramework/2.0/bin:/cbica/software/external/qt/centos7/5.11.1/Tools/QtCreator/bin:/cbica/software/external/qt/centos7/5.11.1/5.11.1/gcc_64/bin:/cbica/software/external/doxygen/centos7/1.8.9.1/bin:/cbica/software/external/texlive/2016/bin/x86_64-linux:/cbica/software/external/texlive/2016/bin:/cbica/software/external/jython/centos7/2.5.3/bin:/cbica/software/external/sge/8.1.9-1/bin/lx-amd64:/cbica/software/external/sge/8.1.9-1/bin:/cbica/software/lab/mico/1.0.0/centos7/bin:/usr/local/cuda-9.0/bin:/cbica/software/external/slicer/centos7/4.8.1:/cbica/software/external/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/bin:/usr/lpp/mmfs/bin:/opt/dell/srvadmin/bin:/data/jag/cnds/nbalderston/software/simnibs/inuse:/cbica/home/nbald/software/simnibs/inuse/bin:/cbica/home/nbald/software/simnibs/inuse/Bash_modules:/cbica/home/nbald/bin:/data/jag/cnds/nbalderston/software/simnibs/inuse:/cbica/home/nbald/software/simnibs/inuse/bin:/cbica/home/nbald/software/simnibs/inuse/Bash_modules:~/bin

PYTHONPATH = /cbica/software/lab/sbiaDti/253/bin:/cbica/software/lab/sbiaUtilities/0.3.3/centos7/bin

R_LIBS = /cbica/software/external/R/gcc5:/cbica/software/external/R:/usr/lib64/R/library:/usr/share/R/library

LD_LIBRARY_PATH = /cbica/software/external/R/gcc5:/cbica/software/external/gcc/centos7/5.2.0/lib64:/cbica/software/external/gcc/centos7/5.2.0/lib:/usr/lib64/mpich/lib:/usr/lib64/openmpi/lib:/cbica/software/lab/captk/centos7/1.7.2/lib:/cbica/software/lab/MUSE/centos7/3.0.5/lib:/cbica/software/lab/MARS/centos7/2.2.2/lib:/cbica/software/external/dcmtk/centos7/3.6.3/lib64:/cbica/software/external/gdcm/centos7/2.6.1/lib:/cbica/software/external/bct-cpp/centos7/396/lib:/cbica/software/lab/dramms/centos7/1.4.2/lib:/cbica/software/external/freesurfer/centos7/5.3.0/lib:/cbica/software/external/nifticlib/2.0.0/lib:/cbica/software/external/fsl/centos7/5.0.11/lib:/cbica/software/external/mosek/7/tools/platform/linux64x86/bin:/cbica/software/external/minc/2.0.13/lib:/cbica/software/lab/mass/1.1.1/lib:/cbica/software/external/dicom3tools/1.00.snapshot.20110207/lib:/cbica/software/external/dependency_bundle/centos7/3817/lib64:/cbica/software/external/dependency_bundle/centos7/3817/lib:/cbica/software/external/ANTs/centos7/2.3.1/lib:/cbica/software/external/qt/centos7/5.11.1/Tools/QtCreator/lib:/cbica/software/external/qt/centos7/5.11.1/5.11.1/gcc_64/lib:/cbica/software/external/sge/8.1.9-1/../../local/8.1.9-1/lib64:/cbica/software/external/sge/8.1.9-1/lib/lx-amd64:/cbica/software/external/cudnn/7.0/cuda-9.0/lib64:/usr/local/cuda-9.0/extras/CUPTI/lib64:/usr/local/cuda-9.0/lib64:/usr/lib64:/usr/lib:/lib64:/lib:/cbica/software/external/matlab/R2018A/bin/glnxa64:/cbica/software/external/matlab/R2018A/runtime/glnxa64:/cbica/software/external/matlab/R2018A/sys/os/glnxa64

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 /cbica/home/nbald/software/afni/inuse

------------------------------ OS specific -------------------------------
which yum            : /usr/bin/yum
yum version          : 3.4.3


=========================  summary, please fix:  =========================
*  login shell 'bash', trusting user to translate code examples from 'tcsh'
*  have python version 3.6.5, some programs need 2.7.x
*  missing R packages (see rPkgsInstall)
*  please run: "suma -update_env" for .sumarc
*  insufficient data for AFNI bootcamp

From there, I noticed that the package "brms" was not installed. However, when I try to install it, I get:

rPkgsInstall -pkgs "brms"
Installing package into ‘/gpfs/fs001/cbica/software/external/R/gcc5’
(as ‘lib’ is unspecified)
Warning in install.packages(pkgs_miss, dep = TRUE, repos = site) :
  'lib = "/gpfs/fs001/cbica/software/external/R/gcc5"' is not writable
Error in install.packages(pkgs_miss, dep = TRUE, repos = site) :
  unable to install packages
Calls: getPkgs -> install.packages
Execution halted

If I try to install it from within R, I get:

> install.packages("brms")
Installing package into ‘/gpfs/fs001/cbica/software/external/R/gcc5’
(as ‘lib’ is unspecified)
Warning in install.packages("brms") :
  'lib = "/gpfs/fs001/cbica/software/external/R/gcc5"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                   2: Australia (Canberra) [https]
 3: Australia (Melbourne 1) [https]   4: Australia (Melbourne 2) [https]
 5: Australia (Perth) [https]         6: Austria [https]
 7: Belgium (Ghent) [https]           8: Brazil (BA) [https]
 9: Brazil (PR) [https]              10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]            12: Brazil (SP 2) [https]
13: Bulgaria [https]                 14: China (Hong Kong) [https]
15: China (Guangzhou) [https]        16: China (Lanzhou) [https]
17: China (Shanghai) [https]         18: Colombia (Cali) [https]
19: Costa Rica [https]               20: Denmark [https]
21: East Asia [https]                22: Ecuador (Cuenca) [https]
23: Ecuador (Quito) [https]          24: France (Lyon 1) [https]
25: France (Lyon 2) [https]          26: France (Marseille) [https]
27: Germany (Erlangen) [https]       28: Germany (Münster) [https]
29: Germany (Regensburg) [https]     30: Greece [https]
31: Hungary [https]                  32: Iceland [https]
33: Indonesia (Jakarta) [https]      34: Italy (Padua) [https]
35: Japan (Tokyo) [https]            36: Korea (Gyeongsan-si) [https]
37: Korea (Seoul 1) [https]          38: Korea (Ulsan) [https]
39: Mexico (Mexico City) [https]     40: Morocco [https]
41: Norway [https]                   42: Philippines [https]
43: Russia [https]                   44: Spain (A Coruña) [https]
45: Sweden [https]                   46: Switzerland [https]
47: Taiwan (Taipei) [https]          48: Turkey (Mersin) [https]
49: UK (Bristol) [https]             50: UK (London 1) [https]
51: USA (IA) [https]                 52: USA (KS) [https]
53: USA (MI 1) [https]               54: USA (MI 2) [https]
55: USA (OH) [https]                 56: USA (OR) [https]
57: USA (TN) [https]                 58: USA (TX 1) [https]
59: Uruguay [https]                  60: (other mirrors)


Selection: 51
also installing the dependencies ‘dygraphs’, ‘xts’, ‘rstan’, ‘shinystan’

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* installing *source* package ‘xts’ ...
** package ‘xts’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c add_class.c -o add_class.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c any.c -o any.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c attr.c -o attr.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c binsearch.c -o binsearch.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c coredata.c -o coredata.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c diff.c -o diff.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c dimnames.c -o dimnames.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c endpoints.c -o endpoints.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c extract_col.c -o extract_col.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c isOrdered.c -o isOrdered.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c isXts.c -o isXts.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c merge.c -o merge.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c na.c -o na.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c period_apply.c -o period_apply.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c period_arithmetic.c -o period_arithmetic.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c period_quantile.c -o period_quantile.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c rbind.c -o rbind.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c rollfun.c -o rollfun.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c runSum.c -o runSum.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c startofyear.c -o startofyear.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c subset.c -o subset.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c subset.old.c -o subset.old.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c toperiod.c -o toperiod.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c totalcols.c -o totalcols.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c tryXts.c -o tryXts.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I../inst/include -I"/gpfs/fs001/cbica/software/external/R/zoo/include" -I/usr/local/include  -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c unique.time.c -o unique.time.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o xts.so add_class.o any.o attr.o binsearch.o coredata.o diff.o dimnames.o endpoints.o extract_col.o init.o isOrdered.o isXts.o merge.o na.o period_apply.o period_arithmetic.o period_quantile.o rbind.o rollfun.o runSum.o startofyear.o subset.o subset.old.o toperiod.o totalcols.o tryXts.o unique.time.o -L/usr/lib64/R/lib -lR
installing to /gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/00LOCK-xts/00new/xts/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘zoo’:
 package ‘zoo’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Error: package ‘zoo’ could not be loaded
Execution halted
ERROR: lazy loading failed for package ‘xts’
* removing ‘/gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/xts’
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
Error in .shlib_internal(args) :
  C++14 standard requested but CXX14 is not defined
* removing ‘/gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/rstan’
ERROR: dependency ‘xts’ is not available for package ‘dygraphs’
* removing ‘/gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/dygraphs’
ERROR: dependencies ‘dygraphs’, ‘rstan’, ‘xts’ are not available for package ‘shinystan’
* removing ‘/gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/shinystan’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’
* removing ‘/gpfs/fs001/cbica/home/nbald/R/x86_64-redhat-linux-gnu-library/3.6/brms’

The downloaded source packages are in
        ‘/scratch/nbald/Rtmp3nrxh9/downloaded_packages’
Warning messages:
1: In install.packages("brms") :
  installation of package ‘xts’ had non-zero exit status
2: In install.packages("brms") :
  installation of package ‘rstan’ had non-zero exit status
3: In install.packages("brms") :
  installation of package ‘dygraphs’ had non-zero exit status
4: In install.packages("brms") :
  installation of package ‘shinystan’ had non-zero exit status
5: In install.packages("brms") :
  installation of package ‘brms’ had non-zero exit status
>

I came across this link,

https://afni.nimh.nih.gov/afni/community/board/read.php?1,160090,160120

However, the solution there requires write access to the default R installation directory. At this point, I think I will need to submit an IT ticket, but I'm not exactly sure where to start.

Is the issue with the lsmeans package or the brms package?
Do I need a root user to install these in the default location?
Is it possible to call local R package installations from afni programs?
Is it possible to change the default installation directory for rPkgsInstall?

Any help is appreciated.
-n