Hello,
I am having some difficulty installing some of the R package dependencies for AFNI on a Linux system (Ubuntu 22.04). I have looked through some previous threads, but most of the ones I saw fixed the issue by updating the R version to 3.5 or later. My R version is 4.3. When I tried to install the R packages that I'm missing individually, I am getting an error that my C++ compiler is not working. I'm a bit stuck and not sure how to proceed.
afni_system_check.py -check_all:
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.2.0-39-generic
version: #40~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 16 10:53:04 UTC 2
distribution: ubuntu 22.04 Jammy Jellyfish
number of CPUs: 32
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/bankslab/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Dec 21 2023
: AFNI_23.3.14 'Septimius Severus'
AFNI_version.txt : AFNI_23.3.14, linux_ubuntu_16_64, Dec 21 2023, official
which python : /home/bankslab/fsl/bin/python
python version : 3.11.6
which R : /usr/bin/R
R version : R version 4.3.2 (x86_64-pc-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/home/bankslab/abin/afni)
R : 1 (/usr/bin/R)
python : 3
/home/bankslab/fsl/bin/python3.11
/home/bankslab/miniconda3/bin/python3.11
/usr/bin/python3.10
python2 : 0
python3 : 3
/home/bankslab/fsl/bin/python3.11
/home/bankslab/miniconda3/bin/python3.11
/usr/bin/python3.10
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : FAILURE
Error in library(data.table) : there is no package called ‘data.table’
Calls: source ... suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
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: gamm4!
These packages are not installed on the computer: data.table!
These packages are not installed on the computer: brms!
R RHOME : /usr/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /home/bankslab/fsl/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.2
++ module loaded: flask
module file : /home/bankslab/fsl/lib/python3.11/site-packages/flask/__init__.py
flask version : 3.0.0
** failed to load module flask_cors
-- flask_cors is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/bankslab/ANTs/:/home/bankslab/freesurfer/bin:/home/bankslab/freesurfer/fsfast/bin:/home/bankslab/freesurfer/tktools:/home/bankslab/fsl/bin:/home/bankslab/fsl/share/fsl/bin:/home/bankslab/freesurfer/mni/bin:/home/bankslab/fsl/share/fsl/bin:/home/bankslab/ANTs:/home/bankslab/freesurfer/bin:/home/bankslab/freesurfer/fsfast/bin:/home/bankslab/freesurfer/tktools:/home/bankslab/fsl/bin:/home/bankslab/fsl/share/fsl/bin:/home/bankslab/freesurfer/mni/bin:/home/bankslab/fsl/share/fsl/bin:/home/bankslab/miniconda3/bin:/home/bankslab/miniconda3/condabin:/home/bankslab/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin:/usr/local/go/bin:/home/bankslab/fsl/bin:/usr/local/go/bin:/home/bankslab/fsl/bin:/home/bankslab/abin
PYTHONPATH =
R_LIBS = /home/bankslab/R
LD_LIBRARY_PATH = :/home/bankslab/fsl/lib:/home/bankslab/fsl/lib
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME (467850M Avail)
top history: ... [gangc]: redo 0.BGA as 1.bga and update run.MSS.txt
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/bankslab/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.11 (amd64)
have Ubuntu system: ubuntu 22.04 Jammy Jellyfish
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Dec 21 2023
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 3 files:
rPkgsInstall -pkgs nloptr
Installing package into ‘/home/bankslab/R’
(as ‘lib’ is unspecified)
trying URL 'http://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpLfsdVB/R.INSTALL16498718789c3/nloptr':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/bankslab/R/nloptr’
The downloaded source packages are in
‘/tmp/RtmpS3pWKs/downloaded_packages’
++ Note: @ 11:23:31
This package has been installed on the computer: nloptr
Warning message:
In install.packages(pkgs_miss, dep = NA, repos = site) :
installation of package ‘nloptr’ had non-zero exit status
g++ --version
g++ (conda-forge gcc 12.3.0-3) 12.3.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Thanks in advance for the help!
Emma