Hello,
I just wanted to add that i got the same error message (see below) trying to install afni on ubuntu (on windows via virtual box; see below for system details). The workaround: Sys.setenv(R_INSTALL_STAGED=FALSE) did not work for me, but maybe I was doing something wrong.
Here is what i did from within the terminal:
R (to open R)
R_INSTALL_STAGED=FALSE
Sys.getenv (“R_INSTALL_STAGED”) (to check variable state)
=False (confirming var is false)
q ()
save = y
R (re open R)
Sys.getenv (“R_INSTALL_STAGED”) (to check variable state)
Sys.getenv (“R_INSTALL_STAGED”) (to check variable state)
=“” (var state not saved)
Next, I tried disabling staged install from inside R and manually downloading packages:
install.packages(“units”,dependencies=TRUE)
This gave me the same error message as before.
Any assistance would be much appreciated!
Here are the results from original R package install error:
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
/usr/lib/R/etc/Makeconf:176: recipe for target 'stan/lang/grammars/term_grammar_inst.o' failed
make: *** [stan/lang/grammars/term_grammar_inst.o] Error 4
ERROR: compilation failed for package ‘rstan’
* removing ‘/home/wtm0004/R/rstan’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/home/wtm0004/R/sf’
ERROR: dependency ‘rstan’ is not available for package ‘shinystan’
* removing ‘/home/wtm0004/R/shinystan’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/home/wtm0004/R/spdep’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’
* removing ‘/home/wtm0004/R/brms’
The downloaded source packages are in
‘/tmp/RtmpPpocAd/downloaded_packages’
++ Note: @ 01:10:52
This package has been installed on the computer: brms
Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘units’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rstan’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘sf’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘shinystan’ had non-zero exit status
5: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘spdep’ had non-zero exit status
6: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘brms’ had non-zero exit status
here is my system info and results from afni_system_check.py -check_all
wtm0004@Linux-VM:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.0.0-25-generic
version: #26~18.04.1-Ubuntu SMP Thu Aug 1 13:51:02 UTC 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 1
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/wtm0004/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Aug 19 2019
: AFNI_19.2.14 ‘Claudius’
AFNI_version.txt : AFNI_19.2.14, linux_ubuntu_16_64, Aug 19 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/wtm0004/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/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
checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: brms!
checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/init.pyc
** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/wtm0004/abin:/home/wtm0004/abin
PYTHONPATH =
R_LIBS = /home/wtm0004/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: 29 Apr 2019 [rickr]: AFNI_pamenc command newline
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/wtm0004/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.11 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Aug 19 2019
========================= summary, please fix: =========================
- login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
- missing R packages (see rPkgsInstall)
