Quick Background:
After a Backup restore, we accidentally filled up the root folder "/" HDD and had no disk space left. I started Ubuntu from a USB, mounted the HDD and found out that the Backup was made in /home on that HDD. However, we have a separate HDD for /home. So I just deleted everything under /home on that HDD, restarted Ubuntu and everything was fixed disk space wise.
I then ran a script that uses R (Rscript) and noticed that I now get this error:
Segmentation fault (core dumped)
When I start R with sudo
it starts without a problem. (sudo R
)
So I thought this is easily fixed with chown
, but it is not. I tried:
sudo chown Myname /home/Myname/ -R
But that didn't fix it. Pretty clueless now. Anyone had a similar issue? I have also uninstalled and reinstalled R.
R gives has a function to get some System and User info. this is what I get when starting R using sudo
:
Sys.info()
sysname
"Linux"
release
"3.16.0-62-generic"
version
"#83~14.04.1-Ubuntu SMP Fri Feb 26 22:52:39 UTC 2016"
nodename
"PC3272796"
machine
"x86_64"
login
"imm_admin"
user
"root"
effective_user
"root"
I also checked where R is installed with:
> R.home()
[1] "/usr/lib/R"
From previous tries, I have already changed the permission for the contents of the folder from root to imm_admin which is the current user.
imm_admin@PC3272796:/usr/lib/R$ ls -l
total 28
drwxrwxrwx 3 imm_admin imm_admin 4096 Sep 6 11:46 bin
lrwxrwxrwx 1 root root 33 Mar 16 04:31 COPYING -> ../../share/common-licenses/GPL-2
drwxrwxrwx 2 imm_admin imm_admin 4096 Sep 6 00:16 etc
drwxrwxrwx 2 imm_admin imm_admin 4096 Sep 6 00:16 lib
drwxrwxrwx 32 imm_admin imm_admin 4096 Sep 6 00:17 library
drwxrwxrwx 2 imm_admin imm_admin 4096 Sep 6 00:16 modules
drwxrwxrwx 3 imm_admin imm_admin 4096 Sep 6 11:46 site-library
-rw-rw-rw- 1 imm_admin imm_admin 46 Mar 16 04:31 SVN-REVISION
Sys.info()
script under the "MyName" user? It just segfaults without outputting anything else?Segmentation fault (core dumped)
message./home
, is the user's$HOME
set up correctly? I.e. if you look in /etc/passwd, does the$HOME
configured there to the one that exists on disk? Does the user's$HOME
belong to the user and his group?