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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
  • and what happens when you run the R Sys.info() script under the "MyName" user? It just segfaults without outputting anything else? – Tomáš Pospíšek Sep 9 '18 at 20:40
  • i cant start R as that user (which is imm_admin). I can only run R with sudo or as root. Anything else gives me the Segmentation error. – Vaxin Sep 9 '18 at 21:40
  • so there's no output when running R as a user except for it segfaulting? – Tomáš Pospíšek Sep 10 '18 at 7:34
  • Yes exactly. I only get the Segmentation fault (core dumped) message. – Vaxin Sep 10 '18 at 8:00
  • Since you have deleted everything under /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? – Tomáš Pospíšek Sep 10 '18 at 17:41

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