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Old 03-01-2020, 11:06 AM   #1
SuzuBell
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Registered: Dec 2013
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Unable to install packages due to storage issue (amount unsuccessful)


I am trying to install an R package on Ubuntu 16.04 R. I have been able to install several packages, but currently, in my R session, when I type:

Code:
install.packages("devtools")
I receive:

Code:
Fatal error: cannot create 'R_TempDir'
Upon issuing the
Code:
 tempdir()
command in R, I see that my temporary directory is located at
Code:
tmp/RtmpD54Esf
. I tried:
Code:
rm -r tmp/RtmpD54Esf
. But the problem remains.

I also tried
Code:
df -h
which results in:

Code:
Filesystem      Size  Used Avail Use% Mounted on
udev             32G     0   32G   0% /dev
tmpfs           6.3G  9.7M  6.3G   1% /run
/dev/sdc2        54G   52G  4.6M 100% /
tmpfs            32G  1.8M   32G   1% /dev/shm
tmpfs           5.0M  4.0K  5.0M   1% /run/lock
tmpfs            32G     0   32G   0% /sys/fs/cgroup
/dev/sda1       2.7T  1.7T  945G  64% /mnt/disk3
/dev/sdb1       2.7T   73M  2.6T   1% /mnt/disk4
/dev/sdf1       2.7T  2.2T  397G  85% /mnt/disk2
/dev/sde1       2.7T  1.9T  683G  74% /mnt/disk1
/dev/sdc1       511M  4.7M  507M   1% /boot/efi
tmpfs           6.3G   40K  6.3G   1% /run/user/1004
I am not sure if the problem is that
Code:
/dev/sdc2
is full. It appears to not be a directory. I tried
Code:
sudo umount -f /dev/sdc2
and
Code:
sudo umount -l /dev/sdc2
but still the problem persisted.

I have searched for several hours but most suggestions to fix this error revolve around erasing contents in the temp directory and unmounting the largest space from df -h. I feel I have tried both these suggestions and am still seeing the error. I do not have lots of Linux management experience and was hoping that by asking this question and following advice very carefully, I can identify if I may be misinterpreting the advice usually available. Thank you for your suggestions!
 
Old 03-01-2020, 11:20 AM   #2
Michael Uplawski
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I cannot well explain it.

What you see on /dev/sdc2 is the "Root" partition, i.e. the top level and starting point of the file-system tree. You are registered on LQ since 2013. This together with
Quote:
I am not sure if the problem is that
/dev/sdc2
is full. It appears to not be a directory. I tried
sudo umount -f /dev/sdc2
raises serious issues. Not only can I not really explain the origin of your troubles, as they are partly mysterious to me, I am not even sure that I want to.

Can you give a little evidence of your Linux knowledge, please:
  • What are the other partitions on /dev/sdc, if there are any.
  • Is there empty space left on the disk (sdc)?
  • Which is the structure of the root-directory ( '/' )?

Something is full and should not be.
The situation that you describe points at one specific directory, but in view of the other problem that you have, going there straight away to “make place” may not be the right strategy.

Last edited by Michael Uplawski; 03-01-2020 at 11:25 AM.
 
Old 03-01-2020, 03:15 PM   #3
bazio101
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Registered: Feb 2020
Location: Greece
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Unable to install packages due to storage issue (amount unsuccessful)

You can use "du" command to find the directory which holds most of these 52G. (most probably your home directory?).
Check its man page and try something like:
"du -ahx . | sort -rh | head -10"
from root "/" directory.
You can't fill 52G by just installing packages.
 
Old 03-04-2020, 01:34 AM   #4
chrism01
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Location: Sydney
Distribution: Centos 7.7 (?), Centos 8.1
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It looks likely that sdc2 incudes /tmp and /var, so it may well be logs that are filling it up.
Easy check
Code:
cd /tmp
df -h .
cd /var
df -h .
 
1 members found this post helpful.
Old 03-04-2020, 06:47 AM   #5
Michael Uplawski
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Quote:
Originally Posted by chrism01 View Post
It looks likely that sdc2 incudes /tmp and /var, so it may well be logs that are filling it up.[/code]
I think it is /var/cache/apt (and archives)
But will it help to clean this up? 54G is monstrous. Something monstrous must happen to fill it up with logs and stale packages... It would help to comprehend the origin of this phenomenon.

Last edited by Michael Uplawski; 03-05-2020 at 02:19 PM. Reason: Kraut2English
 
Old 03-10-2020, 02:58 AM   #6
chrism01
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Unfortunately it's not possible to give an exact answer without being on the system.

Basically you have to drill into each of the (biggest) dirs at each level and see what's there.
Code:
du -sh *
Only then can you research & decide what can be deleted & how (note that some files may need to be deleted via a specific tool, not just a simple rm ...).

Unless you're really sure, you should also backup stuff before deleting it...
 
Old 03-10-2020, 04:39 AM   #7
onebuck
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Moderator Response

Moved: This thread is more suitable in <Ubuntu> and has been moved accordingly to help your thread/question get the exposure it deserves.
 
  


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