Browsed by
Category: Filesystem

Couldn’t delete a failed R package installation

Couldn’t delete a failed R package installation

Today I faced a strange thing, while I tried to install an update to one of my R-packages. As usually, I installed the latest version from it like this


But the installation failed, and when I tried to reinstall it, I got this error message:

Installing package into ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
ERROR: failed to lock directory ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1’ for modifying
Try removing ‘/homeappl/home/<user>/R/x86_64-redhat-linux-gnu-library/4.1/00LOCK-GenomicTools’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp<...>Lv/file3c36<...>34/GenomicTools_0.2.11.tar.gz’ had non-zero exit status

So, I tried to go in said directory and delete the folder manually and there I received another error:

rm: cannot remove '00LOCK-GenomicTools/GenomicTools/libs/.nfs00000001002e2<...>d': Device or resource busy

I tried this and this, but nothing helped to delete that folder, it kept mocking my that the device is busy. Eventually, it helped just to rename the folder list this

mv 00LOCK-GenomicTools/ 00LOCK-GenomicTools-deleteThis/

It is now still hanging there in the folder, but I was able to reinstall the R-package and now I need to revisit the folder in a few days and check, if the device is still busy or if I can delete it then…

Adding an external HDD to fstab

Adding an external HDD to fstab

In order to permanently add an external HDD, the best way is to first identfy the UUID and the corresponding file system by typing

sudo blkid

with that information one can edit the fstab

sudo vim /etc/fstab

and enter then there a line with the format

UUID=<UUID> \tab <mountPoint> \tab <filesystem> \tab <options> \tab 0 \tab 1

Here, the values for <UUID> and <filesytem> we get from the blkid command, the mount point is ‘free choice’ and as option, I choose e.g. errors=remount-ro

Once the fstab is populated like this, just try to mount the disc by typing

sudo mount -a