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Couldn’t delete a failed R package installation

Couldn’t delete a failed R package installation

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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

library("devtools")
install_github("fischuu/GenomicTools")

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…

CDU/CSU Durcheinander

CDU/CSU Durcheinander

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[D] Ich bin ja nun mal weit davon entfernt ein CDU-Wähler zu sein, aber ich kann nicht anders, als mich darüber zu wundern, was da gerade zwischen Laschet/CDU und Söder/CSU abläuft! Wie kann jemand ohne gravierende Gedächtnisprobleme ernsthaft Söder für kanzlertauglich halten?! Klar, die Abgeordneten stehen hinter ihm, da sie sich evtl bessere Chancen auf einen erneuten Sitz im Bundestag ausrechnen – aber trotzdem, da darf auch Mal hinterfragt werden, mit welchem Preis das kommt!

Falls Söder tatsächlich der Kanzlerkandidat wird hoffe ich inständig, dass viele Bürger kein so schlechtes Gedächtnis haben wie momentan viele CDU Mitglieder!

Man darf hoffen, dass andere Parteien da einen Nutzen draus ziehen können…

A little piece of Normality

A little piece of Normality

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Starting today the restaurants are again open in Finland. Of course, Corona is not over yet, there are still many people getting it and one still needs to be careful while being out, but still having a small breakfast out feels quite nice (although the lockdown was not even that long compared to other countries).

However, let’s hope the vaccines will start to have an effect and that severe infections or even deaths will vanish soon and we can start to live normal lifes again.

In that sense, have a nice start into the week!

Eating out after the lockdown
Git submodules

Git submodules

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Today I noticed for the first time the concept of submodules in git. While cloning a repository from GitHub I noticed that one folder in it remained empty. After having a closer look, I noticed a reference to another repository tree like this:

Here, the folder htslib is actually from a tree in a different repository. After I cloned the repository like this (I forked it before):

git clone https://github.com/fischuu/SE-MEI.git

the folder htslib remained empty. That is because files from submodules are not fetched by default. This needs to be done separately by first initializing the submodules (first, cd into the cloned repository)

git submodule init

and then update the files from it

git submodule update

After these steps, the repository should be complete. However, instead of initializing the submodule separately, there is also a shortcut to fetch them all in one step by adding an additional parameter to the cloning like this:

git clone --recurse-submodules https://github.com/fischuu/SE-MEI.git

More details to git submodules can be found here.