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Category: Science

Holiday read arrived

Holiday read arrived

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With the upcoming autumn holiday ahead, my autumn holiday read just arrived in time! Looking forward to having a light read, as my Python become a little rusty lately it is a nice kick-start again to read about it from an introductory perspective. First glance looks really nice!

Creating weighted tables with R / sum of numerics associated to some categorical variable

Creating weighted tables with R / sum of numerics associated to some categorical variable

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The normal table command table() calculates the frequency of each element of a vector like this:

R> df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"))
R> table(df)
df
A B C 
2 2 3

So, it tells us, we have two times A and B and three times C, accordingly.

However, if we have now the situation like this:

df <- data.frame(var = c("A", "A", "B", "B", "C", "C", "C"), value = c(10, 20, 20, 40, 15, 25, 35))

Meaning, we have a categorical variable var and a numeric variable value and for each categorical variable we would like to get the sum over the numerical variable, we can simply use the base-R command aggregate like this

R> aggregate(value ~ var, data = df, FUN = sum)
  var wt
1   A 40
2   B 60
3   C 70

As I often use also the data.table package, here is also a simple solution using this package, assuming we do (respective have a data table from some other source, like fread)

library("data.table")
dt <- data.table(df)

Then we can just sume over a column name with respect to another column like this (and assign the value into a new variable tot) :

setDT(dt)[, .(n = sum(value)), var]
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…

Workshop: “Foundation for the Future Agenda”

Workshop: “Foundation for the Future Agenda”

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I just noticed I haven’t written anything yet about my attendance at the Shared Workshop: “Foundation for the Future Agenda” in Hinxton, UK, during February. This was a workshop organized by EBI for the three H2020 projects GeneSwitch, BovReg and AquaFAANG.

As always, it was an excellent meeting in Hinxton, with lots of good interaction and talks. Also, a visit to the Red Lion is always a nice experience.