R session aborted, R encountered a fatal error, the session was determined

Microbial community profiling
1

Hi,

When using MetaPhlan4 data in my RStudio script, everytime I run into an error, I get a fatal error message and the session gets terminated. When I run the same code with GreenGenes2, this does not happen, instead I receive a normal error message. Does anyone have experience with this error?

I tried with different laptops and different MetaPhlan4 datasets and all give the same issue. Also, I tried with MetaPhlan4 datasets that I used in the past and did not give these fatal error messages.

I am using R 4.4.3, Rtools43 and Rstudio 2025.09. Also, recently I changed to Windows 11, but I guess that should not cause issues?

Hopefully someone can help me. Thanks!

Mirte

2

I think it has to do with the R 4.4.3. Running the same scripts on an old computer with R 3.4.4. does not results in Fatal error messages. So maybe I cannot use MetaPhlan4 datasets for newer R versions :frowning:

3

Hi @mirte,

Would it be possible for you to provide us with a reproducible example so that we can look into this issue?

Thanks,
Jacob

4

Hi Jacob,

Sorry for the late reply, your email ended up in my spam box. Can I send you the example via email? I could share an example dataset and a script. If yes, could you share your email address with me? e.g. via email.

Best,

Mirte