Loading samples in new R takes too long time

[desmodus1984]

I use RStudio, and since I told that the best is to have the latest up-to-date version of the software I installed it, RStudio 2024 B 735 with R 4.4.1.
I am trying to reanalyze a dataset of 44 samples, created with methyldackel, which loaded relatively fast in previous version, but now, it's been almost 5 hours, and the log is frozen in the "Parsing files and constructing 'M' and 'Cov' matrices ..." step.

[read.bismark] Parsing files and constructing valid loci ...
Done in 62.1 secs
[read.bismark] Parsing files and constructing 'M' and 'Cov' matrices ...

I am working in a workstation with huge memory, 400GB; since I was reading 9 files, I realized that that is not my full dataset- since I later found that dmrseq is not limited to pairwise comparison, I tried loading the full 44 samples.
Almost 5 hours and no read.bismark step has finished. With the aim of increasing speed I set the parameter nThread to 8L, and 10L, for 9 samples and full 44 samples dataset.

Do you have any idea why this step is taking so much time to finish now with the new R?
I have to tell that with the new R I had to install dmrseq again, so I don't know what might be slowing it down so much.

Best;

Juan Pablo

[kdkorthauer]

Hi,

As read.bismark is not a function from dmrseq (it is from the bsseq package), I'd suggest you refer to the documentation from that package, and reach out to the respective maintainers if you're still stuck. Thanks!

Best,
Keegan