getFootprints error

[mfrenkel16]

Hi,

I am running into an error when running the tutorial on the BMMCTutorial data. Everything works up until getFootprints which produces the error: Error in { : task 6 failed - "$ operator is invalid for atomic vectors"

I'm running the tutorial interactively in a job with an apptainer that has the dependencies needed. In case you wanted to build the extact container I'm using, I've attached the def file below). I'm using R version 4.2.1. The code that I'm using is attached below "Reproducible_Tutotiral_R_Code.txt". The command that fails is scale <- 50 project <- getFootprints( project, mode = as.character(scale), nCores = 16, footprintRadius = scale, flankRadius = scale)

Everything before this runs ok. There is a Warning for loadTFBSModel that "TF-TRT Warning: Could not find TensorRT" but I'm not sure this matters. I'm not using a GPU for this.

Here's the traceback:

Here's the code which starts in the interactive job outside of R, establishes the environment, and then enters R: Reproducible_Tutorial_R_Code.txt

And if you want to build the apptainer I'm using, here's the def file:

Please let me know if you need any other information or if you know how to fix this.

Thanks! Max

[mfrenkel16]

msfprint.def.txt I forgot to upload the def file for the apptainer in case you wanted to build it, but I don't think the error has to do with this and instead has to do with something in R and the getFootprints code.

[HYsxe]

Hi Max!

Sorry for the late reply. I remember seeing my lab mates ran into this and I vaguely remember it was a R or package version issue. If you try using R4.1.0 do you still get the error?