XGBoost model serializaiton message

[mikelove]

Minor note, when running bambu I see:

 !> se <- bambu(reads = "cell1_sort.bam",
 +             annotations = annotation,
 +             genome = Hsapiens)
 --- Start generating read class files ---
 [20:58:14] WARNING: src/learner.cc:553:
   If you are loading a serialized model (like pickle in Python, RDS in R) generated by
   older XGBoost, please export the model by calling `Booster.save_model` from that version
   first, then load it back in current version. See:

     https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html

   for more details about differences between saving model and serializing.
...

This is at the beginning of a run.

This is with R 4.3.2 and Bioc 3.18 / bambu (3.4.0)

[RnaSeqGal]

Hello, I am encountering the same issue running a single bam file as indicated in the vignette (https://www.bioconductor.org/packages/release/bioc/vignettes/bambu/inst/doc/bambu.html):
test.bam <- system.file("extdata", "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam", package = "bambu")
fa.file <- system.file("extdata", "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa", package = "bambu")
gtf.file <- system.file("extdata", "Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf", package = "bambu")
bambuAnnotations <- prepareAnnotations(gtf.file)
se <- bambu(reads = test.bam, annotations = bambuAnnotations, genome = fa.file)

output:

WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling Booster.save_model from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.

also:

Detected 3 warnings across the samples during read class construction. Access warnings with metadata(bambuOutput)$warnings
--- Start extending annotations ---
WARNING - Less than 50 TRUE or FALSE read classes for NDR precision stabilization.
NDR will be approximated as: (1 - Transcript Model Prediction Score)
Using a novel discovery rate (NDR) of: 0
WARNING - No novel transcripts meet the given thresholds. Try a higher NDR.
--- Start isoform quantification ---
--- Finished running Bambu ---

and also:

Warning message:
Returning more (or less) than 1 row per summarise() group was deprecated in dplyr 1.1.0.
ℹ Please use reframe() instead.
ℹ When switching from summarise() to reframe(), remember that reframe() always returns an ungrouped
data frame and adjust accordingly.
ℹ The deprecated feature was likely used in the bambu package.
Please report the issue to the authors.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.

I just installed R 4.5.1, bambu_3.12.0, NanoporeRNASeq_1.20.0, BiocVersion_3.22.0.

Would installing different versions of any packages fix this?
Any tips are much appreciated, thanks!