Multiple warnings (model from older XGBoost (5 times), deprecated summarize() in dplyr1.1.0

[RnaSeqGal]

Hello,
I'm running bambu for the first time following the "General usage" example, and getting the warnings below. R version 4.5.1 had some issues, so I have used R4.5.2; you indicated you used a patched version of 4.5.1.

Your help in resolving the warnings will be highly appreciated, thank you very much!
Roumi

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(1) [16:34:04] 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.
#5 copies of this warning

(3) 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.

(2) - probably dependent on the example data:
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 ---

This is my sessionInfo():
R version 4.5.2 (2025-10-31)
Platform: x86_64-pc-linux-gnu
Running under: AlmaLinux 8.8 (Sapphire Caracal)

Matrix products: default
BLAS: /hpf/tools/alma8/R/4.5.2/lib64/R/lib/libRblas.so
LAPACK: /hpf/tools/alma8/R/4.5.2/lib64/R/lib/libRlapack.so; LAPACK version 3.12.1

locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

time zone: America/Toronto
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] NanoporeRNASeq_1.20.0 ExperimentHub_3.0.0
[3] AnnotationHub_4.0.0 BiocFileCache_3.0.0
[5] dbplyr_2.5.1 BiocVersion_3.22.0
[7] BiocManager_1.30.27 bambu_3.12.0
[9] BSgenome_1.78.0 rtracklayer_1.70.0
[11] BiocIO_1.20.0 Biostrings_2.78.0
[13] XVector_0.50.0 SummarizedExperiment_1.40.0
[15] Biobase_2.70.0 GenomicRanges_1.62.0
[17] Seqinfo_1.0.0 IRanges_2.44.0
[19] S4Vectors_0.48.0 BiocGenerics_0.56.0
[21] generics_0.1.4 MatrixGenerics_1.22.0
[23] matrixStats_1.5.0

loaded via a namespace (and not attached):
[1] KEGGREST_1.50.0 httr2_1.2.1 rjson_0.2.23
[4] lattice_0.22-7 vctrs_0.6.5 tools_4.5.2
[7] bitops_1.0-9 curl_7.0.0 parallel_4.5.2
[10] tibble_3.3.0 AnnotationDbi_1.72.0 RSQLite_2.4.4
[13] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.7-4
[16] data.table_1.17.8 cigarillo_1.0.0 lifecycle_1.0.4
[19] compiler_4.5.2 Rsamtools_2.26.0 codetools_0.2-20
[22] GenomeInfoDb_1.46.0 RCurl_1.98-1.17 yaml_2.3.10
[25] pillar_1.11.1 crayon_1.5.3 tidyr_1.3.1
[28] BiocParallel_1.44.0 DelayedArray_0.36.0 cachem_1.1.0
[31] abind_1.4-8 tidyselect_1.2.1 purrr_1.2.0
[34] dplyr_1.1.4 restfulr_0.0.16 fastmap_1.2.0
[37] grid_4.5.2 cli_3.6.5 SparseArray_1.10.2
[40] magrittr_2.0.4 S4Arrays_1.10.0 GenomicFeatures_1.62.0
[43] XML_3.99-0.20 withr_3.0.2 filelock_1.0.3
[46] rappdirs_0.3.3 UCSC.utils_1.6.0 bit64_4.6.0-1
[49] xgboost_1.7.11.1 httr_1.4.7 bit_4.6.0
[52] png_0.1-8 memoise_2.0.1 rlang_1.1.6
[55] Rcpp_1.1.0 glue_1.8.0 DBI_1.2.3
[58] jsonlite_2.0.0 R6_2.6.1 GenomicAlignments_1.46.0

[RnaSeqGal]

I found a reply from March 10, 2024, which indicates that it is probably OK to ignore these warnings:
"If you are meaning the xgboost warnings, that is fine to ignore. We just need to update the packages and push the changes. We just keep getting distracted with other tasks but I will hopefully find the time to do this soon.
Given that bambu() finishes running, and the remaining warnings are not result impacting I think its fine to ignore for now. I believe the finally warnings must be happening during the writeBambuOutput() function call. But as you are still getting your outputs I think that should be fine too."

[lingminhao]

Hi @RnaSeqGal, yes it's fine to ignore the warnings from xgboost and dplyr. We will update these during the next release of bambu. To avoid duplications, should I close the issue, as somebody had repored that?

[RnaSeqGal]

Hi @lingminhao,
Thank you very much for your reply. Yes, please close the issue.
R