The deprecated feature was likely used in the bambu package

[alexander-schl]

Hi there,

I use R 4.3.1 and bambu 3.2.6. When using the test set to check if bambu was installed correctly, I encounter the following issue(s) when I execute se <- bambu(reads = test.bam, annotations = bambuAnnotations, genome = fa.file):

--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
[09:01:56] 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.

[09:01:56] 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.

[09:01:56] 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.

[09:01:56] 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.

[09:01:57] 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.

[09:01:57] 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.

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 ---
Warning messages:
1: There was 1 warning in `summarise()`.
ℹ In argument: `intersectWidth = max(intersectWidth)`.
Caused by warning in `max()`:
! no non-missing arguments to max; returning -Inf 
2: 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. 
3: There was 1 warning in `summarise()`.
ℹ In argument: `intersectWidth = max(intersectWidth)`.
Caused by warning in `max()`:
! no non-missing arguments to max; returning -Inf 

Can you help me resolve this issue? Thank you in advance!

[andredsim]

Hi,

If you print(se) could you share the output. From these messages it looks like Bambu was successful and the console output is only a series of warnings (that will be fixed in an upcoming version) that do not negatively impact the output.

Kind Regards,
Andre Sim

[alexander-schl]

Thank you for your quick response! The output of print(se) is

class: RangedSummarizedExperiment 
dim: 105 1 
metadata(2): incompatibleCounts warnings
assays(4): counts CPM fullLengthCounts uniqueCounts
rownames(105): ENST00000190165 ENST00000305248 ... ENST00000622412 ENST00000628764
rowData names(11): TXNAME GENEID ... txid eqClassById
colnames(1): SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000
colData names(1): name

[andredsim]

Thanks, yes it looks like your Bambu is installed correctly and you can continue using it without issue. Be sure to patch Bambu once our next version comes out to remove these deprecated warnings.