dplyr 1.1.0. The deprecated feature was likely used in the bambu package. Warning message

[Michael-m6A]

Hi bambu developers,

I have installed and used the latest bambu v3.2.4.

When running bambu I got the following warning message regarding “dplyr 1.1.0. The deprecated feature was likely used in the bambu package” and asked me to “Please report the issue to the authors”.

Please see the full warning message and session info below.

se.multiSample <- bambu(reads = c(Tx_1, Tx_2, Tx_3, Ctrl_1, Ctrl_2, Ctrl_3), annotations = gtf, genome = fasta)
If you are running bambu multiple times we recommend processing your annotation file first with annotations = prepareAnnotations(gtf.file)

--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
| | 0%[11:20:41] 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.

[11:20:41] 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.

|==============================================================================================================================| 100%

Detected 12 warnings across the samples during read class construction. Access warnings with metadata(bambuOutput)$warnings

--- Start extending annotations ---
Using a novel discovery rate (NDR) of: 0.213
--- Start isoform quantification ---
--- Finished running Bambu ---

Warning messages:
1: 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: There was 1 warning in filter().
ℹ In argument: newGeneId == min(newGeneId).
Caused by warning in min():
! no non-missing arguments to min; returning Inf

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Brisbane
tzcode source: internal

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

other attached packages:
[1] bambu_3.2.4 BSgenome_1.68.0 rtracklayer_1.60.0 Biostrings_2.68.1
[5] XVector_0.40.0 SummarizedExperiment_1.30.2 Biobase_2.60.0 GenomicRanges_1.52.0
[9] GenomeInfoDb_1.36.1 IRanges_2.34.1 S4Vectors_0.38.1 BiocGenerics_0.46.0
[13] MatrixGenerics_1.12.2 matrixStats_1.0.0

loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 dplyr_1.1.2 blob_1.2.4 filelock_1.0.2 bitops_1.0-7
[6] fastmap_1.1.1 RCurl_1.98-1.12 BiocFileCache_2.8.0 GenomicAlignments_1.36.0 XML_3.99-0.14
[11] digest_0.6.31 lifecycle_1.0.3 KEGGREST_1.40.0 RSQLite_2.3.1 magrittr_2.0.3
[16] compiler_4.3.0 rlang_1.1.1 progress_1.2.2 tools_4.3.0 utf8_1.2.3
[21] yaml_2.3.7 data.table_1.14.8 prettyunits_1.1.1 S4Arrays_1.0.4 xgboost_1.7.5.1
[26] bit_4.0.5 curl_5.0.1 DelayedArray_0.26.3 xml2_1.3.4 BiocParallel_1.34.2
[31] withr_2.5.0 purrr_1.0.1 grid_4.3.0 fansi_1.0.4 colorspace_2.1-0
[36] ggplot2_3.4.2 scales_1.2.1 biomaRt_2.56.1 cli_3.6.1 crayon_1.5.2
[41] generics_0.1.3 rstudioapi_0.14 httr_1.4.6 rjson_0.2.21 DBI_1.1.3
[46] cachem_1.0.8 stringr_1.5.0 zlibbioc_1.46.0 parallel_4.3.0 AnnotationDbi_1.62.1
[51] BiocManager_1.30.21 restfulr_0.0.15 vctrs_0.6.3 Matrix_1.5-4.1 jsonlite_1.8.5
[56] hms_1.1.3 bit64_4.0.5 GenomicFeatures_1.52.1 locfit_1.5-9.8 tidyr_1.3.0
[61] glue_1.6.2 codetools_0.2-19 stringi_1.7.12 gtable_0.3.3 BiocIO_1.10.0
[66] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0 rappdirs_0.3.3 GenomeInfoDbData_1.2.10
[71] R6_2.5.1 dbplyr_2.3.2 lattice_0.21-8 png_0.1-8 Rsamtools_2.16.0
[76] memoise_2.0.1 Rcpp_1.0.10 DESeq2_1.40.1 pkgconfig_2.0.3

In addition, congratulations on your recent Nature Methods publication.

Many thanks in advance.

Regards,
Michael

[piechottam]

I have the same warning. I am using bambu 3.2.5.

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

time zone: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
 [1] bambu_3.2.5                 BSgenome_1.68.0
 [3] rtracklayer_1.60.0          Biostrings_2.68.1
 [5] XVector_0.40.0              SummarizedExperiment_1.30.2
 [7] Biobase_2.60.0              GenomicRanges_1.52.0
 [9] GenomeInfoDb_1.36.1         IRanges_2.34.1
[11] S4Vectors_0.38.1            BiocGenerics_0.46.0
[13] MatrixGenerics_1.12.2       matrixStats_1.0.0

loaded via a namespace (and not attached):
 [1] KEGGREST_1.40.0          rjson_0.2.21             lattice_0.21-8
 [4] vctrs_0.6.3              tools_4.3.1              bitops_1.0-7
 [7] generics_0.1.3           curl_5.0.1               parallel_4.3.1
[10] tibble_3.2.1             fansi_1.0.4              AnnotationDbi_1.62.2
[13] RSQLite_2.3.1            blob_1.2.4               pkgconfig_2.0.3
[16] Matrix_1.6-0             data.table_1.14.8        dbplyr_2.3.3
[19] lifecycle_1.0.3          GenomeInfoDbData_1.2.10  compiler_4.3.1
[22] stringr_1.5.0            Rsamtools_2.16.0         progress_1.2.2
[25] codetools_0.2-19         RCurl_1.98-1.12          yaml_2.3.7
[28] tidyr_1.3.0              pillar_1.9.0             crayon_1.5.2
[31] BiocParallel_1.34.2      DelayedArray_0.26.6      cachem_1.0.8
[34] tidyselect_1.2.0         digest_0.6.33            stringi_1.7.12
[37] purrr_1.0.1              dplyr_1.1.2              restfulr_0.0.15
[40] biomaRt_2.56.1           fastmap_1.1.1            grid_4.3.1
[43] cli_3.6.1                magrittr_2.0.3           S4Arrays_1.0.4
[46] GenomicFeatures_1.52.1   utf8_1.2.3               XML_3.99-0.14
[49] rappdirs_0.3.3           filelock_1.0.2           prettyunits_1.1.1
[52] xgboost_1.7.5.1          bit64_4.0.5              httr_1.4.6
[55] bit_4.0.5                png_0.1-8                hms_1.1.3
[58] memoise_2.0.1            BiocIO_1.10.0            BiocFileCache_2.8.0
[61] rlang_1.1.1              Rcpp_1.0.11              glue_1.6.2
[64] DBI_1.1.3                xml2_1.3.5               jsonlite_1.8.7
[67] R6_2.5.1                 GenomicAlignments_1.36.0 zlibbioc_1.46.0

[andredsim]

Hi both, thanks for reporting this. I was able to replicate this warning using the versions you are using (the version available on Bioconductor at the moment). We currently offer version bambu_3.3.4 on the GitHub page and I was unable to reproduce this warning in this version.

[andreas-wilm]

Hello,

I experience the same issue using the following three options:

1. latest Github commit (devtools::install_github("GoekeLab/bambu"))
2. latest release (install.packages('bambu-3.2.4.tar.gz')) and
3. Bioconductor (BiocManager::install("bambu"))

Is there another way to address this issue? It looks like either the shipped model needs updating or XGBoost needs a downgrade.

Thanks, Andreas

[cying111]

Hi @andreas-wilm ,

we have recently fixed the dplyr deprecation related warning. Please feel free to give it a try.

I will close this issue for now. Feel free to re-open it if needed.

Thank you