[Bug]: error in evaluating the argument 'x' in selecting a method for function 'grglist'

[rnaomics]

Affected Area

Transcript Quantification

Issue Description

--- Start generating read class files ---
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://packagemanager.posit.co/cran/__linux__/rhel9/latest
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'grglist': unable to find an inherited method for function ‘seqnames’ for signature ‘x = "GAlignments"’

Minimal Reproducible Example (R Code)

> 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)

Input Data Details

ONT

Reproducibility

Always (every time I run this)

Session Info

Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'grglist': unable to find an inherited method for function ‘seqnames’ for signature ‘x = "GAlignments"’
 

6. | stop(.error_bplist(res))
-- | --

Contribution

• I can provide a small public dataset/toy example for reproduction.

Checklist

• I searched existing issues to avoid duplicates.
• I included a minimal reproducible code snippet.
• I included session/environment information.

[rnaomics]

The error is fixed now. It seems installation error. When I reinstalled bambu and other packages with the following command, it worked

BiocManager::install(c(
"bambu",
"GenomicAlignments",
"GenomicRanges",
"IRanges",
"GenomeInfoDb"
), force = TRUE)