Dear all,

I use a tool called ExomeDepth. 2 months ago I was able to run it and it worked well. Today I decided to analyse different samples and try to count reads:

    library(ExomeDepth)
    data(exons.hg19)
    bams <- c(long vector of bams)
    my.counts <- getBamCounts(bed.frame = exons.hg19, bam.files = bams, include.chr = F, referenceFasta = "/path/to/fasta/hg19.fa")

It worked before and it is exactly what is written in the manual: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf . I have R-3.6.1 and ExomeDepth 1.12 (freshly installed). 

The error:

    Error: RangedData objects are deprecated and the rownames setter for
      RangedData objects is now defunct. Please migrate your code to use
      GRanges or GRangesList objects instead. See IMPORTANT NOTE in
      ?RangedData

(obviously the important note says that it is deprecated)

Is there a way to fix it manually or I should wait for the update of the package?

(This is not a crucial thing, I run this tool for benchmarking, so if I won't be able to run it I'll just write it like it is, but if smb has thoughts how to fix it - I'd do this)
You could try installing from vplagnol github repository (using DevTools) to see if the dependency has been updated (GRanges)

[https://github.com/vplagnol/ExomeDepth][1]

    install.packages("devtools")
    
    library(devtools)
    install_github("vplagnol/ExomeDepth")

If it hasn't then you could try raising an issue on the ExomeDepth repository.

  [1]: https://github.com/vplagnol/ExomeDepth