Genes annotation ranges tampered after project creation

[Baboon61]

Granges coordinates of an handful of genes are modified after project creation (example with CBS, gene_id=875 in TxDb.Hsapiens.UCSC.hg38.knownGene, this gene does not fall into a blacklist region)

ArchR version : ArchR_1.0.2

How to reproduce :

library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
txdb_genes <- genes(txdb)
txdb_genes[txdb_genes$gene_id==875,] #chr21:43053191-43076943

test_genes <- createGeneAnnotation(TxDb = TxDb.Hsapiens.UCSC.hg38.knownGene, OrgDb = org.Hs.eg.db)
test_genes$genes[test_genes$genes$gene_id==875] #chr21:43053191-43076943

addArchRGenome("hg38")
test_arrow <- createArrowFiles(
  inputFiles = fragpath,
  sampleNames = "test",
  geneAnnotation = getGeneAnnotation(),
  genomeAnnotation = getGenomeAnnotation(),
  minTSS = 0,
  minFrags = 0,
  maxFrags = 1e+10,
  addTileMat = FALSE,
  addGeneScoreMat = FALSE,
  offsetPlus = 0,
  offsetMinus = 0,
  force = TRUE
)
test_proj <- ArchRProject(
  ArrowFiles = test_arrow,
  outputDirectory = "my_path")

getGeneAnnotation(test_proj)$genes[getGeneAnnotation(test_proj)$genes$gene_id==875,] #chr21:6444869-43076943

[rcorces]

Hi @Baboon61! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other
responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire
a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know!
In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15.
Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.