DEXSeq hangs

[elenichri]

Hello, I am using proActiv v1.0.0, because I run it on a server where R 4.0.0 is installed. I cannot install a newer version of R (I don't have the rights). Bioconductor 3.12 is the most recent version compatible with R 4.0.0. Any newer version of proActiv is not compatible with Bioc 3.12.

Since I use proActiv v1.0.0, the getAlternativePromoters function is not available. I am running the DEXSeqDataSet, followed by DEXSeq function. DEXSeq hangs my R session. It runs forever with no result, and I have to kill it to get back to my session. The DEXSeqDataSet function seems to work. However, when I checked the rowRanges, I get the below (problematic) output:

head(rowRanges(dxd),3)
GRangesList object of length 3:
$`ENSG00000000003.15:1`
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: no sequences

$`ENSG00000000003.15:2`
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: no sequences

$`ENSG00000000005.6:3`
GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: no sequences

Is the above rowRanges result normal? Is it normal for DEXSeq to take so long to run? How can I proceed? Please note that my result SummarizedExperiment object after running proActiv has dimensions 98780 x 102.

Thank you very much!