Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
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Last seen 4 weeks ago
United States

Hi,

The following code used to work in R 3.3 with Bioconductor 3.4. It now fails on a linux machine I have access to with both Bioc 3.5 and 3.6 but works in my OSX laptop with the same versions.

library(bumphunter)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
gene <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
annotationPackage = 'org.Hs.eg.db')
traceback()
sessionInfo()


This is the error:

Error in .Call2("Rle_constructor", values, lengths, PACKAGE = "S4Vectors") :
Rle of type 'list' is not supported
> traceback()
6: .Call(.NAME, ..., PACKAGE = PACKAGE)
5: .Call2("Rle_constructor", values, lengths, PACKAGE = "S4Vectors")
4: new_Rle(values, lengths)
3: Rle(refseq, TT)
2: Rle(refseq, TT)
1: annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
annotationPackage = "org.Hs.eg.db")


I remember vaguely that this a similar error was solved by re-installing BiocGenerics and/or S4Vectors. So I tried a few times re-installing those packages and other related ones (IRanges, GenomicRanges, Biobase), but the error didn't go away. This is true with both S4Vectors 0.15.9 and 0.14.4 as well as the recently released 0.15.10 and 0.14.5. I'm guessing that there is another package involved that I should re-install but I couldn't find which one it is. I also tried deleting all R packages installed in my user directory and re-installing them, but that didn't work. Changing the order of my .libPaths() to prioritize the system-wide versions vs the versions installed in my user directory didn't help either (note that TxDb.Hsapiens.UCSC.hg38.knownGene is only in my user directory).

Best, Leo