Hello,

promoters() fails on GPos objects; is that expected? If yes, maybe the error message could be made more friendly, for instance by suggesting to use promoters(GRanges(x)).

> gpos1a <- GPos(seqnames=Rle(c("chr1", "chr2", "chr1"), c(10, 6, 4)),
+                pos=c(44:53, 5:10, 2:5))
> gpos1a
UnstitchedGPos object with 20 positions and 0 metadata columns:
       seqnames       pos strand
          <Rle> <integer>  <Rle>
   [1]     chr1        44      *
   [2]     chr1        45      *
   [3]     chr1        46      *
   [4]     chr1        47      *
   [5]     chr1        48      *
   ...      ...       ...    ...
  [16]     chr2        10      *
  [17]     chr1         2      *
  [18]     chr1         3      *
  [19]     chr1         4      *
  [20]     chr1         5      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> promoters(gpos1a)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘update_ranges’ for signature ‘"UnstitchedIPos"’
> sessionInfo()
R Under development (unstable) (2021-10-27 r81107)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bookworm/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicRanges_1.47.4 GenomeInfoDb_1.31.1  IRanges_2.29.0       S4Vectors_0.33.2     BiocGenerics_0.41.1 

loaded via a namespace (and not attached):
[1] zlibbioc_1.41.0        compiler_4.2.0         XVector_0.35.0         tools_4.2.0            GenomeInfoDbData_1.2.7 RCurl_1.98-1.5         bitops_1.0-7

Have a nice day,

Charles

Hi Charles,

This is now addressed in GenomicRanges 1.47.5 (devel) and 1.46.1 (release). Both versions should propagate to the public repos and become available via BiocManager::install() in the next 24 hours in devel and next 72 hours in release.

Generally speaking, GPos objects still lack a few GRanges functionalities but the gap is slowly closing.

Cheers,

H.