read_feats error

[cms72]

Hi,

gggenomes used to work for me, but now I get the following error. I've tried to re-install this using this dev package, but to no avail:
devtools::install_github("thackl/gggenomes@fix-156",force =TRUE)

g0 <- gggenomes::read_feats(list.files(path = "~/Documents/gggenomes/",pattern="*.gbk",full.names = TRUE))
Reading 'gbk' with read_gbk():

• file_id: 1_gggenomes_region [/Users/cmsia/Documents/gggenomes/gggenomes_region.gbk]
  writing directives
  writing features
  Harmonizing attribute names
  • ID -> feat_id
  • Parent -> parent_ids
  • Name -> name
  Error in map2():
  ℹ In index: 1.
  ℹ With name: 1_gggenomes_region.
  Caused by error in loadNamespace():
  ! there is no package called ‘IRanges’
  Run rlang::last_trace() to see where the error occurred.

I hope you can help! Thanks!

[thackl]

Hi,

somehow one of the dependencies (IRanges) was not installed. I will look into why not. Easiest fix for you is to try and install it manually. That should fix it. You can find instructions here:

https://www.bioconductor.org/packages/release/bioc/html/IRanges.html

[thackl]

Note to self, IRanges is currently in "Suggests". Need to check where it's needed and whether to move it to "Depends"

[cms72]

@thackl - manually installing IRanges fixed it. Many thanks!

[iimog]

As IRanges is a bioconductor package, it might be problematic to have in "Depends" for our planned cran submission.