Question: Bug report for GenomicRanges
1
11 months ago by
United States
gabriel.hoffman80 wrote:

GenomicRanges prints a large set of warnings to my terminal when I set a class variable first:

library(GenomicRanges)
setClass("DataFrame")
gr = GRanges(rep(1, 2), IRanges(1:2, 1:2))


This results in this message printed to the terminal:

Found more than one class "DataFrame" in cache; using the first, from namespace '.GlobalEnv' Also defined by ‘S4Vectors’

This occurs on multiple R versions (including v3.5.1) and multiple operating systems.

This is a simplified example. In practice, I run:

# from [https://github.com/Sage-Bionetworks/PythonEmbedInR](https://github.com/Sage-Bionetworks/PythonEmbedInR)
library(PythonEmbedInR)
library(GenomicRanges)
gr = GRanges(rep(1, 2), IRanges(1:2, 1:2))


This produces the same print out as above.

I can see that PythonEmbedInR runs setClass("DataFrame") internally.

Is this something that should be fixed in GenomicRanges, or in PythonEmbedInR?

Note, this is my correspondance about this issue before I create this clearer statement of the problem: https://github.com/Sage-Bionetworks/synapser/issues/201

genomicranges • 244 views
modified 11 months ago by Michael Lawrence11k • written 11 months ago by gabriel.hoffman80
0
11 months ago by
United States
Michael Lawrence11k wrote:

This was a limitation of the methods package. Should be fixed in R-devel now.