Bug report for GenomicRanges
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Entering edit mode
@gabrielhoffman-8391
Last seen 3 months ago
United States

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 • 688 views
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@michael-lawrence-3846
Last seen 2.3 years ago
United States

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

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