Under bioc-devel, I ran
MACPET/vignettes$ R CMD Stangle MACPET.Rmd
and then in R
source("MACPET.R", echo = TRUE)
where the problem manifests as
> summary(MACPET_pintraData,heatmap=TRUE)
Error in .Vector_summary(object, ...) : unused argument (heatmap = TRUE)
You have the S4 class
> getClass(class(MACPET_pintraData))
Class "PIntra" [package "MACPET"]
Slots:
Name: anchor1 anchor2 regions NAMES
Class: integer integer GRanges character_OR_NULL
Name: elementMetadata metadata
Class: DataFrame list
Extends:
Class "GInteractions", directly
Class "Vector", by class "GInteractions", distance 2
Class "Annotated", by class "GInteractions", distance 3
Class "vector_OR_Vector", by class "GInteractions", distance 3
that extends 'Vector'.
You have an S3 generic summary.PIntra, but I guess recently S4Vectors
introduced an S4 method summary,Vector-method. Probably the dispatch system
sees the inherited S4 method before your S3 method, and the solution is to
change your S3 method to S4. Best practice would do this for all S3 methods
defined on S4 classes.
Martin
On 7/8/19, 10:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis"
<bioc-devel-boun...@r-project.org on behalf of ioannis.varda...@ntnu.no> wrote:
Hey,
My package (MACPET) has been crashing lately. The error I get is from the
vignette:
Error in .Vector_summary(object, ...) : unused argument (heatmap = TRUE)
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval
-> summary -> summary
Execution halted
When I call the summary function which is specified on one of my classes.
I realised that for some reason all the methods that I had created and
worked fine for every class, they just don’t work anymore.
I have no idea what causes the error..
Best,
Ioannis
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