[Bioc-devel] Problems with MACPET package

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Mon Jul 8 11:20:34 CEST 2019

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"]


Name:            anchor1           anchor2           regions             NAMES
Class:           integer           integer           GRanges character_OR_NULL

Name:    elementMetadata          metadata
Class:         DataFrame              list

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.


On 7/8/19, 10:46 AM, "Bioc-devel on behalf of Ioannis Vardaxis" <bioc-devel-bounces using r-project.org on behalf of ioannis.vardaxis using ntnu.no> wrote:

    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..
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