[Bioc-devel] Problems with MACPET package

[Ioannis Vardaxis]

I have changed the S4methods now and the Rcheck is working fine locally on my machine. 

I cannot run BiocCheck because I cannot install it on my Mac anymore. It depends on a package named stringdist, which cannot be installed in my Mac. I get an error:
clang: error: unsupported option '-fopenmp'

However I have pushed the changes to the repository now and we will see if the devel version gets fixed.

Best,
Ioannis


> 8. jul. 2019 kl. 11:20 skrev Martin Morgan <mtmorgan.bioc using gmail.com>:
> 
> 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-bounces using r-project.org on behalf of ioannis.vardaxis using 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
> 
>    	[[alternative HTML version deleted]]
> 
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