[Bioc-devel] S4 Method of ExpressionSet Signature Not Found

[Bernd Klaus]

Hi Dario,

side note: if you want to find a bug and load the updated package over and
over again 
it is much easier to use use devtools::load_all()!

It directly loads the updated version 
using the source package directory without the need to detach / recompile /
reinstall.

So you can e.g. do:

1.) change the R code 
2.) load updated package via load_all() from the source (specify pkg dir if
it is not the wd)
3.) check if bug is gone
4.) repeat

Hope that helps,

Bernd



-----Original Message-----
From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
Michael Lawrence
Sent: Friday, October 23, 2015 4:07 AM
To: Dario Strbenac <dstr7320 at uni.sydney.edu.au>
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] S4 Method of ExpressionSet Signature Not Found

They're enclosed in different environments, for one. Basically, all bets are
off if you're doing the unload, reinstall library cycle.

On Thu, Oct 22, 2015 at 7:00 PM, Dario Strbenac <dstr7320 at uni.sydney.edu.au>
wrote:

> Good day,
>
> The variables have the same contents.
>
> Browse[1]> selectParams at featureSelection nonstandardGenericFunction 
> for "DMDselection" defined from package "ClassifyR"
>
> function (expression, ...)
> {
>     standardGeneric("DMDselection")
> }
> <environment: 0x4452b00>
> Methods may be defined for arguments: expression Use  
> showMethods("DMDselection")  for currently available ones.
> Browse[1]> getGeneric("DMDselection")
> nonstandardGenericFunction for "DMDselection" defined from package 
> "ClassifyR"
>
> function (expression, ...)
> {
>     standardGeneric("DMDselection")
> }
> <environment: 0xb4996c8>
> Methods may be defined for arguments: expression Use  
> showMethods("DMDselection")  for currently available ones.
> Browse[1]> c
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function 'DMDselection' for 
> signature '"ExpressionSet"'
>
> It only happens after I use :
>
> detach("package:ClassifyR", unload = TRUE) 
> install.packages("ClassifyR/", repos = NULL)
> library(ClassifyR)
>
> because I'm modifying the package code and installing it repeatedly, 
> to find a bug.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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