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

[Michael Lawrence]

Beware that load_all attaches the entire package namespace to the search
path, so its effect is not consistent with actual usage of the package. I
think devtools has other functionality that is more consistent with Dario's
original approach, and it might work better. But it is also known to break
S4.

On Fri, Oct 23, 2015 at 1:43 AM, Bernd Klaus <bernd.klaus at embl.de> wrote:

> 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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