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

Michael Lawrence

Fri, Oct 23, 2015 3:36 AM

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

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Thread (6 messages)

Dario Strbenac S4 Method of ExpressionSet Signature Not Found Oct 22 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 22 Dario Strbenac S4 Method of ExpressionSet Signature Not Found Oct 22 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 22 Bernd Klaus S4 Method of ExpressionSet Signature Not Found Oct 23 Michael Lawrence S4 Method of ExpressionSet Signature Not Found Oct 23