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List:       bioc-devel
Subject:    Re: [Bioc-devel] build report repeating the same error
From:       "Shepherd, Lori" <Lori.Shepherd () RoswellPark ! org>
Date:       2018-05-30 15:07:19
Message-ID: MW2PR12MB2364B6D0F60821458CC5D430F96C0 () MW2PR12MB2364 ! namprd12 ! prod ! outlook ! com
[Download RAW message or body]

Next time try to add a little more frame of reference (ie.  I've submitted my package \
brainImageR and the tracker build report is showing ERROR)


I cloned your repository and took a quick peak -

You are using roxygen2 to make your man files


So It looks like you updated the documentation in the Comp.R  but never ran the \
document() function to have the man file update and also be pushed to github.  The \
man file example still has the original code that is a table not numeric.





Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces@r-project.org> on behalf of Sara Linker \
                <slinker@salk.edu>
Sent: Wednesday, May 30, 2018 10:43:37 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] build report repeating the same error

Hi at bioc-devel,

I’ve tried a few times now to update the error reported in the build report. I’ve \
pushed the fix to GitHub and bumped the version number, but the same error message \
keeps coming back. Does anyone know how to fix this? I feel like a reboot of some \
kind is needed.

ERROR MESSAGE:


> ### ** Examples
> 
> comp <- methods::new(Class="Comp",
+ tissueExp1 = c(10,12),
+ tissueExp2 =  table(c(rep("A",5), rep("B",5))),
+ composite = matrix(0,nrow=10,ncol=10),
+ random.matrix = data.frame(matrix(0,nrow=10,ncol=10)),
+ refset = "developing"
+ )
Error in validObject(.Object) :
  invalid class "Comp" object: invalid object for slot "tissueExp2" in class "Comp": \
                got class "table", should be or extend class "numeric"
Calls: <Anonymous> -> initialize -> initialize -> validObject
Execution halted

BUT I’ve fixed this and my current code (on GitHub) now reads…
#' @examples
#' comp <- methods::new(Class="Comp",
#' tissueExp1 = c(10,12),
#' tissueExp2 =  c(10,13),
#' composite = matrix(0,nrow=10,ncol=10),
#' random.matrix = data.frame(matrix(0,nrow=10,ncol=10)),
#' refset = "developing"
#' )

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