[Bioc-devel] Should flowCore be importing checkAtAssignment from methods?

[Michael Lawrence]

All S4-based packages should probably have methods in Depends and imported
in NAMESPACE.

On Mon, May 11, 2015 at 4:29 PM, Josef Spidlen <jspidlen at bccrc.ca> wrote:

> Hi guys,
> I just noticed the following:
>
> Contents of my file x.R:
> library("flowCore")
> x <- read.FCS('test.fcs')
>
> Then running the following from a command line:
> Rscript 'x.R'
>
> Outputs:
> Error in object at description[["ORIGINALGUID"]] <- object at description
> [["GUID"]]
> :
>   could not find function "checkAtAssignment"
> Calls: read.FCS -> identifier<- -> identifier<-
> Execution halted
>
> This only happens when executing using Rscript. Adding library("methods")
> to the script resolves this issue. So it looks like flowCore may be
> using checkAtAssignment without declaring so in the NAMESPACE, and this
> issue is normally not noticeable since "methods" are typically loaded
> automatically, but not when using Rscript.
>
> Cheers,
> Josef
>
> --
> Josef Spidlen, Ph.D.
> Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
> 675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
> Tel. +1 604-675-8000, ex. 7755
>
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