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

Josef Spidlen jspidlen at bccrc.ca
Tue May 12 01:29:39 CEST 2015

Hi guys,
I just noticed the following:

Contents of my file x.R:
x <- read.FCS('test.fcs')

Then running the following from a command line:
Rscript 'x.R'

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.


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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