On 05/11/2015 05:37 PM, Michael Lawrence wrote:
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
flowCore doesn't use checkAtAssignment directly. If R can find @<-,
shouldn't it be able to find checkAtAssignment?
The methods package defines but does not use checkAtAssignment in R code,
but it is called from C in main/attrib.c:1479. I guess the C-level
evaluation is in the wrong environment?
Martin
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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