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

[Martin Morgan]

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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>>
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>
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