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

[Michael Lawrence]

Yea, good point, it should probably do that in the methods namespace.
Still, flowCore should probably just import(methods) for the sake of
simplicity.

On Mon, May 11, 2015 at 8:31 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> 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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>>
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>
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