[Bioc-devel] Dependency on windowing systems in the flowCore package

[Martin Morgan]

On 04/17/2014 04:43 PM, Mike wrote:
> I am in the processing of deprecating 'curv2Filter', 'curv1Filter' and
> 'norm2filter' in 'flowCore' and make these three filters available in
> 'flowStats'.
> Here is what I am trying to do:
> 1. add warning message in 'flowCore' through '.Deprecate()'
> 2. copy the S4 classes and methods and constructors of the three filters
> to 'flowStats' so that other packages can make update their NAMESPACE
> and dependencies before they are finally 'Defunct' after 2 release cycles.
>
> However, I'm having these notes when I install the new 'flowStats'
> (installation succeeds though)
>
> Note: the specification for class "curv1Filter" in package 'flowStats'
> seems equivalent to one from package 'flowCore': not turning on
> duplicate class definitions for this class.
> Note: the specification for class "curv2Filter" in package 'flowStats'
> seems equivalent to one from package 'flowCore': not turning on
> duplicate class definitions for this class.
> Note: the specification for class "norm2Filter" in package 'flowStats'
> seems equivalent to one from package 'flowCore': not turning on
> duplicate class definitions for this class.
>
> and the 'filter` method defined in 'flowCore' no longer dispatches
> correctly because of this. Here is reproducible example
> (install modified 'flowStats' from 'curvFilter' branch of
> https://github.com/RGLab/flowStats)
>
> library(flowStats)
> dat <- read.FCS(system.file("extdata","0877408774.B08", package="flowCore"))
> c1f <- curv1Filter(filterId="myCurv1Filter", x=list("FSC-H"), bwFac=2)
> ## Filtering using curv1Filter
> fres <- filter(dat, c1f)
>
> Error in match(x, table, nomatch = 0L) :
>     'match' requires vector arguments

No solution to offer here. It seems like it's actually dispatch to %in%, where 
the method selected is

 > fres <- filter(dat, c1f)
Error in match(x, table, nomatch = 0L) :
   'match' requires vector arguments
 > traceback()
7: match(x, table, nomatch = 0L)
6: x %in% filter
5: x %in% filter
4: .class1(object)
3: as(x %in% filter, "filterResult")
2: filter(dat, c1f)
1: filter(dat, c1f)
 > showMethods("%in%")
Function: %in% (package base)
...
x="flowFrame", table="curv1Filter"
     (inherited from: x="ANY", table="ANY")
...

Before the call to filter there is actually an explicit

 > showMethods("%in%")
Function: %in% (package base)
...
x="flowFrame", table="curv1Filter"

I'm suspecting that the method here is specific to curv1Filter,flowCore-class, 
whereas dispatch is looking for curv1Fitler,flowStats-class.

Maybe a solution is in the fact that 'filter' actually seems to work --

 > selectMethod(filter, c(class(dat), class(c1f)))
...
Signatures:
         x           filter
target  "flowFrame" "curv1Filter"
defined "flowFrame" "filter"

it finds the method for the base class shared by curv1Filter,flowCore-class and 
curv1Filter,flowStats-class, so defining a common class curv1Filter_migration 
and methods on that ?

Martin

>
>
> Before I decide to remove the duplicated definitions from 'flowCore'
> entirely (which is not desired),  Does anyone know how to solve this issue?
>
> Thanks,
> Mike
>
>
>
>
> On 04/16/2014 05:06 PM, Mike wrote:
>> Kevin's fix is already pushed to the latest bioc release and devel.
>>
>> Thanks,
>> Mike
>> On 04/10/2014 11:44 PM, bioc-devel-request at r-project.org wrote:
>>> Subject:
>>> Re: [Bioc-devel] Dependency on windowing systems in the flowCore package
>>> From:
>>> Kieran O'Neill <koneill at bccrc.ca>
>>> Date:
>>> 04/10/2014 05:20 PM
>>>
>>> To:
>>> Kevin Ushey <kevinushey at gmail.com>
>>> CC:
>>> "bioc-devel at r-project.org" <bioc-devel at r-project.org>
>>>
>>>
>>> Thanks Kevin!
>>>
>>> That would have been my proposed option 3 if I had realised it would be
>>> that simple.
>>>
>>> This will make my (and several other analysts I know's) lives a lot easier!
>>>
>>> Cheers,
>>> Kieran
>>>
>>>
>>>
>>>
>>> On 10 April 2014 16:11, Kevin Ushey<kevinushey at gmail.com>  wrote:
>>>
>>>>> Hi Kieran,
>>>>>
>>>>> I've kickstarted the process by sending a pull request here:
>>>>> https://github.com/RGLab/flowCore/pull/21
>>>>>
>>>>> Thanks,
>>>>> Kevin
>>>>>
>>>>>
>>>>> On Thu, Apr 10, 2014 at 3:48 PM, Kasper Daniel Hansen <
>>>>> kasperdanielhansen at gmail.com> wrote:
>>>>>
>>>>>>> My 2ct is that it is worthwhile to have a lean core package.  It sounds
>>>>>>> like it would be trivial to separate gating into a new package, and -
>>>>>>> provided functions are not renamed - would be trivial for downstream
>>>>>>> packages to adapt to.
>>>>>>>
>>>>>>> Especially in situations where competing groups work on the same analysis
>>>>>>> domain, it is great if they can agree on basic data representation, and
>>>>>>> that chance is increased (IMO) if the core package does not include too
>>>>>>> much analysis tools.
>>>>>>>
>>>>>>> Best,
>>>>>>> Kasper
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Apr 10, 2014 at 6:35 PM, Kevin Ushey<kevinushey at gmail.com>wrote:
>>>>>>>
>>>>>>>>> Hi Kieran, Dan,
>>>>>>>>>
>>>>>>>>> I would suggest that you open an issue at
>>>>>>>>> https://github.com/RGLab/flowCore/issues/new.
>>>>>>>>>
>>>>>>>>> Perhaps the easiest solution is to copy featureSignif from feature into
>>>>>>>>> flowCore (giving adequate citation and such, respecting licenses...). It
>>>>>>>>> looks like the function doesn't depend too much on other functionality in
>>>>>>>>> the feature package, so this shouldn't be too much of a problem.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Kevin
>>
>
>
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>
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