[Bioc-devel] Building a package that depends on flowCore

Hi All and thanks for the help.... (yes I know I must RTFM but...)

Anyway I have made this workaround, not sure if it is a good idea:

representation=representation(
		DATA = "environment"
)

With this initializer:

setMethod (
	f = "initialize",
	signature = "GenData",
	definition = function(.Object, flowframe, stain,  ... ) {
		# check data
		flowCore:::checkClass(flowframe, c("flowFrame"))
		.Object at DATA[["Frame"]]<- flowframe
		mt<- stain %in% colnames(flowframe)
		if(!mt) {
         	stop("Invalid stain not matching the flowSet:\n    ", paste(stain, collapse=", "))
         }
		return(.Object)
	}
)


If I have understood the concept of enviroment: I have created a pointer (reference) to our flowFrame.

Best Regards

Davide




On Mar 31, 2011, at 11:14 PM, Nishant Gopalakrishnan wrote:

Hi Davide,

Its hard to guess exactly what the problem is considering that you have not even provided the error message.  It would have been easier for others to help you out if you provided a  snippet of code using which people can reproduce the error you get.

Before you put your class into a package, I would recommend sourcing your code for the class into an R session with the flowCore package loaded and making sure things work without errors.

representation=representation(
      flowframe = "flowFrame",
      [...]
)

 From your example above, it appears that you are  trying to create a new class with a flowFrame as one of its slots. After going through the code for the flowCore package,  I have noticed a bug in the initialize method for flowFrame class which would have prevented you from creating a flowFrame object using just new("flowFrame"). My guess is that you would have done the same for the prototype function for your class. You had to pass in a valid value for the exprs and parameters and description slots to instantiate an object.

I have checked in a fix for this in Version flowCore 1.17.5 and now you should be able to do new("flowFrame") to instantiate an object for filling the slot flowFrame in the prototype for your new class.

Nishant

On 03/30/2011 09:19 AM, Finak, Greg wrote:

Hi, Davide
I'm not as familiar with the R package build system as others on the list, so it's difficult for me to diagnose your problem from the information given, but I can offer a few suggestions. In the Namespace file, try explicitly importing just the classes, methods and functions from flowCore that your package actually uses. I think you woukd want flowCore in the Depends field of your Description file. Finally, have a look at other packages that extend flowCore, like the flowMerge package for example, and see how they handle it. In my experience, masked methods don't usually lead to installation failure. Perhaps you could provide more output from R CMD check, and the content of your Namespace and Description files.
Cheers
Greg

Sent from my iPhone

On 2011-03-30, at 2:10 AM, "Davide Rambaldi"<davide.rambaldi at ifom-ieo-campus.it>   wrote:

Hi all, I am trying to pack my code in a package for submission to bioconductor.

The package depends on flowCore, so for example I have an S4 class with a "slot" that is a flowFrame object.

representation=representation(
       flowframe = "flowFrame",
       [...]
)

Now I am trying to build the package:

without depends in DESCRIPTION or NAMESPACE:

If I omit the dependecy from flowCore in the DESCRIPTION file I get this warning during R CMD check:

Warning: undefined slot classes in definition of "GenData": flowframe(class "flowFrame")


Then I tried to define the dependency from flowCore:

If I put the

Depends: flowCore

in DESCRIPTION

I get:

checking whether package ?flowFit? can be installed ... ERROR
Installation failed.

The log file say:

Attaching package: 'flowCore'

The following object(s) are masked from 'package:stats':

   alias, filter

Execution halted


I tried to add in NAMESPACE:

import(flowCore)

I tried also to move flowCore from Depends to Imports in DESCRIPTION but seems that it always halt at that point.

What I should try now?

Thanks and Best Regards




Davide Rambaldi, Bioinformatics PostDoc.
-----------------------------------------------------
IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303870
[e] davide.rambaldi at ifom-ieo-campus.it


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aa

Davide Rambaldi, Bioinformatics PostDoc.
-----------------------------------------------------
IFOM-IEO Campus
Via Adamello 16, Milano
I-20139 Italy
[t] +39 02574303870
[e] davide.rambaldi at ifom-ieo-campus.it