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

[Finak, Greg]

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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