[Bioc-devel] Circular dependencies and vignette building

[Jonathan Cairns]

Hi,

I am attempting to submit a software package "Chicago", and a corresponding data package "PCHiCdata", to Bioconductor. However, I have an issue with circular dependencies.

Chicago "suggests" PCHiCdata, because one of the data sets in PCHiCdata is used to build the vignette. As a result, when BioC attempts to R CMD BUILD Chicago, it cannot build the vignette and thus returns an error. However, PCHiCdata "depends" on Chicago, because the data use a class from Chicago, so I can't build and install it first. (I got around this issue on my local machine by installing Chicago before building the vignette.)

One issue is that we found it impossible to create a data set that was small enough to fit in the software package, but large enough to have enough information to run the full Chicago workflow on. This is why the vignette depends on the external data package.

I imagined this situation would be common, but I couldn't find any advice on it. Is there a sensible/recommended way to resolve this dependency?

Thanks,

Jonathan

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