[Bioc-devel] Circular dependencies and vignette building

[Hervé Pagès]

Hi Jonathan,

This is indeed a very common situation and you are doing the right
thing. Please upload PCHiCdata to our issue tracker in the same issue
as Chicago. We'll make sure that the build system installs the 2
packages (Chicago and PCHiCdata, in that order) before it tries to
build Chicago.

Thanks,
H.

On 10/06/2015 09:55 AM, Jonathan Cairns wrote:
> 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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-- 
Hervé Pagès

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