From: "Herv? Pag?s" <hpages at fredhutch.org>
To: "Jonathan Cairns" <Jonathan.Cairns at babraham.ac.uk>, bioc-devel at r-project.org
Cc: "Mikhail Spivakov" <Mikhail.Spivakov at babraham.ac.uk>, "Paula Freire-Pritchett"
<Paula.Freire-Pritchett at babraham.ac.uk>
Sent: Tuesday, October 6, 2015 11:25:05 AM
Subject: Re: [Bioc-devel] Circular dependencies and vignette building
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
The Babraham Institute, Babraham Research Campus, Cambridge CB22
3AT Registered Charity No. 1053902.
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