Re: [Bioc-devel] Circular dependencies and vignette building

2015-10-07 Thread Jonathan Cairns
re-Pritchett" > > <paula.freire-pritch...@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

Re: [Bioc-devel] Circular dependencies and vignette building

2015-10-06 Thread 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.

Re: [Bioc-devel] Circular dependencies and vignette building

2015-10-06 Thread Dan Tenenbaum
vel@r-project.org > Cc: "Mikhail Spivakov" <mikhail.spiva...@babraham.ac.uk>, "Paula > Freire-Pritchett" > <paula.freire-pritch...@babraham.ac.uk> > Sent: Tuesday, October 6, 2015 11:25:05 AM > Subject: Re: [Bioc-devel] Circular dependencies and vignette building &

[Bioc-devel] Circular dependencies and vignette building

2015-10-06 Thread 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,