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. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
