Yes, please upload PCHiCdata to the same issue as Chicago, do not start a new issue. Thanks, Dan
----- Original Message ----- > From: "Hervé Pagès" <hpa...@fredhutch.org> > To: "Jonathan Cairns" <jonathan.cai...@babraham.ac.uk>, > bioc-devel@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 > > 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 > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel