[Bioc-devel] Circular dependencies and vignette building

Dan Tenenbaum dtenenba at fredhutch.org
Tue Oct 6 21:39:44 CEST 2015


Yes, please upload PCHiCdata to the same issue as Chicago, do not start a new issue.
Thanks,
Dan


----- Original Message -----
> From: "Hervé Pagès" <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.
> > 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 at 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: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



More information about the Bioc-devel mailing list