[Bioc-devel] Problem of circular depedencies in package

Benilton Carvalho beniltoncarvalho at gmail.com
Mon Sep 19 16:44:52 CEST 2016

My understanding is that plasFIA should be in the Suggests field (and not
in Depends).

On Mon, Sep 19, 2016 at 11:31 AM DELABRIÈRE Alexis <Alexis.DELABRIERE at cea.fr>

> Hi,
> I hope that it is the good place to ask this, as it is related to
> Bioconductor guidelines.
> I have an issue of package dependency, I'm developing a package for the
> processing of mass spectrometry data(proFIA), it works on raw data which
> are quite heave (6 cleaned files weight 50 mega), so I wanted to provide a
> data package to test the functions(plasFIA) and build the vignettes. The
> two package are finished but I have an issue following the Bioconductor
> submission guidelines about submitting two packages, which require to
> submit the package which does not depend of the other in first :
> My first package proFIA which is the processing package require plasFIA to
> build the vignette. I used a preprocessed object in the example to avoid 3
> mins processing times in each examples, without that CHECK installation
> will be too long. To access the visualization function, the raw data are
> necessary, that's why the dependence to plasFIA is mandatory.
> My second package plasFIA contains the data and the processing files. In
> data directory, there is an RData file which contain an object from proFIA
> package of class "proFIAset" to store the information about the package.
> The complicated part now : this object require a path to the raw file to
> allows the visualization function to work. So in the .onLoad function I do
> the following thing :
> .onLoad <- function(libname, pkgname)
> {
>       #Finding and loading the RData object
>      pfile=file.path(find.package("plasFIA"), "data","plasSet.rda")
>      load(pfile)
>       #Creating the new paths to raw files in the meML directory.
>      nms <- file.path(system.file(package="plasFIA"),"mzML",
>          gsub("/", .Platform$file.sep, basename(attr(plasSet,
> "classes")[,1])))
>      #Setting the new paths
>      plasSet at classes[,1] <- nms
>      plasSet at path<-file.path(find.package("plasFIA"), "mzML")
>     #Saving the object.
>      save(plasSet,file=pfile)
> }
> Which work, but if I don't put "proFIA" in depend "plasFIA" CHECK fails.
> And if I put it I have a circular dependency.
> I know that a similar issue exists for "faahko" and "xcms" package in
> Bioconductor, and I did not find a better solution.
> Do you know a solution to overcome the circular dependency or, is this
> okay for BioConductor in this setup ?
> I just opened an issue in the contribution part or Bioconductor, so you
> can go there to see the code.
> Alexis Delabriere
> PhD Student,
> Laboratoire d'Analyse de Données et d'Intelligence des Systèmes,
> CEA Saclay,
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