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@classes[,1] <- nms
plasSet@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 Donn�es et d'Intelligence des Syst�mes,
CEA Saclay,
DRT/LIST/DM2I/LADIS
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