On 09/19/2016 07:44 AM, Benilton Carvalho wrote:
My understanding is that plasFIA should be in the Suggests field (and not
in Depends).


Right. That's the typical way to go. And your users will benefit
from having the software package Suggests and not Depends on the
data package, because then they won't be forced to download tens or
hundreds of mega of data that they don't need for their analysis.

Cheers,
H.


On Mon, Sep 19, 2016 at 11:31 AM DELABRIÈRE Alexis <alexis.delabri...@cea.fr>
wrote:

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 Données et d'Intelligence des Systèmes,
CEA Saclay,
DRT/LIST/DM2I/LADIS


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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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