[Bioc-devel] NAMESPACE question

Robert Castelo robert.castelo at upf.edu
Sun Oct 5 22:39:12 CEST 2014


i have the following warning message when installing the devel version 
(0.99.5) of my package 'qpgraph':

** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::as.vector' when loading 
* DONE (qpgraph)

after investigating the issue i think it has to do with the fact that in 
the NAMESPACE of 'qpgraph' i'm importing the whole Matrix package and 
later the 'as.vector()' method defined in IRanges. The NAMESPACE file 
looks like this:





... (few lines later) ...


... (rest of the file) ...

from what i have learned while reading documentation and googling about 
this issue, it seems that the solution would be to import every 
function/method i use from Matrix before i do the import from IRanges, 
but i use the dspMatrix-class all over the package and i don't know how 
would i find out what set of functions/methods i have to explicitly 
import. i can import a few of the methods from Matrix i know from the 
top of my head that the package is using but i'm afraid i'll be missing 
other methods that will break the package when using it in situations 
outside current examples and unit tests.

i'd appreciate if you have a suggestion about what to do in this situation.


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