[Bioc-devel] help with imports for new package and other questions

Hi,

I am trying to get right my new package (
http://github.com/lpantano/isomiRs). But I am having some problems with
the packages I import.

The main problem is that I get warnings while loading my packages because
some dplyr replaces functions in others packages like S4Vectors and others.

This is my NAMESPACE

import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomicRanges)
import(SummarizedExperiment)
import(dplyr)
importFrom(plyr, join_all)
import(DESeq2)
import(methods)
import(RColorBrewer)
import(gplots)
import(ggplot2)
import(GGally)
import(DiscriMiner)

and these are the warnings:

** preparing package for lazy loading
Warning: replacing previous import by ?dplyr::slice? when loading ?isomiRs?
Warning: replacing previous import by ?dplyr::collapse? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::intersect? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::setdiff? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::union? when loading ?isomiRs?
Warning: replacing previous import by ?dplyr::rename? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::combine? when loading
?isomiRs?
Warning: replacing previous import by ?dplyr::desc? when loading ?isomiRs?
Warning: replacing previous import by ?gplots::space? when loading
?isomiRs?
** help


I need to solve this to avoid warnings. I tried something like use
`importFrom` to only import some functions but don't know if importFrom is
something I shouldn't use or I should.

I would also appreciate very much if some one can point me to the right
way to solve the following:

* I failed to create good documentation for some functions, data of my
package. Can anyone point me to a good example of a dataset documentation,
so I could create a good one for my dataset example.

* I have some problems with my coding style, like sometimes I have `=`
insted of `<-` and I forgot to add spaces like this ` <- `. Any one knows
of a plugin for any editor to help me find that. Because I am always
missing some of them by eye.

Thanks a lot in advance for any help in any point.

Lorena