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

[Lo]

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