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

Hi Lorena,

For your last question about coding style, you could look into the lintr package:
https://github.com/jimhester/lintr

You can run it either as an R function, or add it as a plugin to some editors. The developer, Jim Hester, is also part of the Bioconductor team!

Adrienne

On Aug 14, 2015, at 6:57 AM, Lo <lorena.pantano at gmail.com> wrote:

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