oh! that's cool! super nice, will try it.
thanks a lot!
On 08/20/2015 12:46 PM, Adrienne Stilp wrote:
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.pant...@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
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