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

[Lo]

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.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
>>
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