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

[Kasper Daniel Hansen]

Indeed, you need to use importFrom to selectively import.

In this process you'll realize how great it would be to have a function
called
  importEverythingFromExcept(  PACKAGE, NOT_THESE_FUNCTIONS)
but last time I raised this issue on R-devel, I was gently shut down.

In the meantime you should use the codetoolsBioC package (only available in
subversion; you need to check it out and build/install it by hand).  This
package has a function (writeNamespaceImports) which can analyze your code
and tell you exactly which functions you use from which package.  Trust me,
it'll save you days of work to use this.

SVN url is
  svn co
https://hedgehog.fhcrc.org/gentleman/bioconductor/trunk/madman/Rpacks/codetoolsBioC

Best,
Kasper

On Fri, Aug 14, 2015 at 9:57 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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>

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