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

[Lo]

Hi,

thanks a lot for the link!, I would definitely try that one...you save 
me a lot of time!

On 08/14/2015 10:03 AM, Kasper Daniel Hansen wrote:
> 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 
> <mailto: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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