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

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