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

[Kasper Daniel Hansen]

As I understand it, the function sometimes gives false positives (I have
never experience it myself though - Michael Lawrence has, but perhaps his
use cases are more complicated).  My guess is that this is a showstopper
for including it in codetools (where it would be great to go, in my
opinion).

At least I think it should be released in Bioconductor with binaries etc.
The NAMESPACE analysis is amazingly useful.

Kasper


On Fri, Aug 14, 2015 at 10:19 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

>
>
> On Fri, Aug 14, 2015 at 10:03 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> 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.
>>
>
> I was trying to remember the location of this utility ... should be in our
> developers guide
>
> I don't see it here
>
>
> http://bioconductor.org/developers/how-to/buildingPackagesForBioc/#namespace
>
> Any chance that it could be promoted into R?  getting namespaces right can
> be quite
> time-consuming.
>
>
>>
>> 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
>> >
>> > _______________________________________________
>> > Bioc-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

	[[alternative HTML version deleted]]