On Fri, Aug 14, 2015 at 10:03 AM, Kasper Daniel Hansen < [email protected]> 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 <[email protected]> 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 > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
