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.pant...@gmail.com > <mailto:lorena.pant...@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@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
