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 <st...@channing.harvard.edu> wrote: > > > On Fri, Aug 14, 2015 at 10:03 AM, Kasper Daniel Hansen < > kasperdanielhan...@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.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 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 >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel