Hi Lorena, In your particular case it seems to me that you're using dplyr internally for convenient data frame transformations (nothing that couldn't be done with plain R BTW), and that you're only using a few dplyr symbols for this. The codetoolsBioC package could be useful to help you identify these things and import them selectively. It seems to me that these things are: %>%, group_by, filter, and summarise, but I could be missing some. OTOH your package defines the IsomirDataSeq class which extends the SummarizedExperiment class, and thus relies largely on the GenomicRanges/SummarizedExperiment infrastructure. So I would highly recommend that you *fully* import BiocGenerics, S4Vectors, IRanges, and SummarizedExperiment. That will make the maintenance of your NAMESPACE file much easier in the long run than importing selectively from these packages.
I also remember seeing selective imports from the methods package in NAMESPACE files generated with codetoolsBioC. Unless there is a good reason for doing so, these should be avoided and the methods package fully imported. Cheers, H. On 08/14/2015 06:57 AM, Lo 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
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
