Hi Michael, Thanks for the suggestion. When I depend my package on GenomicRanges the warning is now gone.
Regards, Andreas ---------------------------------------------------------- Chantriolnt - Andreas Kapourani PhD Candidate in Data Science, School of Informatics, University of Edinburgh e-mail : c.a.kapour...@sms.ed.ac.uk <c.a.kapour...@sms.ed.ac.uk> : kapouranis.andr...@gmail.com On Tue, Feb 16, 2016 at 11:28 AM, Michael Lawrence < lawrence.mich...@gene.com> wrote: > If you are expecting the user to manipulate that granges then you should > depend on GenomicRanges. > > I guess R is loading the data to check the docs. When the methods > namespace is loaded, it conveniently attaches the package defining the > class. > On Feb 16, 2016 3:48 AM, "Andreas Kapouranis" < > kapouranis.andr...@gmail.com> wrote: > >> Hi Michael, >> >> Thanks for the reply. >> >> I created a minimal reproducible package with the issue. As it seems the >> warning comes because I have a 'data' folder where I have stored some >> example data, and one of the data is stored in GRanges format. >> If I delete the GRanges example data and keep any other data, I get no >> warning. >> >> So the issue is only when I import the 'methods' package and I have data >> locally stored as GRanges objects in the 'data' folder. >> >> You can download and install the simple example package by typing: >> >> devtools::install_github("andreaskapou/simplePackage") >> >> >> Or you can see the code in the following link, which just contains a >> simple function to call the methods::is() function and create a GRanges >> object. >> https://github.com/andreaskapou/simplePackage >> >> Thanks, >> Andreas >> >> ---------------------------------------------------------- >> Chantriolnt - Andreas Kapourani >> PhD Candidate in Data Science, >> School of Informatics, >> University of Edinburgh >> >> e-mail : c.a.kapour...@sms.ed.ac.uk <c.a.kapour...@sms.ed.ac.uk> >> : kapouranis.andr...@gmail.com >> >> On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence < >> lawrence.mich...@gene.com> wrote: >> >>> It would be helpful to have a reproducible example, i.e., your actual >>> package or a skeleton of it that reproduces the issue. Btw, you might >>> be able to debug this behavior by: >>> >>> debug(tools::undoc) >>> tools::undoc(dir=yourPackageDir) >>> >>> >>> >>> On Mon, Feb 15, 2016 at 7:52 AM, Andreas Kapouranis >>> <kapouranis.andr...@gmail.com> wrote: >>> > Hi, >>> > >>> > I am developing a package for Bioconductor, and I have a weird issue >>> when >>> > importing the 'methods' package. Before I add the 'methods' package in >>> > Imoprts in the DESCRIPTION file, I pass the CMD check without any >>> warnings. >>> > >>> > However, when I add the 'methods' package in the Imports field, I get a >>> > warning during CMD check. (I need the methods package since I use the >>> > methods::is() function, and if I call it just as is(), when running the >>> > package from Rscript will fail since by default it does not load the >>> > 'methods' package.) >>> > >>> > I read a similar issue here: >>> > https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008193.html >>> > and I updated all my packages from Bioconductor including IRanges and >>> > GenomicRanges. >>> > >>> > This is the warning that I get, which is exactly the same as the >>> previous >>> > issue in Bioc-Devel, and I understand that for some reason the >>> BiocGenerics >>> > is attached only when the 'methods' package is imported. >>> > >>> > * checking for missing documentation entries ... WARNING >>> > >>> > Attaching package: ‘BiocGenerics’ >>> > >>> > The following objects are masked from ‘package:parallel’: >>> > >>> > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >>> > clusterExport, clusterMap, parApply, parCapply, parLapply, >>> > parLapplyLB, parRapply, parSapply, parSapplyLB >>> > >>> > The following objects are masked from ‘package:stats’: >>> > >>> > IQR, mad, xtabs >>> > >>> > The following objects are masked from ‘package:base’: >>> > >>> > Filter, Find, Map, Position, Reduce, anyDuplicated, append, >>> > as.data.frame, as.vector, cbind, colnames, do.call, duplicated, >>> > eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, >>> > lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, >>> > pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, >>> > tapply, union, unique, unlist, unsplit >>> > >>> > All user-level objects in a package should have documentation entries. >>> > See chapter ‘Writing R documentation files’ in the ‘Writing R >>> > Extensions’ manual. >>> > >>> > >>> > >>> > My DESCRIPTION file when I add the 'methods' package is the following: >>> > ... >>> > Depends: R (>= 3.2.0) >>> > LazyData: TRUE >>> > RoxygenNote: 5.0.1 >>> > Imports: GenomicRanges, >>> > IRanges, >>> > assertthat, >>> > S4Vectors, >>> > graphics, >>> > data.table, >>> > methods >>> > Suggests: knitr, >>> > rmarkdown, >>> > testthat >>> > VignetteBuilder: knitr >>> > >>> > >>> > >>> > Regards, >>> > Andreas >>> > >>> > [[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