[Bioc-devel] BiocGenerics attaches when methods package is imported
Hi Andreas, for a good understanding: just mentioning the methods package in the DESCRIPTION file isn't doing a thing if you don't also add import(methods) to the NAMESPACE file. So it looks like the warning occurs when the package indicates that the methods package is imported when it actually isn't. Do you still get that warning if you update the NAMESPACE file? Cheers Joris On Mon, Feb 15, 2016 at 4:52 PM, Andreas Kapouranis <
kapouranis.andreas at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Mathematical Modelling, Statistics and Bio-Informatics tel : +32 9 264 59 87 Joris.Meys at Ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[alternative HTML version deleted]]