[Bioc-devel] BiocGenerics attaches when methods package is imported

[Michael Lawrence]

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.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]]
>
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