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

Joris Meys Joris.Meys at Ugent.be
Mon Feb 15 17:16:38 CET 2016

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


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?


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
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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
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