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

[Andreas Kapouranis]

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.kapourani at sms.ed.ac.uk  <c.a.kapourani at sms.ed.ac.uk>
           : kapouranis.andreas at gmail.com

On Mon, Feb 15, 2016 at 4:22 PM, Michael Lawrence <lawrence.michael at 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.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
>

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