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

[Andreas Kapouranis]

Hi Joris,

Apologies for not including the NAMESPACE file, but I have included the
methods package also there, although I have used:

importFrom(methods,is)

since I just need the is() function for the time being.

Regards,
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 4:16 PM, Joris Meys <Joris.Meys at ugent.be> wrote:

> 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
> -------------------------------
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>

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