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

[Andreas Kapouranis]

Hi Michael,

Thanks for the suggestion. When I depend my package on GenomicRanges the
warning is now gone.

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 Tue, Feb 16, 2016 at 11:28 AM, Michael Lawrence <
lawrence.michael at gene.com> wrote:

> If you are expecting the user to manipulate that granges then you should
> depend on GenomicRanges.
>
> I guess R is loading the data to check the docs. When the methods
> namespace is loaded, it conveniently attaches the package defining the
> class.
> On Feb 16, 2016 3:48 AM, "Andreas Kapouranis" <
> kapouranis.andreas at gmail.com> wrote:
>
>> 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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