[Bioc-devel] some new warnings in a package

[Martin Morgan]

On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
> I encounter the same issue with EnrichmentBrowser - and apparently,
> several other packages too, e.g. ensembldb, erma, ExiMiR ...
>
> The warnings seem to be, at first glance, linked to messages e.g. for
> masking:
>
> -----------------------------------------------------------------------
>
> * checking S3 generic/method consistency ... WARNING
>
>
> Attaching package: 'EnrichmentBrowser'
>
> The following object is masked from 'package:BiocGenerics':
>
>      normalize
>
> See section 'Generic functions and methods' in the 'Writing R
> Extensions' manual.
>
> ------------------------------------------------------------------------
>
> However, even when renaming the function, so that masking is not necessary
> (and the message is thus not given anymore), the issue persists.
>
> There seems to be something weird with the current R-devel (2016-04-29
> r70565), as R CMD check as prompts me to import from base packages:
>
> -------------------------------------------------------------------------
> Undefined global functions or variables:
>    available.packages browseURL capture.output col2rgb data dev.off
>    formula head mad median memory.limit model.matrix p.adjust par pchisq
>    phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
>    segments symbols text unzip write.table
> Consider adding
>    importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
>    importFrom("graphics", "par", "segments", "symbols", "text")
>    importFrom("stats", "formula", "mad", "median", "model.matrix",
>               "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
>               "quantile", "rnorm", "runif", "sd")
>    importFrom("utils", "available.packages", "browseURL",
>               "capture.output", "data", "head", "memory.limit",
>               "read.delim", "unzip", "write.table")
> to your NAMESPACE file.
> ---------------------------------------------------------------------------

the advice here -- to import from base packages -- is correct. This 
ensures that a user cannot define a function, e.g., col2rgb, that masks 
the one in grDevices. It is appropriate because these base packages are 
not by default imported into your package namespace, so symbols are 
resolved by looking on the search() path. The only exception to this is 
the actual 'base' package, which _is_ imported by default.

The advice is conservative, in that it does not say that you should add 
Imports: grDevices etc to your NAMESPACE file. This is also correct, in 
that the grDevices package is always installed.

So yes, you should update the NAMESPACE file following the warning 
message you see in your build report.

Martin

>
> Somebody an idea? Or just waiting for the next R-devel snapshot?
>
> Thx,
> Ludwig
>
>
>>
>>
>>
>> On Fri, 29-04-2016, at 23:49, Martin Morgan
>> <martin.morgan at roswellpark.org> wrote:
>>> On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
>>>> Dear All,
>>>>
>>>> In case it matters, and since we are past the 22, I just noticed that a
>>>> package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g.,
>>>> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
>>>> that, if I recall correctly, were not being given around the 22nd. I
>>>> think
>>>> these warnings have started appearing with the latest Rs in BioC
>>>> (around
>>>> r70549?). I haven't been able to understand the ultimate cause of the
>>>> warnings (as they seem to refer to issues that are not in the code of
>>>> my
>>>> package), but they disappear when I move a package from Imports to
>>>> Depends.
>>>
>>> They seem to come from GLAD's use of packageStartupMessage() in .onLoad
>>> (e.g., when the package is imported) rather than the recommended
>>> .onAttach (when the package is attached to the search() path, e.g., via
>>> library() or Depends: in the DESCRIPTION file).
>>>
>>> I updated GLAD to use packageStartuupMessage() in .onAttach; I think the
>>> warnings will go away.
>>
>> Martin, thanks for the reply and details. And sorry for my
>> not-particularly-explicit message; yes, GLAD is the package that I moved
>> to
>> Depends. And I did not say (though I had intended too ---time to go to
>> bed)
>> that I had committed my changes to svn.
>>
>> Anyway, should I revert my changes to keep GLAD in Imports?
>>
>> Best,
>>
>> R.
>>
>>
>>>
>>> Martin
>>>
>>>>
>>>>
>>>> Best,
>>>>
>>>> R.
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> This email message may contain legally privileged and/or confidential
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>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>>
>> Phone: +34-91-497-2412
>>
>> Email: rdiaz02 at gmail.com
>>         ramon.diaz at iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
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>
>


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