[Bioc-devel] some new warnings in a package

[Ludwig Geistlinger]

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

Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.
However all remaining NOTEs and WARNINGs that appeared in the latest build
persist, for example

* checking for code/documentation mismatches ... WARNING

just issues a warning with any further details.

Thx,
Ludwig


>
>
> 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.
>

>
> 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
>>>> information.  If you are not the intended recipient(s), or the
>>>> employee
>>>> or agent responsible for the delivery of this message to the intended
>>>> recipient(s), you are hereby notified that any disclosure, copying,
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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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
>
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-- 
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
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80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de