[Bioc-devel] some new warnings in a package

Martin Morgan martin.morgan at roswellpark.org
Tue May 3 00:30:19 CEST 2016 


On 05/02/2016 12:37 PM, Ludwig Geistlinger wrote:
>> 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.

yes, these warnings are relative new.

> 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.

ok thanks for pointing that out.

I believe this is a change in R, but the immediate culprit is 
BiocInstaller (indirectly loaded by AnnotationHub and other dependencies 
of your package). R CMD check would try and capture the 'stderr' stream 
to check for errors. BiocInstaller would try and capture the 'stderr' 
stream on package load to check for https capabilities [primarily a 
left-over from earlier version of R, where a output went directly to 
stderr rather than to a message or warning). BiocInstaller interfered 
with R CMD check.

This is fixed in BiocInstaller 1.21.7.

Thanks for the bug report and your persistence.

Martin


>
> 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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>>>>> received this message in error, please notify the sender immediately
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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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>>
>
>


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