[Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

[Obenchain, Valerie]

Hi,

I noticed this before the release - many packages are affected with a 
similar error. Something this pervasive is likely due to a change (bug?) 
in base R and not something you need to fix. It may also be fixed in a 
later version of R version than what's on the build machines.

Now that the release is over we'll start focusing on the Bioc 3.9 builds 
and we'll look into this.

Thanks.
Valerie



On 11/1/18 2:56 AM, Christopher John wrote:
> Hi
> 
> I also have a warning after the upgrade, just for the development version
> (I have not changed).
> 
> I am not sure why this happened as I can't find the ape in the namespace
> and previously had no warning before upgrade.
> 
> Thanks.
> 
> * checking whether package ‘M3C’ can be installed ... WARNING
> Found the following significant warnings:
>    Warning: S3 method ‘ape::as.phylo.dendrogram’ was declared in
> NAMESPACE but not found
> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/M3C.Rcheck/00install.out’ for details.
> 
> 
> On Thu, 1 Nov 2018 at 08:09, Jakob Willforss <jakob.willforss using immun.lth.se>
> wrote:
> 
>> Hi! Getting closer to release, exciting!
>>
>> Today I saw that the build for my package NormalyzerDE gave a warning
>> after the release version bumps,
>> but only on the Windows build machine. No code has been changed from
>> previously succeeding builds.
>>
>> It seems to be unable to find certain functions in the libraries xts and
>> ggplot2 (see warning below). It seems to build fine on the Ubuntu and Mac
>> machines.
>>
>> Do you think this is something to worry about, or is it likely to be
>> something temporary to the build machines? I wonder in particular as my
>> work environment (and debugging environment of choice) is Linux, where the
>> problem don't seem to be reproduced.
>>
>> Best wishes,
>> Jakob
>>
>> The warning:
>>
>> * checking whether package ‘NormalyzerDE’ can be installed ... WARNING
>> Found the following significant warnings:
>>    Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE
>> but not found
>>    Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were
>> declared in NAMESPACE but not found
>> See ‘/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck/00install.out’
>> for details.
>>
>>          [[alternative HTML version deleted]]
>>
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>>
> 
> 	[[alternative HTML version deleted]]
> 
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