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

[Pages, Herve]

Just to clarify we see these warnings on Mac only:

https://bioconductor.org/checkResults/3.9/bioc-LATEST/NormalyzerDE/merida2-checksrc.html

https://bioconductor.org/checkResults/3.9/bioc-LATEST/M3C/merida2-checksrc.html

They seem to indicate problems with CRAN packages xts, ggplot2, and ape. 
For some unclear reason, we only see this problem on the Mac builder. 
Other CRAN packages (rgl, igraph, biglm, network, strucchange, etc..) 
are actually causing the same type of warnings on the BioC 3.9 build 
report. 359 Bioconductor software packages are affected.

We'll need to investigate. Safe to ignore for now.

Cheers,

H.

On 11/1/18 05:05, Obenchain, Valerie wrote:
> 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]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zbRfJqGI0IrvvjNQYWzYZ1IZI3KlU4K3SAfArdCEFJI&s=NFc2ZKQEuLA6u4oI3K6GZ9TGwHOUkR9XqlgMRfRZOHw&e=
>>>
>> 	[[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zbRfJqGI0IrvvjNQYWzYZ1IZI3KlU4K3SAfArdCEFJI&s=NFc2ZKQEuLA6u4oI3K6GZ9TGwHOUkR9XqlgMRfRZOHw&e=
>>
>
>
> 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, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=zbRfJqGI0IrvvjNQYWzYZ1IZI3KlU4K3SAfArdCEFJI&s=NFc2ZKQEuLA6u4oI3K6GZ9TGwHOUkR9XqlgMRfRZOHw&e=

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319