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

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 at 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.

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