[Bioc-devel] Warnings about man pages for assignment operators on Windows builds

[Mike Smith]

Hi Vince and Stephanie,

There was some discussion in the Bioconductor slack about these warnings,
and they definitely seem to be related to a change in R-devel, which tries
to create files with names that are invalid on the Windows filesystem.

However, the reason you may not see them on your local machine is due to
the way the Bioconductor build system runs the package checks, which are a
little more convoluted than you probably run locally.  Using my typical
approach I see the warning messages printed in the output of R CMD INSTALL,
but it doesn't trigger anything in R CMD check.

I suspect that the build system warnings will persist for a while longer as
the issue is still there, but I don't think there's anything you can do as
a package developer, so there's no need to worry about it for now.
Hopefully a fix will make it's way into R-devel fairly soon.

Mike

On Wed, 30 Dec 2020 at 12:04, Vincent Carey <stvjc using channing.harvard.edu>
wrote:

> Hi Stephanie
>
> I see similar problems for GenomicFiles, so it is not a problem unique to
> your package.
> I was not able to generate this error with r79717 in Windows 10, so I
> conjecture that this
> will go away when the R-devel for windows is upgraded.
>
> Best regards
> Vince
>
> On Tue, Dec 29, 2020 at 1:58 PM Stephanie Gogarten <sdmorris using uw.edu>
> wrote:
>
> > Hi all,
> >
> > Several of my packages have a set of warnings on the Windows devel builds
> > that have persisted for a while now, all of this form:
> >
> > Rd warning: cannot open file
> >
> >
> 'C:/Users/biocbuild/bbs-3.13-bioc/meat/SeqVarTools.buildbin-libdir/00LOCK-SeqVarTools/00new/SeqVarTools/help/lastFilter<-.html':
> > Invalid argument
> >
> > I have the following in my .Rd file:
> >
> > \alias{lastFilter<-}
> > \alias{lastFilter<-,SeqVarIterator,numeric-method}
> >
> > Is there a different way I should be documenting assignment operators in
> > R-devel?
> >
> > thanks,
> > Stephanie
> >
> >         [[alternative HTML version deleted]]
> >
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> >
>
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