[Bioc-devel] Rd warnings in Windows bioc-devel check

[Deepayan Sarkar]

This has been fixed in R, and should go away once the binaries have caught
up. See

https://bugs.r-project.org/bugzilla/show_bug.cgi?id=18090

Best,
Deepayan

On Sat, May 1, 2021, 4:44 PM Benjamin Jean-Marie Tremblay <
benjamin.tremblay using uwaterloo.ca> wrote:

> Dear Bioc-devel,
>
> For a little while now I've been getting a couple of odd Rd warnings in
> the Windows check of the devel branch of my package:
>
> Found the following significant warnings:
>   Rd warning: Previous alias or file overwritten by alias:
> convert_motifs,PWM-method
>   Rd warning: cannot open file
> 'D:/biocbuild/bbs-3.13-bioc/meat/universalmotif.buildbin-libdir/00LOCK-universalmotif/00new/universalmotif/help/[<-,universalmotif-method.html':
> Invalid argument
> See 'D:/biocbuild/bbs-3.13-bioc/meat/universalmotif.Rcheck/00install.out'
> for details.
>
> These warnings do not appear in the release branch Windows check, so I am
> a bit confused as to what may be happening. My guess is that the first
> warning is happening due to the presence of another alias
> (convert_motifs,pwm-method) which might pose a problem if the Rd aliases or
> filenames were case insensitive. The second warning I suspect is relating
> to some of the characters in '<-' not playing nice with Rd aliases or
> filenames, but again I find it strange that this has suddenly become a
> problem. I have noticed that I'm not alone in getting these warnings
> though, for example I can see that IRanges, BiocGenerics, etc are getting
> them too.
>
> Any insight would be helpful. The deadline for passing R CMD check is in a
> couple of weeks, and I am a loss as to what to do. The fact that core
> Bioconductor packages are getting similar warnings suggests to me that
> these might be considered 'acceptable warnings' as mentioned in the release
> schedule, but I wanted to ask ahead of time to be sure.
>
> Thanks,
>
> Benjamin
>
>
> https://bioconductor.org/checkResults/devel/bioc-LATEST/universalmotif/riesling1-checksrc.html
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