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

Benjamin Jean-Marie Tremblay benj@m|n@tremb|@y @end|ng |rom uw@ter|oo@c@
Sat May 1 13:14:26 CEST 2021

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.




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