Usage of 'sapply()' and '1:length()' become a warning instead of a NOTE.

[nturaga]

• Change the Rmd document to show WARNING instead of NOTE.
• Did not bump version in the document.
• Add NEWS file change to log issue.
• This PR addresses #63

[mtmorgan]

If this is to be a warning then we must be confident that there are no false positives, because people take 'heroic actions' to overcome warnings. Have you run this check (not the whole BiocCheck...) over common Bioconductor packages to get a sense for whether there are false positives?

Also, are there situations where there is nothing or very little to be gained by the change? for instance any(sapply(x, is, "Rle")) evaluates correctly when length(x) == 0 and sapply() returns a list instead of the expected logical vector...

Sometimes when people have corrected 1:length(x) they have written this as seq_len(length(x)) instead of seq_along(x); maybe it makes sense to add some detail in the vignette https://github.com/Bioconductor/BiocCheck/blob/4687a90efd5a30218320af9eb79f778463397d2e/vignettes/BiocCheck.Rmd#L382

[grimbough]

Sometimes when people have corrected 1:length(x) they have written this as seq_len(length(x)) instead of seq_along(x); maybe it makes sense to add some detail in the vignette

Just thought I'd add that I see this all the time in our groups' internal code reviews.

[nturaga]

Thanks for the feedback @mtmorgan. I will check for false positives and the other aspects and get back to you with some details.

[lshep]

@nturaga It looks like you are still working on the updates for checking for false positives and other aspects ?