Passing BiocCheck()

[hackdna]

Errors

• "At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not:"
• "Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."
• "Invalid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/"
• "No biocViews terms found."
• "No 'vignettes' directory."
• "Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/ ."

Warnings

• "Description field in the DESCRIPTION file is too concise"
• "Evaluate more vignette chunks."
• "Remove set.seed usage (found 5 times)"
• "Avoid T/F variables; If logical, use TRUE/FALSE (found 51 times)"
• "The following files are over 5MB in size: '.git/objects/33/d794a2db6598e9fd6808ee815a21af38fb1f48 .git/objects/77/40f0f0d0abee5c3fee0c13d1eeeea044c62fa7 .git/objects/pack/pack-c37633e5c2521abc60f069884252e737552ee3dc.pack'"

Notes

• " 'sessionInfo' not found in vignette(s)"
• " Avoid the use of 'paste' in condition signals"
• "Recommended function length <= 50 lines."
• "Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements."
• "Consider shorter lines; 6 lines (0%) are > 80 characters long."
• "Consider multiples of 4 spaces for line indents, 758 lines(32%) are not."
• "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel"
• " Avoid sapply(); use vapply()"
• " Avoid 1:...; use seq_len() or seq_along()"
• "'LazyData:' in the 'DESCRIPTION' should be set to false or removed" - [x] "Update R version dependency from 2.10 to 4.1.0."

[hackdna]

Closed by mistake in PR.

[pouryany]

Just added the PanomiR tag to my Bioc support profile.

[pouryany]

There is a conflict between the indenting 4 spaces rule and Roxygen generated manuals (where they automatically have 2 indents in the \usage{} field). Upon submission, this should be clarified as discussed in the issue below.

r-lib/roxygen2#332