F1000 REVIEW: Things I spotted while reviewing

[HenrikBengtsson]

I'm reviewing the F1000 submission. While doing this I spotted a few "random" things related to the package per se. I figured it's more convenient to just post these things here rather than via the review process. If I spot more, I'll post them to this issue.

Help pages

• A few \title{}:s are in all lower case, e.g. "get bioconductor download stats". Easy to spot if you look at the HTML index page.

• The help pages use all lower case for the value sections, e.g. "a character string of the email" in help("biocBuildEmail"). Is that intentional?

• Bioconductor is sometimes referred to as 'bioconductor' (lower case) or just 'bioc' and 'Bioc'.

• xml -> XML (for the initialism XML)

• github -> GitHub

• The help pages could need some more cross links. For example, help(dataciteXMLGenerate) says the value us "an xml element", e.g. exactly what is an "xml element". A link to the corresponding \pkg{XML} or \pkg{xml2} documentation would be helpful.

Vignette

• Broken URL: https://bioconductor.org/packages/3.9/BiocViews in Section 6.3 'Integration with [BiocViews]' (in the header) - automatically detected by R CMD check --as-cran (awesome flag; hint, hint, nudge, nudge to the Bioconductor community)

[HenrikBengtsson]

Miscellaneous

• Is dependency 'SnowballC' used anywhere? A 'grep' on all files didn't give anything.

• spelling::spell_check_package() reveals several typos/spelling mistakes.

• Several URLs used in the package code uses the HTTP although HTTPS is available/supported for them.

• Does the internal download.file() call need a mode = "wb" to avoid obscure misbehaviors due to different newline endings?

[LiNk-NY]

Hi Henrik, @HenrikBengtsson
I've made some changes in PR #42.

• A few \title{}:s are in all lower case, e.g. "get bioconductor download stats". Easy to spot if you look at the HTML index page.
• The help pages use all lower case for the value sections, e.g. "a character string of the email" in help("biocBuildEmail"). Is that intentional?
• Bioconductor is sometimes referred to as 'bioconductor' (lower case) or just 'bioc' and 'Bioc'.
• xml -> XML (for the initialism XML)
• github -> GitHub
• The help pages could need some more cross links. For example, help(dataciteXMLGenerate) says the value us "an xml element", e.g. exactly what is an "xml element". A link to the corresponding \pkg{XML} or \pkg{xml2} documentation would be helpful.

Vignette

* [ ] Broken URL: https://bioconductor.org/packages/3.9/BiocViews in Section 6.3 'Integration with [BiocViews]' (in the header) - automatically detected by R CMD check --as-cran (awesome flag; hint, hint, nudge, nudge to the Bioconductor community)

Miscellaneous

• Is dependency 'SnowballC' used anywhere? A 'grep' on all files didn't give anything.
• spelling::spell_check_package() reveals several typos/spelling mistakes.
• Several URLs used in the package code uses the HTTP although HTTPS is available/supported for them.
• Does the internal download.file() call need a mode = "wb" to avoid obscure misbehaviors due to different newline endings?