Resolve any issues reported by R CMD check about codyn HOT 5 CLOSED

All issues identified by devtools::check() have been resolved except for:

• checking R code for possible problems ... NOTE
  community_stability: no visible binding for global variable ‘stability’

This looks like a simple problem from community_stability.R, line 19, maybe one of the
authors could fix this.

Also, running check on Max OSX (I'm on 10.9.5) produces this error:

• checking PDF version of manual ... WARNING
  LaTeX errors when creating PDF version.
  This typically indicates Rd problems.
  LaTeX errors found:
  ! LaTeX Error: File `inconsolata.sty' not found.

This appears to be an error with the library 'texinfo @5.2.2' that is incompatible with R, and has been an issue for awhile. This error does not occur on Ubuntu 14.04, so this appears to be an issue with R and
not the codyn package. If you are interested, the problem is described here:

http://markmail.org/search/?q=list%3Aorg.r-project.r-devel+inconsolata.sty#query:list%3Aorg.r-project.r-devel%20inconsolata.sty+page:1+mid:arxwlgn5jkvzpibd+state:results

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Actually, R CMD check --as-cran gives three new NOTEs which all are easy to fix.

In the first case check even gives the solution: capitalize initial letters

The Title field should be in title case, current version then in title case:
‘Community dynamics metrics’
‘Community Dynamics Metrics’

Second is more cryptic: you have to mean that in R "complete sentence" means any string ending with full stop (period). See https://stat.ethz.ch/pipermail/r-help/2015-July/430057.html . This also got into Twitter.

* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

These were old things, but new R also wants you to explicitly import packages in stats, graphics etc. Fortunately the new check also gives you the text you need to add to your NAMESPACE:

Undefined global functions or variables:
  aggregate as.formula cor cov lm quantile sd stability var
Consider adding
  importFrom("stats", "aggregate", "as.formula", "cor", "cov", "lm",
             "quantile", "sd", "var")
to your NAMESPACE.

This adds several new unknown names in addition to stability.

The coding of stability is really opaque, though. I had to look code for a long time before noticing that you referred to a column in output. I would consider more transparent coding.

Please do not use is.na(stability) == F but use instead !is.na(stability).

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Fixed all issues with non-ASCII characters in doc files.

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Confirmed that all checks are working on:

• Mac OS X 10.3.3, R 3.2.2
• Debian, R 3.2.2
• Debian, R-devel
• Windows, R 3.2.2
• Windows, R-devel

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All checks resolved.

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