Changes required for CRAN resubmission

[Jason Vander Heiden]

Non-FOSS package license (CC BY-NC-SA 4.0)

Can't you use a FOSS license?

* checking R code for possible problems ... NOTE
collapseDuplicates: no visible global function definition for 'na.omit'
estimateAbundance: no visible global function definition for
 'txtProgressBar'
estimateAbundance: no visible global function definition for
 'rmultinom'
estimateAbundance: no visible binding for global variable 'sd'
estimateAbundance: no visible global function definition for 'qnorm'
estimateAbundance: no visible global function definition for
 'setTxtProgressBar'
getPhylipEdges: no visible global function definition for 'read.table'
getPhylipInferred: no visible global function definition for
 'read.table'
getPropertyData: no visible global function definition for 'data'
getPropertyData: no visible binding for global variable 'aaindex'
getPropertyData: no visible binding for global variable 'pK'
multiggplot: no visible global function definition for 'plot'
plotAbundance: no visible global function definition for 'plot'
plotDiversityCurve: no visible global function definition for
 'setNames'
plotDiversityCurve: no visible global function definition for 'plot'
rarefyDiversity: no visible global function definition for 'setNames'
rarefyDiversity: no visible global function definition for
 'txtProgressBar'
rarefyDiversity: no visible global function definition for 'rmultinom'
rarefyDiversity: no visible binding for global variable 'sd'
rarefyDiversity: no visible global function definition for 'qnorm'
rarefyDiversity: no visible global function definition for
 'setTxtProgressBar'
readChangeoDb: no visible global function definition for 'read.delim'
stoufferMeta: no visible global function definition for 'qnorm'
stoufferMeta: no visible global function definition for 'pnorm'
testDiversity: no visible global function definition for 'setNames'
testDiversity: no visible global function definition for
 'txtProgressBar'
testDiversity: no visible global function definition for 'rmultinom'
testDiversity: no visible global function definition for
 'setTxtProgressBar'
testDiversity: no visible global function definition for 'combn'
testDiversity: no visible global function definition for 'ecdf'
testDiversity: no visible global function definition for 'sd'
testDiversity: no visible binding for global variable 'sd'
writeChangeoDb: no visible global function definition for 'write.table'
writePhylipInput: no visible global function definition for 'setNames'
writePhylipInput: no visible global function definition for
 'write.table'
Undefined global functions or variables:
 aaindex combn data ecdf na.omit pK plot pnorm qnorm read.delim
 read.table rmultinom sd setNames setTxtProgressBar txtProgressBar
 write.table

Consider adding

 importFrom("graphics", "plot")
 importFrom("stats", "ecdf", "na.omit", "pnorm", "qnorm", "rmultinom",
            "sd", "setNames")
 importFrom("utils", "combn", "data", "read.delim", "read.table",
            "setTxtProgressBar", "txtProgressBar", "write.table")

to your NAMESPACE.

Please fix.

For the vignette:

In principle one should be able to rebuilds vignettes. Anyway, from WRE:

The ‘BuildVignettes’ logical field can be set to a false value to stop R CMD build from attempting to build the vignettes, as well as preventing R CMD check from testing this.

Please follow this advice then.

[Jason Vander Heiden]

Apparently CRAN runs checks on R-devel versions, not released versions of R. From: https://developer.r-project.org/blosxom.cgi/R-devel/NEWS

‘R CMD check --as-cran’ now checks code usage (via ‘codetools’) with only the base package attached, so that functions from default packages other than base which are used in the package code but not imported are reported as undefined globals.

Hence, all the 'no visible global function definition' notes from packages that would normally be attached by default.

We should try checking with codetools::checkUsagePackage() and http://win-builder.r-project.org.

[Jason Vander Heiden]

The current license is listed in https://svn.r-project.org/R/trunk/share/licenses/license.db

[Jason Vander Heiden]

All fixed. Will resolve if this passed resubmission.

[Jason Vander Heiden]

Accepted!