R CMD check NOTES:

[Jason Vander Heiden]

#1

* checking DESCRIPTION meta-information ... NOTE
Deprecated license: CC BY-NC-SA 3.0

#2

* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.

#3

* checking R code for possible problems ... NOTE
countClones: no visible binding for global variable ‘SEQ_COUNT’
countClones: no visible binding for global variable ‘COPY_COUNT’
countGenes: no visible binding for global variable ‘SEQ_COUNT’
countGenes: no visible binding for global variable ‘COPY_COUNT’
estimateAbundance: no visible binding for global variable ‘COUNT’
estimateAbundance: no visible binding for global variable ‘P’
getPropertyData: no visible binding for global variable ‘aaindex’
getPropertyData: no visible binding for global variable ‘pK’
plotAbundance: no visible binding for global variable ‘RANK’
plotAbundance: no visible binding for global variable ‘P’
plotAbundance: no visible binding for global variable ‘GROUP’
plotAbundance: no visible binding for global variable ‘.x’
plotAbundance: no visible binding for global variable ‘LOWER’
plotAbundance: no visible binding for global variable ‘UPPER’
plotDiversityCurve: no visible binding for global variable ‘group’
plotDiversityCurve: no visible binding for global variable ‘lower’
plotDiversityCurve: no visible binding for global variable ‘upper’
plotDiversityCurve: no visible binding for global variable ‘.x’
rarefyDiversity: no visible binding for global variable ‘COUNT’
rarefyDiversity: no visible binding for global variable ‘SEQUENCES’
testDiversity: no visible binding for global variable ‘COUNT’
testDiversity: no visible binding for global variable ‘SEQUENCES’

[Jason Vander Heiden]

Using License: file LICENSE in the DESCRIPTION file solves the first two.

Avoiding non-standard evaluation in dplyr, tidyr and ggplot calls should solve the third.

[Namita Gupta]

Valid licenses according to CRAN: https://svn.r-project.org/R/trunk/share/licenses/license.db

[Jason Vander Heiden]

CRAN says we need to use 'CC BY-NC-SA 4.0'. Using this also solves NOTE 1. We can just delete the file for NOTE 2.

[Jason Vander Heiden]

These:

getPropertyData: no visible binding for global variable ‘aaindex’
getPropertyData: no visible binding for global variable ‘pK’

Are due to loading data objects from seqinr. Had to do some non-sense with the with function and a temporary environment to fix them.

These:

plotAbundance: no visible binding for global variable ‘.x’
plotDiversityCurve: no visible binding for global variable ‘.x’

Are due to the special variable in math_format(10^.x) calls. I couldn't find a satisfactory fix, so I went with adding .x <- NULL right before the plotting routines.

Everything else could be fixed by using standard evaluation.

[Jason Vander Heiden]

Fixed all no visible binding notes and updated license to CC BY-NC-SA 4.0 in 6f28192.