Issue #32 resolved
Jason Vander Heiden
created an issue

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’

Comments (6)

  1. Jason Vander Heiden reporter

    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.

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