R CMD check issues

If you are interested in joining the CRAN cult, here's the things that need to be fixed according to codetools and R CMD check.

From codetools::checkUsagePackage('tigger'):

plotNovel: local variable ‘alpha’ assigned but may not be used (functions.R:434)
plotNovel: local variable ‘y_intercept’ assigned but may not be used (functions.R:433)

From R CMD check --as-cran:

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

* checking whether package ‘tigger’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘grid::arrow’ when loading ‘tigger’
  Warning: replacing previous import by ‘grid::unit’ when loading ‘tigger’

Fixable with explict @importFrom directives. Check alakazam/R/Alakazam.R for an example.

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

It's okay to bump the license to version 4.0

* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘findLowerY’ ‘mutationRangeSubset’ ‘positionMutations’
  ‘superSubstring’

Remove internal :::.

* checking R code for possible problems ... NOTE
cleanSeqs: no visible binding for global variable ‘.’
findNovelAlleles: no visible binding for global variable ‘.’
findNovelAlleles: no visible binding for global variable ‘a’
findNovelAlleles: no visible binding for global variable ‘POSITION’
findNovelAlleles: no visible binding for global variable ‘OBSERVED’
findNovelAlleles: no visible binding for global variable ‘MUT_COUNT’
findNovelAlleles: no visible binding for global variable ‘MUTATED’
findNovelAlleles: no visible binding for global variable ‘PASS’
findNovelAlleles: no visible binding for global variable ‘POS_MUT_RATE’
findNovelAlleles: no visible binding for global variable ‘Y_INT_MIN’
findNovelAlleles: no visible binding for global variable
  ‘SEQUENCE_IMGT’
findNovelAlleles: no visible binding for global variable ‘SNP_STRING’
findNovelAlleles: no visible binding for global variable ‘STRING_COUNT’
findNovelAlleles: no visible binding for global variable
  ‘MUT_COUNT_MINUS_SUBSTRING’
findNovelAlleles: no visible binding for global variable ‘J_CALL’
findNovelAlleles: no visible binding for global variable ‘J_GENE’
findNovelAlleles: no visible binding for global variable
  ‘JUNCTION_LENGTH’
findNovelAlleles: no visible binding for global variable ‘COUNT’
findNovelAlleles: no visible binding for global variable ‘FRACTION’
findNovelAlleles: no visible binding for global variable ‘TOTAL_COUNT’
findNovelAlleles: no visible binding for global variable ‘MAX_FRAC’
findUnmutatedCalls: no visible binding for global variable ‘.’
genotypeFasta: no visible binding for global variable
  ‘POLYMORPHISM_CALL’
genotypeFasta: no visible binding for global variable ‘GERMLINE_CALL’
genotypeFasta: no visible binding for global variable ‘NOVEL_IMGT’
getPopularMutationCount: no visible binding for global variable
  ‘V_CALL’
getPopularMutationCount: no visible binding for global variable
  ‘SEQUENCE_IMGT’
getPopularMutationCount: no visible binding for global variable
  ‘V_GENE’
getPopularMutationCount: no visible binding for global variable
  ‘V_SEQUENCE_IMGT’
getPopularMutationCount: no visible binding for global variable
  ‘V_SEQUENCE_IMGT_N’
getPopularMutationCount: no visible binding for global variable
  ‘V_GENE_N’
getPopularMutationCount: no visible binding for global variable
  ‘V_SEQUENCE_IMGT_N_MAX’
getPopularMutationCount: no visible binding for global variable
  ‘V_SEQUENCE_IMGT_P_MAX’
inferGenotype: no visible binding for global variable
  ‘POLYMORPHISM_CALL’
inferGenotype: no visible binding for global variable ‘GERMLINE_CALL’
inferGenotype: no visible binding for global variable ‘NOVEL_IMGT’
inferGenotype: no visible binding for global variable ‘.’
mutationRangeSubset: no visible binding for global variable ‘.’
mutationRangeSubset: no visible binding for global variable ‘MUT_COUNT’
plotGenotype: no visible binding for global variable ‘GENE’
plotGenotype: no visible binding for global variable ‘ALLELES’
plotNovel: no visible binding for global variable ‘SEQUENCE_IMGT’
plotNovel: no visible binding for global variable ‘V_CALL’
plotNovel: no visible binding for global variable ‘J_CALL’
plotNovel: no visible binding for global variable ‘JUNCTION_LENGTH’
plotNovel: no visible binding for global variable ‘POSITION’
plotNovel: no visible binding for global variable ‘OBSERVED’
plotNovel: no visible binding for global variable ‘MUT_COUNT’
plotNovel: no visible binding for global variable ‘MUTATED’
plotNovel: no visible binding for global variable ‘PASS’
plotNovel: no visible binding for global variable ‘.’
plotNovel: no visible binding for global variable ‘MUT_COUNT_NOVEL’
plotNovel: no visible binding for global variable ‘POS_MUT_RATE’
plotNovel: no visible binding for global variable ‘Polymorphic’
plotNovel: no visible binding for global variable ‘NT’
plotNovel: no visible binding for global variable ‘J_GENE’
positionMutations: no visible binding for global variable ‘.’
positionMutations: no visible binding for global variable
  ‘SEQUENCE_IMGT’
positionMutations: no visible binding for global variable ‘POSITION’
positionMutations: no visible binding for global variable ‘NT’
positionMutations: no visible binding for global variable ‘GERM_NT’
selectNovel: no visible binding for global variable ‘GERMLINE_CALL’
selectNovel: no visible binding for global variable ‘NOVEL_IMGT’
sortAlleles: no visible binding for global variable ‘GENE1’
sortAlleles: no visible binding for global variable ‘GENE’
sortAlleles: no visible binding for global variable ‘GENE2’
sortAlleles: no visible binding for global variable ‘FAMILY’
sortAlleles: no visible binding for global variable ‘ALLELE’
updateAlleleNames: no visible binding for global variable ‘.’
writeFasta: no visible binding for global variable ‘.’

Most of these can be fixed by switching from non-standard evaulation in dplyr, ggplot, tidyr calls to standard evaluation. For example, by using mutate_ instead of mutate and aes_string instead of aes. Tedious, but easy. For the . you'll likely need to set . <- NULL at the top of the function that uses it.

Examples with CPU or elapsed time > 5s
                  user system elapsed
inferGenotype    7.382  0.100  11.584
reassignAlleles  6.516  0.123  10.765
plotGenotype     4.507  0.122   8.764
genotypeFasta    4.033  0.107   8.282
findNovelAlleles 1.171  0.073   5.331
selectNovel      0.792  0.106   5.041

Examples need to be less than 5 second run time.

Warning messages:
1: character(0) 
2: character(0)

These will go away when the dplyr import conflicts are resolved.

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