R CMD check: NOTE no visible binding for global variable

[ssnn]

R CMD check reports many cases of 'no visible binding for global variable'

* checking R code for possible problems ... NOTE
binMutationsByRegion: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcBaseline: no visible binding for global variable ‘IMGT_V_NO_CDR3’
calcBaseline: no visible binding for global variable ‘HS5FModel’
calcBaseline: no visible binding for global variable ‘i’
calcBaselineHelper: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcDBExpectedMutations: no visible binding for global variable
  ‘HS5FModel’
calcDBExpectedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcDBExpectedMutations: no visible binding for global variable ‘i’
calcDBObservedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcDBObservedMutations: no visible binding for global variable ‘i’
calcExpectedMutations: no visible binding for global variable
  ‘HS5FModel’
calcExpectedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calculateMutationalPaths: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calculateTargeting: no visible binding for global variable ‘HS5FModel’
calculateTargeting: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
collapseByClone: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
collapseByClone: no visible binding for global variable ‘CLONE’
collapseByClone: no visible binding for global variable ‘yidx’
collapseByClone: no visible binding for global variable ‘i’
distSeqMat: no visible binding for global variable ‘M1NDistance’
distSeqMat: no visible binding for global variable ‘HS1FDistance’
distToNearest: no visible binding for global variable ‘HS5FModel’
distToNearest: no visible binding for global variable ‘V’
distToNearest: no visible binding for global variable ‘J’
distToNearest: no visible binding for global variable ‘L’
distToNearest: no visible binding for global variable ‘yidx’
distToNearest: no visible binding for global variable ‘i’
groupBaseline: no visible binding for global variable ‘yidx’
groupBaseline: no visible binding for global variable ‘i’
mutationType: no visible global function definition for
  ‘translateAminoAcidToTraitChange’
plotBaselineDensity: no visible binding for global variable ‘SIGMA’
plotBaselineDensity: no visible binding for global variable ‘DENSITY’
plotBaselineDensity: no visible binding for global variable
  ‘GROUP_COLLAPSE’
plotBaselineDensity: no visible binding for global variable ‘REGION’
plotBaselineSummary: no visible binding for global variable ‘REGION’
plotBaselineSummary: no visible binding for global variable
  ‘BASELINE_SIGMA’
plotBaselineSummary: no visible binding for global variable
  ‘BASELINE_CI_LOWER’
plotBaselineSummary: no visible binding for global variable
  ‘BASELINE_CI_UPPER’
plotMutability: no visible binding for global variable ‘pos3’
plotMutability: no visible binding for global variable ‘pos1’
plotMutability: no visible binding for global variable ‘pos2’
plotMutability: no visible binding for global variable ‘pos4’
plotMutability: no visible binding for global variable ‘pos5’
plotMutability: no visible binding for global variable ‘pos’
plotMutability: no visible binding for global variable ‘char’
plotMutability: no visible global function definition for ‘one_of’
plotMutability: no visible binding for global variable ‘x’
plotMutability : <anonymous>: no visible binding for global variable
  ‘text_y’
plotMutability: no visible binding for global variable ‘text_y’
plotMutability: no visible binding for global variable ‘text_label’
plotMutability: no visible binding for global variable ‘score’
plotMutability: no visible binding for global variable ‘motif’
summarizeBaseline: no visible binding for global variable ‘i’

[Jason Vander Heiden]

For reference: http://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when

[Jason Vander Heiden]

Some solutions in:
https://bitbucket.org/kleinstein/alakazam/issues/32/r-cmd-check-notes

[Jason Vander Heiden]

codetools::checkUsagePackage('shm')

plotMutability: no visible global function definition for ‘one_of’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)

analyzeMutations2NucUri: local variable ‘paramSeqUri’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1391)
calculateTargeting: local variable ‘tmp’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:928)
clearConsole: local variable ‘nproc’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/Core.R:144)
createMutabilityMatrix : .fillHot: local variable ‘Nei’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:591)
createMutabilityMatrix: local variable ‘seqAtMutation’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:500)
distSeq5mers: local variable ‘a’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:60-76)
getClosestBy5mers: local variable ‘indexJunctionsCounts’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:258)
getClosestMat: local variable ‘indexJunctionsCounts’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:302)
plotMutability: local variable ‘orient_x’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1315)
plotMutability: local variable ‘orient_y’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1316)
plotMutability: local variable ‘sub_rect’ assigned but may not be used (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1278)

calcBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:489-495)
calcBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:489-495)
calcDBExpectedMutations: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:729-732)
calcDBExpectedMutations: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:729-732)
calcDBObservedMutations: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:390-394)
calcDBObservedMutations: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:390-394)
collapseByClone: no visible binding for global variable ‘CLONE’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:117)
collapseByClone: no visible binding for global variable ‘yidx’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:118)
collapseByClone: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:146-149)
collapseByClone: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/MutationProfiling.R:146-149)
distToNearest: no visible binding for global variable ‘yidx’ (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:485)
distToNearest: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:502)
distToNearest: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:503-507)
distToNearest: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:513)
distToNearest: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/DistToNearest.R:514-517)
groupBaseline: no visible binding for global variable ‘yidx’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:771)
groupBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:821)
groupBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:833)
plotBaselineDensity: no visible binding for global variable ‘SIGMA’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1314-1316)
plotBaselineDensity: no visible binding for global variable ‘DENSITY’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1314-1316)
plotBaselineDensity: no visible binding for global variable ‘GROUP_COLLAPSE’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1314-1316)
plotBaselineDensity: no visible binding for global variable ‘REGION’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1343-1344)
plotBaselineSummary: no visible binding for global variable ‘REGION’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1488)
plotBaselineSummary: no visible binding for global variable ‘BASELINE_SIGMA’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1506)
plotBaselineSummary: no visible binding for global variable ‘BASELINE_CI_LOWER’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1507-1514)
plotBaselineSummary: no visible binding for global variable ‘BASELINE_CI_UPPER’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1507-1514)
plotBaselineSummary: no visible binding for global variable ‘REGION’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1524-1525)
plotMutability: no visible binding for global variable ‘pos3’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1213)
plotMutability: no visible binding for global variable ‘pos3’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1228)
plotMutability: no visible binding for global variable ‘pos1’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1232)
plotMutability: no visible binding for global variable ‘pos2’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1232)
plotMutability: no visible binding for global variable ‘pos4’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1232)
plotMutability: no visible binding for global variable ‘pos5’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1232)
plotMutability: no visible binding for global variable ‘pos5’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1235)
plotMutability: no visible binding for global variable ‘pos4’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1235)
plotMutability: no visible binding for global variable ‘pos2’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1235)
plotMutability: no visible binding for global variable ‘pos1’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1235)
plotMutability: no visible binding for global variable ‘pos’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)
plotMutability: no visible binding for global variable ‘char’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)
plotMutability: no visible binding for global variable ‘x’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)
plotMutability: no visible binding for global variable ‘pos’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)
plotMutability: no visible binding for global variable ‘char’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1242-1244)
plotMutability : <anonymous>: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1277)
plotMutability: no visible binding for global variable ‘x’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1281-1297)
plotMutability: no visible binding for global variable ‘pos’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1281-1297)
plotMutability: no visible binding for global variable ‘char’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1281-1297)
plotMutability: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1281-1297)
plotMutability: no visible binding for global variable ‘text_label’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1281-1297)
plotMutability: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1301-1304)
plotMutability: no visible binding for global variable ‘text_label’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1301-1304)
plotMutability: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1301-1304)
plotMutability: no visible binding for global variable ‘text_label’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1301-1304)
plotMutability: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1306-1309)
plotMutability: no visible binding for global variable ‘text_label’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1306-1309)
plotMutability: no visible binding for global variable ‘text_y’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1306-1309)
plotMutability: no visible binding for global variable ‘text_label’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1306-1309)
plotMutability: no visible binding for global variable ‘x’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1317-1331)
plotMutability: no visible binding for global variable ‘x’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1317-1331)
plotMutability: no visible binding for global variable ‘score’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1317-1331)
plotMutability: no visible binding for global variable ‘motif’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1317-1331)
plotMutability: no visible binding for global variable ‘x’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1338-1350)
plotMutability: no visible binding for global variable ‘score’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1338-1350)
plotMutability: no visible binding for global variable ‘motif’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1338-1350)
plotMutability: no visible binding for global variable ‘motif’ (/home/jason/workspace/igpipeline/shm/R/TargetingModels.R:1338-1350)
summarizeBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1093)
summarizeBaseline: no visible binding for global variable ‘i’ (/home/jason/workspace/igpipeline/shm/R/Baseline.R:1096)

[Jason Vander Heiden]

Not yet sure what to do about .I (from data.table) and one_of (from dplyr).

[Jason Vander Heiden]

tidyr::gather_ does not appear to support dropping of columns by name. See dplyr::select_vars_ for a workaround. Re: 'no visible binding' from tidyr::gather calls.

[Jason Vander Heiden]

Remaining issues from codetools::checkUsagePackage('shm'):

analyzeMutations2NucUri: local variable ‘paramSeqUri’ assigned but may not be used (TargetingModels.R:1384)
calculateTargeting: local variable ‘tmp’ assigned but may not be used (MutationProfiling.R:939)
createMutabilityMatrix : .fillHot: local variable ‘Nei’ assigned but may not be used (TargetingModels.R:591)
createMutabilityMatrix: local variable ‘seqAtMutation’ assigned but may not be used (TargetingModels.R:500)
distSeq5mers: local variable ‘a’ assigned but may not be used (DistToNearest.R:60-76)
getClosestBy5mers: local variable ‘indexJunctionsCounts’ assigned but may not be used (DistToNearest.R:258)
getClosestMat: local variable ‘indexJunctionsCounts’ assigned but may not be used (DistToNearest.R:302)

Remaining issues from R CMD check --as-cran:

binMutationsByRegion: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcBaseline: no visible binding for global variable ‘IMGT_V_NO_CDR3’
calcBaseline: no visible binding for global variable ‘HS5FModel’
calcBaselineHelper: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcDBExpectedMutations: no visible binding for global variable
  ‘HS5FModel’
calcDBExpectedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcDBObservedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calcExpectedMutations: no visible binding for global variable
  ‘HS5FModel’
calcExpectedMutations: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calculateMutationalPaths: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
calculateTargeting: no visible binding for global variable ‘HS5FModel’
calculateTargeting: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
collapseByClone: no visible binding for global variable
  ‘IMGT_V_NO_CDR3’
distSeqMat: no visible binding for global variable ‘M1NDistance’
distSeqMat: no visible binding for global variable ‘HS1FDistance’
distToNearest: no visible binding for global variable ‘HS5FModel’

[Jason Vander Heiden]

All of the IMGT_V_NO_CDR3 visibility issues should be resolvable by setting the default to NULL, but we need to ensure this works as expected in all cases (see issue #48).

[ssnn]

Jason:

Maybe we need to use utils::globalVariables(). Would prefer not. So gross.

[Namita Gupta]

These have all been resolved with commit f382c26