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gapit3documentation's Issues

GAPIT3documentation::GAPIT() function calls

I've migrated GAPIT3::GAPIT() to GAPIT3documentation::GAPIT() so I can explore how it works (i.e., so I can break it). It appears to be a wrapper to other GAPIT function calls. Because many of these were left in GAPIT3 they are now obvious as WARNINGS. However, some calls are not to GAPIT3 so they should be prefixed with package:: to make them work. The below WARNING can be used as a checklist.

   GAPIT: no visible global function definition for ‘GAPIT.0000’
   GAPIT: no visible global function definition for ‘GAPIT.DP’
   GAPIT: no visible global function definition for ‘GAPIT.Phenotype.View’
   GAPIT: no visible global function definition for ‘GAPIT.Judge’
   GAPIT: no visible global function definition for ‘GAPIT.IC’
   GAPIT: no visible global function definition for ‘GAPIT.SS’
   GAPIT: no visible global function definition for ‘GAPIT.ID’
   GAPIT: no visible global function definition for ‘GAPIT.Genotype’
   GAPIT: no visible global function definition for ‘write.table’
   GAPIT: no visible global function definition for
     ‘GAPIT.Phenotype.Simulation’
   GAPIT: no visible global function definition for
     ‘GAPIT.Multiple.Manhattan’
   GAPIT: no visible global function definition for
     ‘GAPIT.Circle.Manhatton.Plot’
   GAPIT: no visible global function definition for ‘GAPIT.Interactive.GS’
   Undefined global functions or variables:
     GAPIT.0000 GAPIT.Circle.Manhatton.Plot GAPIT.DP GAPIT.Genotype
     GAPIT.IC GAPIT.ID GAPIT.Interactive.GS GAPIT.Judge
     GAPIT.Multiple.Manhattan GAPIT.Phenotype.Simulation
     GAPIT.Phenotype.View GAPIT.SS write.table
   Consider adding
     importFrom("utils", "write.table")
   to your NAMESPACE file.

Omit GAPIT.0000

The function GAPIT.0000() appears to only install dependencies. This should be handled by the R dependency handling system, so the function appears unnecessary. Perhaps we need to make sure the R documentation is set up correctly so that this dependency handling can take place before we omit it?

Use HapMap header

The HapMap format has a header. However, instructions to read in HapMap data include header=FALSE. This seems non-intuitive. Can we fix this?

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