R CMD Check: new warnings and notes

[teunbrand]

I found that the dev branch now generates more warnings and notes than before (which was only the bigwrig import warning).

Warnings

> checking contents of ‘data’ directory ... WARNING
  Files not of a type allowed in a ‘data’ directory:
    ‘hg19_cytobandAcen.bed’ ‘martExport.Rdata’
  Please use e.g. ‘inst/extdata’ for non-R data files

> checking files in ‘vignettes’ ... WARNING
  Files in the 'vignettes' directory but no files in 'inst/doc':
    ‘GENOVA.R’, ‘GENOVA.Rmd’, ‘GENOVA.bib’, ‘GENOVA.html’, ‘GENOVA.log’,
      ‘GENOVA.pdf’, ‘logo_GENOVA.png’
  The following files look like leftovers/mistakes:
    ‘GENOVA.log’
  Please remove them from your package.

> checking package vignettes in ‘inst/doc’ ... WARNING
  dir.exists(dir) is not TRUE
  Package vignette without corresponding single PDF/HTML:
     ‘GENOVA.Rmd’

Notes

> checking installed package size ... NOTE
    installed size is  6.6Mb
    sub-directories of 1Mb or more:
      data   5.7Mb

> checking top-level files ... NOTE
  Non-standard file/directory found at top level:
    ‘3Ddev_subsampling.pdf’

[teunbrand]

Fixed some of these in 022f08f39f5ec630db4a674fbc6459897eabe0f4

[teunbrand]

@robinweide do you need the hg19_cytobandAcen.bed and martExport.Rdata files still? I think they were used in creating the vignette

[robinweide]

Yes, these are used for the vignette.

[teunbrand]

But do we need to have these inside the package distribution?

[robinweide]

If we keep them on Shannon, for when we want to re-compile the vignette, it's fine to remove them from the distribution.

[teunbrand]

I managed to reduce the new checks and warnings to just the following:

> checking dependencies in R code ... WARNING
  '::' or ':::' import not declared from: ‘bigwrig’

But that might be a different issue altogether