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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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devtools::check fails on documentation issue #169

Closed Kdreval closed 1 year ago

Kdreval commented 1 year ago

The devtools::check() returns a series of warnings indicating problems with package build. This one refers to the documentation:

❯ checking for unstated dependencies in examples ... WARNING
  Warning: parse error in file 'lines':
  35: unexpected symbol
  217:                                   custom_colours = c("#onecolour, "#anothercolour", "athirdcolour"),
  218:                                   classification_column
                                         ^
Kdreval commented 1 year ago

Also this is related to the documentation:

❯ checking Rd cross-references ... WARNING
  Missing link or links in documentation object 'FtestCNV.Rd':
    ‘3’ ‘"GRAPH"’

  Missing link or links in documentation object 'calculate_pga.Rd':
    ‘0..1’

  Missing link or links in documentation object 'prettyChromoplot.Rd':
    ‘0-1’

  See section 'Cross-references' in the 'Writing R Extensions' manual.
Kdreval commented 1 year ago

And this:

❯ checking for unstated dependencies in examples ... WARNING
  Warning: parse error in file 'lines':
  6: unexpected symbol
  1562: MYC_expr = get_gene_expression(hugo_symbols = c("MYC"), join_with = "mrna")
  1563: Read full
             ^
Kdreval commented 1 year ago

The list extended to other issues as well. Apparently, devtools reported these syntax issues one at a time. All were resolved in #177