CRAN Check Failure for Upcoming broom Release

[simonpcouch]

Hi there! The broom dev team just ran reverse dependency checks on the upcoming broom 0.7.0 release and found new errors/test failures for the CRAN version of this package. I've pasted the results below, which seem to result from our decision to no longer export the fix_data_frame() function (for maintainability purposes.)

• checking tests ...

   ERROR
  Running the tests in ‘tests/testthat.R’ failed.
  Last 13 lines of output:
    [1mBacktrace:[22m
    [90m 1. [39mgenerics::tidy(dds)
    [90m 2. [39mbiobroom::tidy.EList(dds)
    [90m 3. [39mbiobroom:::tidy_matrix(x$E)
    [90m 7. [39mbroom::fix_data_frame
    [90m 8. [39mbase::getExportedValue(pkg, name)
    
    ══ testthat results  ═══════════════════════════════════════════════════════════
    [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
    1. Error: limma tidier works as expected (@test-limma_tidiers.R#5) 
    2. Error: voom tidier adds weight column (@test-limma_tidiers.R#26) 
    3. Error: voomWithQualityWeights tidier adds weight and sample.weight columns (@test-limma_tidiers.R#49) 
    
    Error: testthat unit tests failed
    Execution halted
  

I've pasted the most recently exported function definition below as a place to start from in making the necessary fixes.🙂

fix_data_frame <- function(x, newnames = NULL, newcol = "term") {
  if (!is.null(newnames) && length(newnames) != ncol(x)) {
    stop("newnames must be NULL or have length equal to number of columns")
  }

  if (all(rownames(x) == seq_len(nrow(x)))) {
    # don't need to move rownames into a new column
    ret <- data.frame(x, stringsAsFactors = FALSE)
    if (!is.null(newnames)) {
      colnames(ret) <- newnames
    }
  }
  else {
    ret <- data.frame(
      ...new.col... = rownames(x),
      unrowname(x),
      stringsAsFactors = FALSE
    )
    colnames(ret)[1] <- newcol
    if (!is.null(newnames)) {
      colnames(ret)[-1] <- newnames
    }
  }
  as_tibble(ret)
}

We hope to submit this new version of the package to CRAN in the coming weeks. If you encounter any problems fixing these issues, please feel free to reach out!