Error in testthat due to NA handling in test-17-bedgraph.r when exporting meth.diff as log-transformed value

[alexg9010]

The recent Bioconductor check on nebbiolo1 for the methylKit package version 1.33.0 encountered an error in testthat.R.
An error occurred in the test suite tests/testthat.R, specifically in test-17-bedgraph.r:19:1. The error was caused by a scan() function call in R, where it expected a numeric (real) value but encountered 'NA'.

Reason

This error occurs when we want to export the meth.diffvalue as log transformed value. This will lead to NA output, which causes rtracklayer to complain upon import. similiar to perc.meththe meth.diff value should not be allowed to be transformed.

Summary of Error:

In test-17-bedgraph.r:

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-17-bedgraph.r:19:1'): (code run outside of test_that()) ──────
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, flush = flush, encoding = encoding, skipNul = skipNul): scan() expected 'a real', got 'NA'

Details:

• Line 19 causes failure:

  methylKit/tests/testthat/test-17-bedgraph.r

  Lines 10 to 19 in 0a5581c

  	# getting a bedgraph file from a methylDiff object containing differential
  	# methylation percentages
  	outFile <- tempfile(pattern = "mdiff.",tmpdir = outDir,fileext = ".bed")
  	bedgraph(methylDiff.obj, file.name=outFile, col.name="meth.diff",
  	unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="")
  	tt <- rtracklayer::import.bedGraph(outFile)
  	outFile2 <- tempfile(pattern = "mdiff.",tmpdir = outDir,fileext = ".bed")
  	suppressWarnings(bedgraph(methylDiff.obj,col.name = "meth.diff",
  	log.transform = TRUE,negative = TRUE,file.name = outFile2))
  	tt2 <- rtracklayer::import.bedGraph(outFile2)

• Error Message:

Error in scan(file = file, ...): scan() expected 'a real', got 'NA'

• Environment: Linux (Ubuntu 24.04.1 LTS), R Under development (unstable), gcc 13.2.0.

Suggested Fixes

• Disallow transformation of meth.diff values
• update tests

Testthat Log

Expand

methylKit.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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> library(testthat)
> library(methylKit)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:generics':

    intersect, setdiff, setequal, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff,
    setequal, table, tapply, union, unique, unsplit, which.max,
    which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> 
> 
> test_check("methylKit")
Using internal DSS code... 
Using internal DSS code... 
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 224 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-17-bedgraph.r:19:1'): (code run outside of `test_that()`) ──────
Error in `scan(file = file, what = what, sep = sep, quote = quote, dec = dec, 
    nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE, 
    fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip, 
    multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, 
    flush = flush, encoding = encoding, skipNul = skipNul)`: scan() expected 'a real', got 'NA'
Backtrace:
     ▆
  1. ├─rtracklayer::import.bedGraph(outFile2) at test-17-bedgraph.r:19:1
  2. └─rtracklayer::import.bedGraph(outFile2)
  3.   ├─BiocIO::import(con, "bedGraph", ...)
  4.   └─BiocIO::import(con, "bedGraph", ...)
  5.     ├─BiocIO::import(FileForFormat(con, format), ...)
  6.     └─rtracklayer::import(FileForFormat(con, format), ...)
  7.       └─rtracklayer (local) .local(con, format, text, ...)
  8.         ├─rtracklayer::import.ucsc(...)
  9.         └─rtracklayer::import.ucsc(...)
 10.           └─rtracklayer (local) .local(con, ...)
 11.             ├─rtracklayer::import.ucsc(...)
 12.             └─rtracklayer::import.ucsc(...)
 13.               ├─BiocIO::import(con, "ucsc", ...)
 14.               └─BiocIO::import(con, "ucsc", ...)
 15.                 ├─BiocIO::import(FileForFormat(con, format), ...)
 16.                 └─rtracklayer::import(FileForFormat(con, format), ...)
 17.                   └─rtracklayer (local) .local(con, format, text, ...)
 18.                     ├─BiocGenerics::lapply(seq_along(trackLines), makeTrackSet)
 19.                     └─base::lapply(seq_along(trackLines), makeTrackSet)
 20.                       └─rtracklayer (local) FUN(X[[i]], ...)
 21.                         ├─BiocIO::import(...)
 22.                         └─BiocIO::import(...)
 23.                           ├─BiocIO::import(FileForFormat(con, format), ...)
 24.                           └─rtracklayer::import(FileForFormat(con, format), ...)
 25.                             └─rtracklayer (local) .local(con, format, text, ...)
 26.                               ├─S4Vectors::DataFrame(...)
 27.                               └─utils::read.table(...)
 28.                                 └─base::scan(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 224 ]
Error: Test failures
Execution halted