Changes in version 2.59.3                        

Bug fixes

  - methylumIDAT() reads IDAT files from per-slide subdirectories, which
    is the layout Illumina's own software produces
    (<idatPath>/<Slide>/<Slide>_<Array>_Grn.idat). Both the
    file-presence check and the code that actually opened the files
    assumed a flat directory, so a nested run reported every sample as
    missing. Flat layouts are unaffected. If the same basename appears
    under more than one subdirectory the read now errors and lists the
    candidates rather than picking one. getBarcodes() had the same blind
    spot and is fixed too. (#19)

  - diagnostics() works on objects with no color-channel annotation,
    such as the bundled GoldenGate mldat. Three if (annotation(x) ==
    "...") tests errored outright on a zero-length annotation, and past
    those, the plotting loop split probes on a COLOR_CHANNEL column that
    such objects do not have, so every panel would have been drawn from
    zero probes. The long-reported call to the non-existent
    plot.density() was real, on the same path, and is also fixed. (#23)

  - methylumi.bgcorr() explains itself when asked for noob correction on
    an object that has no out-of-band intensities. Objects built from
    GEO series matrices or GenomeStudio output via methylumiR() carry
    only methylated/unmethylated/p-value data; OOB probes come only from
    reading raw IDATs. This used to fail deep inside method dispatch
    with "unable to find an inherited method for 'intensities.OOB'".
    (#24)

Deprecated and defunct

  - The gamma-family background corrections — method = "goob", "gamma"
    and "mode" — have been removed. They called gamma.mle(),
    gamma.mode() and gamma.integral() from rGammaGamma, a GitHub-only
    package that is not available from CRAN or Bioconductor and was
    never declared as a dependency, so these methods have errored for
    years. Requesting one now produces an error saying so. method =
    "noob" (the default) is unaffected. (#18)

Internal changes

  - qc.probe.plot(), plotNAs() and plotProbeNAs() no longer use
    ggplot2's deprecated qplot(). Plot output is unchanged except in
    plotNAs(), where the segment layer now maps linewidth rather than
    the also-deprecated size; scale_linewidth uses a linear palette
    where scale_size used an area one, so line widths differ slightly.
    (#40)

  - A pkgdown site is published to https://seandavi.github.io/methylumi/
    from a GitHub Actions workflow. (#43)

                       Changes in version 2.59.2                        

Bug fixes

  - The package installs again. lattice removed parallel() from its
    exports (it was renamed parallelplot() years ago, then deprecated,
    then made defunct). Because the import resolved at lazy-load time,
    this broke R CMD INSTALL for the whole package rather than just
    parplot(), and took several downstream packages with it.

  - QCdata() is no longer silently lost when a MethyLumiSet is subset.
    eSet's [ method drops the QC slot, and the previous guard tried to
    subset it after that had already happened — NULL[, j, drop = FALSE]
    returns NULL without erroring, so the guard was a no-op. QC data is
    now captured before dispatch and reattached. Feature indices no
    longer apply to QC probes, which live in their own feature space;
    only sample selection does. As a consequence combine() no longer
    reports "Dropped control probes" when combining subsets.

  - The example dataset mldat no longer shares its assayData between
    copies. It had been saved with storageMode = "environment" instead
    of "lockedEnvironment", so x <- mldat; methylated(x) <- ... silently
    mutated the original. The assay values themselves are unchanged.

  - plotNegOob() works again. It had two independent ggplot2 breakages:
    scale_y_continuous(breaks = NA) (now NULL) and opts() (removed from
    ggplot2 years ago, now labs()).

Internal changes

  - .mclapply() is now a thin wrapper around BiocParallel::bplapply()
    instead of parallel::mclapply() behind a require(). mclapply()
    forks, so it degraded to serial on Windows regardless. The signature
    is unchanged, and parallel results are verified identical to serial
    results. Configure it the standard Bioconductor way, with
    BiocParallel::register().

  - require() calls inside package code have been replaced with declared
    imports, or with requireNamespace() guards that produce an
    actionable error for genuinely optional packages (MASS, Biostrings,
    lumi). require() returns FALSE rather than erroring, so a missing
    package used to change behaviour silently.

  - Bare T/F are now TRUE/FALSE throughout (105 occurrences). These are
    ordinary variables, not reserved words, so a user with a variable
    named T in scope could change the meaning of a default argument.

  - 1:length(x), 1:nrow(x) and 1:ncol(x) are now seq_along()/seq_len(),
    which behave correctly when the length is zero.

  - Base-package functions used by the package are now properly
    imported, rather than resolving by accident because the packages
    happened to be attached.

Documentation

  - Most man pages are generated from roxygen blocks now. The S4 class
    and generic documentation remains hand-written on purpose; see the
    note in R/data.R.

  - extractBarcodeAndPosition() was documented as returning three
    columns with numeric row and column. It returns five, and row/column
    are strings such as "R006"; the numeric ones are
    rowNumber/columnNumber.

Testing and infrastructure

  - The package has a test suite for the first time: 36 tests covering
    import from IDAT and text, normalization, background correction,
    coercions, filtering, subsetting and every plotting entry point.

  - CI runs R CMD check against Bioconductor devel on GitHub Actions,
    replacing a .travis.yml that had not run in years.

Known issues

  - methylumi.bgcorr() with method = "gamma" or method = "mode" does not
    work. It calls gamma.mle(), gamma.mode() and gamma.integral() from
    rGammaGamma, which is not declared as a dependency and is not
    available from CRAN or Bioconductor. The default noob method is
    unaffected.

  - qc.probe.plot(), plotNAs() and plotProbeNAs() still use ggplot2's
    deprecated qplot().