Address CRAN reviewer feedback for 0.4.1

[murraystokely]

Summary

Addresses the four items raised in CRAN's pre-acceptance review of the 0.4.0 resubmission:

• Method references in DESCRIPTION. Adds DOI/ISBN-linked citations for the bin-by-bin distance measures (Rubner/Tomasi/Guibas 2000, Swain/Ballard 1991, Puzicha/Hofmann/Buhmann 1997) and average shifted histograms (Scott 2015), in the form CRAN requires (<doi:...> / ISBN:... with no spaces inside the angle brackets).
• \value tags in every Rd file. Adds a \value section to every exported function listed in the reviewer's note (ash, bindist, binning, ecdfofhist, histogram-message, informationloss, intersect, merge, mergebuckets, message-histogram, plot, plothist, quantiles, scale, subset, trimsparse). Functions that draw on the current device explicitly state "No return value, called for side effects".
• \dontrun{} cleanup. man/dtrace.Rd no longer needs \dontrun{} — the example now uses the package's bundled inst/extdata/buildkernel-readsize-dtrace.txt sample, so it runs without a live DTrace install. man/informationloss.Rd unwraps the PlotKSDCC/PlotEMDCC calls; they complete in well under five seconds.
• Restoring user state in vignettes. HistogramTools.Rnw and HistogramTools-quickref.Rnw now capture par() and options() at the top and restore them at the end, so building the vignettes no longer mutates the caller's graphics parameters or options.

Bumps Version to 0.4.1 and records the changes in NEWS.md.

Test plan

• R CMD build .
• R CMD check --as-cran HistogramTools_0.4.1.tar.gz — confirm the four reviewer notes are gone (no missing \value, no stray \dontrun{}, references parsed, no "user options changed" diagnostic from the vignettes).
• Spot-check ?KSDCC, ?ReadHistogramsFromDtraceOutputFile, ?PlotRelativeFrequency for readable \value text.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[murraystokely]

Verification (after installing ash/Hmisc/emdist/gdata/testthat locally)

GitHub Actions R-CMD-check matrix on this branch — all green: macOS-latest, Windows-latest, Ubuntu × release / devel / oldrel-1.

R CMD check --as-cran HistogramTools_0.4.1.tar.gz (R 4.3.3, local) reports every reviewer-flagged stage as OK:

• checking DESCRIPTION meta-information ... OK — DOI/ISBN references parse.
• checking Rd files ... OK, checking Rd contents ... OK, checking for missing documentation entries ... OK — every new \value tag accepted.
• checking examples ... OK — no \dontrun{} left; the dtrace example runs against the bundled sample file.
• checking re-building of vignette outputs ... OK — both Sweave vignettes rebuild cleanly with par()/options() restored.
• checking tests ... OK.

Remaining local diagnostics are tooling-only (no pandoc, no qpdf, no tidy, missing inconsolata.sty for the local PDF manual build, and RProtoBuf not installed because the system lacks protobuf-dev — RProtoBuf is in Enhances:). None of these come from package content, and the CI matrix exercises the PDF and HTML manuals on machines with the full toolchain.