NEWS.md

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Rclade News

Rclade 1.1.5 (2026-09-15)

CRAN resubmission. Addresses the three issues raised by the CRAN reviewer for 1.1.4:

• Single quotes in Description: Single quotes are now reserved for R package names only ('ggtree', 'deeptime', 'ape'). Quotes were removed around acronyms and database names (GTDB, Silva, NCBI, MRCAs, LUCA, LACA, LBCA), and "geoscales" is now described in words as geologic time scales because it is not a package name.
• Reference format in Description: The bibliographic references now use the authors (year) <doi:...> form with the year in parentheses: Yu et al. (2017) , Gearty (2025) , and Paradis and Schliep (2019) .
• Console output in R/selftest.R: run_rclade_selftest() and its internal helpers now report progress with message() (stderr) instead of cat(), so all self-test output can be suppressed with suppressMessages(). A new verbose argument (default TRUE) allows fully silent runs. The returned exit code (0/1) and the outcome of every individual check are unchanged.

No changes to package behaviour, exports, or test outcomes relative to 1.1.4.

Rclade 1.1.4 (2026-09-08)

CRAN resubmission. Fixes the 2 WARNINGs and 1 NOTE reported by the CRAN incoming pre-test for 1.1.3:

• Pre-built vignettes: The package has a VignetteBuilder: knitr field in DESCRIPTION, but inst/doc did not exist and no pre-built vignette HTML files were shipped. CRAN requires that packages with a VignetteBuilder field include pre-built vignette outputs in inst/doc/. All three vignettes (quick_start.Rmd, publication_ready.Rmd, taxonomy_formats.Rmd) are now pre-built as HTML files and placed in inst/doc/ alongside their .Rmd sources, so CRAN's checking infrastructure finds them without needing to re-build them (which requires package dependencies not available on the CRAN check machines).
• Possibly misspelled words in DESCRIPTION: The flagged words (Gearty, Paradis, Schliep, Yu, et, al) are author surnames and the Latin abbreviation "et al." from the bibliographic references cited in the Description field (Yu et al. 2017, Gearty 2025, Paradis and Schliep 2019). They are not misspellings. Documented in cran-comments.md.

No changes to package code, exports, or behaviour relative to 1.1.3.

Rclade 1.1.3 (2026-09-07)

CRAN resubmission. Fixes the issue raised by the CRAN reviewer (Uwe Ligges) for 1.1.2:

• Single-quoted software names in Description: The software names ggtree, deeptime, and ape in the bibliographic reference paragraph of the Description field were not enclosed in single quotes. They have been changed to 'ggtree', 'deeptime', and 'ape'. The .mimosa/ development directory is now also excluded via .Rbuildignore.

No changes to package code, exports, or behaviour relative to 1.1.2.

Rclade 1.1.2 (2026-09-04)

CRAN resubmission. Fixes the two NOTEs reported by the win-builder incoming pre-test for 1.1.1:

• Non-standard top-level files: LICENSE.md, MANIFEST.tsv, and REPRODUCIBILITY.md are now excluded from the built tarball via .Rbuildignore (they are development/reproducibility artefacts, not intended for distribution; the standard LICENSE file required by License: MIT + file LICENSE remains).
• Possibly misspelled words in DESCRIPTION: the flagged words (ggtree, deeptime, Yu, et, al, Gearty, Paradis, Schliep) are R package names and author surnames from the methodological references cited in the Description field; they are not misspellings. Documented in cran-comments.md.

No changes to package code, exports, or behaviour relative to 1.1.1.

Rclade 1.1.1 (2026-09-03)

CRAN resubmission. All issues raised by the CRAN reviewer (Leonore Hochhauser) for the 1.0.0 submission have been addressed:

• DESCRIPTION references: Added methodological references to the Description field (Yu et al. 2017, Gearty 2025, Paradis & Schliep 2019) with DOIs in the required format.
• Missing \value tags: Added \value sections to print.rclade_options.Rd, run_rclade_shiny.Rd, set_log_enabled.Rd, set_log_file.Rd, and set_log_level.Rd.
• Examples for unexported functions: Removed \examples sections from all @keywords internal Rd files (batch_with_interrupt, build_path, managed_tempfile, resolve_group, resolve_special_identifier, validate_taxonomy_no_cycles, with_graceful_interrupt).
• \dontrun → \donttest: Removed all \dontrun{} wrappers from exported function examples. Where examples referenced external files (not available on CRAN), the example code was removed entirely. Where examples used bundled data(example_tree), they are now executable without wrappers.
• Console output: Replaced cat() with message() in save_session_info() and summarize_multi_trees() so output can be suppressed via suppressMessages().
• try-error in functionTree(): Resolved by converting \dontrun{} examples to \donttest{} (the error originated from example evaluation on CRAN servers).

Rclade 1.1.0 (2026-08-26)

Revision release implementing the fixes required by the pre-submission independent review ("Rclade-审稿意见", 2026-08-24). Contains one user-visible behavior change.

• BREAKING / fail-safe unit contract (issue 1): plot_timetree() now aborts with an informative error when add_timescale = TRUE and unit is NULL. Previously the pipeline silently defaulted to "Ga" (multiplying edge lengths by 1000), which could label a non-time-calibrated tree with a plausible-looking but wrong geological axis. Rclade does not infer branch-length units and does not verify chronogram status; pass unit = "Ma" / unit = "Ga" explicitly, or set add_timescale = FALSE. The CLI reports the same condition as a parameter error (exit code 2). Added: non-finite edge-length check (error) and an auditable root-to-tip dispersion warning for non-ultrametric/heterochronous inputs.
• Group-status accounting (issues 2/8): rclade_info and summarize_timetree() now report groups_total, groups_collapsed, groups_singleton, groups_skipped_non_monophyletic, and groups_skipped_other (with group names), fixing the previous "Collapsed groups" label that reported parsed candidates instead of clades actually collapsed. Non-monophyletic groups are skipped with a warning by default ("warn and skip"); strict = TRUE terminates at the first such group.
• Accuracy evaluation fix (issue 5): the built-in example accuracy script now aligns predictions with ground truth positionally and asserts cardinality; the previous label-based merge inflated 50 tips to 250 rows.
• Portable benchmark scripts (issue 6): run_process_level.sh resolves Rscript from PATH (override with RSCRIPT=) instead of a machine-specific absolute path.
• Honest CI description (issue 7): the former min-deps job is renamed deps-smoke and documented as a current-release dependency resolution check (DESCRIPTION lower bounds are NOT verified by CI); coverage upload remains best-effort (fail_ci_if_error: false) and is documented as a monitoring metric, not an enforced quality gate. The NEWS entry for v1.0.1 §12.1 was corrected accordingly.

Rclade 1.0.2 (2026-08-22)

• Refreshed benchmark results: all benchmarks were re-run against the v1.0.1 code base (which includes the 2026-08-16 Newick bracket-balance vectorization and parsing-pipeline fixes). In-session rendering at 10,000 tips improved from ~1.4 s to ~0.9 s (median); real-data timing on the GTDB ar53 tree (10,122 tips, 25 phyla) is now reported: 4.3 s in-session (median of 3) and 5.6 s process-level including R startup. Deterministic accuracy checks are unchanged (100% GTDB/example parsing accuracy; zero straight-edge deviation).
• Reproducibility scripts: adds scripts/benchmark_real_timing.R (real-data in-session timing, manuscript Table 4 source) and scripts/make_ncbi_rank_shift_example.R (deterministic regeneration of ncbi_rank_shift_example.csv, byte-identical to the committed file).
• No changes to package code relative to 1.0.1; DESCRIPTION and .zenodo.json versions bumped for archival.

Rclade 1.0.1 (2026-08-21)

• Evaluation data: adds the evaluation/ directory with real-data parsing-accuracy results (parsing_accuracy_real_data.csv; complete GTDB R232 ar53 taxonomy table, 10,122 labels x 7 ranks: 100% non-NA rate and 100% exact-match agreement) and a reproducible verification script (verify_gtdb_parsing_accuracy.R), supporting the parsing-accuracy evaluation reported in the accompanying manuscript.
• No changes to package code. evaluation/ is excluded from R builds via .Rbuildignore; DESCRIPTION and .zenodo.json versions bumped for archival.

Robustness and rendering fixes (2026-08-16, Rclade 1.0.1)

• Collapse-triangle alignment: collapse triangles were horizontally offset from their clades when every tip in the tree was collapsed (e.g. collapsing all phyla at once). The cause was revts() (time-axis reversal) being applied a second time after collapse — with all tips collapsed away, max(x) is the shallowest MRCA instead of 0, so the second application shifted the whole tree while the fixed-coordinate triangle polygons stayed behind. Vertical positions were unaffected. revts() is now applied exactly once; triangle apexes align with their MRCA again.
• Long-label guard: Newick labels longer than 500 characters are now truncated to 400 characters + _RCLADE_TRUNC (with a warning) before parsing, because ape 5.8.1's Newick parser aborts the whole R process (glibc "stack smashing detected", exit 134) on labels longer than ~512 characters on Linux. Documented in read_tree_auto() and plot_timetree(); truncate-aware notes added to README (EN/CN).
• Adversarial-input messages: control characters and Unicode BiDi markers detected in node names are now reported as <U+XXXX> escapes instead of raw characters, so error messages can no longer corrupt terminal output (and no longer trip C-level formatting).
• Tests: the two timing-ratio performance tests now measure calibrated blocks of repeats (>= ~100 ms per size) instead of single sub-millisecond system.time() reads, which made the max/min ratio pure clock-quantization noise (constant 8x failure on macOS and CI alike).
• CI/docs: pkgdown site now builds and deploys (dataset topics indexed, site URL added to DESCRIPTION, write permission granted); codecov upload failures no longer fail R-CMD-check (no token configured); the bilingual FAQ claim of "52 exported functions" corrected to 26.
• theme_timetree() now returns a list: the return value changed from a single ggplot2 theme object to list(theme, coord) where coord carries clip = "off" (breaking change for direct callers: use p + th$theme, then add_clip_off(p, layout) for clipping control). The rendering pipeline no longer adds the returned coord unconditionally — add_clip_off() applies coord_polar(...) (circular) or coord_cartesian(clip = "off") (rectangular) only when no timescale coordinate is present, preventing the coordinate from overwriting the polar / deeptime geo coordinate systems (T05).

License and attribution compliance (2026-08-04, Rclade 1.0.1)

• License corrections: the deeptime license was incorrectly listed as "MIT" in the logo, CLI help, and README files; it is actually GPL (>= 3). The treeio license was incorrectly listed as "GPL-2+"; it is actually Artistic-2.0. Both have been corrected in R/logo.R, R/cli.R, README.CN.md, and README.EN.md.
• Third-party notices: a new inst/THIRDPARTY file now provides a centralized declaration of all third-party dependencies, bundled data, and their licenses.
• Citation file: inst/CITATION now includes recommended citations for ggtree (Yu et al. 2017), deeptime (Gearty 2025), and GTDB (Parks et al. 2020) alongside the Rclade citation.
• GTDB data license: the bundled ar53_r232.tree is now explicitly declared as CC BY 4.0 in README files and inst/THIRDPARTY.
• Vignette references: all three vignettes now include a "References & Acknowledgments" section listing key dependencies and data sources.
• Function documentation: plot_timetree() Rd now includes a \references{} section with ggtree, deeptime, and ape citations.
• Copyright headers: all R source files now carry a copyright and license notice at the top of each file.

Manuscript-review hardening (2026-08-03, Rclade 1.0.1)

Addresses the editor/reviewer pass over the 1.0.0 manuscript (real-data parsing evaluation, unified benchmark protocol):

• Format detection (M-B3): the GTDB detection rule now additionally requires a semicolon-delimiter majority. Accession-prefixed embedded labels with double-underscore rank separators (e.g. GCA_xxx_d__Archaea_p__X) previously matched the [dpcofgsk]__ pattern and were misclassified as GTDB; they are now correctly detected as embedded (real-world case: 700-tip LACA timetree, §3.5 of the manuscript).
• Embedded parsing: parse_embedded() (all three delimiter modes) now tolerates double-underscore rank separators (_p__value), and leading underscores left over from such schemes are trimmed from parsed values.
• Tests: new test-straight-vdiffr.R adds vdiffr visual-regression snapshots of collapsed circular/rectangular renderings to guard against rendering drift across ggplot2/ggtree updates (executed when NOT_CRAN=true).
• Scripts: adds evaluate_parsing_real_data.R, measure_straightness.R, benchmark_real_session.R, benchmark_bac120_subsample.R, and run_process_level.sh; benchmark_synthetic.R unified to >=3 replicates at every scale; fixes a fragile regexpr() construct in baseline_manual_workflow.R.

Remediation round 2 (2026-08-01, Rclade 1.0.1)

Addresses remaining items from 修改计划_Rclade_v1.0.0.md:

• API surface convergence (P0-2): 27 infrastructure functions (logging, timers, temp-file helpers, validators, etc.) moved from exported to internal (@keywords internal); NAMESPACE reduced from 52 to 26 exports. New rclade_options() constructor provides a validated parameter object for plot_timetree(opts = ...) (route B1: backward-compatible, explicit args take precedence).
• Manuscript: supplementary "Searched alternatives" table added (CN/EN); §2.6.1 formalizes NCBI/Silva 0.3 threshold alongside GTDB/embedded 0.6; §2.6.3 computational-complexity table added; abstract notes single-run measurements at n >= 5000; §2.7 cross-references the searched-alternatives table; Chinese §4.3 adds O(n·k) notation.
• Docs: run_rclade_cli() Rd documents exit-code contract with examples; run_rclade_shiny() Rd adds a Concurrency section warning about global state; test-performance.R header clarifies catastrophic-regression intent.
• Engineering: environment.yml removes r-devtools from runtime deps; README (CN/EN) adds lockfile reproducibility guidance; tests/functional/ test IDs and comments fully translated to English.

Post-review hardening (2026-07-30, Rclade 1.0.1)

A structured editor-style review of the 1.0.0 manuscript and codebase was fully addressed (see 主编审阅报告_Rclade_v1.0.0.md in the project workspace). User-visible changes:

• Rendering/time axis: the x-axis range is now adaptive (compute_x_min() floors at -4567 Ma only when the tree root actually reaches into the Hadean); the erroneous injection of "Hadean" into the eras table (a Hadean is an eon, not an era) was removed; displayed-leaves counting after collapse no longer includes backbone internal nodes.
• CLI: -u/--unit default changed from Ga to auto (aligned with the R API; Ga still converts x1000); work around an optparse >= 1.8 prefix-collision that leaked sibling defaults into --highlight, --clade and --taxonomy_file; --strip_annotations now drops treedata columns by annotation pattern (support/rate/height/HPD/NHX/taxid).
• R API: ignore_malformed = TRUE is now honoured in the multiPhylo batch path (failed trees become NULL placeholders, as documented); delimiter_mode defaults unified to "reverse" across all exported functions; format-detection clear-majority threshold (score >= 0.6) made tolerant to binary floating-point error; Newick bracket-balance validation vectorized (large-tree speedup).
• Docs/metadata: DESCRIPTION lists the embedded format; third-party attribution in the logo/CLI help corrected (ggtree >= 4.0, deeptime Gearty 2025); withr added to Suggests; non-ASCII characters removed from shiny-app.R; Shiny no longer loads remote fonts; the Dockerfile installs from source (no bundled tarball), uses R 4.5.3 and propagates the documented Unix exit codes via q(status = ...).
• Tests/CI: new tests for displayed-leaves counting, adaptive x_min and the Shiny app; stale functional-test expectations aligned with intentional behaviour (duplicate-tip warning, non-interactive overwrite="ask", Silva detection fallback); CI Stage B now uses stop_on_failure = TRUE and a declared-minimum-dependencies job was added; codecov.yml uses the standard flags + status schema.

Rclade 1.0.0 (2026-07-09, First Stable Release)

First stable release. Consolidates the 0.2.0 development series into a formal release and aligns the manuscript with the project code.

• Unified version to 1.0.0 to mark the first stable release.
• All examples and result figures now use FigTree_withLACA_GBM_95CI.tree.recover (the 700-tip archaeal timetree published by Moody et al. 2025, Phil. Trans. R. Soc. B 380:20240097, doi:10.1098/rstb.2024.0097; redistributed with attribution).
• Manuscript supplementary material now fully includes the circular-layout straight-edge technical document.
• Cleaned junk files from the project code (.DS_Store, tests/testthat/_problems/, tests/functional/output/, empty directories).
• Fixed path references, version wording, and bibliography citations in the manuscript.
• Fixed geological timescale rendering under ggplot2 4.x, regenerated roxygen documentation, and synced dependency declarations and docs.

1.0.0 Clean redistribution (2026-08-13)

• Clean redistribution (2026-08-13): removed all bundled third-party reference data (data-external/ and GTDB reference files under inst/extdata/) and GTDB-dependent scripts/tests (scripts/extract_gtdb_node_taxonomy.R, scripts/benchmark_bac120_subsample.R, scripts/evaluate_parsing_real_data.R, scripts/benchmark_real_session.R, tests/testthat/external/); updated README, CITATION, THIRDPARTY, cran-comments, CI workflow, and vignettes to drop bundled GTDB references; renamed format-specific benchmark helpers to format-neutral names.

See the language-specific release notes for full historical details:

• English
• 中文

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.