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CRAN resubmission. Addresses the three issues raised by the CRAN reviewer for 1.1.4:
'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.authors (year) <doi:...> form
with the year in parentheses: Yu et al. (2017) doi:10.1111/2041-210X.12628, Gearty (2025) doi:10.1080/20964471.2025.2537516, and Paradis and
Schliep (2019) doi:10.1093/bioinformatics/bty633.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.
CRAN resubmission. Fixes the 2 WARNINGs and 1 NOTE reported by the CRAN incoming pre-test for 1.1.3:
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).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.
CRAN resubmission. Fixes the issue raised by the CRAN reviewer (Uwe Ligges) for 1.1.2:
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.
CRAN resubmission. Fixes the two NOTEs reported by the win-builder incoming pre-test for 1.1.1:
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).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.
CRAN resubmission. All issues raised by the CRAN reviewer (Leonore Hochhauser) for the 1.0.0 submission have been addressed:
\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 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{} 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.cat() with
message() in save_session_info() and
summarize_multi_trees() so output can be suppressed via
suppressMessages().\dontrun{} examples to \donttest{} (the error
originated from example evaluation on CRAN servers).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.
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.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.run_process_level.sh resolves Rscript from
PATH (override with RSCRIPT=) instead of a
machine-specific absolute path.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.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)..zenodo.json versions bumped for archival.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.evaluation/ is excluded
from R builds via .Rbuildignore; DESCRIPTION and
.zenodo.json versions bumped for archival.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._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).<U+XXXX> escapes instead of raw characters, so error
messages can no longer corrupt terminal output (and no longer trip
C-level formatting).system.time() reads, which made the
max/min ratio pure clock-quantization noise (constant 8x failure on
macOS and CI alike).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).R/logo.R, R/cli.R, README.CN.md,
and README.EN.md.inst/THIRDPARTY file now provides a centralized declaration
of all third-party dependencies, bundled data, and their licenses.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.ar53_r232.tree is now explicitly declared as CC BY 4.0 in
README files and inst/THIRDPARTY.plot_timetree() Rd now includes a
\references{} section with ggtree, deeptime, and ape
citations.Addresses the editor/reviewer pass over the 1.0.0 manuscript (real-data parsing evaluation, unified benchmark protocol):
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).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.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).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.Addresses remaining items from
修改计划_Rclade_v1.0.0.md:
@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).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.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.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:
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.-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).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).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 = ...).stop_on_failure = TRUE and a
declared-minimum-dependencies job was added; codecov.yml uses the
standard flags + status schema.First stable release. Consolidates the 0.2.0 development series into a formal release and aligns the manuscript with the project code.
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)..DS_Store,
tests/testthat/_problems/,
tests/functional/output/, empty directories).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:
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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