version bump 1.33.3
 

 use tryCatch to send warning when download fails and fall back to using cached file
 

 Merged in DavidRach's ggcyto fixes as well as a few things from the bioconductor branch that had gotten away from me. Added a few missing dependencies from said ggcyto fix.
 

 Brough over Bioconductor flowGate version 1.13.1 differences to bring both GitHub and Bioconductor brances to being equivalent (except for preparePlot, which still double checking with unit tests for the Bioconductor version vs the ggcyto changes).
 

 AdjustAll argument for applyGateCloseSwap to adjust all specimens within a GatingSet in one go if so desired
 

 SpanGate adjustments and openCyto template exports are operational
 

 Modified gs_gate_interactive_adjust to show existing gate, and if done is clicked directly exit out without any adjustments being conducted. Seems to be recalculating correctly, as the downstream plots are showing the appearance of singlets subsequently, and when viewing gate coordinates the vertices are specimen specific. So one object off the list, wooh! Updating to 0.99.3 for internal tracking.
 

 Rollback requirement to R >= 4.4 for Cytometry in R class
 

 Unit test for all four interactive plot types. Need to check ggplot2 v3 next to see if back-compatible or not.
 

 Worked through Shiny capture options, gate is being created, but returning a colname not found on recompute from flowWorkspace.
 

 With ggplot2 switching to v4, and ggcyto shifts, flowGate is failing on shiny launch. Creating unit test systematically as I go (as likely will need to refer some of this up to ggcyto as well).
 

 Merge branch 'master' of github.com:NKInstinct/flowGate
 

 Post bioconductor review changes - just some documentation cleanup!
 

 Fixed for July submission
 

 DO.scVI now correctly saves the model
 

 Merge remote-tracking branch 'origin/master'
 

 Merge remote-tracking branch 'origin/master'
 

 Update NEWS.md 

 bug fix: bug fix for user-provided LRN, citation info
 

 Validate ontology graph structure.
Check for node names, duplicated nodes, missing node names, and a single root.
 

 bump version to 0.99.5
 

 Add onto_cache parameter to plotResult tests and vignette examples
 

 Refactor utils functions to use `onto_cache` parameter.

`.getHierarchicalPredSets`: now accepts an `onto_cache` argument and reuses it instead of calling igraph directly inside the loop. The old `.ancestors()` and `.children()` helpers (which made direct igraph calls) are removed;

`.scores()`: computes a node's score as the sum of predicted probabilities for its leaf children, intersected with prediction matrix columns.

`.precomputeCellScores()`: precomputes per-cell ancestor scores in one call (returns the predicted class, ancestors, their scores, and tie-breaking distances from each ancestor to the predicted class.

Updated prediction set functions (`.predSets`, `.predSetsSimple`, `.predSetsStep`, `.predSetsRank`) all now take `onto_cache` and `cell_cache`.
 

 Update R package manager URL in CI workflow 

 igblastr 1.3.12: 100x speedup or more to percent_mutation()
 

 version bump 1.49.25
 

 update grepl patterns for Authors@R NOTE
 

 ci: retrigger build
 

 fix: move loop docstring next to function, regenerate docs

The roxygen block was separated from the loop function by internal
helpers, causing loop.Rd to be lost. Also removed BiocParallel
references from docs since we now use parallel::parLapply.
 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: trigger build
 

 ci: retrigger build
 

 perf: return invisible from loop() to suppress knitr output for side-effect calls
 

 fix: export caller environment to PSOCK cluster workers
 

 perf: use mclapply on POSIX, parLapply on Windows, enable on macOS
 

 perf: replace BiocParallel with parallel::mclapply in loop()
 

 ci: trigger build
 

 ci: trigger build
 

 perf: vectorize mapping construction and model param extraction
 

 ci: trigger build
 

 ci: trigger build
 

 fix: use data.table instead of data.frame in predict helper
 

 fix: restore assertions in predict_efficacy_from_conc
 

 Merge pull request #198 from gdrplatform/GDR-3438

perf: optimize pipeline performance 

 ci: retrigger build
 

 ci: retrigger build
 

 ci: trigger build
 

 ci: trigger build
 

 perf: remove hardcoded parallelize=TRUE from average_SE
 

 ci: trigger build
 

 ci: trigger build
 

 perf: cache aggregate_ref, pre-compute ref mappings, vectorize isobologram smoothing
 

 ci: trigger build
 

 fix: use approved imperative verb in NEWS.md
 

 perf: rbindlist in isobolograms and rbindParallelList, eliminate redundant id column in normalize
 

 perf: optimize pipeline performance
 

 bug fix
 

 Replace S4 table() method with breakpointTable() generic
 

 Fixes on code coverage
 

 bugfix in intro
 

 merge
 

 after Biorxiv
 

 bump and bugfix in violin
 

 efficiency improvement of graph merging
 

 bump
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 support "sb" tag from new Space Ranger for 2um spot coordinates.
 

 Version bump in devel
 

 Merge branch 'devel' of git.bioconductor.org:packages/CoSIA into devel
 

 Fix path issue in test suite
 

 Clean up trailing white space
 

 Add validation for gene expression plot error
 

 Add validation script for tidyr fix
 

 Fix VST parsing in plotSpeciesGEx and plotTissueGEx

Replace deprecated tidyr::separate_rows with tidyr::unnest for the VST
list column. separate_rows no longer handles list columns correctly in
current tidyr, causing all VST values to become NA and breaking violin
plot rendering.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

 Version bump to fix windows testing error
 

 Don't memcpy a 0-length vector (#66) 

 Merge pull request #65 from MichaelChirico/patch-3

Remove '...' which is not in \usage 

 Bump version
 

 Add batchtools to suggests
 

 Add a comment at the end of the HPC vignette indicating that the current implementation does not handle partial completion
 

 Fix in the code selecting the SnowParam parallel backend for Windows
 

 When running on Windows, gsvaMap() will run parallel calculations within a node using a SnowParam() backend
 

 mapReduce() also verifies that input chunks contain the expected total number of rows/columns
 

 In the HPC support, create the internal HDF5Array_dump directory using an absolute path, just in case the working directory in a worker node is not work.dir
 

 Fixes in the code and documentation of gsvaBatchtoolsSlurmParam()
 

 Switch back lapply() used for debugging and testing to bplapply() in gsvaMap()
 

 gsvaMap() can return paths to serialized resulting objects, and gsvaReduce() can takes those paths as input
 

 Fix on parallel error recovering and object QC in gsvaMap()
 

 Added gsvaMap() and gsvaReduce(), documentation and unit tests
 

 Merge branch 'devel' of git.bioconductor.org:packages/BASiCStan into devel
 

 Fix doc errors
 

 explain omp on multi-OS
 

 Update the typo.
 

 Merge remote-tracking branch 'origin/main' into devel
 

 Temporary patch in response to changed geneontology.org GAF file naming convention.
 

 Update nb_consensus: signed/median modes, retention & robust_PCs fixes

Integrate the reworked nb_consensus()/nb_consensus_transfer():
- module_retention ("all"/"any"/"median") and new min_pc1_cor threshold are
  now honoured (previously retention silently used a hard-coded mean >= 0.8).
- robust_PCs=TRUE rank-transforms the data behind the stored rotation so it is
  consistent with the rank-based projection in nb_consensus_transfer().
- Added network_type="signed" and consensus_method="median".
- Sign alignment guarded against zero-variance (NA) inputs; PC2+ oriented
  deterministically.

Bug fixes found during integration:
- nb_consensus_transfer() no longer errors when zero modules are retained
  (paste0("ME", integer(0)) returned "ME", mismatching ncol = 0).
- Filter-mask cache key now includes a data fingerprint, so caches are not
  reused across different datasets sharing dimensions/method/stepno; key is
  sanitised to a valid filename on Windows.
- Returned per-dataset filter indices mapped back to full feature space under
  progressive ("min") subsetting.
- stepno coerced to integer; summary uses min_pc1_cor (was hard-coded 0.8).

Bioconductor/cleanliness:
- sapply -> vapply; utils::head; removed non-ASCII em-dashes; examples are now
  runnable (dropped \donttest). Regenerated man pages; bump to 2.21.5.
 

 Changed checking order in cleanVariants
 

 Updated NEWS
 

 check-meshdb
 

 update bioc version
 

 Fix S4 method signature for table() under R-devel
 

 update to reflect new GEOquery usage
 

 Merge pull request #6 from Bisaloo/vignette-typo

Fix typo 

 Don't need ':::' for exported functions (#129) 

 Merge pull request #25 from MichaelChirico/patch-1

Remove Imports as duplicate of Depends 

 Bump version from 0.51.4 to 0.51.5

Reflecting merged PR on typo 

 Fix typo IRange::IRanges --> IRanges::IRanges 

 try avoiding new(class1(x)) by using [0L] to create an empty prototype in parallelVectorNames
 

 set-auto-update
 

 Version bump after bugfix
 

 Merge obsolete Bioconductor devel tip; superseded by rebased history
 

 update-actions-immApex-coverage
 

 Merge origin/devel into clonal-cluster

Bring the full-length sequence retention and dowser export work (PR #579)
into the clonalCluster performance branch, which was based on a devel
state that predated it. Resolve the NEWS.md 2.9.1 conflict by unifying
both changelogs into one entry: the full-length sequence features plus
the clonalCluster threshold/expand changes, with immApex (>= 1.7.1)
recorded under DEPENDENCIES. DESCRIPTION auto-merged (version 2.9.1,
immApex pin, dowser in Suggests).

 

 clonalCluster edit

clonalCluster() passed the loose similarity threshold (for example 0.85)
to buildNetwork() and then refiltered the returned edges in R to the
tight bound (0.15). The engine therefore computed a large edge list that
was mostly discarded, and the wide internal band hid the new candidate
indexing in immApex.
- Pass 1 - threshold when threshold is below 1 so the engine prunes
  early. The downstream `dist <= 1 - threshold` filter becomes a no-op.
  Raw thresholds (>= 1) are passed through unchanged.
- Select the edge expansion from cluster.method. Connected-components
  clustering uses the memory-efficient "star" expansion, which is exact
  for components. Community methods use "clique" for exact multiplicity.
 

 robustness hardening

Harden retain.sequences against heterogeneous samples and NA joins
combineBCR now resolves retained columns against the intersection of
columns shared by all samples instead of the first sample only. This
fixes an "undefined columns selected" crash (and a silent column drop in
the reverse order) when samples carry different fields, e.g. mixing an
Immcantation-annotated sample that has sequence_alignment/germline_alignment
with a raw 10x sample that does not. combineTCR already resolved per
sample and is unchanged.
Add .cleanSeqJoin to drop "NA" placeholder tokens left when a contig in a
multi-contig chain lacks a full-length sequence. "seqA1;NA" collapses to
"seqA1" and an all-placeholder value becomes a real NA. Wired into the TCR
rename step and the BCR output columns. The helper is grepl-gated, so clean
joins pass through untouched and the default path keeps its zero overhead.
Adds regression tests for both cases and a BUG FIXES note to NEWS.
 

 dowser bridge

Add `exportDowser` bridge for dowser/Immcantation
New `exportDowser()` and e`xportClones(format = "dowser")` reshape combined
data into an AIRR frame with clone_id/sequence_id/junction_length for
`dowser::formatClones()`. Guards with guidance when the IMGT-gapped
sequence_alignment/germline_alignment fields are absent (e.g. raw 10x).
Adds dowser to Suggests. Closes #578.
 

 single-cell passthrough

Carry retained sequence columns through `combineExpression`
Present sequence_* columns now flow into Seurat/SCE metadata alongside
the CT* columns. Present-only and additive; no-op when nothing was
retained.
 

 import retention

Add `.computeFullSeq()`: every loaded contig table now carries a
standardized sequence/sequence_aa column. AIRR-family inputs copy the
native fields; 10x and MiXCR reconstruct the full V(D)J from
framework/CDR region columns; CDR3-only formats (TRUST4, WAT3R,
ParseBio) get NA. sequence_alignment/germline_alignment pass through
when present.

Purely additive - no existing column changes. Groundwork for #535.
 

 optimize
 

 improve tcss
 

 bug fixed in Wang method SV caching, #30
 

 Fix Wang method: normalise GO.db relationship names so edge weights apply

GO.db parent maps (GOBPPARENTS etc.) emit relationship names as "isa" and
"part of", but getSV() keys its weight table on "is_a" and "part_of". Since
neither spelling matches, every edge fails the membership test and is remapped
to "other", so Wang similarity silently uses a uniform 0.7 weight for all
87,439 edges instead of is_a = 0.8 / part_of = 0.6 (Wang et al. 2007).

Normalise the GO.db spellings to the weight-table keys before the existing
membership test. regulates / positively regulates / negatively regulates
continue to map to "other" (0.7), unchanged.
 

 openSesame: forward min_beads to per-prefix calls (fix #217)

min_beads (and func) were dropped in the multi-prefix/SigDF-list
bplapply recursion, so only single-prefix calls honored min_beads.
Bump to 1.31.1.
 

 Merge pull request #21 from BorchLab/refine-networks

Refine networks 

 update documentation Roxy 8.0.0
 

 Update README.md 

 Address reviewer comments
 

 Optimize code redundancy
 

 missing man files
 

 version bump 1.31.10
 

 version bump 1.31.9
 

 add if interactive to biocDownloadStats

- service temp disrupted
 

 justify use of Authors@R and document NOTE in vignette
 

 Refactor NAMESPACE and code structure, add package-level doc, update datasets doc, and fix BiocCheck warnings
 

 install GEOquery from github at Github Actions 

 version bump 1.49.23
 

 Use params = FALSE in curl_parse_url()
 

 Bump version
 

 Add attributes field to `zarr_overview()`
 

 chore(ci): bump GitHub Actions to Node 24-compatible releases (#93)

* chore(DESCRIPTION): bump minimum R version to 4.6.0

Resolves BiocCheck NOTE: Update R version dependency from 4.5.0 to 4.6.0.
Updates versions.env and CI workflow to R 4.6.0 / Bioconductor 3.23.

* chore(check-bioc.yml): update cache keys and artifact name to R 4.6.0 / Bioc 3.23

Cache keys still referenced RELEASE_3_18/r-4.3.1 causing stale compiled
packages to be restored under R 4.6.0, breaking data.table (SETLENGTH
symbol removed in R 4.6.0). Bumped cache-version to cache-v5 to force
a clean build.

* fix(ci): version-aware cache keys in Bioc workflow

* fix(devcontainer): fall back to source installs for R >= 4.6

For R/Bioc release pairs not yet packaged on conda, skip the conda
package list and install R packages from source via install.R. Adds a
MESA_VARIANT-aware block so full-variant genome/annotation packages are
installed only for the full image.

* refactor(check-bioc.yml): read R/Bioc versions from versions.env

Add a read-versions pre-job that parses .devcontainer/versions.env and
exposes r-version, bioc-version, and bioc-release outputs. The build job
matrix now consumes these instead of hardcoded values, making
versions.env the single source of truth for CI.

* docs(UPGRADE_GUIDE): drop manual check-bioc.yml edits

check-bioc.yml now reads versions from versions.env, so it no longer
needs hand-editing on upgrade. Remove it from the files-to-touch list,
rewrite Step 6, refresh the version map, and note the slim source-install
fallback.

* docs(NEWS): document devcontainer fix and versions.env single source

* fix(devcontainer): copy install.R into image for source-install fallback

The R >= 4.6 fallback invoked .devcontainer/install.R by relative path,
but the file was never copied into the image, so the slim build failed
with 'cannot open file'. COPY it to /opt/install.R and call that path.

* chore(devcontainer): add R→Bioc resolver and repurpose versions.env

Add resolve_versions.sh — the single place the R→Bioconductor mapping
lives. It parses R (>= X.Y) from DESCRIPTION, derives the latest
released Bioc version for that R via bioconductor.org/config.yaml,
and emits R_VERSION / BIOC_VERSION / BIOC_RELEASE. Works on BSD and
GNU awk; sources versions.env only as an optional pin override.

Repurpose versions.env: remove the hardcoded R_VERSION / BIOC_VERSION
entries (now derived) and IMAGE_TAG_* (unused). The file now serves
only as an optional override comment block, absent by design.

* chore(devcontainer): re-base Dockerfile on bioconductor/bioconductor_docker

Replace FROM continuumio/miniconda3 with:
  FROM bioconductor/bioconductor_docker:${BIOC_RELEASE}

where BIOC_RELEASE is passed in as a build-arg (computed by
resolve_versions.sh), so the tag is always derived — never hardcoded.

Drop all conda machinery: miniconda base, mamba, channel config,
mesa_env, conda activate.d script, package_list COPYs, and the
hardcoded 4.5/3.22 special-case branches. R and the full Bioc stack
come from the base image — the same one CI uses.

Use ENV to expose R_VERSION and BIOC_VERSION inside the container
(install.R reads them). Install deps by running install.R against a
staged DESCRIPTION copy, keeping the dep layer cache-stable. Add
chown of /usr/local/lib/R/site-library so the vscode user can install
mesa at postCreateCommand time.

* chore(devcontainer): rewrite install.R with DESCRIPTION-driven deps

Remove the conda user-lib path gymnastics and hardcoded "3.22" fallback.

Dependencies are now derived from DESCRIPTION via
remotes::dev_package_deps() — no hand-maintained package lists.
DESCRIPTION is the source of truth for which packages; the Bioc
version is read from the BIOC_VERSION env var set by the Dockerfile.

The slim/full difference is a single explicit full_only blocklist
(9 heavy genome/annotation data packages). slim omits them; the test
suite gates those cases with skip_if_not_installed() / skip_long_checks()
so slim tests skip gracefully. Genuine extras not in DESCRIPTION
(languageserver, imsig, ggtree dev, immunedeconv) are still installed.

* chore(devcontainer): update devcontainer.json for bioconductor base image

- R paths: /opt/conda/envs/mesa_env/bin/R → /usr/local/bin/R
- Remove postStartCommand (conda activate no longer needed)
- Simplify postCreateCommand to install only mesa from the live
  workspace; all deps are already in the image

* chore(ci): use resolve_versions.sh in both workflows

check-bioc.yml: replace the inline versions.env parse with a call to
resolve_versions.sh appended to GITHUB_OUTPUT. The emitted
bioc-release value is now the resolver's BIOC_RELEASE (computed from
DESCRIPTION), keeping the matrix consistent with the devcontainer.

build-image.yml: replace the Load versions step with resolve_versions.sh
appended to GITHUB_ENV; add BIOC_RELEASE to the Dockerfile build-args
so the FROM tag is wired through the same derivation chain.

Both workflows now reflect: DESCRIPTION R (>=) → resolver →
RELEASE_X_Y tag, with zero hardcoded version literals.

* chore(devcontainer): remove conda package lists

conda/package_list.{slim,full}.txt are no longer used — the new
Dockerfile installs deps via install.R reading from DESCRIPTION, not
conda package lists. Delete the now-empty conda/ directory too.

* docs(devcontainer): rewrite UPGRADE_GUIDE for single-file workflow

The upgrade procedure is now: edit DESCRIPTION's R (>=) line — done.
resolve_versions.sh derives the Bioc version and Docker tag; both CI
and the image build pick them up automatically.

- Replace the 11-step conda/source-install procedure with the
  simplified flow; add a TL;DR section at the top.
- Document the optional versions.env pin (for staying on a non-latest
  Bioc within an R series).
- Remove conda-activation steps in the devcontainer verification
  section; R is on the default PATH in the bioc base image.
- Remove the source-fallback Note block (no longer applicable).
- Genericise check_bioc_compat.R usage example to remove stray
  version literals from its header comment.

* docs(NEWS): document devcontainer re-base and single-file upgrade

* chore(devcontainer): address Copilot review comments on PR #92

- resolve_versions.sh: emit R_VERSION_FULL (full X.Y.Z from DESCRIPTION)
  alongside the existing R_VERSION (major.minor used for Bioc lookup).
  Falls back to bare major.minor if DESCRIPTION omits the patch.
- check-bioc.yml: replace eval+.0 pattern with >> GITHUB_ENV (consistent
  with build-image.yml) and use R_VERSION_FULL for the r-version output,
  removing the hardcoded .0 patch assumption.
- install.R: pin both install_github() calls to specific SHAs for
  reproducible image builds (ggtree has no release tags; immunedeconv
  pinned to SHA for v2.1.4).

* chore(devcontainer): suppress InvalidDefaultArgInFrom lint in Dockerfile

BIOC_RELEASE has no ARG default because any hardcoded value would need
to be updated on each Bioc upgrade, breaking the single-file workflow.
The workflow always supplies it via --build-arg; the directive silences
the lint without affecting builds or the upgrade path.

* fix(devcontainer): move check=skip directive to top of Dockerfile

Parser directives must precede all other content (including comments)
to be recognised by BuildKit; placement after the header comment block
caused the directive to be silently ignored.

* fix(ci): separate cache keys per devcontainer variant

Parallel slim and full matrix jobs wrote to the same registry cache tag,
so whichever job finished last would overwrite the other's entries. Give
each variant its own tag (cache-slim, cache-full) to eliminate the race.

* test(mouse): skip annotation tests when full-only packages absent

TxDb.Mmusculus.UCSC.mm10.knownGene and org.Mm.eg.db are full-only
packages not installed in the slim devcontainer. The test block was
failing instead of skipping on slim.

* fix(devcontainer): use noble RSPM binaries and harden version resolver

- RSPM/Posit codename jammy -> noble in install.R and check-bioc.yml; the
  bioconductor_docker:RELEASE_3_23 base is built on rocker 4.6.0 / ubuntu noble
  (24.04), so jammy (22.04) binaries were ABI-mismatched or fell back to source.
- check-bioc.yml read-versions: write resolver output to a file then source it,
  so a resolver failure aborts the step instead of being swallowed inside
  source <(...).
- Drop the now-unused R_VERSION build-arg/ENV (install.R reads only BIOC_VERSION).
- NEWS: point the R 4.6 / Bioc 3.23 upgrade at #92 (#91 was closed unmerged).

* docs(NEWS.md): add PR 92 reference

* chore(ci): bump GitHub Actions to Node 24-compatible releases

actions/checkout, docker/setup-buildx-action, docker/login-action and
docker/build-push-action targeted the deprecated Node 20 runtime. Pin
them to current Node 24 releases to clear the build-image CI warnings.

Also bump the same deprecated actions (plus actions/cache,
actions/upload-artifact@master and docker/metadata-action) in
check-bioc.yml for consistency.

* docs(NEWS.md): shorten PR #93 desciption

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: fpmartinez10 <eriperules@gmail.com>
Co-authored-by: Claude <noreply@anthropic.com> 

 docs: fix LaTeX Unicode errors and wrap slow example in \donttest{} (#88)

* chore(DESCRIPTION): bump version to 0.99.4.9000

* docs(NEWS): open 0.99.4.9000 development section

* docs: replace Unicode math symbols with ASCII in roxygen and Rd files

LaTeX (used to build the PDF manual) cannot render bare Unicode characters
such as U+2265 (>=), U+2264 (<=), and U+2208 (in) without extra packages,
causing R CMD check to error. Replace all occurrences with ASCII equivalents
in both the roxygen2 source comments and the generated .Rd files.

* docs(analyseDMRs): wrap summariseDMRsByGene example in \donttest{}

The example runs calculateDMRs + annotateWindows which takes ~52 s,
pushing R CMD check past the 10-minute CRAN limit. \donttest{} keeps
the example runnable locally and on Bioconductor builds while excluding
it from standard CRAN checks.

* docs(NEWS): record LaTeX Unicode fixes and donttest for summariseDMRsByGene

* docs: reregenerate roxygen files

* Add trailing newline to .gitignore

Fixes BiocCheckGitClone 'incomplete final line' warning from readLines().

* docs(NEWS): correct Unicode-symbol description in changelog

The 0.99.4.9000 entry listed the ASCII replacements (`>=`, `<=`, `in`)
as the "Unicode math symbols" that were removed, which is contradictory.
Name the actual Unicode glyphs (≥, ≤, ∈) as the originals and the ASCII
characters as the replacements. Addresses Copilot review on #88.

Co-Authored-By: Claude <noreply@anthropic.com>

* docs: fix proportion constraint from <= 1 to < 1 in mixThreeQsetSamples

* docs(NEWS.md): add blank space to allow Steven to approve PR

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk>
Co-authored-by: Claude <noreply@anthropic.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> 

 Bump version: 1.11
 

 Bump version: 1.0.1
 

 Edit README.md file
 

 Fix percentile_norm()
 

 remove error when checking directly on untarred directories
 

 add install method in BiocPackage class docs
 

 check for non-derived default show methods for S4 class
 

 use .BiocPackage install method in unit tests
 

 edgeR 4.11.3
- Fix catchSalmon.Rd args.
 

 fix getGEO usage in examples
 

 update script to use versioning
 

 add ai folder to .Rbuildignore and .gitignore
 

 use roxygen2 v8
 

 add internal catalog_versions dataset
 

 version bump 1.1.2
 

 use roxygen2 v8
 

 use separate bfc object for writing

assisted-by: claude sonnet 4.6
 

 Do not render docs for read_chunk()
 

 Document support for sharding in NEWS
 

 Document sharding as supported for reading
 

 Fix transposing mess
 

 Add tests for sharded dataset
 

 Add first draft for sharding codec decoder
 

 Refine read_data() args
 

 List sharding_indexed in list of supported codecs
 

 Create test dataset for sharding
 

 Avoid extra nrow() call
 

 Skip S3 tests on CI

At least for now until EMBL S3 instability has resolved
 

 Remove pre-rendered figure
 

 Run all code chunks
 

 Use knitr caching on S3 vignette
 

 Skip more S3 tests where necessary
 

 Vectorise the motif_coocc() max.distance spatial columns

Setting max.distance turns on the descriptive spatial columns
(both.clustered, median.distance), and computing them was dramatically
slower than the rest of the function. The old code looped pair by pair
and sequence by sequence, looked each sequence's hits up in a
string-keyed list (a linear scan over names), and built a full
outer() distance matrix through an R closure just to take its minimum,
so it scaled poorly with the number of hits.

Every hit is now mapped to a single global coordinate, sequence.i * BIG
+ (start - minstart) with BIG = 2 * (max - min) + 1, so that two hits in
the same sequence are always closer than two hits in different
sequences. A single sorted findInterval() per motif pair then resolves
every within-sequence nearest (A, B) pair at once (cross-pairs), or
diff() of the sorted coordinates gives the adjacent gaps (self-pairs),
with no per-sequence loop, no outer() matrix, and no string-keyed
lookups. The both.clustered and median.distance output is identical
(checked against the previous implementation over 40 randomised inputs
covering self-pairs and multi-hit sequences); it is roughly 9x faster on
a 30-motif, 1000-sequence, ~137k-hit benchmark, and the gap widens as
the hit table grows.
 

 Merge pull request #82 from seandavi/fix-issue-81-recursive-revdeps

Fix pkgBiocRevDeps(recursive = TRUE) leaking forward dependencies 

 Fix pkgBiocRevDeps(recursive = TRUE) leaking forward dependencies

Recursing reverse dependencies over 'Suggests' / 'Enhances' edges explodes
to nearly the entire repository (e.g. thousands of packages 'Suggests'
knitr), which pulled in the queried package's own forward (non-reverse)
dependencies. Restrict the recursion to strong dependencies so only genuine
reverse dependencies are returned.

For Rarr this reduces the recursive result from 25,613 packages to 4.

Adds a regression test and bumps the version with a NEWS entry.

Fixes #81

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 

 bump version
 

 bump version
 

 Bump version
 

 Define rotate() as a method

As requested by Hervé Pagès in https://github.com/Bioconductor/BiocGenerics/issues/24#issuecomment-4550063899
 

 # update README
 

 # update README
 

 Refre to geneome biology paper
 

 update description
 

 bump version
 

 # MSA2dist 1.17.5 (2026-06-24)

BUG FIXES

* fixed vignette
 

 Version bump
 

 Changed table loader class checker stringency
 

 Add BugReports field to DESCRIPTION

Addresses the BiocCheck NOTE 'Provide BugReports field(s)'. Points to the
maintainer email; the archived PascalSchlosser/netboost GitHub repo is stale
and has issues disabled.
 

 fix: journal preprint
 

 Bumped version
 

 version bump 1.1.1
 

 set default redownload=FALSE arg in .download_catalog
 

 version bump
 

 update the bigwig export methods.
 

 add message to check where cost the memory.
 

 add: link to ISC bencmark repo
 

 add: citation
 

 bump new z version
 

 update with latest roxygen
 

 Bump version to 1.5.3
 

 Update README.md

Change citation from bioarxiv to published manuscript 

 chore: as per review
 

 chore: add prism data
 

 BNPARAM in args, default to Kmkknn
 

 Fix package metadata and bump version to 1.3.1
 

 Bump version to 1.3.1 and fix vignette build issues
 

 Fix vignette dependency on mia and address BiocCheck notes
 

 Update installation instructions for DspikeIn

Added instructions for installing DspikeIn from Git. 

 Update README.md 

 Update README to remove core functions installation link

Removed the link to DspikeIn core functions installation. 

 Remove .DS_Store files and add to .gitignore
 

 Bump version to 0.99.27 for clean Bioconductor rebuild
 

 Describe your update briefly
 

 Add GeomxTools to package suggests
 

 Add GeoMxSet import bridge and SpatialDecon negative probes
 

 Merge pull request #55 from DavisLaboratory/ningbioinfo-patch-2

Update README with DDC file input instructions 

 Upgrade actions/cache from v2 to v4 

 Fixes #51 

 update readGeoMx to fix a bug when reading multiple negprobe and remove
 

 fix bug in findNCGs and add outAssay options in batchCorrection so people can retain the original logcounts
 

 update plotRLExpr function by adding the sce_thres parameter.
 

 fix bug: add new para to document
 

 document the new parameter in plotpairpca
 

 Update pcaOtherPlotting.R

Added missing comma from function arguments 

 update: fix a bug when finding NCG, added a buffer to avoid log0.
 

 i Please enter the commit message for your changes. Lines starting
 

 version bump
 

 version bump
 

 version bump
 

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
 

 fix bug with tests for R4.4
 

 Update README.md, add citation 

 update version number
 

 Update helper methods for processing gene body regions
 

 Re-structured vignette references
 

 Attempt to resolve MultipleAlignment build failure
 

 Merge branch 'fix-xgboost-module' into devel
 

 Update the Version and NEWS.
 

 Merge remote-tracking branch 'upstream/devel' into fix-xgboost-module
Fix the conflict with the updates.
 

 Update the Modeling function.
 

 ModelingRF_nowights.R.
 

 Make sure it could test on HPC.
 

 Test XGBoost on HPC.
 

 Set up for RF on HPC.
 

 Set up for HPC and added the details in vignette.
 

 Fix the issue of the EvaluateModel function.
 

 Changed the typo.
 

 Changed the vignette.
 

 Deleted the .pdf.