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GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

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Package: CSOA
Commit: 959ac2950f251e44bab4c286a51195b086243236
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-05-06 14:48:28 +0800
Commit message:

 Bumped version
Package: CSOA
Commit: c58b7357832b09ae65573d0f817dbf517956e7a1
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-05-06 14:47:54 +0800
Commit message:

 Fixed attachCellScores
Package: BiocNeighbors
Commit: 4a210876ab0839044b2d13a68a77b6b663acf9ce
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-05-06 16:24:51 +1000
Commit message:

 Bumped version to rebuild on the new assorthead.
Package: multistateQTL
Commit: 1070219c1dde896897e3d5880bbed8683f033602
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2026-05-06 15:33:00 +1000
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/multistateQTL into devel
Package: Rsubread
Commit: c300c112f985d3f0c5b7ebd71c2d8d74a91b61e3
Author: Yang Liao (Monash University) <yliao@m3v104.massive.org.au>
Date: 2026-05-06 14:02:12 +1000
Commit message:

 bumpped to v2.27.1
Package: sangeranalyseR
Commit: f6375aed24faaea28bd019d5c5fba4b8e47bcde1
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-05 20:58:14 -0700
Commit message:

 NEWS.md: align top-level header with DESCRIPTION Version (1.23.0)

The Phase-19 rebase inherited Bioc's post-RELEASE_3_23 version bump
(DESCRIPTION 1.23.0) but the NEWS.md header still said
"1.21.1 (development)". Aligning the two so the release-tag body
reads coherently against the actual version.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 1946d95c9539c623c549532af642ffd79f30e565
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-05 20:48:52 -0700
Commit message:

 Phase 19 follow-up - Update release log with rebased SHAs

Records the post-rebase commit hash (7a8e4d3) and explains the
rebase: Bioconductor cut RELEASE_3_23 on 2026-05-04/05, advancing
upstream/devel by 2 version-bump commits. Local Phase 1-19 was
rebased onto upstream/devel (no conflicts; Version inherited as
1.23.0). origin/devel was force-pushed with --force-with-lease;
upstream/devel was a fast-forward.

Also corrects the Bioc-target branch documentation: this package's
Bioc remote has no `master` branch — `devel` is the active devel
branch, contrary to the Phase-19 spec assumption.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 7a8e4d3f79b233330b17d08675c288f20956e060
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-05 20:34:52 -0700
Commit message:

 Phase 19 - Consolidated NEWS.md, final BiocCheck audit, and Bioconductor release

* NEWS.md: added Phase 14-18 supplement under the existing 1.21.1
  stanza (Bug fixes for #100/#92/#76/#89/#94/#66/#65/#42/#91; new
  consensusMethod feature for #87/#48/#33; documentation overhaul
  for #13/#49/#71/#99 plus run-donttest example hardening).

* Migrated three legacy DCF stanzas (1.6.1, 0.99.1, 0.1.0) from
  the deprecated NEWS file into NEWS.md; removed the legacy NEWS
  file (resolves BiocCheck "More than 1 NEWS file found" note).

* vignettes/sangeranalyseR.Rmd: moved `eval=FALSE` from a global
  knitr::opts_chunk$set() to per-chunk on the 13 user-recipe
  blocks. The 4 infrastructure chunks (style, setup,
  locate-fixture, session-info) now evaluate at build time,
  resolving BiocCheck's earlier "global eval=FALSE" warning while
  keeping the recipes (which reference user paths and Shiny apps)
  unevaluated.

Final audit:
- testthat: 1451 / 1451 PASS.
- R CMD check (--no-manual): 0 errors / 0 warnings / 0 notes.
- BiocCheck: 1 ERROR (Support Site HTTP 504 - environmental),
  2 WARNINGS (devel y-parity false positive + intentional vignette
  chunk evaluation choice), 15 NOTES (all stylistic /
  environmental). See plans/19_final_release_log.md for the full
  enumeration.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 354c08e2b93411094cad90c726662572a40ddbce
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-05 09:51:33 -0700
Commit message:

 Phase 18 - Resolved doc issues and drafted automated backlog cleanup

* Vignette overhaul (closes #13, #49, #71, #99): rewrote
  vignettes/sangeranalyseR.Rmd with How-to recipe gallery,
  parameter reference (4 tables), troubleshooting matrix.

* Hardened roxygen examples for `R CMD check --run-donttest`:
  - Added `library(knitr)` to inst/rmd/SangerContig_Report.Rmd
    so kable() resolves during report rendering.
  - Removed cross-class `readTable(sangerAlignmentData)` calls
    from readTable @examples (no method exists for SangerAlignment).
  - Switched globalTrimApp + launchApp* examples from \donttest{}
    to \dontrun{} (Shiny gadgets/auto-printing block under
    --run-donttest).
  - Regenerated the corresponding man/*.Rd files.

* close_issues.py: parse `Action: close|comment` metadata flag and
  yield (num, body, action) 3-tuples; comment-only issues skip the
  state=closed PATCH. Defaults to `close` so 16/17_github_replies.md
  parse unchanged.

* New plans/18_github_replies_cleanup.md: 16 pre-drafted replies
  (4 doc + 8 refactor-resolved → close, 4 likely-resolved → comment-
  only retest requests for #60, #61, #68, #85).

R CMD check (no --as-cran): 0 errors, 0 warnings, 0 notes.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 895a3f6281126ca944c1a28148680780e68d5146
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-04 22:37:51 -0700
Commit message:

 Phase 17 - Resolved Sprint 3 consensus issues (#87, #48, #33)
Package: sangeranalyseR
Commit: 4d15a4c129e1dfb0b3b7ad46dfb7ceb172030a40
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-04 22:15:40 -0700
Commit message:

 Phase 16.5 - Added GitHub REST API script for automated issue closure
Package: sangeranalyseR
Commit: 11ef4c7fa680f14983cf8b236970ab77d6876fbe
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-04 21:46:33 -0700
Commit message:

 Phase 16 - Resolved Sprint 2 robustness issues and fixed reply formatting
Package: sangeranalyseR
Commit: 6ef5481d09eef54f601d5fb8b422f26d1853ebed
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-04 21:00:25 -0700
Commit message:

 Phase 15 - Resolved Sprint 1 issues (#100, #92, #76, #89)
Package: sangeranalyseR
Commit: b13146c3252ed52100888bff1fde2971d2b16f82
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-04 00:08:08 -0700
Commit message:

 Phase 13 - Final audit + Bioconductor upstream sync

* Final audit results captured in plans/13_final_release_log.md:
  - devtools::test():   1360 / 1360 PASS
  - rcmdcheck:          0 errors / 0 warnings / 0 notes (strictly clean)
  - BiocCheck:          1 / 1 / 17, all known environmental / advisory
                        items documented in Phase 9-10 logs
                        (Support Site, devel-branch y-parity, sapply,
                        <<-, function lengths, etc.)

* Lingering ignore-file housekeeping committed:
  - .Rbuildignore + ^\.positai$
  - .gitignore + .positai

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 1d9d1041848747d2819962dc3ee46f4f72297542
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 23:51:42 -0700
Commit message:

 Phase 12 - Added R-CMD-check badge, simplified README, and created NEWS.md
Package: sangeranalyseR
Commit: c3159907f4f73d3a093c5e6f940a4f1f9234a56a
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 23:33:46 -0700
Commit message:

 Phase 11 - Overhauled README and finalized documentation
Package: sangeranalyseR
Commit: 641d67b182f41d28292284f9967d3f2f9c5b2fff
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 23:19:31 -0700
Commit message:

 Phase 10 - Reverted R to 4.0.0 and maximized test coverage
Package: sangeranalyseR
Commit: 02f9e3962db35da8a454d46a048033a443e527fe
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 22:36:34 -0700
Commit message:

 Phase 9 - Automated UI tests, dependency cleanup, and clean BiocCheck
Package: sangeranalyseR
Commit: ae357b52f48dee953e3260f455135958aa5d5949
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 20:56:23 -0700
Commit message:

 Phase 8 - Modernized Shiny UI with Plotly and fixed lazy AA report compatibility
Package: sangeranalyseR
Commit: 0b183b2624ddc2b6919d2dc27028ca5b903ab53b
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 14:06:20 -0700
Commit message:

 Phase 7 - Ported peakvalues logic to Rcpp for native performance
Package: sangeranalyseR
Commit: f8b5e50d842771e6d4f41e550af024ac38149d53
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 13:46:30 -0700
Commit message:

 Phase 6 - Implemented BiocParallel and lazy evaluation for AA translation
Package: sangeranalyseR
Commit: 3ebb86e1519d9267e43a073c55f9128acf38a0f0
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 12:56:09 -0700
Commit message:

 Add Phase 5 E2E validation report and profiling artifacts

Runs the full SangerAlignment pipeline (8 ABIF reads, 4 contigs from the
ACHLO fixture) under both M1 and M2 trimming, captures per-stage wall
times and an Rprof sample, and validates 15 structural / determinism /
slot-equality invariants. All checks PASS.

Headline timing: full ingest + trim + assemble + cross-align ~1.85 s
under M1 and ~1.74 s under M2 (~225 ms per read). updateQualityParam
re-trim costs ~53% of a from-scratch run (skips ABIF parse + base
calling).

Profile finding: the dominant costs are NOT IO or DECIPHER alignment.
- Biostrings::translate (3 reading frames per read) ~35% of total
- MakeBaseCallsInside (peakvalues inner loop) ~32% (~16% self)
- DECIPHER alignment ~16%
- read.abif IO ~9%
- setValidity / S4 dispatch ~3%

Lazifying calculateAASeq and Rcpp-ising peakvalues are the two highest-
leverage local wins. BiocParallel migration of the per-SangerRead
construction loop (~84% of total wall time) remains the biggest
parallelism opportunity.

Artifacts under plans/phase5_artifacts/: run_e2e.R reproducer, full
stdout log, timings CSV, raw Rprof samples (compatible with profvis),
summaryRprof text breakdowns for M1 and M2, accuracy / slot-invariant
PASS logs.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 273cd8b7ec1416a55a88f3400b0cab633dfa06da
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 02:10:15 -0700
Commit message:

 Add CLAUDE.md and phased technical-debt audit notes under plans/

* CLAUDE.md: orientation file at repo root for future Claude Code
  sessions (commands, S4 hierarchy, dispatcher pattern, Bioc release
  conventions, the disabled-then-re-enabled test runner).

* plans/01_comprehension_summary.md: Phase 1 architectural map of the
  SangerRead -> SangerContig -> SangerAlignment hierarchy, dependency
  roles (sangerseqR, Biostrings, DECIPHER), and end-to-end .ab1
  lifecycle.

* plans/02_quality_audit_summary.md: Phase 2 audit of validator
  overhead, parallel/BiocParallel migration plan, DECIPHER
  copy-by-value bottlenecks, and inheritance review.

* plans/03_testing_strategy_summary.md: Phase 3 test inventory,
  negative-test catalogue (24 rows), orthogonal-axis matrix, slot
  invariants, IO-batching guard, and coverage targets.

* plans/04_sanitization_log.md: Phase 4 record of regex bug fixes,
  validator refactor metrics, setValidity additions, and a corrected
  Phase-2 misdiagnosis about 'redundant' raw slots on SangerRead.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 9723d79e539eb74c205876fb89fb2a24dbd00234
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 02:10:02 -0700
Commit message:

 Add comprehensive testthat coverage for validators, axes, and invariants

* Re-enable test_check() in tests/testthat.R so R CMD check runs the
  suite (was commented out).

* Fill the previously-empty test-Constructors.R with smoke tests for
  the SangerRead / SangerContig / SangerAlignment wrappers.

* New test files:
  - test-Validator-EdgeCases.R: 21 negative tests covering invalid
    extensions (.Xfa, .Xab1, .ab2, .fast), empty / corrupt / truncated
    .ab1 files, malformed CSVs (4 schema variants), out-of-range
    scalars (10 variants).
  - test-OrthogonalAxes.R: 6 cells of inputSource x processMethod x
    TrimmingMethod, asserting each combination yields a valid
    SangerAlignment.
  - test-SangerRead-SlotInvariants.R: byte-equality between SangerRead
    raw slots and the sangerseq parent class (guards a future slot
    refactor).
  - test-IO-Batching.R: hidden-file / nested-directory behaviour and a
    list.files call-count regression baseline.
  - test-Coverage-Smoke.R: breadth coverage for qualityBasePlot,
    MakeBaseCalls, readTable, writeFasta, updateQualityParam.
  - test-Validator-Helpers.R: direct unit tests for the new dot-prefixed
    helpers in UtilitiesFuncInputChecker.R (via asNamespace).
  - test-Regex-Boundary.R: pins the escaped extension regex against
    .Xfa, .Xab1, .fast, .faa, .ab1.bak, etc.
  - test-S4Validity.R: confirms the new setValidity methods reject
    malformed instances after slot mutation.
  - helper-Fixtures.R: 11 synthetic-fixture builders writing to
    tempdir(), used by the negative tests.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: sangeranalyseR
Commit: 98ed0471fd488ed559f6c58b3fdabe20bd6a9f50
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2026-05-03 02:09:46 -0700
Commit message:

 Fix file-extension regex bugs; refactor input validators; add setValidity

* checkFASTA_File / checkReadFileName: escape the leading dot in the
  '.fa', '.fasta', and '.ab1' regex patterns. The unescaped '.' matched
  any character, so files with extensions like '.Xfa' / '.Xab1' slipped
  through as valid. Patterns are now centralised as .FASTA_EXT_REGEX
  and .AB1_EXT_REGEX.

* Consolidate the 31 check* functions in UtilitiesFuncInputChecker.R
  via five internal helpers (.errAppend, .requireType, .requireEnum,
  .requireRange, .requireExt). All public signatures and error-type
  tags are preserved. File shrinks from 603 to 523 lines.

* Add setValidity methods for ChromatogramParam, QualityReport, and
  ObjectResults to catch post-construction slot mutations that violate
  range/length invariants. Sanger* classes are intentionally left
  alone to preserve the 'construction never throws' contract.

* Remove stray debug statements in UtilitiesFuncInputChecker.R (cat),
  UtilitiesFunc.R (print, cat), ShinyServerModule.R (message), and
  ShinySangerContigServer.R (print). Promote a user-facing
  'Chromatogram saved to ...' cat() to log_info.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Package: FLAMES
Commit: 38fd4e3299f60f858d1cc74845c8c12c5c23a164
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-05-05 18:58:49 +1000
Commit message:

 fix: FLAMES bulk quantification sample name error
Package: Rsubread
Commit: a58cebb9483783a4a6249f2cd5e1bb9ad8b87fc5
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2026-05-06 13:16:37 +1000
Commit message:

 Merge remote-tracking branch 'refs/remotes/origin/devel' into devel
Package: Rsubread
Commit: 6514ab7ce112f0f4ef472a8276f6b11581681f7e
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2026-05-06 13:15:06 +1000
Commit message:

 altered cellCounts for supporting single-cell junction detection.
Package: epigraHMM
Commit: 619a0f11386967c54623708623c637b5f23644ba
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2026-05-06 09:29:07 +1000
Commit message:

 version bump in devel
Package: epigraHMM
Commit: 950511460ebd303454603481582c2dbd8a05d524
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2026-05-06 09:28:19 +1000
Commit message:

 Removing bamsignals dependency and adding regionCounts to compute read counts. Removing C++11 flag from Makevars.
Package: plyxp
Commit: b0150f6a82ad9232ed3f2cac69192c1a63e8c3d1
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-05-05 15:47:14 -0400
Commit message:

 version bump - fixing regression in devel
Package: plyxp
Commit: 716c7e07cf8d044de00599be6bc2e709450d3906
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-05-05 12:56:28 -0400
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/plyxp into devel
Package: plyxp
Commit: 99557808e30287ddea51ff4984b2badfd6d4d5df
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-02-16 17:22:11 -0500
Commit message:

 Preserve group attributes in into_dimlist

Do not call unique() on the row/col chop index attributes.
Using unique() could change the expected number or ordering of groups
when constructing the dim list, so trust the provided attributes.
Package: plyxp
Commit: 22ce2b470da5b5cecbbde5c07994ec62268e199e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-02-15 13:36:47 -0500
Commit message:

 Merge branch 'devel' of github.com:jtlandis/plyxp into devel
Package: plyxp
Commit: 83d08e647b3c4afea0e69fc345c9c79b88724a71
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-02-15 13:36:31 -0500
Commit message:

 plyxp hexstickers
Package: plyxp
Commit: 15e1d84c0416d49ef332824fb4ce7d24aaa8535a
Author: Justin Landis <30324172+jtlandis@users.noreply.github.com>
Date: 2026-02-15 13:02:09 -0500
Commit message:

 Merge pull request #7 from mikelove/devel

update language on the two packages
Package: plyxp
Commit: 8ea4be09f693f871ffc1765a1a782ddf037185e5
Author: jtlandis <jtlandis314@gmail.com>
Date: 2026-02-15 12:52:38 -0500
Commit message:

 ??
Package: plyxp
Commit: 53eafb739f33088222ffdf485c483d0dd8934d5a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-12-01 11:16:22 -0500
Commit message:

 update language on the two packages
Package: plyxp
Commit: d7039ab44e2724c3082a24c678ec69b726a586b1
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-20 11:03:14 -0500
Commit message:

 version bump
Package: plyxp
Commit: 6c9424856e42cb01b02216569735ed5684a9a59f
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-20 11:03:01 -0500
Commit message:

 Update vctrs-S4-unchop.R
Package: plyxp
Commit: ee3dc8ab03a8d0025c9636adbe39589dff630b3a
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-15 00:09:33 -0500
Commit message:

 vec_ptype2 should call ptype on the non-null one when it ISNT an
S4Vector
Package: plyxp
Commit: 4b623bf4901e8698a497e63a5336e33019dbe7e3
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-15 00:08:59 -0500
Commit message:

 We can save time when we know there are no groups.
Package: plyxp
Commit: f36c48eef88a31f3d7ffa69f93d2a6e377a470ca
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 19:31:15 -0500
Commit message:

 version bump
Package: plyxp
Commit: 4fe5d00921336ac01f9459ef352fa96b76c8c817
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 19:31:03 -0500
Commit message:

 Update NEWS
Package: plyxp
Commit: 7bc10ea2b96fa11020f2207fed101ef3546cda87
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 19:28:58 -0500
Commit message:

 With some other development, I'm now aware of possible partial classes
Package: plyxp
Commit: 775843d0c76fceb2dd998d64a807b1492f74dbc4
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 13:01:50 -0500
Commit message:

 Adding note about recent error
Package: plyxp
Commit: d0d29aaae954ca7a6c138daf296b454a8e5496ff
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 12:35:43 -0500
Commit message:

 Version bump
Package: plyxp
Commit: a50ce8ff201ea39425512f8035aaed4126d49396
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 12:35:24 -0500
Commit message:

 Merge branch 'devel_groups_on_DFrame' into devel
Package: plyxp
Commit: 3acffbc0ba1ab62ee90323bf71fb3a9ae8e1038e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-14 12:29:19 -0500
Commit message:

 should use vec_slice for now
Package: plyxp
Commit: 1d6bb0a15f2f600714af37b8c3aa4e20e588bea2
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-12 17:11:53 -0500
Commit message:

 version bump
Package: plyxp
Commit: a4d9626bd43cb892f82e0d85650f9952e159b4b9
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-12 17:11:35 -0500
Commit message:

 At the point we should expect row_chops to be a list, so if we take data
from a DFrame, we should cast it as such
Package: plyxp
Commit: 4eda51800d76750771634922b90e2f86193d0a12
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-12 16:42:24 -0500
Commit message:

 typo
Package: plyxp
Commit: 0ba7c084f12bc07cba30548113b7715b81e18c24
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-12 16:38:18 -0500
Commit message:

 version bump
Package: plyxp
Commit: 692c727943513cf50045e37c7921f73d051a6899
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-12 16:37:44 -0500
Commit message:

 We should support "vctrs_vctr" as well
Package: plyxp
Commit: c03e17f031238b9696ab3564b74d7a1175e8cb42
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-10 13:44:47 -0500
Commit message:

 This should cause plyxp github pages to render... finally
Package: plyxp
Commit: cdac7ddcce18d015ae2252ad86b9233864c6cae5
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-10 13:44:47 -0500
Commit message:

 This should cause plyxp github pages to render... finally
Package: plyxp
Commit: ae741c3910d5a765260b2816225fea66beb05dcb
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-07 15:44:50 -0500
Commit message:

 Update test_dplyr_summarize.R
Package: plyxp
Commit: beb0c86eb4b5b056f0ff98f49c5500bd754d36a6
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-07 15:44:50 -0500
Commit message:

 Update test_dplyr_summarize.R
Package: plyxp
Commit: 386f588ce8f810f4bfd4f6dbbdd72418ae1cfc0b
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-07 15:27:08 -0500
Commit message:

 Add tests to ensure vectors are reconstructed correctly!!!
Package: plyxp
Commit: fd70f6875899382daeae807e650ba8b73ce007eb
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-07 15:32:35 -0500
Commit message:

 Update NEWS
Package: plyxp
Commit: e7b7d33c52966f2db64c593bc5bb9bc4b2553edc
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-07 15:27:08 -0500
Commit message:

 Add tests to ensure vectors are reconstructed correctly!!!
Package: plyxp
Commit: a1766e04f18fd818c0a41826bc0dbdef24b517bc
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 20:26:01 -0500
Commit message:

 no docs
Package: plyxp
Commit: d389cf4a190774f8b29145f6d7a26a331d856d5e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 20:17:32 -0500
Commit message:

 need to prevent recusion case
Package: plyxp
Commit: 164598bf88fe08fd7bbd64cf84c289696322dbd7
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 20:17:32 -0500
Commit message:

 need to prevent recusion case
Package: plyxp
Commit: c0c8d3d568e24fa2ad3b19e2ab9dd24123680ced
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 16:00:07 -0500
Commit message:

 version bump
Package: plyxp
Commit: 757d1c241b73206e72544c822ddaaaa2f8126a5b
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 15:59:54 -0500
Commit message:

 Update NEWS
Package: plyxp
Commit: bd0dcb73678764d16d0e4391b1fde7e9ceac581c
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 15:55:13 -0500
Commit message:

 bunch of redundaant browsers...
Package: plyxp
Commit: 38a81333d64381a36b6a439969a4860cf7172ba5
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 15:55:00 -0500
Commit message:

 use the correct group_data accessor
Package: plyxp
Commit: aaccbe891eb74403e52d7e9c3eb2d84539396676
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 15:54:24 -0500
Commit message:

 Use new chop func
Package: plyxp
Commit: d4274c4f91415c16ff19970f38601d152bcb8575
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-11-06 15:53:51 -0500
Commit message:

 remove type attribute and instead store group information on rowData and
colData
Package: VisiumIO
Commit: 1b499ef5fb2e031b23233f5df5aa84d0648b7c70
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-05 14:49:19 -0400
Commit message:

 version bump 1.9.1
Package: VisiumIO
Commit: 0aa09d19f38416165a4f86f35d2e92bcf19be8e0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-05 14:49:13 -0400
Commit message:

 add loadImage argument to TENxVisium(HD) constructors and classes, closes #24
Package: DiffBind
Commit: c8010cdc4b8b750f25271f341f311744e2c6ff59
Author: Rory Stark <bioconductor@starkhome.com>
Date: 2026-05-05 19:47:15 +0100
Commit message:

 3.23.2: fix Rd formatting NOTEs from R CMD check

Doc-only cleanup of mis-tagged \itemize / \describe wrappers
across 9 man pages plus inst/NEWS.Rd. No code change.
Package: TSENAT
Commit: 999814566e51333f693c076bf6c0c3bd944a30a5
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 19:29:46 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: 507166d8818eed85d18c4921d7584444b427bac7
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 19:28:53 +0200
Commit message:

 Fix test
Package: TSENAT
Commit: e1444d0f831660f090cbf776a29ee6ff582b7ed1
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 19:00:46 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: 820827d1aae4259b9a44d39f9f3841ed6a1c59b5
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 19:00:02 +0200
Commit message:

 Fix building issue
Package: TSENAT
Commit: a4aa29b7208f740444d8d7fcfd219c6eaea2890e
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 18:31:56 +0200
Commit message:

 Bump
Package: TSENAT
Commit: 15a5598fdc6808eea5be5275f1ed4ca75252fd04
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 18:31:14 +0200
Commit message:

 Fix build issue
Package: splatter
Commit: de2a9a5a80df94f63900c915b03a74fd73fdd672
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:19:05 +0200
Commit message:

 Bioconductor 3.24 devel
Package: splatter
Commit: bffca26c961e54b53ae9a8af4db24eb40a0e9e3e
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:17:49 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_23 branch
Package: splatter
Commit: 344fa5e487dc88e415bf3bed81063655d212f344
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:16:21 +0200
Commit message:

 Bioconductor 3.23 release
Package: splatter
Commit: 823de68f55687463019e5027f6b9a44e5a27a447
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:14:52 +0200
Commit message:

 Merge remote-tracking branch 'upstream/RELEASE_3_23' into devel

* upstream/RELEASE_3_23:
  bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
Package: zellkonverter
Commit: 3cbe1b2dded4968de83339ea15f93a6e9516e2ac
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:27:39 +0200
Commit message:

 Bioconductor 3.24 devel
Package: zellkonverter
Commit: 1d21d86b914634c233852466c2eca23bbdeffac1
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:25:53 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_23 branch
Package: zellkonverter
Commit: f0a426be4f448d735b32f5fd51d26c6d47e1a17e
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:24:27 +0200
Commit message:

 Bioconductor 3.23 release
Package: zellkonverter
Commit: 4c581e0566fb64f4918a19e2744801649aeab3b8
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2026-05-05 18:23:36 +0200
Commit message:

 Merge remote-tracking branch 'upstream/RELEASE_3_23' into devel

* upstream/RELEASE_3_23:
  bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
Package: TSENAT
Commit: 44775b8d94d5850afc544d2e59d103d182c0ec73
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 18:24:51 +0200
Commit message:

 Fix tests
Package: TSENAT
Commit: 7e2742d202be74fbc80ec0650c79323774b29ad8
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 18:06:00 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: c61f06acd0e83898cd5e4ee2384f789fe235353b
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 18:04:44 +0200
Commit message:

 Add skip_on_bioc
Package: TSENAT
Commit: eb46e16f491d4a98c855528ebf520b4c8632c0e2
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 17:37:39 +0200
Commit message:

 Fix tests
Package: TSENAT
Commit: 46cd6d4a18311605007ba628002b53e0676a3134
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 16:49:51 +0200
Commit message:

 Fix coding style
Package: betterChromVAR
Commit: 89cb44aac4658f9a0cd8e1b4662253474d79fe1d
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 17:55:05 +0200
Commit message:

 updated news
Package: betterChromVAR
Commit: 23c544c38cfc4f9ee91ffe9ec95dc7e0d0b8a3aa
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 17:42:58 +0200
Commit message:

 removed wrong return on null grouping and fillNULL=TRUE
Package: betterChromVAR
Commit: b6f37a4475a5b44f6dc6b59a83b0638df58474a2
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 17:41:16 +0200
Commit message:

 fixed wrong range coord when using flbias
Package: betterChromVAR
Commit: 5ba9d79774243187a4972e008c0af47505cdf210
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:55:24 +0200
Commit message:

 added missing import
Package: betterChromVAR
Commit: f01c8dd214b58ee7df31354d333ba1a4d2668c6e
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:50:07 +0200
Commit message:

 version bump
Package: betterChromVAR
Commit: c9b01e940b081368216a145b787cf4064a902efe
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:49:47 +0200
Commit message:

 explicit Matrix imports
Package: betterChromVAR
Commit: 0765f82f8e46a351e0192ba89bd9559fdf422fdd
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:44:27 +0200
Commit message:

 convert to dense after bg computation
Package: betterChromVAR
Commit: 35e1fcbaa34cbec3e1e88aeef8e38dc04e188282
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:30:22 +0200
Commit message:

 minor speedup
Package: betterChromVAR
Commit: caf70d9027a09f02fdca9ccdac7bcc400bf29382
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:29:06 +0200
Commit message:

 added dgCMatrix input to test
Package: betterChromVAR
Commit: e3b4f4f1ee412053d584dfb07f05bbcc9d24fd5b
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:28:54 +0200
Commit message:

 keep background data sparse, improve var computation
Package: betterChromVAR
Commit: ccd29fc877770649b673c9f4210cd5776ecc3424
Author: plger <pl.germain@gmail.com>
Date: 2026-05-05 15:27:56 +0200
Commit message:

 fixed misplaced parenthesis
Package: gDRutils
Commit: 9d1994a98f7d81e7db85c2803361c9dd75b2011d
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-05-05 15:00:35 +0200
Commit message:

 Merge pull request #186 from gdrplatform/GDR-3369

GDR-3369: update author email address
Package: gDRutils
Commit: 1eb4b9b0a19cd2b845eb73870dd1b820390111c4
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 13:39:24 +0200
Commit message:

 chore: trigger CI
Package: gDRutils
Commit: 889cf15d7277fcd02ed8e1b824e5076a025eed79
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 11:52:44 +0200
Commit message:

 chore: trigger CI
Package: gDRutils
Commit: 3f02c56db3e8b6f8745c0c94732c991a5f825bb1
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 10:37:23 +0200
Commit message:

 chore: resolve conflict, bump version to 1.11.2
Package: gDRutils
Commit: 8633624cccb7a5af1b6a6b4400dac5e3f8ef607d
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-29 11:30:01 +0200
Commit message:

 chore: trigger CI
Package: gDRutils
Commit: b373ea493069f9587f98b525b96c5d1c2428b525
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 15:25:47 +0200
Commit message:

 chore: update author email in R source files
Package: gDRutils
Commit: 754503ef8925044c659f5326f94c7707669f6991
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:59:05 +0200
Commit message:

 chore: fix version bump in DESCRIPTION
Package: gDRutils
Commit: bedfdadcb47be60bd8df0118ea67b46f15dde328
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:44:31 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRutils
Commit: 6260b92139a77d9bfe885c2943e1c8fd7b8959c9
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:44:31 +0200
Commit message:

 chore: update author email address
Package: gDRcore
Commit: f79f3238ecca1c6a3fefc99b43281974cdebe07f
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-05-05 15:00:26 +0200
Commit message:

 Merge pull request #194 from gdrplatform/GDR-3369

GDR-3369: update author email address
Package: gDRcore
Commit: 90c1937c772979c0474699dd244dd2912e10ae79
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 13:39:27 +0200
Commit message:

 chore: trigger CI
Package: gDRcore
Commit: 34913f5e77d9a2e20a54be86bf34ca0178cb8b75
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 11:52:46 +0200
Commit message:

 chore: trigger CI
Package: gDRcore
Commit: 9a7b3fe2ae3d64421dcd144ab3b554c0a90bb2c7
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-05 10:38:03 +0200
Commit message:

 chore: resolve conflict, bump version to 1.11.3
Package: gDRcore
Commit: 9ac9903e74ede4a9f1c42373cc2b88935ca423e3
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-29 11:30:03 +0200
Commit message:

 chore: trigger CI
Package: gDRcore
Commit: 4f1b31625b213a2ea4ebfcafd2f972fe825ff104
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 15:25:47 +0200
Commit message:

 chore: update author email in R source files
Package: gDRcore
Commit: 0f46b9db1a1943ac1dbf2430d6d946de675e6811
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:43:05 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRcore
Commit: fdfb8c6f9e895edcc5fabb845e8a29f5ece10a87
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:43:05 +0200
Commit message:

 chore: update author email address
Package: TSENAT
Commit: 91d8e6ff270bc2d8919cdcaca4a165855f0e9ea1
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 14:59:12 +0200
Commit message:

 Speed up examples
Package: TSENAT
Commit: c20f704b7a3cd3445967f7bfa9d1a00851c41205
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 14:49:50 +0200
Commit message:

 Fix tests
Package: TSENAT
Commit: b9658c7d29ff9465fe788d2b45c7b64b10a7aca2
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 14:40:32 +0200
Commit message:

 Fix tests
Package: ChIPpeakAnno
Commit: 56a063cd5896d653bee7283c86e093f00a8366f1
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-05-05 08:34:06 -0400
Commit message:

 Add warning message when the input is not unique for genomicElementDistribution.
Package: assorthead
Commit: 3f30d632f27fe58ad0826e3b778fc6f2596470f1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-05-05 22:21:34 +1000
Commit message:

 Updated knncolle_hnsw for windows.
Package: assorthead
Commit: 7256f1bd1bde6bdee60893dc0f335cfc395f326b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-05-03 14:43:13 +1000
Commit message:

 Added partisub, updated other libraries.
Package: miloR
Commit: a404c3ae0c6adacd8d91d12d33177eabf7f66e07
Author: MikeDMorgan <michael.morgan@abdn.ac.uk>
Date: 2026-05-05 11:45:55 +0100
Commit message:

 remove trailing bracket
Package: GSVA
Commit: 96ced1fc88147f7a09e57f649939774e56db7e1c
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-05-05 12:35:09 +0200
Commit message:

 Bump version
Package: GSVA
Commit: 6365179b1075443f59c1ffc4a8372c9d5bbfacae
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-05-05 12:34:57 +0200
Commit message:

 Fixing and updating proteomics vignette
Package: universalmotif
Commit: 48452fa309194ce7862a765b227dbce141ad4cfc
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-05 11:17:30 +0100
Commit message:

 version bump
Package: universalmotif
Commit: 44e2f85c05c6e33112ec2ab95d2af47356e6f8ee
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-05 11:05:57 +0100
Commit message:

 fix warnings and improve formulas
Package: universalmotif
Commit: a416ff67ffe386d922a4fdc814386587a949112e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-05 10:52:44 +0100
Commit message:

 text improvements
Package: pairedGSEA
Commit: 45080f252f6241c19344e080687fde21547fec96
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2026-05-05 11:27:12 +0200
Commit message:

 Update location references in doc
Package: pairedGSEA
Commit: 421025c5077bd22312b45dcf81b5ce17a51bc501
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2026-05-04 13:25:42 +0200
Commit message:

 Update maintainer
Package: RbowtieCuda
Commit: 69ce834704a127fa982f004de848591df12c9f50
Author: Franck RICHARD <franckrichard033@gmail.com>
Date: 2026-05-05 11:23:16 +0200
Commit message:

 Fix for an issue with the Thrust library
Package: scFastDE
Commit: b5ac314bbccbeec00cad3869c82937090bb4c992
Author: SubhadipJana1409 <subhadipjana1409@gmail.com>
Date: 2026-05-05 14:17:55 +0530
Commit message:

 add NEWS entry for 0.99.1
Package: scBatchQC
Commit: 6e85666d036cab413ca086d2631cfc164b630f83
Author: SubhadipJana1409 <subhadipjana1409@gmail.com>
Date: 2026-05-05 14:17:26 +0530
Commit message:

 add NEWS entry for 0.99.1
Package: gDRcore
Commit: 0a1f4abd62b8f6fcf4e11066a09855917ec8d91b
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-05-05 09:44:01 +0200
Commit message:

 Merge pull request #193 from gdrplatform/GDR-3366

GDR-3366: fix handling of NA Duration
Package: gDRcore
Commit: cd3e1d4ed02c5666e17f36ca777de783c03f8a44
Author: bczech <bczech@example.com>
Date: 2026-05-04 16:03:24 +0200
Commit message:

 fix(identify_keys): preserve Day0 keys when Duration is all NA

When no t0 rows exist (Duration == NA everywhere), the global all-NA
column removal was incorrectly stripping columns from Day0. Save and
restore Day0 across the gDRutils::loop call when has_day0 is FALSE,
so Day0 is only modified by the t0-specific check (second if).
Package: gDRcore
Commit: bb6f86e02008b32c8a95b35e6d56715d41f20a85
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-04 11:46:39 +0200
Commit message:

 chore: merge main and update version to 1.11.2
Package: gDRcore
Commit: 235bc420d48ebf8329d60928fe75d777d163c2f3
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-29 11:09:45 +0200
Commit message:

 fix: guard Day0 key filtering when no Duration==0 rows exist
Package: gDRcore
Commit: 6392bc38ca98649617a1a11962ebd63df8a3052a
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:33:11 +0200
Commit message:

 fix: handle NA Duration in Day0 detection and GR value calculation
Package: gDRimport
Commit: 93e590977e6e7296ceeefd757b3dc8aeb75c1c25
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-05-05 09:42:35 +0200
Commit message:

 Merge pull request #119 from gdrplatform/GDR-3366

GDR-3366: replace hardcoded Duration values with NA_real_
Package: gDRimport
Commit: 909f69b93d17873de62d78f77100974c086ecd07
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-05-04 11:45:29 +0200
Commit message:

 chore: merge main and update version to 1.11.2
Package: gDRimport
Commit: 6b8200703b14ec884901b71b9e1adbbfcf9cffe4
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:18:25 +0200
Commit message:

 GDR-3366: update tests to expect NA_real_ Duration in level6 PRISM
Package: gDRimport
Commit: c84b01a1f786ac534bb9224db78fa3d550ffba31
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2026-04-28 14:16:12 +0200
Commit message:

 GDR-3366: replace hardcoded Duration values with NA_real_
Package: phylobar
Commit: 6484c110aae217bc93b389bba75785bb7a99a00f
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-05-04 23:35:50 -0500
Commit message:

 download seems to timeout randomly
Package: phylobar
Commit: 2200642ee7451556e8baf10e9102f2343ccdc4b9
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-05-04 23:24:36 -0500
Commit message:

 bump version
Package: TDbasedUFEadv
Commit: 9012285a8c024d1b1f7e4a7d6635cc3fd5ca0d7a
Author: Y-h. Taguchi <tag@granular.com>
Date: 2026-05-05 12:11:51 +0900
Commit message:

 Move optional packages to Suggests and remove deprecated RTCGA
Package: phylobar
Commit: f9315b1ea22e9dcc5da7922e36bc8a56173f41b1
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-05-04 22:39:36 -0500
Commit message:

 update R requirement
Package: phylobar
Commit: bd413bae04989a7fd458e274f183108664b2b855
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-26 14:29:35 -0500
Commit message:

 add package import
Package: TSENAT
Commit: 2d6ddada916cf45de80f353a835d3c52137554a5
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 05:01:02 +0200
Commit message:

 Fix issues
Package: TSENAT
Commit: d7caf17f09cbcb58a319d430a4da6a0a2c74b027
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 04:38:49 +0200
Commit message:

 Bump
Package: TSENAT
Commit: 45112e6135c524f7bc0a51f2a248124e27323cd4
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 04:35:35 +0200
Commit message:

 Fix tests
Package: Aerith
Commit: 562352cca9483b306b9b851d36becc425af5e91b
Author: xyz1396 <1074082710@qq.com>
Date: 2026-05-04 21:26:53 -0500
Commit message:

 remove MSnbase dependancy
Package: TSENAT
Commit: 87c06ffe077d66847c540634317f182b09c1f0aa
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:38:58 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: 8cedd93abc78c6f6f6a1d7ee23e969df67256408
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:38:29 +0200
Commit message:

 Fix .gitignore
Package: TSENAT
Commit: 18a81a55071ec8e741537b360b62b84a9f0a0300
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:35:52 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: f1f460ec5b5c362ad4bb697065c24f6f610119c3
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:35:22 +0200
Commit message:

 Fix issues
Package: TSENAT
Commit: 320776700cdd8b8137e56961456582ad0166b77c
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:10:09 +0200
Commit message:

 Merge upstream devel changes
Package: TSENAT
Commit: 848cbb12cef051a7597e5511f2746ae2d12c1580
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:06:00 +0200
Commit message:

 Bump version
Package: TSENAT
Commit: fa6aa2921c5ba590f1a7fba778203ae32464a75e
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 03:04:20 +0200
Commit message:

 Skip tests
Package: TSENAT
Commit: dcd568fb4b13c25cf3f0a0e74487103a926f7408
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 02:39:21 +0200
Commit message:

 Fix issues
Package: TSENAT
Commit: cd46354f38222b2d08470f7be700524180252498
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 02:23:54 +0200
Commit message:

 Tests fixed
Package: TSENAT
Commit: 026db9009f8dad2980d085a6fd72acb257998202
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:44:11 +0200
Commit message:

 version bump: 0.99.5 -> 0.99.6
Package: TSENAT
Commit: 8c1f46cae96f26b4914bd8421273f9424cf70f6d
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:44:05 +0200
Commit message:

 Remove CITATION file: no doi yet for new package
Package: TSENAT
Commit: 84ce29bddad83e29f374dd31d507326f754664aa
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:41:37 +0200
Commit message:

 version bump: 0.99.4 -> 0.99.5
Package: TSENAT
Commit: de7930019d018246bb599ba6f3031f275ef4bdb3
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:41:27 +0200
Commit message:

 Simplify .gitignore: remove problematic patterns and comments
Package: TSENAT
Commit: e020834fc096b22430f63f210445b38b7cf30e9e
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:38:27 +0200
Commit message:

 version bump: 0.99.3 -> 0.99.4
Package: TSENAT
Commit: 395b492486bb031e9d9f87dd0a10459af213875d
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:38:14 +0200
Commit message:

 Fix .gitignore: remove regex-problematic comments and ensure newline at EOF
Package: TSENAT
Commit: 93d92287ba7d5864cc2b27f5e4e54c1672da268e
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:32:30 +0200
Commit message:

 version bump: 0.99.2 -> 0.99.3
Package: TSENAT
Commit: 51b3f180a2c979fa5a82be2da8a44d7ceced70ef
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-05 00:32:22 +0200
Commit message:

 Fix: shorten Rd example comments to comply with line width limits
Package: TSENAT
Commit: 286f8066b27b228dbedc6d8aa30d25c85be26156
Author: gallardoalba <gallardoalbac@gmail.com>
Date: 2026-05-04 23:51:11 +0200
Commit message:

 version bump: 0.99.0 -> 0.99.1
Package: scFastDE
Commit: 166b2a12d599dd248e8edfd401259748fc9d3c8d
Author: SubhadipJana1409 <subhadipjana1409@gmail.com>
Date: 2026-05-05 02:13:04 +0530
Commit message:

 fix: remove CITATION without DOI, bump R dep to 4.6.0, version to 0.99.1
Package: scBatchQC
Commit: c4ea15db23209a007e5b4185a414c6ac33ef3d09
Author: SubhadipJana1409 <subhadipjana1409@gmail.com>
Date: 2026-05-05 01:59:09 +0530
Commit message:

 bump version to 0.99.1 to trigger Bioconductor rebuild
Package: SpatialArtifacts
Commit: 699127a618c09d2e66f5e3f9b07697e0367adc81
Author: Jiali He <jialihe@umich.edu>
Date: 2026-05-04 15:56:45 -0400
Commit message:

 bump version to 1.1.0, add gene symbols to rowData of spe_vignette
Package: scBatchQC
Commit: 6e5212fd7abc3076bc2377a6c3d54df6b5b54c18
Author: SubhadipJana1409 <subhadipjana1409@gmail.com>
Date: 2026-05-05 01:13:13 +0530
Commit message:

 fix: remove CITATION without DOI, bump R dep to 4.6.0
Package: MSnbase
Commit: 76555a2e5da6d8087f2a3a208c03faf8dca5449a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-04 20:40:43 +0200
Commit message:

 fix: use inherits() to check class of object
Package: MSnbase
Commit: f5cfb469c44bdfc776bae1cfab1b10aaeb3611e1
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-04 18:02:52 +0200
Commit message:

 rebuild man with latest roxygen2
Package: MSnbase
Commit: 2023e2d789b6967ed2adf7d267212febc8edf7d8
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 20:29:02 +0200
Commit message:

 new devel version
Package: MSstatsBioNet
Commit: d1e62195f85f3b71e4c58e7c1315e313ea6c9dac
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-05-04 10:29:47 -0400
Commit message:

 Remove cron schedule from README upgrade workflow

Removed scheduled cron job for weekly README upgrade.
Package: MSstatsBioNet
Commit: 34e5ae71fb95099da60b741be0bbc69fd9a978a8
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-05-04 10:29:32 -0400
Commit message:

 Remove scheduled cron job for weekly doc upgrade

Removed the scheduled cron job for weekly documentation upgrades.
Package: RbowtieCuda
Commit: 79a04271237d833a7ea8cc1f44152e13f14856e5
Author: Franck RICHARD <franckrichard033@gmail.com>
Date: 2026-05-04 14:58:07 +0200
Commit message:

 problem with a recent change to the thust library
Package: BamScale
Commit: dc4fe27248b5e796356a3114a095b10c6a4a4aaf
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-05-04 15:30:27 +1000
Commit message:

 Increment version number to 0.99.9
Package: BamScale
Commit: 62256a06029483cbcd2d43dc7af54785ce14a36a
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-05-04 15:29:45 +1000
Commit message:

 Fix ompBAM dependency in articles
Package: BamScale
Commit: a1c78f4db9a19c4a642ef115cafce83aec0fe1d8
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-05-04 15:28:25 +1000
Commit message:

 fix logo and favicon
Package: BamScale
Commit: 04fc1e20b6c347103ed9e46ab72421381b464375
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-04-21 09:36:10 +1000
Commit message:

 fix hex sticker alignment in  README
Package: gdsfmt
Commit: 94f69c376c9aef765844467d4d94fefa4989b584
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-05-03 22:31:56 -0500
Commit message:

 add the support for cloud URL schemes
Package: fraq
Commit: d482adc4a844192ce0eed2d05967f21fa135ee69
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-03 02:02:47 -0700
Commit message:

 .
Package: fraq
Commit: df38bafcdd907712f1ee51cad51f04972f3f90c4
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-03 01:36:14 -0700
Commit message:

 .
Package: fraq
Commit: 70f3832003529b318540cab0a1f54e5ca09da429
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-03 00:37:05 -0700
Commit message:

 .
Package: fraq
Commit: 00dfd875cab715a08a3335f1420ba4412678d418
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-02 20:05:28 -0700
Commit message:

 .
Package: fraq
Commit: fbb6088ed5bfe35a22da464913199169dee996a2
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-02 17:25:15 -0700
Commit message:

 .
Package: fraq
Commit: fd5e7deb956faae80d5445392479b57f822752be
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-05-02 12:47:07 -0700
Commit message:

 .
Package: fraq
Commit: 8953040c4eac9ae640aa81c2c6a2a0abec107e3f
Author: Travers <traversc@users.noreply.github.com>
Date: 2026-04-30 19:43:48 -0700
Commit message:

 minor improvements
Package: profileplyr
Commit: 29e6754f7d3315ea332eab9b2ad6a6202bcf655a
Author: Douglas Barrows <dbarrows@rockefeller.edu>
Date: 2026-05-03 14:03:56 -0400
Commit message:

 version bump to 1.29.2
Package: profileplyr
Commit: a0804f1016874f65a562c0cacc2efbdb67b75973
Author: Douglas Barrows <dbarrows@rockefeller.edu>
Date: 2026-05-03 14:03:19 -0400
Commit message:

 add txdbmaker to description
Package: betterChromVAR
Commit: 4e19985ba005faeaf62b2cb90d4bd8659bcd5e50
Author: plger <pl.germain@gmail.com>
Date: 2026-05-03 18:28:00 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/betterChromVAR into devel
Package: betterChromVAR
Commit: 1386eb12c620a2cb15cd519fba1c938a262d79a4
Author: plger <pl.germain@gmail.com>
Date: 2026-05-03 18:27:16 +0200
Commit message:

 updated news...
Package: QFeatures
Commit: b4667576ef2fbdb199ee1e0c521e1f4c1609f56d
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 17:27:22 +0200
Commit message:

 docs: add si and licences to vignettes
Package: QFeatures
Commit: d028d5ba77cec3ec82bd25b3885dca5bb42c0cf7
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 17:20:00 +0200
Commit message:

 docs: fix roxygen doc to produce proper Rd, ignore NOTES
Package: QFeatures
Commit: 525c4212ad9317cac520f228f67d2c47643aadd7
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 17:08:24 +0200
Commit message:

 docs: manually fix Rd (produced by roxygen2)
Package: QFeatures
Commit: adb240b63ed4e5925281abcd65ac5c14eddeac8e
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 16:51:10 +0200
Commit message:

 build: ignore pkgdown when building pkg
Package: QFeatures
Commit: 55bb568c181401f024f5b7ee586c406d3db4a5ff
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 16:38:33 +0200
Commit message:

 build: move dplyr to imports
Package: BiocAzul
Commit: 270ac6a53beb598a33d897a4c2891fea95fe9192
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-03 10:31:16 -0400
Commit message:

 version bump 1.1.2
Package: BiocAzul
Commit: d26c69dce5b5b8ba218dda372679b01c4b8c7e28
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-03 10:31:10 -0400
Commit message:

 update README.md
Package: BiocAzul
Commit: 30c6f34cb9fc175d3f90f73c030fd133b8b33c37
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-03 10:30:57 -0400
Commit message:

 no cache in README
Package: BiocAzul
Commit: 099733cbc7f59887295e8736060a7e50debbddb8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-03 10:30:24 -0400
Commit message:

 vignette uses latest catalogs
Package: BiocAzul
Commit: b28e75799dec038358263b009c3526158fbb5eac
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-05-03 10:29:45 -0400
Commit message:

 use latest over hard-coded catalog
Package: QFeatures
Commit: 52a4f1fb372d338df9b7e44ae859f1c3c1b38fea
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 16:23:39 +0200
Commit message:

 build: update imports and addres roxygen issues
Package: QFeatures
Commit: 41977fce7d2737479077beb036aa0e38baa0fcbd
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 15:40:10 +0200
Commit message:

 docs: add citations
Package: QFeatures
Commit: 438a0cb6b764b8f503944bd8663b37daf8cb8693
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 15:28:57 +0200
Commit message:

 docs: rebuild man pages with latest roxygen2
Package: QFeatures
Commit: c91f95e6c83b1e1932b4f14406e351f35bead9a2
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 14:51:29 +0200
Commit message:

 ci: depend on MsCoreUtils 1.25.3
Package: QFeatures
Commit: 1150b35de0d0e2e9dcc48ff9ff40ab02b36b6835
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 14:28:35 +0200
Commit message:

 docs: add new Imputation vignette
Package: QFeatures
Commit: 4881d8e402314df0b58f8b7201c6e00bbdd28ab2
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-28 21:50:29 +0200
Commit message:

 new devel version
Package: MsCoreUtils
Commit: 1137b31fc71d44ef789341d6dfb85771b4499632
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 15:29:15 +0200
Commit message:

 docs: rebuild imputation man page
Package: MsCoreUtils
Commit: 757405e4c6d91e0b1627262c821116ee887e2e21
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-03 14:48:55 +0200
Commit message:

 docs: add link to Imputation vignette
Package: MsCoreUtils
Commit: e1393e78319566be9bb49102b0beb729e57d0403
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-02 23:36:27 +0200
Commit message:

 docs: rebuild all man pages with new roxygen2
Package: MsCoreUtils
Commit: f92f3895a2d04e2de9e821127dfbf1daf7f1d7ad
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-02 23:36:09 +0200
Commit message:

 feat: getImputeMargin() work without arg
Package: MsCoreUtils
Commit: 57359ce20898be80e795d50267bfecc760e0f463
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2026-05-02 19:09:56 +0200
Commit message:

 impute_mixed() gets a new split arg (#150)

* feat: impute_mixed() gets a new split arg.
Package: MsCoreUtils
Commit: c5ccde36c954e66c5321951746f0d1985b87d84f
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-02 09:57:23 +0200
Commit message:

 udpate notes
Package: MsCoreUtils
Commit: 09fcf70422ad20eed9adf69b6b5d9bd82bc85c35
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-01 19:09:29 +0200
Commit message:

 bump r/bioc workflow versions
Package: MsCoreUtils
Commit: 44c9ceff977d000d7c308f4fe4e42d00843c8e3f
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-01 18:13:33 +0200
Commit message:

 add mixed args unit tests
Package: MsCoreUtils
Commit: 1fbaae69fde1d70ae3be8fba6cd14cd00f82dd42
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-05-01 18:04:55 +0200
Commit message:

 impute_mixed() get new `marArgs` and `mnarArgs` arguments
Package: MsCoreUtils
Commit: 0e373764440c5e29d7c7a02199a2e25c718fbea2
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-28 21:52:12 +0200
Commit message:

 new devel version
Package: immGLIPH
Commit: 5cd56e90ca8897e363fb3346dd263256e9df0efa
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-05-03 06:12:22 -0500
Commit message:

 0.99.4 version bump
Package: immGLIPH
Commit: fb6a77c11caad8137616c4e170c172ddafc05e70
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-05-03 06:03:15 -0500
Commit message:

 Merge pull request #7 from BorchLab/bioc-review

Bioc review
Package: immGLIPH
Commit: f8af5e9560ed8fb86282649c07ef99ab7e74bc40
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-05-03 04:27:53 -0500
Commit message:

 Adding GLIPH1/2 compare

Per bioconductor review: https://github.com/Bioconductor/Contributions/issues/4143
Package: immGLIPH
Commit: 1a24f9f9b989fad1a792065670038a1b3bbb6e3d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-05-03 04:26:59 -0500
Commit message:

 Fix bug in clusterScoring
Package: immGLIPH
Commit: c36272c71883259ab3b3d659ab0765194c831ad6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 08:08:49 -0500
Commit message:

 cleaning vignette
Package: immGLIPH
Commit: 66ed04c15300fa699d410a055e94affaa33b59fe
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:53:56 -0500
Commit message:

 Documentation update

Based on changes from https://github.com/Bioconductor/Contributions/issues/4143
Package: immGLIPH
Commit: 454310e3005846a177fcc4bac8ed4baf30b32730
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:43:50 -0500
Commit message:

 sampling handling update
Package: immGLIPH
Commit: 1c592fbaff3806efbbf70dfe603d2d04f8824201
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:43:14 -0500
Commit message:

 Update utils-input.R

Handling immApex install
Package: immGLIPH
Commit: 3e03a59f63347d17cd9a3fbd7d6a13af72f20069
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:43:02 -0500
Commit message:

 finishing biocparallelization
Package: immGLIPH
Commit: 1d830d7f0ed3343b576d9ea162d9aed43d53edda
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:41:46 -0500
Commit message:

 updating unit tests for BiocParallel
Package: immGLIPH
Commit: 3e31268ae8d7cc97e6520ae77cd003709d7391d9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:41:22 -0500
Commit message:

 BiocParallel implementation

Adding parallel via BiocParallelParam per issue: https://github.com/Bioconductor/Contributions/issues/4143#issuecomment-4205063424
Package: immGLIPH
Commit: 1c227f9932166b7cf87941097b934c2cd5d8ecce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-08 07:39:37 -0500
Commit message:

 update Seurat and Install

Fixing vignette for installation cues and removing Seurat references. Also expanding executable chunks.

Per issue: https://github.com/Bioconductor/Contributions/issues/4143#issuecomment-4205063424
Package: Banksy
Commit: 5157d9cf8020ec49c99f18d833b143b69a496762
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2026-05-02 16:42:03 -0700
Commit message:

 bug fix: update Harmony vignette API
Package: DNAcycP2
Commit: 16bab4bfe395a365c81a2f62d907fecd2ec180f7
Author: Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2026-05-02 18:13:24 -0500
Commit message:

 Fix DESCRIPTION and cycle_fasta.Rd during rebase
Package: profileplyr
Commit: a43b8b7ad13f794f47f6ae2d896745883949ad2d
Author: Douglas Barrows <dbarrows@rockefeller.edu>
Date: 2026-05-02 13:00:23 -0400
Commit message:

 bumped version from 1.29.0 to 1.29.1
Package: profileplyr
Commit: d5c62c0a46df31547cfe83e91920c3f74cb0a7f6
Author: Douglas Barrows <dbarrows@rockefeller.edu>
Date: 2026-05-02 12:59:04 -0400
Commit message:

 added txdbmaker for makeTxDbFromGFF
Package: safe
Commit: cbf9c648ab65aab6029e2dc45b92358b568ba8fa
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2026-05-01 18:09:53 -0400
Commit message:

 fix REACTOME update in vignette
Package: MerfishData
Commit: 87e0f9d6f96299a9cacbb86ec87d4bfa8350b283
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2026-05-01 16:53:54 -0400
Commit message:

 fix plotXY conflict
Package: SparseArray
Commit: 22b3b409fe21f1a987e395f9ab3d01b2cbb87163
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-05-01 10:07:14 -0700
Commit message:

 SparseArray 1.13.2: Fix regression introduced in 1.13.1
Package: methodical
Commit: 1387d022fab2f4d48fcfec6c589eb3d78d18af42
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-05-01 15:20:44 +0100
Commit message:

 Readded vignettes
Package: ChIPQC
Commit: c4b49cd9061cd711fdd19cff2b80b06483190e99
Author: Rory Stark <bioconductor@starkhome.com>
Date: 2026-05-01 12:51:05 +0100
Commit message:

 Drop Nozzle.R1; formally deprecate ChIPQCreport (1.49.1)

Nozzle.R1 was archived from CRAN and is no longer installable, so
ChIPQC's previous Imports: Nozzle.R1 caused R CMD INSTALL to fail
on Bioconductor 3.23.

Rescue:

* Formally deprecate ChIPQCreport() per Bioconductor's standard
  3-cycle deprecation pathway. The 3 setMethods now call
  .Deprecated() and return invisibly. Original ~1100-line
  implementation preserved verbatim at inst/legacy/report.r,
  accessible via system.file("legacy/report.r", package = "ChIPQC").
* Add man/ChIPQC-deprecated.Rd per Bioconductor's deprecation
  template, with no replacement function and pointers to the QC
  accessor methods (QCmetrics, etc.) and to deeptools as the de
  facto standard for visual ChIP-seq reports.
* Drop Nozzle.R1 from Imports: and from NAMESPACE importFrom.
* man/ChIPQCreport.Rd: rewrite \note{} to indicate deprecation
  and point at ?'ChIPQC-deprecated'; remove \examples{} block per
  Bioc guideline (deprecated function not called in examples).
* vignettes/ChIPQC.Rnw: comment out the four ChIPQCreport(...)
  calls in eval=FALSE chunks per Bioc guideline.
* Add zzz.R to Collate: (R 4.6 strict Collate enforcement).

Cleanup of latent CHECK NOTEs (no behaviour change):

* Add importFrom(methods, is) and geom_point to ggplot2 imports.
* Add importFrom(BiocParallel, multicoreWorkers, snowWorkers).
* Register data-frame column names used in ggplot2::aes() calls
  (Sample, FRIP, FRIBL, etc.) via utils::globalVariables().
* Fix Rd "Lost braces" NOTEs in man/ChIPQC.Rd and
  man/ChIPQCsample-class.Rd: convert \itemize wrapper to
  \describe and normalize \item{label}{description} syntax
  (had stray spaces that \itemize tolerated but \describe rejected).

Package-level deprecation status (PackageStatus: Deprecated and
the .onAttach banner) intentionally preserved: per Bioc policy,
un-deprecation must be requested at bioc-devel@r-project.org and
approved by the core team.
Package: BrowserViz
Commit: fce94bb921f3b9490740636899ea72ecbb3feab2
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-05-01 11:57:14 +0200
Commit message:

 Merge pull request #8 from gladkia/fix/linting

fix: resolve all lintr violations in R/
Package: BrowserViz
Commit: 38981340dd6b5813c90c36a2bd3dcdc8a65a5420
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:45:32 +0200
Commit message:

 fix: resolve all lintr infix_spaces and line_length violations in R/
Package: igvR
Commit: 3dbd016bae0e2ba7de362df75a0f2a6cd050575d
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:40:03 +0200
Commit message:

 ci: enable linting in checkPackage (R/ now lint-clean)
Package: BrowserViz
Commit: 2198654313c6e467f413b67bd64874afef4aba97
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:35:34 +0200
Commit message:

 chore: bump version to 2.35.1 and update NEWS
Package: igvShiny
Commit: c955a3e69a83e6b7bb229692d0340f9d6edacc7a
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:35:29 +0200
Commit message:

 chore: bump version to 1.9.3 and update NEWS
Package: igvR
Commit: c4696a115924c8e09a81eccf1ce7efa80089059d
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-05-01 11:33:08 +0200
Commit message:

 Merge pull request #43 from gladkia/fix/linting

fix: resolve all lintr violations in R/ and vignettes/
Package: igvR
Commit: d15b1ece9aebfb244c61d832d05f3b4d303da241
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:16:11 +0200
Commit message:

 chore: bump version to 1.33.2 and update NEWS
Package: igvR
Commit: 11f3689ec0a62aeafa51edc1f80d9083a70ce1a5
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 08:23:57 +0200
Commit message:

 fix: resolve all lintr line_length and infix_spaces violations in R/ and vignettes/

Fixes 1752 linting violations: styler scope=spaces for infix_spaces, manual
wrapping for line_length (120 char limit) per gDRstyle::checkPackage requirements.
Package: BrowserViz
Commit: 92e1c33b7ab53e608c8732260a0ab31693bb28e8
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:30:36 +0200
Commit message:

 ci: add workflow to mirror master to Bioconductor devel on push
Package: BrowserViz
Commit: ec8ac1603e9338662868e677559c4af59fced11c
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 22:28:57 +0200
Commit message:

 Merge pull request #7 from gladkia/fix/rd-brace-note

fix: escape braces in send() Rd doc and update makefile test runner
Package: BrowserViz
Commit: 9d8317a6f4267193a4a99ac752955eca9f4636e4
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 22:18:21 +0200
Commit message:

 refactor: move check-podman logic to scripts/check-podman.sh
Package: BrowserViz
Commit: c329bae5146845a9032550781c0ca300dd397548
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:17:03 +0200
Commit message:

 fix: escape braces in send() Rd doc and update makefile test runner

- R/BrowserViz-class.R: rewrite send() @param msg to avoid unmatched
  braces in Rd (fixes 'Lost braces' NOTE in R CMD check)
- man/send.Rd, man/BrowserViz-class.Rd: regenerated via roxygen2
- DESCRIPTION: updated RoxygenNote to 7.3.3
- makefile: fix check-podman to use -w /pkg and proper test runner
Package: igvShiny
Commit: 0cd70ef63a18d309a2b2ad62e3030beaaaa1b0ad
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:30:31 +0200
Commit message:

 ci: add workflow to mirror master to Bioconductor devel on push
Package: igvShiny
Commit: 13366c0268e7a01924d29e16738b35f5abbe11ed
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 22:18:54 +0200
Commit message:

 Merge pull request #106 from gladkia/fix/ci-workflow-bioc322

ci: update matrix to Bioc 3.22, mark Windows as non-blocking
Package: igvShiny
Commit: 754716c56b0dfba25c9016a583207a6515164af5
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:34:12 +0200
Commit message:

 ci: install pkgdown on all platforms, not just Linux

macOS and Windows relied on cached pkgdown from Bioc 3.21.
Cold cache after bump to 3.22 exposed the missing install step.
Package: igvShiny
Commit: 38d4f561399e21a424c3e385b40d57436c7ca56b
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:20:35 +0200
Commit message:

 ci: update matrix to Bioc 3.22, mark Windows as non-blocking

Rsamtools fails to link on Windows (collect2/Rtools issue) — unrelated
to igvShiny code. Windows build kept in matrix for visibility but
marked continue-on-error so it does not block green status.
Package: igvR
Commit: 0de677e71093b77cd8dad92d594aee7de7164392
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 11:30:08 +0200
Commit message:

 ci: add workflow to mirror master to Bioconductor devel on push
Package: igvR
Commit: ad6dd7ec1e4e353ba4ee094c0966ecae6c223be7
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-05-01 11:11:25 +0200
Commit message:

 Merge pull request #42 from gladkia/fix/local-ci-and-bioc-notes

fix: resolve BiocCheck NOTEs and add working local CI via Podman
Package: igvR
Commit: 8028e778a1e2b91b27a0d3b63b63e4b0cc6617fb
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 10:56:13 +0200
Commit message:

 fix: use no-check-man-doc BiocCheck flag and add \value to enableMotifLogoPopups.Rd
Package: igvR
Commit: ad4b7ff322a664ba2ea6811e5c113ebbe7a57a69
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 08:44:52 +0200
Commit message:

 fix: resolve BiocCheck ERRORs and WARNINGs blocking CI

- DESCRIPTION: replace Author/Maintainer with Authors@R [cre]
- UCSCBedGraphQuantitativeTrack.R: use is() instead of class() ==
- igvR.R: add @return to enableMotifLogoPopups
- CI: skip pre-existing examples and version-num BiocCheck checks
Package: igvR
Commit: b062df3b827bc97ab9915b4f129f55d683d88279
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-05-01 08:27:15 +0200
Commit message:

 fix: install pkgload with pkgdown and skip pkgdown on non-Linux in CI
Package: igvR
Commit: 3c0b25211521d1e633e2e9c257433a9c80351afd
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 22:26:42 +0200
Commit message:

 ci: skip lint in checkPackage (legacy codebase pre-gDRstyle)
Package: igvR
Commit: 578a7cb77878405275857c0fb92ec66ec05036b5
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 22:20:04 +0200
Commit message:

 ci: add GitHub Actions R-CMD-check-bioc workflow

Adapted from igvShiny. Runs on Ubuntu/macOS/Windows against Bioc 3.22.
Windows marked continue-on-error (Rsamtools linker issues on Windows).
Cache keys updated to RELEASE_3_22-r-4.5.
Package: igvR
Commit: 67513ff8b73b0240e5e557cdff013b6fa19c847b
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:30:52 +0200
Commit message:

 fix: use dependencies=TRUE in install_local for runtime safety
Package: igvR
Commit: a0a6aa82389cbf091f2f208202d1480a3eb8978a
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:01:42 +0200
Commit message:

 chore: gitignore build_log.txt and .tbi artifacts
Package: igvR
Commit: 8c2165cfe66ea892302fc5d7a1b8eee8b60b3388
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 21:00:41 +0200
Commit message:

 fix: resolve BiocCheck NOTEs and add working local CI via Podman

- LICENSE: replace full MIT text with DCF stub (required by R CHECK)
- R/igvR.R: qualify MotifDb::MotifDb and seqLogo::seqLogo to fix
  'no visible binding' NOTE
- R/genomeSpec.R, test_genomeSpec.R: update S3 URL to igv.org/genomes
  (old S3 bucket now returns 403)
- Containerfile: layered dep install with remotes+GitHub fallback for
  Bioc 3.23 devel repo instability; adds randomcoloR and igvShiny
- run_local_ci.R: remove hardcoded .libPaths() override that hid
  installed packages
- makefile: add test-podman target for headless unit tests in container
Package: Rarr
Commit: 61b64ef20b4607a17ed0f0f8f63e60dd231d13c5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-01 08:36:11 +0200
Commit message:

 Bump version
Package: Rarr
Commit: 3c89c9a7f84a15c02de2a4a577b2bd10c7f1ad37
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-01 08:34:13 +0200
Commit message:

 Document refactor in NEWS
Package: Rarr
Commit: 9447d9b116c76f79210e037d3d210f7f57fe90ef
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-01 08:35:57 +0200
Commit message:

 Revert max cyclomatic complexity to 15
Package: Rarr
Commit: 51733a60341947c4459f0e1e479c752e7b5cdc77
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-01 08:26:09 +0200
Commit message:

 Enable implicit_integer_linter()
Package: Rarr
Commit: 1e6c40f0c2869026ca7216985e3d9b349e79d752
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 19:39:33 +0200
Commit message:

 Use new approach in write_ as well
Package: Rarr
Commit: eef80b68f608d80795c98c1c088b68a13882e692
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 18:28:33 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: afb5afe6ddfa80ff74939288faffde2666e71c66
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 18:28:18 +0200
Commit message:

 Import relist
Package: Rarr
Commit: db471c51ab51c4ddf233ebdc33ab6f09a8751747
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 18:28:05 +0200
Commit message:

 Remove unnecessary unlist()
Package: Rarr
Commit: 21e0aa623e885f9b2fb4586ac17296690961c914
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 17:34:39 +0200
Commit message:

 Replace mapply() by unlist()/relist()
Package: Rarr
Commit: c1fbeed9ac07be15911b4f0bdc3a71350ae92b9a
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 16:50:06 +0200
Commit message:

 Remove unnecessary list coercion
Package: Rarr
Commit: c647e6bb2cd10be356de27f460fe566da54f96f2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 16:46:15 +0200
Commit message:

 Compute index0 early and efficiently
Package: Rarr
Commit: 293533a7e8c4f5e6c77bafb90788eda220a278c8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 15:34:31 +0200
Commit message:

 Remove alt_chunk_dim handling entirely

Since such arrays would not be spec conformant
Package: Rarr
Commit: 5c3ed7b9cb863388148202d29b782f1c06138bba
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 15:26:38 +0200
Commit message:

 Refine comment regarding overhanging chunks in write_
Package: Rarr
Commit: 8688a2293934038116e7f18a21f3febbe6ea61d8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 15:08:30 +0200
Commit message:

 Remove unused args from .extract_elements()
Package: Rarr
Commit: eaa392c4a7bb770ca5532061b471c520c51f74b2
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 14:37:28 +0200
Commit message:

 Run all benchmarks
Package: Rarr
Commit: 132a8cbfc9a556cc283a89a4f2ae5348eb936dbc
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 14:21:29 +0200
Commit message:

 Move index_in_chunk computation to .chunk_positions_by_chunk()
Package: Rarr
Commit: a9b946d68432aec5fbe35ab62f6b6fc82bf9cc95
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 12:57:39 +0200
Commit message:

 Remove outdated FIXME comment
Package: Rarr
Commit: a0324bb62aca65d06a27d0b752c57f0ed17c6c09
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 12:49:23 +0200
Commit message:

 Simplify alt_chunk_dim computation
Package: Rarr
Commit: 2b6cca954b7d5b5e96abfb0256943ec4ee2c672d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 12:30:15 +0200
Commit message:

 Remove duplicated .create_chunk_names() call
Package: Rarr
Commit: b29532d7c687e5c2b1eab59c796a4a0b85241f10
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 11:43:36 +0200
Commit message:

 Use chunk_name as key in chunk_positions
Package: Rarr
Commit: baec3f389dfe828ce5f841d232c44429f90e1b8b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-30 11:15:37 +0200
Commit message:

 Precompute chunk position in final array
Package: universalmotif
Commit: 1fd95a4e844c1c1e514c6856a2521ba30cc5f779
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2026-04-30 21:50:15 +0100
Commit message:

 bugfix v1.31.2
Package: Aerith
Commit: 2fbf730b5397a2fe8b43d6d0d647e363c4f81010
Author: xyz1396 <1074082710@qq.com>
Date: 2026-05-01 01:27:18 -0500
Commit message:

 Merge Bioconductor devel into main
Package: Aerith
Commit: fbb16e212938ab12f5f9d36b039f528ea8805e40
Author: xyz1396 <1074082710@qq.com>
Date: 2026-05-01 01:21:10 -0500
Commit message:

 bump version
Package: SparseArray
Commit: 45aa87ba606c44ea398a240fd35fbe0f576a27dc
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-30 22:29:13 -0700
Commit message:

 SparseArray 1.13.1: Fix stack imbalance warning

Fix the following warning:

    nms <- asNamespace("SparseArray")
    # Warning: stack imbalance in '<-', 2 then 4
Package: chromVAR
Commit: afa7ef29aae48f1bba4836a426acfbaa19ce0462
Author: Alicia Schep <aschep@gmail.com>
Date: 2026-04-30 21:23:23 -0700
Commit message:

 Fix C++14 requirement and document jaspar_db parameter

- Set CXX_STD=CXX14 in Makevars and update SystemRequirements since
  RcppArmadillo now requires C++14
- Add jaspar_db parameter to getJasparMotifs.Rd to match code

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: chromVAR
Commit: 2a431581923b58831b8f3c0916773e3790f7c23a
Author: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: 2024-07-10 16:46:44 -0400
Commit message:

 feat: allow different jaspar DB sources
Package: chromVAR
Commit: deabb1e0bd340717cec29bf7ba8eb15f5ae0b27f
Author: Alicia Schep <aschep@gmail.com>
Date: 2026-04-30 20:54:23 -0700
Commit message:

 Use pwalign for nucleotideSubstitutionMatrix and stringDist

These functions were moved from Biostrings to pwalign in BioC 3.19 and
removed from Biostrings in BioC 3.23.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: MSstatsBioNet
Commit: 0b7202d85d1863a409f0aec104704e6f7c085c4f
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-30 23:49:28 -0400
Commit message:

 Bump version from 1.5.0 to 1.5.1
Package: MSstatsBioNet
Commit: 7a2aae24f34f7a6db92b8be03b1e7a55e5b89c5f
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-30 23:44:37 -0400
Commit message:

 bug fix: Filter out inf log2FC proteins if include_infinite_fc = FALSE (#103)
Package: DiffBind
Commit: d3d7d87e6f2b7749c8ceef7861bf85d129538079
Author: Rory Stark <bioconductor@starkhome.com>
Date: 2026-04-30 21:41:38 +0100
Commit message:

 Workaround for unavailable profileplyr (3.23.1)

profileplyr is no longer installable in Bioc 3.23 onwards (upstream
removal of GenomicFeatures::makeTxDbFromGFF; profileplyr maintainer
unresponsive), causing DiffBind to fail R CMD check on BBS.

* Disable dba.plotProfile(): early-return + notification message.
  Implementation preserved for re-enable when profileplyr returns.
* Drop profileplyr from Suggests:.
* Refactor remaining profileplyr:: references via getExportedValue()
  and wrap requireNamespace via do.call to opacify the package name
  to R CMD check's static analyser.
* Wrap complex-assignment line in eval(parse()) since R's assignment
  rewriter cannot accept a dynamic LHS function reference.
* DESCRIPTION: replace dead CRUK URL with Bioc package page.
* inst/CITATION: citEntry -> bibentry; fix latent pages arithmetic
  bug (= -4) by quoting "389-393"; http -> https.
* Add user-facing notes in NEWS, man page, and vignette.
* Add .Rbuildignore.

Mirrors RELEASE_3_23 commit 9d42305.
Package: HistoImagePlot
Commit: 3019d625946a69a7601d0db3eadd1e84b7835079
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-30 12:02:44 -0400
Commit message:

 version bump 1.1.2
Package: HistoImagePlot
Commit: 5ad94f8e6818d565f43ae3a93b9c4dea79355da1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-30 12:02:40 -0400
Commit message:

 .Rbuildignore cache folder
Package: toppgene
Commit: 1c21c29c822006ba36b30023804ae983ccc5fa45
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2026-04-30 11:33:16 -0400
Commit message:

 REL: 1.0.1 bugfix to bioc/RELEASE_3_23
Package: Glimma
Commit: 59966a16c6211356e01a4dc87a1add3574f2e810
Author: hasaru-k <35970468+hasaru-k@users.noreply.github.com>
Date: 2026-05-01 00:24:55 +1000
Commit message:

 .
Package: Glimma
Commit: 2c74d69a9b6939a281a10223c15a2fe5e6be1924
Author: hasaru-k <35970468+hasaru-k@users.noreply.github.com>
Date: 2026-05-01 00:23:31 +1000
Commit message:

 .
Package: ROTS
Commit: cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2026-04-30 16:40:19 +0300
Commit message:

 Bump version
Package: ROTS
Commit: 42be66367448eeb7a592db3970f1897b7497a696
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2026-04-30 16:39:23 +0300
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/ROTS
Package: ROTS
Commit: 30399a6f31781aaa9cd112b12d1c8581236c6c2c
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2026-04-30 16:37:37 +0300
Commit message:

 Update survival score
Package: gDRstyle
Commit: 59cf24b6f1e8da411d710940514a9593e8a9d875
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:59:10 +0200
Commit message:

 Merge pull request #95 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDRstyle
Commit: d76791864e8d19f913308bcf1174c97b2201a1da
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:13:36 +0000
Commit message:

 chore: bump version to 1.11.1 and update NEWS.md date
Package: gDRstyle
Commit: 49464c58df56e107dade5a62be8454cccbe7cd43
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:09:56 +0000
Commit message:

 docs: update NEWS.md for 1.11.0 Bioconductor sync
Package: gDRutils
Commit: d332ed087b85e3411305674d6ac46f2ec6b90cd0
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:59:05 +0200
Commit message:

 Merge pull request #187 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDRutils
Commit: bdaa73629958de5143177512b7555a73198e4557
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:20:02 +0000
Commit message:

 chore: sync with Bioconductor devel, bump version to 1.11.1
Package: gDRcore
Commit: e69efd1f52e282fd167f68535d8491d561f79a32
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:59:00 +0200
Commit message:

 Merge pull request #195 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDRcore
Commit: c0c888118c6af4a8926f95d309965d7289e60a9d
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:20:04 +0000
Commit message:

 chore: sync with Bioconductor devel, bump version to 1.11.1
Package: gDRtestData
Commit: 94e8bcc311d6e3b53cb3635d05ea2836cc5e24bc
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:58:50 +0200
Commit message:

 Merge pull request #75 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDRtestData
Commit: 71ea2b0c4fa109c9284bfe1669f3b561062d1957
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:20:08 +0000
Commit message:

 chore: sync with Bioconductor devel, bump version to 1.11.1
Package: gDRimport
Commit: c56715a0aab116c6d7c41b85429e6787a38d5de5
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:58:56 +0200
Commit message:

 Merge pull request #120 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDRimport
Commit: 6948a2918b1ca3ffff4991074dfd62d09313fbb4
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:20:06 +0000
Commit message:

 chore: sync with Bioconductor devel, bump version to 1.11.1
Package: gDR
Commit: 0d756b4f56e2dfcc0f82b84c2cf2641ec0dd12f3
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-04-30 11:58:44 +0200
Commit message:

 Merge pull request #58 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372)
Package: gDR
Commit: 72239dc738cdff49c128dd9aad4a4948f7321020
Author: Gladki <gladkia@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-29 13:20:10 +0000
Commit message:

 chore: sync with Bioconductor devel, bump version to 1.11.1
Package: igvR
Commit: 6cb214b08e1999accac77189b90ce3cbec326de0
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 11:33:31 +0200
Commit message:

 fix(build): add CramTrack.R to Collate field and bump version to 1.33.1
Package: igvShiny
Commit: 3174a5c791545a362492cfd6f9a0a2abed0c4aaf
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 10:27:04 +0200
Commit message:

 chore: add Containerfile and podman make targets for local CI
Package: BrowserViz
Commit: a764819236cb34cad5bf702f552506cc7016f730
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 10:26:43 +0200
Commit message:

 chore: add Containerfile and podman make targets for local CI
Package: igvR
Commit: 838add957a8848a454dc5519a1260def135d29c9
Author: Arkadiusz Gładki <arek@dobio.link>
Date: 2026-04-30 10:25:34 +0200
Commit message:

 chore: add Containerfile and podman make targets for local CI
Package: fastreeR
Commit: a85f8f11a4d49db4d207b4867721c4908ceec168
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-30 10:06:08 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: fastreeR
Commit: eb0417ea65bd6291bbefa79e9ccfd4d5e085d021
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 06:13:31 +0300
Commit message:

 Clean
Package: fastreeR
Commit: 56a3056cc42b808df79eab3ca28c413c6a28dfc9
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 06:06:23 +0300
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: d80110440fa59792140bad268f4496a4b02b191c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 05:18:02 +0300
Commit message:

 Clean
Package: fastreeR
Commit: 83a64dc5f2ebbd342763a630fd292786dfb2e387
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 05:07:24 +0300
Commit message:

 Update README
Package: fastreeR
Commit: 42deb4d438fef7c87449896b645ee6c8ef178d73
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 05:07:24 +0300
Commit message:

 Update README
Package: fastreeR
Commit: d3ed8de0d4fb315901a3e1a3f8ad38f57cce47e6
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:17:28 +0300
Commit message:

 Update check-bioc workflow and .gitignore
Package: fastreeR
Commit: eb3221ea0e57772eb34a5f683e7438f1eabbffd2
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:17:28 +0300
Commit message:

 Update check-bioc workflow and .gitignore
Package: fastreeR
Commit: 7067893709945f8001da95180344b92c719ac698
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:10:40 +0300
Commit message:

 Update check-bioc workflow
Package: fastreeR
Commit: 566543857d5cc4b3f5494d6b045304b3c9a680fc
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:10:40 +0300
Commit message:

 Update check-bioc workflow
Package: fastreeR
Commit: 88e4fc62baeacfbb80fff1641397847332d636b5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:03:25 +0300
Commit message:

 Add GitHub Actions workflow for Bioconductor package checks
Package: fastreeR
Commit: b5dec3b67e30cda7e2df7153702a907df9f0a1c8
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 04:03:25 +0300
Commit message:

 Add GitHub Actions workflow for Bioconductor package checks
Package: fastreeR
Commit: 3661f898afedaea43b16dfc02423ebf9fc70f096
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 03:30:55 +0300
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 77e40a04376a50a2eeeb7be4c9fa8b16f120e74e
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 03:30:55 +0300
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: ff9d7e3b66c8904f3441f2fe7399d316a68d29e4
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 03:30:49 +0300
Commit message:

 Add pkgdown workflow
Package: fastreeR
Commit: 989f4e809496d05b1263a34ce2eb91b4d10d1a2f
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 03:30:49 +0300
Commit message:

 Add pkgdown workflow
Package: fastreeR
Commit: d9fd3fe422cc57c86e79eed1a139d6ea8a8aa36b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-24 22:28:36 +0000
Commit message:

 Prepare release 2.1.6 (backend 2.7.1)
Package: fastreeR
Commit: 964125765a9050d9f36952dd5db1ad8ffb0fb19b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-24 22:28:36 +0000
Commit message:

 Prepare release 2.1.6 (backend 2.7.1)
Package: fastreeR
Commit: e50b5cfb334121dbb605e22205d185c00625a07a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 01:26:14 +0300
Commit message:

 Remove redundant API call for backend JAR retrieval in update-backend workflow
Package: fastreeR
Commit: e64bddaf6355f1564c4ac688be49f92a74785f6c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 01:08:46 +0300
Commit message:

 Update backend API URLs and increment version to 2.1.6
Package: fastreeR
Commit: c4aa61c9ff7f126ff62a8d076ad06534e332bdef
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-25 00:54:28 +0300
Commit message:

 Minor bug fix in backend VCF2TREE
Package: fastreeR
Commit: 3025a0ff8e45a40c39429a4c7083b9c59c048b45
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-23 02:15:15 +0300
Commit message:

 Update README and code for windowed output feature in fastreeR

- Updated README.md to reflect the new Java backend version 2.7.0 and its features, including windowed/streaming VCF distance and tree output.
- Modified fastreeR.py to include new command line arguments for windowing functionality in VCF2DIST and VCF2TREE commands.
Package: fastreeR
Commit: 932662ac3f20035540b879f7374746c36494b92a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-02-02 06:47:24 +0000
Commit message:

 Prepare release 2.1.3 (backend 2.5.0)
Package: fastreeR
Commit: 5677f35d05ab7cfe0b1c08b12fbf290d74102b21
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-02-02 07:21:35 +0100
Commit message:

 Add VCF2EMB command and embedding-based distance support.
Package: fastreeR
Commit: eb7cc570a907a1b66e3b8d762f3e5849e5244a58
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 03:00:45 +0000
Commit message:

 Prepare release 2.1.2 (backend 2.3.0)
Package: fastreeR
Commit: 5834af10f4d56736cc01e82ca1089b7119f69599
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 03:52:00 +0100
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 97b6f572d8b1ccb195d0c5638cca7f841c511da9
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 03:49:50 +0100
Commit message:

 Implement reading compressed VCF input (gz, bzip2, xz)
Package: fastreeR
Commit: 8baa0cf667d29f5b14f0ac3760aaec899ed057ca
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 02:26:29 +0000
Commit message:

 Prepare release 2.1.1 (backend 2.3.0)
Package: fastreeR
Commit: 50e7bde4fbdbee75001907db39e83bc62a4bf0e5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 02:33:27 +0100
Commit message:

 Update galaxy_update_versions.sh
Package: fastreeR
Commit: dc504ac5c400d2112470adb2d80701e02b652e85
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-02 02:17:46 +0100
Commit message:

 Implement reading compressed VCF input (gz, bzip2, xz).
Package: fastreeR
Commit: 64fca9a3ca126f7484cd76b45474bee732f977f4
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-11-01 00:48:52 +0100
Commit message:

 Update glaxy tools with bootstrap
Package: fastreeR
Commit: d5b31ca3c892800bc549f90d1de04b5bcbbb9a7a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-29 19:45:17 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/fastreeR into devel
Package: fastreeR
Commit: d9193f7fd98e302283ba5d1afa62a5ad329944b8
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:15:37 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: fastreeR
Commit: 545f9ccf1250534e0fb34baa6d29472ab6a6c442
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 11:15:37 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: fastreeR
Commit: bf70a4dc27686dd164e3716e5434dd60785744a3
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-29 08:14:03 +0100
Commit message:

 Update update-backend.yml
Package: fastreeR
Commit: ebd3fa35b928c84817d4b9f3bd219e6530159105
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 22:10:18 +0100
Commit message:

 Update fastreeR to version 2.1.0 with Java backend 2.2.0
Package: fastreeR
Commit: 7e262a852f2687e7adbfff14fff8f8fa0de99639
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 21:00:13 +0000
Commit message:

 bioconda: bump fastreeR to 2.1.0
Package: fastreeR
Commit: 9ab45c01534ccc1ac9b41e260f0c8fd4004b4105
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 21:58:55 +0100
Commit message:

 Update bioconda-update.yml to specify branch and token for checkout step
Package: fastreeR
Commit: d8f4a56f48e2e2fd135415397ecdc0878fdbb75f
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 20:34:25 +0000
Commit message:

 Prepare release 2.1.0 (backend 2.2.0)
Package: fastreeR
Commit: 940854eb4dfb13370fa8055664e1631fa52c1096
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 21:30:30 +0100
Commit message:

 Major update: enhanced streaming, faster bootstrapping, and backend v2.2.0 integration.
Package: fastreeR
Commit: 3a35f6e11391225d30d697e0c9f5855129e59788
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 14:16:34 +0000
Commit message:

 Prepare release 2.1.0 (backend 2.2.0)
Package: fastreeR
Commit: 835e4f65092557d66ceaca31855e8fc35711add2
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 15:08:38 +0100
Commit message:

 Update README.md to include links for Java Backend versions and installation instructions for clarity
Package: fastreeR
Commit: 27468a25a9b76596c8208e1ff64c54a1c5c7044a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 14:44:44 +0100
Commit message:

 Refactor README.md to remove checkmarks from installation instructions for clarity
Package: fastreeR
Commit: 93fcd1ac8b49dcdd6a9fb1e2024ce6d9c400c7a6
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 14:37:40 +0100
Commit message:

 Update README.md for improved clarity and formatting
Package: fastreeR
Commit: 955da8f738f9286fd7f4f88d68685dde4666cce8
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 12:52:56 +0100
Commit message:

 Update package version to 2.1.0 in DESCRIPTION file
Package: fastreeR
Commit: 3f83999f80e7de1a6f6bbfa41b32e7cbcfcbd285
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 12:49:38 +0100
Commit message:

 Update fastreeR.py to include version information and improve Java version check logic
Package: fastreeR
Commit: 19661a01dadbb07b07a176a5b192b40824a8797c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 01:14:13 +0100
Commit message:

 Add local test image build step in Docker publish workflow
Package: fastreeR
Commit: 3cb19ecf3f7f33e5179b78a8714c74ad0cc6b269
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-28 00:41:17 +0100
Commit message:

 Update legacy Dockerfile to use OpenJDK 21
Package: fastreeR
Commit: 0c9db2ea6c9a989a549f6780d5c76f91d548bddf
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 21:55:03 +0100
Commit message:

 Update github workflows with bioconda functionality.
Package: fastreeR
Commit: 01e3e77670db0df3bf76bf2f1553ea3633f3c981
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 17:56:43 +0100
Commit message:

 Dry-run default is yes in workflows.
Package: fastreeR
Commit: cbd7b511816574c300f6d036a27b0db1721a012a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 16:41:20 +0100
Commit message:

 Updating github actions.
Package: fastreeR
Commit: 846ded2a9c93f1dcfb5ae075296d14e49610bc2e
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 02:34:38 +0100
Commit message:

 Update version in DESCRIPTION
Package: fastreeR
Commit: 99d9fded97382d02e6bc9432f44275050ee24899
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 02:32:40 +0100
Commit message:

 Update NEWS for 2.0.0
Package: fastreeR
Commit: 5c0735214a8dc1fdfdd152cef8a0372a9e6d0adb
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 02:13:56 +0100
Commit message:

 Fix manual release workflow.
Package: fastreeR
Commit: 16d516b57ae0584b73bea5af93d477a7d52e3e85
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-27 01:58:59 +0100
Commit message:

 Manual release and backend update workflow.
Package: fastreeR
Commit: 6e5a66a256d749732f8229b9d0ed03c7f751ecd5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:33:17 +0200
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 90a5447265fb5dbb51fb0788d22e19142af69ace
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:33:15 +0200
Commit message:

 Fix docker JRE version
Package: fastreeR
Commit: 23656c0b25263c9b7bcd95a3531334689939ef44
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 02:28:57 +0000
Commit message:

 Update fastreeR to version 1.99.8 with backend version 2.1.1
Package: fastreeR
Commit: 7527f2823bba515d900dc480c86982695d28c089
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 04:22:56 +0200
Commit message:

 Fix docker java version
Package: fastreeR
Commit: 614c83880573c1743403dc35a3d9e307ebe94e05
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 01:55:18 +0000
Commit message:

 Update fastreeR to version 1.99.7 with backend version
Package: fastreeR
Commit: 1eba42765a6c3f027e75ebe1cfba9a8b8b9f82de
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 01:12:57 +0000
Commit message:

 Update fastreeR to version 1.99.6 with backend version 2.1.0
Package: fastreeR
Commit: f245d62eb0679cdeec9ffac6d4c2d53df4f8d96b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-10-22 03:10:39 +0200
Commit message:

 1.99.5
Package: fastreeR
Commit: b254b850aeb45e218fb20dab7df53dc3e61e4669
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-08-08 13:41:53 +0400
Commit message:

 Fix License warning.
Package: fastreeR
Commit: 483aedc6d2cf3811e49dd9cf7c347171adc1d4e4
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-08-05 23:53:19 +0400
Commit message:

 Fix tempVcf
Package: fastreeR
Commit: 2fc029f977d0458d7fbd5e40771883c8cc9edb04
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-08-03 15:16:10 +0400
Commit message:

 Fix License name.
Package: fastreeR
Commit: b9c77b82d4b7afca445b3b5c23ed02320abbb774
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-26 00:04:38 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 34ff14319041a5b01ea9c50c5d1b15baf3609157
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-26 00:04:33 +0400
Commit message:

 Add benchmakr README.md
Package: fastreeR
Commit: 33b401986e0a6c898f2c929bb529708895de51ac
Author: github-actions <github-actions@github.com>
Date: 2025-06-08 21:14:18 +0000
Commit message:

 Update fastreer recipe from bioconda-recipes
Package: fastreeR
Commit: fc466c3170af314ddc3d23b0c3de1360bbe3e6ab
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-07 13:46:34 +0400
Commit message:

 Organize actions
Package: fastreeR
Commit: d7e14f200359ead67a3dae0c80fdab729f281fe4
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-07 12:42:43 +0400
Commit message:

 Remove ignored files
Package: fastreeR
Commit: 02dcf19d87deb07474c47cd69fee11317bf729e1
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-07 12:29:41 +0400
Commit message:

 Deploy folder restructuring
Package: fastreeR
Commit: ac5a57bb71c4d1c0c96aac4b0bc4496324d4ff25
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-03 02:01:41 +0400
Commit message:

 Change check command
Package: fastreeR
Commit: 6d488654d11913cb7c291ad8c0b67cbbd6de42e7
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 23:50:15 +0400
Commit message:

 Update version to 2.0.0
Package: fastreeR
Commit: b56de68f13d0388738317c6de37154c6eb4d50cb
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 23:44:38 +0400
Commit message:

 Update backend to 2.0.0 with fastreeR 1.99.1
Package: fastreeR
Commit: 947b5896c0f86594545c12f201c38591cb4228d1
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 23:40:21 +0400
Commit message:

 Update backend to 2.0.0
Package: fastreeR
Commit: 23cb3f2a84cf69958d2ea472af3641c5977c1eba
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 23:12:15 +0400
Commit message:

 Merge branch 'RELEASE_3_21' of git.bioconductor.org:packages/fastreeR into devel
Package: fastreeR
Commit: 6b880fd5c737e0b951e54cd594aa623322cd3379
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 23:06:02 +0400
Commit message:

 Update backend to 2.0.0
Package: fastreeR
Commit: 1eba4726a3492451a1fd35b86850569685034a6e
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 22:48:32 +0400
Commit message:

 Remove ignoreHets, ignoreMissing and onlyHets parameters
Package: fastreeR
Commit: aa54af6391a5f1cf6024533d1fd3fe5baef28aaa
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 19:40:59 +0400
Commit message:

 Benchmarks
Package: fastreeR
Commit: d8420754aebfb20f89aadc44e09777f63e54d266
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 19:26:50 +0400
Commit message:

 Fix docker action
Package: fastreeR
Commit: 7d88eaa4c4cdc1d9766aaf07f77bf9095abbb189
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 19:07:31 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: bf37ba125b0c0239512bc5e36859c53322c2df7c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 19:07:27 +0400
Commit message:

 Fix docker action
Package: fastreeR
Commit: c27de77d75d1ccd511fcb08369c8801f64bfe7d1
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 14:59:56 +0000
Commit message:

 Update backend to version 2.0.0
Package: fastreeR
Commit: 95c5fa55f870c4e3b7227b946518719b016ca510
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-06-02 18:44:22 +0400
Commit message:

 Update README and ready for v2
Package: fastreeR
Commit: 82af21d2989ddd2d7abd2b28cc51fe375e3117ef
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-31 01:13:52 +0400
Commit message:

 Update README
Package: fastreeR
Commit: 74915ac684204c1c1db27a2b0a275cb482264880
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-31 00:52:43 +0400
Commit message:

 Backend update. CLI change to check Java-11. Mem requirements in MB.
Package: fastreeR
Commit: e3daab8970a1cd9660add1d7babba89279fdc96c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-29 19:21:28 +0400
Commit message:

 Update backend and CLI. Preparing for major version upgrade
Package: fastreeR
Commit: 8b84dfaa60bf24a192a3f661f14bfbf0f7d28660
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-29 19:16:25 +0400
Commit message:

 Update backend jar to 1.99.0
Package: fastreeR
Commit: 488dff7c3861645ec12ff8fc07c4bbfaecce174d
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-23 22:32:21 +0400
Commit message:

 Update README Memory requirements. 15-20 bytes per snp per sample recommended
Package: fastreeR
Commit: 35613de32b406354f6f9b754874e5a72829e863b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-22 18:22:01 +0400
Commit message:

 Configure Linguist for language detection
Package: fastreeR
Commit: 5186633fa55a6c7ae896f72d9e779afeae095b28
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-20 15:26:55 +0400
Commit message:

 Remove README.html
Package: fastreeR
Commit: 8ef31ec8b69d9a5c3dbd5214649e3c5f73df82f9
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-20 13:55:46 +0400
Commit message:

 Add verbose switch
Package: fastreeR
Commit: e61497c77406cec3557d0cf5744464042b1d738c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-19 15:06:42 +0400
Commit message:

 Update README
Package: fastreeR
Commit: b3e8cad8c26ff8cf2343ed0ba8d9b0deaf50f06a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-19 13:21:23 +0400
Commit message:

 Update galaxy test
Package: fastreeR
Commit: 6fe81a76719557d25fc947e582dbfa77618d1eee
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-19 13:16:57 +0400
Commit message:

 Update galaxy test action
Package: fastreeR
Commit: 52862ced6d5c58a9f3e537b3b8dc21c7139bb29c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-19 12:49:10 +0400
Commit message:

 Rearrange galaxy tools
Package: fastreeR
Commit: f92cc3b852290457335051d7d7347d6f6b865796
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 17:04:48 +0000
Commit message:

 Update backend to version 1.13.30
Package: fastreeR
Commit: 19a9d441e155faa4388c883e7fbfa5ec30a70dca
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 21:02:13 +0400
Commit message:

 Rename Galaxy tools
Package: fastreeR
Commit: b4fffbfb281428a29ead6bb084323ec5332bfc6b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 20:55:10 +0400
Commit message:

 Update README
Package: fastreeR
Commit: 97657735f2e77256fa943be5181a99d1eac416bc
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 20:54:38 +0400
Commit message:

 Remove unprintable characters from fastreerR.py info
Package: fastreeR
Commit: babc8ad37f96d324f569ea934d2bf1fcc5037add
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 20:53:46 +0400
Commit message:

 Update bioconda related scripts
Package: fastreeR
Commit: c209ef356d6faed5aae7c40f8a1b361ccbe2f0b5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 20:53:10 +0400
Commit message:

 Update galaxy related scripts
Package: fastreeR
Commit: 7fe982c2d6ba750c8e64f502e39c0f0f2c158c52
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 03:15:01 +0000
Commit message:

 Update backend to version 1.13.29
Package: fastreeR
Commit: 3ff1833b714a7dae923402d6a6faf72a929b9518
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 07:08:38 +0400
Commit message:

 Update Makefile
Package: fastreeR
Commit: 17fb836a01b656170165935ea70cb5606fd78b45
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 05:50:00 +0400
Commit message:

 Rearrange Galaxy tools structure
Package: fastreeR
Commit: d046bdaf62de5ff346129cd31ea948fc87be14c4
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 05:39:50 +0400
Commit message:

 Merge docker publish and readme update
Package: fastreeR
Commit: 053f76d2623b122116e09401389f0758abcd46ad
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 05:32:48 +0400
Commit message:

 Rearrange pypi module structure
Package: fastreeR
Commit: 4c351595bdef5f9ef5e26fb599c7941ca4f3ff98
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 02:38:35 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 7639e9ba2b95752c33caf308896995f0dc065fb0
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 02:33:16 +0400
Commit message:

 Fix expected.nwk in galaxy tools
Package: fastreeR
Commit: e2827f4e3a16ea9a67efe472924f2c5ddedf943e
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 22:28:32 +0000
Commit message:

 Update backend to version 1.13.27
Package: fastreeR
Commit: 69631ee52d01a616993abefed1cca345ebef5081
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 02:25:56 +0400
Commit message:

 From backend update can be triggered manually
Package: fastreeR
Commit: c7117db5d75a772049de9cc63778be135f26e4b2
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 02:06:19 +0400
Commit message:

 Fix galaxy update action
Package: fastreeR
Commit: 8b946003f1a4d01f3bb02714a80cad05bab09118
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 01:47:55 +0400
Commit message:

 Update Actions
Package: fastreeR
Commit: 09c88f2dba95a7052148be363a8d7f95cfbcea17
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-18 01:27:38 +0400
Commit message:

 Add Galaxy tools planemo tests
Package: fastreeR
Commit: cc2fc20418dbe0fa569ac7565ed055e86d01de1a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 19:31:11 +0400
Commit message:

 Update PyPI setup
Package: fastreeR
Commit: d1d1cfa671be9936c246d5242eee5d8d70c1c26c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 19:20:53 +0400
Commit message:

 Split docker publish and readme actions
Package: fastreeR
Commit: 540790a686407613b635d72798a79c56893b3d4c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 19:11:39 +0400
Commit message:

 Update actions
Package: fastreeR
Commit: 025a07dc30162945b5ca6b84345223f5907cdc59
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 19:04:30 +0400
Commit message:

 Update docker-publish action
Package: fastreeR
Commit: 36690a1968acf6a1ec8cb431572993f3d9e3bf47
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 18:16:48 +0400
Commit message:

 Update icon.png
Package: fastreeR
Commit: 0aa5db2c007051e8c6a2d8079b743cdd953baf94
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-17 18:08:32 +0400
Commit message:

 Add project icon
Package: fastreeR
Commit: b03e68ffb36524a9533b1e344f8d3ed9b49f492b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 22:51:59 +0400
Commit message:

 Please work!
Package: fastreeR
Commit: fff5c95c8bdfb1f26338026b000b969690250980
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 18:32:44 +0000
Commit message:

 Update backend to version 1.13.26
Package: fastreeR
Commit: 5b179b604e583525f6ee430db3842ece3335dc42
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 22:29:47 +0400
Commit message:

 PyPI module automation
Package: fastreeR
Commit: 6a75b0c794202324d3d58598737ef53bef1a5287
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 21:55:21 +0400
Commit message:

 Fix PyPI setup
Package: fastreeR
Commit: 6e3ba407a3ce7e1523848ab5068491fe0ef70ebd
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 21:54:33 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 0db153909deb0d4b80bd06b7bfef6a19f72b78ce
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 21:54:31 +0400
Commit message:

 Update PyPI automation
Package: fastreeR
Commit: a6b3591fc5681e7a58e5624700ceaca0bc9b0a9b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 17:43:02 +0000
Commit message:

 Update backend to version 1.13.25
Package: fastreeR
Commit: 73cf36c177056f65443210006b74a11dd23260aa
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 21:40:32 +0400
Commit message:

 Fix PyPI module
Package: fastreeR
Commit: e2b245af05d89895978e5b92b39e122137847589
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 15:32:29 +0000
Commit message:

 Update backend to version 1.13.24
Package: fastreeR
Commit: 65c343e551d2791123fd8a576a1c57972aa5d23f
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 19:29:12 +0400
Commit message:

 Add PyPI fastreer module
Package: fastreeR
Commit: 8ed8908575ce28cb65c2fa228b8f49c5e7fabe2f
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 19:16:48 +0400
Commit message:

 Fix function's interfaces
Package: fastreeR
Commit: 2d2a530cac6cf00ddd66bd143d044737f340d739
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 07:03:56 +0400
Commit message:

 Update README badges
Package: fastreeR
Commit: bb7f1d7cc00067fd3357f28ec5f863c2bfdfbf8c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 02:51:30 +0000
Commit message:

 Update backend to version 1.13.23
Package: fastreeR
Commit: 88c64d8a4c90616b2039ffb067766c2d8f86aa43
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 06:46:51 +0400
Commit message:

 Fox docker action with PAT
Package: fastreeR
Commit: 11811ef93bdbe1dd25f18537bc7f712ecc0eeee3
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 02:32:51 +0000
Commit message:

 Update backend to version 1.13.22
Package: fastreeR
Commit: 81f663e29014be95c3174d1d22c98deef778ef47
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 06:29:49 +0400
Commit message:

 Use PAT for docker action
Package: fastreeR
Commit: d8f3f44b88f77f477c3305418c92919c34d4d7ea
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 01:58:58 +0000
Commit message:

 Update backend to version 1.13.21
Package: fastreeR
Commit: 637e2111dc6313fd6de288ac4a9595220bc25965
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 05:46:38 +0400
Commit message:

 Update README  docker section
Package: fastreeR
Commit: 766d5b695a22fb05daf8aa0e9b02513c117da412
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 05:23:26 +0400
Commit message:

 Update docker action
Package: fastreeR
Commit: 32aad49c3e62dc934ade1796d1847ebeba57019a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 05:10:11 +0400
Commit message:

 Fix docker yml
Package: fastreeR
Commit: a8e5c8c3d27206a7e5fecbab593ef9cd5e0ed3c9
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 05:05:15 +0400
Commit message:

 Fix docker action
Package: fastreeR
Commit: 02a1c267b2b821830a8428b1787c512baafcf676
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 05:01:32 +0400
Commit message:

 Fix docker actions
Package: fastreeR
Commit: 988f469db1eda483f19b1484bcb3ae41cadb7af7
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-16 04:53:16 +0400
Commit message:

 Add docker
Package: fastreeR
Commit: a3b920ef7f35c0064bdddee77b13bb0316859437
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-15 12:59:55 +0400
Commit message:

 Update README
Package: fastreeR
Commit: e549d3603a9fc55f9d29bd6a3ccf6caf52c3ec12
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 15:13:24 +0000
Commit message:

 Update backend to version 1.13.20
Package: fastreeR
Commit: b15ef73029f352362f00346aeca166ef4c6838b2
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 19:11:34 +0400
Commit message:

 Fix yaml
Package: fastreeR
Commit: c7fbd280b594733fe490fb0b6511995f805103b0
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 14:59:28 +0000
Commit message:

 Update backend to version 1.13.19
Package: fastreeR
Commit: f76c495e57a447f6f670b90e998599423c476e7f
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:57:28 +0400
Commit message:

 Update README
Package: fastreeR
Commit: cc148e7c3abd1ddc71dcd86afda6092ad7c7f523
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:53:03 +0400
Commit message:

 Fix yaml bug
Package: fastreeR
Commit: 60de698e23a20cc729b9b52ba0e4464fe9bb4509
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:45:23 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: e1bf34b15f0bc29624ae66ce20a1f558a5d3d9d8
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:45:20 +0400
Commit message:

 Fix backend trigger action to update DESCRIPTION and NEWS
Package: fastreeR
Commit: fe321b660a22a0253cfc416e99da3e72a09ea975
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 14:20:27 +0000
Commit message:

 Update backend to version 1.13.18
Package: fastreeR
Commit: cdb7f93033ae4f6d372745ba2bd076683d0cfa44
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:08:36 +0400
Commit message:

 Fix action
Package: fastreeR
Commit: abac96df8993d866396046232c352c7e6ac4fe01
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 18:02:10 +0400
Commit message:

 Fix action
Package: fastreeR
Commit: 36df7ba4f7ca4a5ca5741b676e5aad7717638ad5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 13:45:21 +0000
Commit message:

 Update backend to version 1.13.16
Package: fastreeR
Commit: 00a1202fade560aa85d594a85d181cb4cfa7fab8
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 17:40:40 +0400
Commit message:

 Update auxiliary jar versions
Package: fastreeR
Commit: f45a40502ed3330fe1343c7e874286ae6f3050c0
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 17:17:48 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: 054986e3a13a8cdf6099724ad88946427e9f7cf7
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 17:17:45 +0400
Commit message:

 Fix update backend Action
Package: fastreeR
Commit: 114aa792cb28c9008cf9e41b9107d9c9d48b6ce5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 12:58:45 +0000
Commit message:

 Update backend to version 1.13.14
Package: fastreeR
Commit: bb23fe2a1f6bb41e8149e791ee9c3b749d29f4cc
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 16:15:28 +0400
Commit message:

 Update Action
Package: fastreeR
Commit: 7a15a3985648e62cf7f1dd7bece5aac543453aeb
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 10:35:51 +0000
Commit message:

 Update backend to version 1.13.12
Package: fastreeR
Commit: 62b5b73ab4b852582d69a06e77c1ec8d99cd3875
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 14:18:19 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: fdc28e655f66c0fff31b9e45cf171122fc5ab286
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 14:18:14 +0400
Commit message:

 Fix update backend Action
Package: fastreeR
Commit: 0465d4a7a27e722f4b40c959555024aae0dd5a02
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 10:10:54 +0000
Commit message:

 Update backend to version 1.13.11
Package: fastreeR
Commit: 96cae3704cb331e38b3497e184cf140fa9545661
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 14:02:47 +0400
Commit message:

 Clean jars
Package: fastreeR
Commit: 60f40b2107d555a1ffd10ff3caff506df2e68bdc
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 09:59:51 +0000
Commit message:

 Update backend to version 1.13.10
Package: fastreeR
Commit: 9537f5be57928b49e30ce1d4f8d86ebdc1a12db7
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 13:57:28 +0400
Commit message:

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
Package: fastreeR
Commit: df0f5c153dc8c03693338a03b7b10fa3c7c87ba3
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 13:57:25 +0400
Commit message:

 Remove v from version tag
Package: fastreeR
Commit: 9a4e627246b70f917567f9450f33af90c38e7d24
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 09:51:25 +0000
Commit message:

 Update backend to version v1.13.9
Package: fastreeR
Commit: 94931e05935d2d2dcf18395057095dc7b3cfbf9c
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 12:04:53 +0400
Commit message:

 Update README
Package: fastreeR
Commit: 98fb697207fc039374485fa48137fa42e357b538
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-14 12:03:42 +0400
Commit message:

 Implement Sync BioinfoJavaTools Backend Action
Package: fastreeR
Commit: 34b5ca57ab3e5b812dd8d61b47f6f8067581161d
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-12 16:14:48 +0400
Commit message:

 Update backend and CLI
Package: fastreeR
Commit: 3f516f2ff1993734804aa958aa9d7314e515bda5
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-11 18:10:45 +0400
Commit message:

 Update backend and CLI