Bump version
 

 Bump version
 

 Bump
 

 Bioconductor 3.24 devel
 

 Bioconductor 3.23 release
 

 Bioconductor 3.24 devel
 

 Bioconductor 3.23 release
 

 Fix tests
 

 Add skip_on_bioc
 

 Fix coding style
 

 removed wrong return on null grouping and fillNULL=TRUE
 

 added missing import
 

 explicit Matrix imports
 

 minor speedup
 

 keep background data sparse, improve var computation
 

 Merge pull request #186 from gdrplatform/GDR-3369

GDR-3369: update author email address 

 chore: trigger CI
 

 chore: trigger CI
 

 chore: fix version bump in DESCRIPTION
 

 chore: update author email address
 

 chore: trigger CI
 

 chore: resolve conflict, bump version to 1.11.3
 

 chore: update author email in R source files
 

 chore: update author email address
 

 Fix tests
 

 Add warning message when the input is not unique for genomicElementDistribution.
 

 Added partisub, updated other libraries.
 

 Bump version
 

 version bump
 

 text improvements
 

 Update maintainer
 

 add NEWS entry for 0.99.1
 

 Merge pull request #193 from gdrplatform/GDR-3366

GDR-3366: fix handling of NA Duration 

 chore: merge main and update version to 1.11.2
 

 fix: handle NA Duration in Day0 detection and GR value calculation
 

 chore: merge main and update version to 1.11.2
 

 GDR-3366: replace hardcoded Duration values with NA_real_
 

 bump version
 

 update R requirement
 

 Fix issues
 

 Fix tests
 

 Bump version
 

 Bump version
 

 Merge upstream devel changes
 

 Skip tests
 

 Tests fixed
 

 Remove CITATION file: no doi yet for new package
 

 Simplify .gitignore: remove problematic patterns and comments
 

 Fix .gitignore: remove regex-problematic comments and ensure newline at EOF
 

 Fix: shorten Rd example comments to comply with line width limits
 

 fix: remove CITATION without DOI, bump R dep to 4.6.0, version to 0.99.1
 

 bump version to 1.1.0, add gene symbols to rowData of spe_vignette
 

 fix: use inherits() to check class of object
 

 new devel version
 

 Remove scheduled cron job for weekly doc upgrade

Removed the scheduled cron job for weekly documentation upgrades. 

 Increment version number to 0.99.9
 

 fix logo and favicon
 

 add the support for cloud URL schemes
 

 .
 

 .
 

 .
 

 version bump to 1.29.2
 

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

 docs: add si and licences to vignettes
 

 docs: manually fix Rd (produced by roxygen2)
 

 build: move dplyr to imports
 

 update README.md
 

 vignette uses latest catalogs
 

 build: update imports and addres roxygen issues
 

 docs: rebuild man pages with latest roxygen2
 

 docs: add new Imputation vignette
 

 docs: rebuild imputation man page
 

 docs: rebuild all man pages with new roxygen2
 

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

* feat: impute_mixed() gets a new split arg. 

 bump r/bioc workflow versions
 

 impute_mixed() get new `marArgs` and `mnarArgs` arguments
 

 0.99.4 version bump
 

 Adding GLIPH1/2 compare

Per bioconductor review: https://github.com/Bioconductor/Contributions/issues/4143
 

 cleaning vignette
 

 sampling handling update
 

 finishing biocparallelization
 

 BiocParallel implementation

Adding parallel via BiocParallelParam per issue: https://github.com/Bioconductor/Contributions/issues/4143#issuecomment-4205063424
 

 bug fix: update Harmony vignette API
 

 bumped version from 1.29.0 to 1.29.1
 

 fix REACTOME update in vignette
 

 SparseArray 1.13.2: Fix regression introduced in 1.13.1
 

 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.
 

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

 chore: bump version to 2.35.1 and update NEWS
 

 Merge pull request #43 from gladkia/fix/linting

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

 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.
 

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

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

 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
 

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

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

 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.
 

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

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

 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
 

 ci: skip lint in checkPackage (legacy codebase pre-gDRstyle)
 

 fix: use dependencies=TRUE in install_local for runtime safety
 

 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
 

 Document refactor in NEWS
 

 Enable implicit_integer_linter()
 

 Run devtools::document()
 

 Remove unnecessary unlist()
 

 Remove unnecessary list coercion
 

 Remove alt_chunk_dim handling entirely

Since such arrays would not be spec conformant
 

 Remove unused args from .extract_elements()
 

 Move index_in_chunk computation to .chunk_positions_by_chunk()
 

 Simplify alt_chunk_dim computation
 

 Use chunk_name as key in chunk_positions
 

 bugfix v1.31.2
 

 bump version
 

 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>
 

 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>
 

 bug fix: Filter out inf log2FC proteins if include_infinite_fc = FALSE (#103) 

 version bump 1.1.2
 

 REL: 1.0.1 bugfix to bioc/RELEASE_3_23
 

 .
 

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

 Merge pull request #95 from gdrplatform/GDR-3372

chore: sync main with Bioconductor devel (GDR-3372) 

 docs: update NEWS.md for 1.11.0 Bioconductor sync
 

 chore: sync with Bioconductor devel, bump version to 1.11.1
 

 chore: sync with Bioconductor devel, bump version to 1.11.1
 

 chore: sync with Bioconductor devel, bump version to 1.11.1
 

 chore: sync with Bioconductor devel, bump version to 1.11.1
 

 chore: sync with Bioconductor devel, bump version to 1.11.1
 

 chore: add Containerfile and podman make targets for local CI
 

 chore: add Containerfile and podman make targets for local CI
 

 Clean
 

 Clean
 

 Update README
 

 Update check-bioc workflow and .gitignore
 

 Update check-bioc workflow
 

 Add GitHub Actions workflow for Bioconductor package checks
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Add pkgdown workflow
 

 Prepare release 2.1.6 (backend 2.7.1)
 

 Update backend API URLs and increment version to 2.1.6
 

 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.
 

 Add VCF2EMB command and embedding-based distance support.
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Prepare release 2.1.1 (backend 2.3.0)
 

 Implement reading compressed VCF input (gz, bzip2, xz).
 

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

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

 Update fastreeR to version 2.1.0 with Java backend 2.2.0
 

 Update bioconda-update.yml to specify branch and token for checkout step
 

 Major update: enhanced streaming, faster bootstrapping, and backend v2.2.0 integration.
 

 Update README.md to include links for Java Backend versions and installation instructions for clarity
 

 Update README.md for improved clarity and formatting
 

 Update fastreeR.py to include version information and improve Java version check logic
 

 Update legacy Dockerfile to use OpenJDK 21
 

 Dry-run default is yes in workflows.
 

 Update version in DESCRIPTION
 

 Fix manual release workflow.
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update fastreeR to version 1.99.8 with backend version 2.1.1
 

 Update fastreeR to version 1.99.7 with backend version
 

 1.99.5
 

 Fix tempVcf
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update fastreer recipe from bioconda-recipes
 

 Remove ignored files
 

 Change check command
 

 Update backend to 2.0.0 with fastreeR 1.99.1
 

 Merge branch 'RELEASE_3_21' of git.bioconductor.org:packages/fastreeR into devel
 

 Remove ignoreHets, ignoreMissing and onlyHets parameters
 

 Fix docker action
 

 Fix docker action
 

 Update README and ready for v2
 

 Backend update. CLI change to check Java-11. Mem requirements in MB.
 

 Update backend jar to 1.99.0
 

 Configure Linguist for language detection
 

 Add verbose switch
 

 Update galaxy test
 

 Rearrange galaxy tools
 

 Rename Galaxy tools
 

 Remove unprintable characters from fastreerR.py info
 

 Update galaxy related scripts
 

 Update Makefile
 

 Merge docker publish and readme update
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 1.13.27
 

 Fix galaxy update action
 

 Add Galaxy tools planemo tests
 

 Split docker publish and readme actions
 

 Update docker-publish action
 

 Add project icon
 

 Update backend to version 1.13.26
 

 Fix PyPI setup
 

 Update PyPI automation
 

 Fix PyPI module
 

 Add PyPI fastreer module
 

 Update README badges
 

 Fox docker action with PAT
 

 Use PAT for docker action
 

 Update README  docker section
 

 Fix docker yml
 

 Fix docker actions
 

 Update README
 

 Fix yaml
 

 Update README
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 1.13.18
 

 Fix action
 

 Update auxiliary jar versions
 

 Fix update backend Action
 

 Update Action
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update backend to version 1.13.11
 

 Update backend to version 1.13.10
 

 Remove v from version tag
 

 Update README
 

 Update backend and CLI
 

 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 Preparing for next Bioconductor Release.
 

 Update R version requirement.
 

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
 

 add support for haploid GT in vcf
 

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
 

 Ready for Bioconductor Release 3.17
 

 Bump y following creation of RELEASE_3_16 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
 

 Update vignette minor bug.
 

 Update vignette to handle getting sample files through https failure.
 

 BioC badge.
 

 Merge remote-tracking branch 'upstream/master'
 

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 

 Updates after the 1st Bioconductor review.
 

 Update vignette's use of dist2hist.
 

 Update java backend.
 

 Update zzz.R
 

 Update vignette to use BiocFileCache
 

 Update zzz.R 

 Last of 2022-03-22
 

 Update NEWS.md
 

 Update examples.
 

 Update fasta2dist formatting
 

 Update tree2clusters example
 

 Update manual
 

 Remove depends on R >=4.2
 

 Update fastreeR_vignette.Rmd
 

 Update fastreeR_vignette.Rmd
 

 update BioInfoJavaUtils backend to 1.2.2
 

 update BioInfoJavaUtils backend to 1.2.1
 

 Update check-bioc.yml 

 Update BioInfoJavaUtils-1.0.0.jar
 

 Update check-bioc.yml