fix typo
 

 remove extra handleCheck
 

 move citation check to BiocCheckSource
 

 Call parse_s3_path() only once
 

 Document new `attributes` field in NEWS
 

 chore(version): bump to 0.99.5 (#94)

Bump DESCRIPTION Version and rename the NEWS.md devel heading from
0.99.4.9000 to the 0.99.5 release, mirroring PR #86.

Co-authored-by: Claude <noreply@anthropic.com> 

 chore(devcontainer): re-base both devcontainer variants on bioconductor_docker (#92)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* chore(devcontainer): remove conda package lists

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

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

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

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

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

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

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

* chore(devcontainer): suppress InvalidDefaultArgInFrom lint in Dockerfile

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

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

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

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

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

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

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

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

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

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

* chore(devcontainer): harden resolve_versions.sh error handling

Guard against an empty release_version (e.g. if Bioconductor changes the
config.yaml format) so the script fails with a clear, specific message
instead of a silent set -e abort.

Also correct the header comment to document all four KEY=VALUE lines the
script prints; R_VERSION_FULL was emitted but undocumented.

---------

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

 chore(DESCRIPTION): bump version to 0.99.4.9000 (#87)

* chore(DESCRIPTION): bump version to 0.99.4.9000

* docs(NEWS): open 0.99.4.9000 development section 

 Update SVM for prediction
 

 Add visualization of prediction
 

 Bug fix: normalized_mutual_info function
 

 version bump 1.49.22
 

 version bump 1.49.21
 

 add unit tests for show method check
 

 remove old install helper
 

 add install method for .BiocPackage class
 

 - New function splitGencodeTxNames()
- catchSalmon() etc now detect and unpack Gencode tx names
 

 add dir exists check
 

 add script to delete empty files
 

 version bump 1.1.3
 

 add version parameter to getCatalog

- latest catalog version as default
 

 # MSA2dist 1.17.7 (2026-06-25)

BUG FIXES

* fixed Rd files
 

 update for roxygen2 v8
 

 add ai folders to .Rbuildignore and .gitignore
 

 Update NEWS
 

 Bump version
 

 Support index at the start of the shard
 

 Pass fill value down to sharding codec
 

 Fix index shape
 

 Make bytes/bytes codec arg simpler
 

 Run devtools::document()
 

 Move some read_chunk() steps in .extract_elements()

So read_chunk() can be reused in sharding codec
 

 Pass down chunk_dim to internal functions

- To avoid looking for it repeatedly (efficiency)
- To allow reuse of read_chunk() in sharding codec
- To prepare for the use of irregular grids
 

 Use 2 spaces for JSON indents
 

 Remove unnecessary relist()
 

 Pre-render S3 vignette
 

 Remove outdated mentions of Rarr limitations
 

 Add Mike as vignette coauthor
 

 Move S3 content to dedicated vignette
 

 bump version
 

 Replace the binnedAverage by binAverage.
 

 Merge remote-tracking branch 'origin/devel' into fix-issue-81-recursive-revdeps

# Conflicts:
#	DESCRIPTION
#	NEWS
 

 fixes on getDataGEO() to be compatible with new GEOquery returnType SummarizedExperiment (#171)

* fixes on getDataGEO() to be compatible with new GEOquery returnType SummarizedExperiment

* removed unused Biobase from import packages

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk> 

 Vectorise the motif_coocc() pairwise test

motif_coocc() called stats::fisher.test() once per motif pair, which
dominated the runtime for large numbers of motif combinations. The
one-sided (greater) Fisher exact p-value for a 2x2 table is exactly the
upper tail of the hypergeometric distribution of the top-left cell
given the margins, so all pairs now get their p-value from a single
vectorised phyper() call. With the default integer table this matches
fisher.test() to floating-point precision.

The per-pair contingency counts were also rebuilt: the 'both' counts
for every pair are the entries of a single crossprod() of the
sequence-by-motif presence matrix, replacing the per-pair intersect()
loop and the per-iteration data.frame assignments (themselves
quadratic in the number of pairs). The descriptive spatial columns
still loop, but only over co-occurring pairs and only when
max.distance is set.

odds_ratio is now the sample odds ratio (both*neither)/(a_only*b_only)
rather than the conditional-MLE estimate from fisher.test, which has no
closed form and cannot be vectorised cheaply; the documentation is
updated to match. Around 34-60x faster on 100-500 motifs with identical
counts and p-values.
 

 Guard get_consensus() against non-column input

get_consensus() and get_consensusAA() passed their position argument
straight to C++, where get_consensusC()/get_consensusAAC() index a
fixed number of entries with no bounds checks. A non-numeric value
(for example a whole universalmotif object) aborted the R session
during the S4-to-double conversion rather than raising a catchable
error, and a vector shorter than the alphabet read out of bounds.

Both functions now check that position is a numeric vector of the
expected length (4 for DNA/RNA, 20 for amino acids) before reaching
C++, with a regression test and a NEWS entry.
 

 Mention generics/methods changes in NEWS
 

 Remove custom generic for image()

Following Hervé Pagès' recommendation in https://github.com/Bioconductor/BiocGenerics/issues/24#issuecomment-4548115193
 

 # update README
 

 # update DESCRIPTION
 

 Bump version for Bioconductor devel
 

 remove the imported package preseqR and adjust the authorship.
 

 Reword documentation to avoid the term "user"

Reword the vignettes, roxygen blocks (and their generated man pages),
and the README so that mentions of "user"/"users" are phrased more
neutrally, e.g. "meets the user's qvalue cutoff" becomes "meets the
chosen qvalue cutoff".
 

 # MSA2dist 1.17.4 (2026-06-24)

* update DESCRIPTION
* update dnastring2dist to handle unique sequence patterns

NEW FEATURES

* added collapseChar
* added collapseXStringSet
* added normpop
* added dnastring2weightedPi
* added rcpp_weightedPi
* added rcpp_weightedPi_pop
* added dnastring2dxy
* added rcpp_dxy_fst_pop
* added dist2dxy to calculate dxy per pop from dnastring2dist result
 

 Updated package in line with readr updates
 

 Refine DESCRIPTION wording and drop comment in netboost.R

- DESCRIPTION: simplify the method summary, broaden the omics scope, and remove
  the MC-UPGMA citation sentence.
- R/netboost.R: remove the explanatory comment about WGCNA loading.
 

 Resolve BiocCheck WARNINGs and expand DESCRIPTION

- R/netboost.R: drop the top-level Sys.setenv(ALLOW_WGCNA_THREADS)/require(WGCNA)
  block. WGCNA functions are namespace-qualified or imported via @importFrom, so
  the package no longer attaches WGCNA at load. This clears the BiocCheck
  'Avoid Sys.setenv' and 'Avoid library/require' WARNINGs.
- DESCRIPTION: replace author Yaniv Loewenstein with Alex Waterhoelter, expand
  the Description to a multi-sentence summary of the method, bump to 2.21.4.
 

 minor fixes
 

 Visualization changes
 

 update NEWS.md
 

 update catalog to version 1.1.0
 

 missing test files
 

 fix a bug when sketch reduction in the dataset.
 

 Update the bigwig export methods.
 

 fix: typo git stars
 

 add: citations and bioc badges
 

 add: allow control over centering and scaling in pca computation
 

 add: update torxigen note to latest for R 4.6
 

 Fix feature specific covariates formula
 

 Merge pull request #80 from gdrplatform/GDR-3448

[GDR-3448] Update vignette 

 doc: add prism data
 

 Update getGEO command to match new behaviour of GEOquery
 

 Clean .gitignore
 

 Merge upstream devel and bump version to 1.3.1
 

 Merge MGhotbi into devel
 

 1
 

 Document alternative installation for DspikeIn

Added alternative installation method for DspikeIn. 

 Update README.md 

 Update README.md 

 Remove system files (.DS_Store) and add to .gitignore
 

 Remove system files (.DS_Store) and add to .gitignore
 

 Merge pull request #25 from mghotbi/devel

Bump version to 0.99.25 for Bioconductor rebuild 

 Update README latest news
 

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

# Conflicts:
#	DESCRIPTION
 

 Update README with DDC file input instructions

Added instructions for input with DDC files to README. 

 Merge pull request #52 from pcantalupo/devel

Fixes #51 

 version bump
 

 change email
 

 version bump
 

 version bump
 

 version bump
 

 Merge pull request #38 from dkcoxie/patch-1

Update pcaOtherPlotting.R 

 Update pcaOtherPlotting.R

Updated `plotPairPCA` function to add argument for legend placement within ggpubr::ggarange() call 

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

 fix bug in citation page
 

 add citation document
 

 update docker for github check
 

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

 version bump
 

 Merge pull request #25 from DavisLaboratory/ningbioinfo-patch-1

Update README.md, add citation 

 Merge updates to devel
 

 Fix bugs related to vignette build
 

 Fix tests in Windows and increase coverage
 

 Re-structured vignette references
 

 Update the wrong touch.
 

 Bump version,update NEWS and Merge the branch.
 

 Bump version and update NEWS
 

 Update the Modeling function.
 

 Update the function.
 

 Make sure it could test on HPC.
 

 Test XGBoost on HPC.
 

 Test on HPC
 

 Set up for XGboost on HPC.
 

 Changed some titles.
 

 Changed the typo for the documentation.
 

 Changed the typo.
 

 Revert "Deleted the .pdf."

This reverts commit 7e8c942a38e85b9667741c2b8074dab53776ddab.
 

 Update the vignette,qcByCmdscale,NormalizeData and CreatCrcBiomeScreenObject to make them more detailed and completed.
 

 Fix XGBoost caret compatibility with recent xgboost versions and add compatible caret model specification for XGBoost.
 

 double ensure clean slate when testing watched tags
 

 missing 'fnd' role produces message instead of NOTE, closes #251
 

 missing CITATION files produce message instead of note, closes #250
 

 fix Rproj unit test
 

 update NEWS
 

 remove *.Rproj from bad files list
 

 version bump 1.49.15
 

 version bump 1.49.14
 

 include "Additional_repositories" field in checkRemotesUsage
 

 add cli headings to unit tests

assisted-by: gemini 3.5 flash
 

 pass libloc to dots for checkManDocumentation
 

 add .BiocCheck folder to Rbuildignore and gitignore
 </pre>
    </div>
  
    

      Package: BiocCheck

      Commit: a724905517fc781d820547f0e91dc4c4dea60965

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-12 17:13:25 -0400

      Commit message:


	  
		
 don't unload namespace if previously loaded
 
    
  
    

      Package: BiocCheck

      Commit: c591bfdc9e399969fa2e1490cb779ba3a8c8170b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-12 17:12:58 -0400

      Commit message:


	  
		
 add else statements for callr calls
 
    
  
    

      Package: BiocCheck

      Commit: 5c43825d56b31754993d689065e7a572975dc2b9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-12 16:28:30 -0400

      Commit message:


	  
		
 rename pkgname to packageName in NEWS and vignette
 
    
  
    

      Package: BiocCheck

      Commit: e38e6a328651a31dd843f35ad7cdcf0142cdc339

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-12 16:27:10 -0400

      Commit message:


	  
		
 update docs for BiocCheck and BiocCheckGitClone
 
    
  
    

      Package: BiocCheck

      Commit: a1ae7869397af8c58402030d4725744ae7897009

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-12 16:26:31 -0400

      Commit message:


	  
		
 simplify and combine BiocCheck and BiocCheckGitClone
 
    
  
    

      Package: BiocCheck

      Commit: 5335ba24604cbd8ca011d8050104d58ab3fe3ea2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-02 14:56:35 -0400

      Commit message:


	  
		
 version bump 1.49.12
 
    
  
    

      Package: BiocCheck

      Commit: 768bbf0e65809dc8d58013f253faa8cb534853f7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-02 14:55:10 -0400

      Commit message:


	  
		
 Add validation check for install_param prefix before log extraction
 
    
  
    

      Package: BiocCheck

      Commit: 57a8a170437547d9a3f80f97c642678a8f5ae1ca

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:27:16 -0400

      Commit message:


	  
		
 version bump 1.49.11
 
    
  
    

      Package: BiocCheck

      Commit: 6f3b52376b19f29027addcbc48b334c36cec76e3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:27:11 -0400

      Commit message:


	  
		
 update NEWS
 
    
  
    

      Package: BiocCheck

      Commit: fa92e65d6da5773f4a0e8427db7d01f2c855edc1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:15:32 -0400

      Commit message:


	  
		
 version bump 1.49.10
 
    
  
    

      Package: BiocCheck

      Commit: bdf48eefeec624d904a21a4b8c2274f33fd8bb12

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:10:14 -0400

      Commit message:


	  
		
 rename internal function to start with dot
 
    
  
    

      Package: BiocCheck

      Commit: 72be0b9b88cc461dab070d08deb812a1e0ed6f15

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:09:06 -0400

      Commit message:


	  
		
 use code to indicate types in param docs
 
    
  
    

      Package: BiocCheck

      Commit: f8a4a1aea942f48c6e5cc30b6fc07a966068d930

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:08:46 -0400

      Commit message:


	  
		
 simplify checkForVersionNumberMismatch
 
    
  
    

      Package: BiocCheck

      Commit: d9c7e1440de4c8d3bcb0ad4d5d195718ad37eb14

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-06-01 17:08:18 -0400

      Commit message:


	  
		
 use isSourceDir output and simplify code in BiocCheck and BiocCheckGitClone
 
    
  
    

      Package: BiocCheck

      Commit: bfc0df918c54f069c81b1538cde0b8aa012174a5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 17:26:34 -0400

      Commit message:


	  
		
 identify source directories and git clones
 
    
  
    

      Package: BreastSubtypeR

      Commit: 435e0e17f1e97f8a0b9216037b3e2cc05317df75

      Author:  Qiao Yang <yq.kiuo@gmail.com> 

      Date: 2026-06-22 17:28:51 +0200

      Commit message:


	  
		
 Updates: TNBC cohort detectoion
 
    
  
    

      Package: BreastSubtypeR

      Commit: ba216e654ad5f1e6851232f2b7ddab85dde36f01

      Author:  Qiao Yang <yq.kiuo@gmail.com> 

      Date: 2026-06-22 17:20:49 +0200

      Commit message:


	  
		
 Fix TNBC cohort detection
 
    
  
    

      Package: Moonlight2R

      Commit: 3d3ec69442b08ba91e5e24897b1bddece35eec9e

      Author:  Matteo Tiberti <matteo.tiberti@gmail.com> 

      Date: 2026-06-22 16:58:18 +0200

      Commit message:


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

      Package: Moonlight2R

      Commit: e8bb2029aeec7512518c9039ac7ef321b7b416a6

      Author:  AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com> 

      Date: 2026-06-22 16:50:33 +0200

      Commit message:


	  
		
 Fix moonlight z-score and updated datasets accordingly (#169)

* Fix moonlight z-score and updated datasets accordingly

* Fix overlap pool of genes for fgsea z-score calculations

* Removed Exp.Log.Ratio column from DiseaseList; fixes in FEA fgsea; updated datasets accordingly

* fixed typo error on tests and updated NEWS.md summary

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk> 
    
  
    

      Package: Moonlight2R

      Commit: 0439e0d001678f6a54637435376086afa96e7cc4

      Author:  Matteo Tiberti <matteo.tiberti@gmail.com> 

      Date: 2026-04-29 11:27:38 +0200

      Commit message:


	  
		
 Merges upstream for BioC 3.23 release (#167)

* bump x.y.z version to even y prior to creation of RELEASE_3_23 branch

* bump x.y.z version to odd y following creation of RELEASE_3_23 branch

---------

Co-authored-by: A Wokaty <andres.wokaty@sph.cuny.edu> 
    
  
    

      Package: ivygapSE

      Commit: e705549d5fd5889c7b9519ac7ba500f650ba41e2

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-06-22 10:43:39 -0400

      Commit message:


	  
		
 fix BiocFileCache problem with r-univ
 
    
  
    

      Package: TFEA.ChIP

      Commit: aead7d72aef4034cbbcf5977aed559742692420a

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2026-06-22 16:00:51 +0200

      Commit message:


	  
		
 Fix bump v2
 
    
  
    

      Package: TFEA.ChIP

      Commit: 606cbea4e4baf14a9d844d180cf2f9c5ae3f0174

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2026-06-22 15:59:01 +0200

      Commit message:


	  
		
 Fix bug
 
    
  
    

      Package: omicsPrint

      Commit: 055a518b1e7a9a58c21e9af9cf8fb8a634fa9604

      Author:  DavyCats <davycats.dc@gmail.com> 

      Date: 2026-06-22 14:45:59 +0200

      Commit message:


	  
		
 fix vignette
 
    
  
    

      Package: GExPipe

      Commit: 1fb56b969672c87818c0d16281db82fd8ce12f2f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 16:32:19 +0500

      Commit message:


	  
		
 Release 0.99.17: drop dev/ from source to fix empty-dir build warning
 
    
  
    

      Package: GExPipe

      Commit: be3c090d1cddfe9ce2f0820bd712d7fd1ef0d93e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 16:16:31 +0500

      Commit message:


	  
		
 Release 0.99.16: remove empty scripts/ from package build
 
    
  
    

      Package: OMA

      Commit: b5689fd109cbbfbc195a7c81f69bb4d13ef3cf26

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-06-22 14:07:21 +0300

      Commit message:


	  
		
 Add tool list (#866) 
    
  
    

      Package: OMA

      Commit: 0e8bf07e1a9cb57e24a7bccb18b5f563fd61f942

      Author:  Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com> 

      Date: 2026-05-24 07:42:12 +0000

      Commit message:


	  
		
 Update biocbook workflows (#854)

Co-authored-by: Leo Lahti <leo.lahti@iki.fi> 
    
  
    

      Package: OMA

      Commit: d02425a6a6fed441556e8dc4638e112d810dbe97

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2026-05-24 10:16:13 +0300

      Commit message:


	  
		
 Minor improvements to DAA and mediation sections (#857)

Seems OK so I take the freedom to merge. 
    
  
    

      Package: GExPipe

      Commit: 04baa48bd4bda606269297a9678718ee4b3322f3

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 15:52:00 +0500

      Commit message:


	  
		
 Release 0.99.15: fix BiocCheck errors and set.seed warning
 
    
  
    

      Package: GExPipe

      Commit: 66b947621112904dd336807d502ada5330c7e775

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 15:43:41 +0500

      Commit message:


	  
		
 Release 0.99.14: remove empty inst/scripts from package build
 
    
  
    

      Package: GExPipe

      Commit: efd0159c51dcbe6f22dbcf3deb78edc3e1142b7a

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 15:18:12 +0500

      Commit message:


	  
		
 Merge upstream/devel (keep main) for Bioconductor SPB 0.99.13
 
    
  
    

      Package: GExPipe

      Commit: 0e57872469d74485a5bb13601471298f234aea97

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-22 15:15:11 +0500

      Commit message:


	  
		
 Release 0.99.13: SPB push with clean R CMD check

Bump version for Bioconductor build; bundle vignette screenshot; convert all R
sources to ASCII; vignette reviewer updates. Full R CMD check passes with
vignettes built (0 errors, 0 warnings).
 
    
  
    

      Package: GExPipe

      Commit: f4b0ea3a4b44ff31b203243d6523a93fb284f6ac

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-19 13:30:01 +0500

      Commit message:


	  
		
 Release 0.99.12: SPB revision, check fixes, vignette build fix
 
    
  
    

      Package: GExPipe

      Commit: 7964276c3d0fc7dd734d88beec76f654879aaf8a

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-19 13:06:30 +0500

      Commit message:


	  
		
 Bioconductor revision readiness (v0.99.11): gate runtime install, docs, vignette
 
    
  
    

      Package: GExPipe

      Commit: ef310207fbb7c0edc783955e8544f0da1c0f9a0f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-17 16:30:28 +0500

      Commit message:


	  
		
 Fix glmnet 5.x API: LASSO, Elastic Net, Ridge work again.
 
    
  
    

      Package: GExPipe

      Commit: 3cbaa39947e795327749d95ca579ed9cd46e3b45

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-17 15:21:27 +0500

      Commit message:


	  
		
 Release 0.99.9: document GitHub update path and glmnet/PVCA fixes.
 
    
  
    

      Package: GExPipe

      Commit: 2cec5e7982f8028df2fc46b4d8f5122216a82d6f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-17 15:11:50 +0500

      Commit message:


	  
		
 Never skip glmnet ML methods; use subprocess fallback without R restart.
 
    
  
    

      Package: GExPipe

      Commit: 8251edace81856e8ce447dab0fd34d333fa9efa8

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-17 14:36:17 +0500

      Commit message:


	  
		
 Fix PVCA and helpers when running from GitHub install.

Load platform helpers into Shiny server modules via package namespace, source gexp_platform_helpers.R in global.R, and route PVCA through .gexpipe_call so runGitHub and install_github paths find gexpipe_pvca_df.
 
    
  
    

      Package: GExPipe

      Commit: e0be5179009e8421c5ef82fc6f4273578871d943

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-17 12:46:35 +0500

      Commit message:


	  
		
 Fix mixed-platform normalization, batch PVCA, and pipeline stability.

Align metadata through normalization and batch steps, add global-quantile guidance for merged microarray/RNA-seq, repair PVCA before/after plots, use edgeR filterByExpr, and expand platform helper tests.
 
    
  
    

      Package: GExPipe

      Commit: 3f7820e1dce0be66694104ee7626f59022a795d4

      Author:  Safa Rafique <safa.sandhu@gmail.com> 

      Date: 2026-06-16 17:20:13 +0500

      Commit message:


	  
		
 Improve merged-platform integration and native package handling.

Rebuild glmnet before first DLL load to avoid manual R restarts after upgrades; add mixed microarray/RNA-seq platform covariates, merged-mode caveats, and Platform PCA diagnostics; fix redundant WGCNA module-trait heatmap column.
 
    
  
    

      Package: GExPipe

      Commit: f2d41f14ff8a96987d15bad617c836264a9bd30c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-08 18:01:05 +0500

      Commit message:


	  
		
 Fix R 4.6 install: use dcurves instead of archived rmda, with runtime rmda fallback for nomogram DCA

Co-authored-by: Cursor <cursoragent@cursor.com>
 
    
  
    

      Package: GExPipe

      Commit: 1589241ca5b480de8cfce9b2d247e821ffa1abdb

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-05 19:14:05 +0500

      Commit message:


	  
		
 Docs: clarify Shiny app launch as two steps (runGExPipe() then shiny::runApp())

Replace the nested one-liner shiny::runApp(GExPipe::runGExPipe(), ...) with the
explicit two-step pattern across README, vignette, runGExPipe() examples,
man page, and the gexpipe_setup() fallback message, per reviewer request.

 
    
  
    

      Package: GExPipe

      Commit: 0fc6ec44c093f01a57d1e30686687a5c2694c20d

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 15:44:36 +0500

      Commit message:


	  
		
 Fix GSEA results not showing: clusterProfiler::GSEA returns gseaResult not enrichResult; accept both classes in summary, status, workspace checks

 
    
  
    

      Package: GExPipe

      Commit: 552112f50ae28e65553bd2c0e5690573c9a9a7e9

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 15:38:33 +0500

      Commit message:


	  
		
 Fix Continue to ROC button: add missing next_page_validation_to_roc entry to client-side nav map

 
    
  
    

      Package: GExPipe

      Commit: b4d1925e67ce8e74bf954d04096de64587005c6b

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 15:34:08 +0500

      Commit message:


	  
		
 Auto-rebuild glmnet and other native packages for current R: remove stale copies from all libs, reinstall before app load

 
    
  
    

      Package: GExPipe

      Commit: 427451377cba8190271cce20157123e5f1170c0c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 15:23:37 +0500

      Commit message:


	  
		
 Aesthetic WGCNA module-eigengene correlation heatmap: corrplot with module-coloured labels, adaptive sizing, clean margins

 
    
  
    

      Package: GExPipe

      Commit: adc4ef74a06ff28b3159a4fd287772d0087f85df

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 14:11:03 +0500

      Commit message:


	  
		
 Auto-fix broken DLL packages (e.g. glmnet after R upgrade): detect, reinstall, reload at startup and runtime

 
    
  
    

      Package: GExPipe

      Commit: 1fa3ac5192defa146fe06c1f6eb5accd67236f03

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 13:28:23 +0500

      Commit message:


	  
		
 Download fallback: parse supplementary series_matrix/text files when no ExpressionSet returned

 
    
  
    

      Package: GExPipe

      Commit: 5f15e6c9e460ceb1bcde9bc380ea2d57c0283d27

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-04 12:31:56 +0500

      Commit message:


	  
		
 Fix DE method help: replace hidden tooltip with always-visible guide table; fix radio button label rendering

 
    
  
    

      Package: GExPipe

      Commit: 686f30fa151227b8b79e8e3dc750861c15aad282

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 19:14:55 +0500

      Commit message:


	  
		
 Align package dependencies with app code (v0.99.8).

- Update DESCRIPTION Imports, pkg_versions.txt, install lists, and README
- Add alignment check scripts; sole author Safa Rafique

 
    
  
    

      Package: GExPipe

      Commit: 0617ba6d933d2dd6af4c565746dba002bb031bfe

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 17:52:28 +0500

      Commit message:


	  
		
 Sync local to GitHub: vcf_acmg app, gitignore cleanup

Added:
- inst/shinyapp/vcf_acmg/app.R: standalone VCF Annotation &
  ACMG Classification Shiny app (VariantAnnotation + MyVariant.info
  REST API, no Python/reticulate required)

.gitignore:
- Added vignettes/saved_workspaces/ (runtime workspace saves)
- Added GExpipe_1/ and GExpipe_*/ (old project copies/scratch dirs)

Deleted:
- Garbage cookie file accidentally named with a Python ngrok command
  (vignettes/import sys,json; ...) — was a libcurl cookie leftover

 
    
  
    

      Package: GExPipe

      Commit: 6d5886a82aa607dfbfdd07fb5ba23babb8a94834

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 16:42:01 +0500

      Commit message:


	  
		
 Bump version to 0.99.8; fix UI file routing and visual consistency

Version bump 0.99.7 -> 0.99.8 ensures remotes::install_github()
always triggers a reinstall even with force = FALSE.

UI file routing fix (from previous commit 9046c3b):
.gexp_inst_file() now only uses getwd()-relative paths when running
from the GExPipe source root (DESCRIPTION has Package: GExPipe).
When running a GitHub-installed or CRAN-installed version from any
other working directory, system.file() is used directly — preventing
stale UI files from old local copies (e.g. GExpipe_1/) or old
workspaces from overriding the properly installed interface.

Visual consistency:
- All CSS/styling is embedded inline in interface_app.R (no external
  www/ files) so both local and GitHub versions render identically
- shinydashboard >= 0.7.3 declared as minimum (0.7.3 is latest CRAN)
- Updated Roxygen documentation metadata

 
    
  
    

      Package: GExPipe

      Commit: 35c4518ba76caadfb13f2122956a4f3fccc9e774

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 16:14:55 +0500

      Commit message:


	  
		
 Fix: GitHub-installed app was loading stale UI files from wrong directory

.gexp_inst_file() previously checked getwd()-relative paths first,
regardless of whether the user was in the GExPipe source root.
This caused the GitHub-installed version to show an old/different
UI when:
  - getwd() was a user's home or Documents folder that happened to
    contain an old inst/shinyapp/ copy (e.g. GExpipe_1/)
  - getwd() was any directory with an older local checkout

Fix: detect dev mode by checking whether getwd() (or its parent)
contains a DESCRIPTION file with "Package: GExPipe". Only then do
local inst/ files take precedence (for developers). In all other
cases (GitHub install, CRAN install, any non-source directory),
system.file() is used directly to guarantee the installed files
are always the ones loaded — regardless of working directory.

Before: local run = new UI, GitHub install = possibly old UI
After:  local run = new UI, GitHub install = always installed UI

 
    
  
    

      Package: GExPipe

      Commit: b9e523a36727894c451508c910d2afe554af1f4c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 13:31:11 +0500

      Commit message:


	  
		
 Add NA-sample detection/removal and per-GSE sample summary

Microarray + RNA-seq download:
- Detect samples (columns) that are >90% NA/NaN/Inf and remove them
  automatically with a clear log message showing which samples were
  dropped and the count (e.g. "2/15 sample(s) removed (>90% NA): S3, S7")
- Detect samples with 10-90% NA and report them in the log (kept
  but flagged so the user knows)
- If ALL samples are NA, fail early with "all samples were NA"

server_download.R:
- Added Step 1 sample summary block after all downloads complete:
  lists each GSE with its sample count and gene/probe count so the
  user sees exactly how many samples were loaded from each dataset
- Shows total samples loaded across all datasets

 
    
  
    

      Package: GExPipe

      Commit: 971104a08804bf20988234087e2c3e0ab344f8b4

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 13:02:09 +0500

      Commit message:


	  
		
 Fix: combine split GSEMatrix files so all samples are retained

GEO splits large series across multiple GSEMatrix files
(e.g. _series_matrix-1.txt.gz + _series_matrix-2.txt.gz).
getGEO() returns one ExpressionSet per file.

The previous code used which.max(n_feat) which picked the first
file and silently dropped the rest — causing GSE100026 (15 samples)
to appear as only 8 samples in the app.

Fix in gexp_download_one_microarray_gse:
- Group returned ExpressionSets by platform
- When multiple files share the same platform and identical probe rows,
  cbind() their expression matrices and rbind() their pData to recover
  all samples
- Deduplicate columns if the same GSM ID appears in more than one file
- If row sets differ (truly different platforms), fall back to the
  largest single matrix as before
- Select the platform group with the most combined samples
- Log message now reports "(N matrix files combined)" when merging

 
    
  
    

      Package: GExPipe

      Commit: 58dce1df592e8e2465183e25d0780af41fc4dfa3

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-06-03 10:37:01 +0500

      Commit message:


	  
		
 Fix CodeLink probe ID conversion and harden download pipeline

Probe ID mapping (GPL1449 / CodeLink UniSet Human 20K):
- map_microarray_ids: case-insensitive fData column search so
  Gene.Symbol / GENE_SYMBOL / gene symbol all resolve correctly;
  treat GEO placeholder "---" and other missing-value strings as NA
- probe_ids_to_symbol_gpl: case-insensitive probe-ID and symbol-column
  detection; try tempdir() then getwd() as destdir to reuse cached GPL
  files; case-insensitive probe-ID matching as final fuzzy step;
  filter "---" / N/A / null placeholders before matching
- gexp_download_normalize_ids_for_overlap: new micro_eset_list param;
  when any_id_to_symbol fails, fall back to fData from the already-
  downloaded ExpressionSet (no extra network call needed)
- server_download.R: pass micro_eset_list to normalize call

Download pipeline hardening (earlier sessions):
- tryCatch result-return pattern throughout (no <<- in main blocks)
- Safe [[ access on named vectors (fix "subscript out of bounds")
- ExpressionSet parse guard for list/NULL/empty returns from getGEO
- GPL list-unwrapping for newer GEOquery versions
- Length-mismatch guard before every rownames<- assignment
- All-downloads-failed early exit with clear log message
- Combined-matrix cleared on each new run to avoid stale data reuse

UI / server improvements (earlier sessions):
- Batch, ML, normalize, results server modules hardened
- global.R: package-check error page on startup
- ui_normalize.R tweaks

 
    
  
    

      Package: GExPipe

      Commit: b7c4de354eafac688693bf13d992c8557124a95d

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-29 18:41:54 +0500

      Commit message:


	  
		
 Suppress BiocManager interactive update prompt completely

In RStudio, interactive() returns TRUE so BiocManager shows
"Enter one or more numbers to skip updates" even when ask=FALSE
is passed to install(). Fix: set options(BiocManager.ask=FALSE)
globally right after BiocManager is confirmed available, before
any install call. Also suppress "install from source?" prompt via
install.packages.check.source="no". Same options added to the
subprocess script so it never prompts there either.

 
    
  
    

      Package: GExPipe

      Commit: 0dcb1ab4fc3a32c7e5d25fdf328c3d989281a40c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-29 17:11:25 +0500

      Commit message:


	  
		
 Block app launch if required packages missing; show error page with fix

If packages fail to install (e.g. network reset during download):
1. Retry install once more for each failed package
2. If still missing after retry — BLOCK the app from opening
3. Show a dark-theme error page listing exactly which packages
   failed and the exact R code to fix it (copy-paste ready)
4. Print the same info to the R console for non-browser users

Previously the app opened silently and crashed mid-analysis when
a missing package was first called (e.g. org.Hs.eg.db during
RNA-seq gene ID conversion). Now the missing package is caught
at startup before the interface opens.

 
    
  
    

      Package: GExPipe

      Commit: f55712c4a29d8122f76cf2f835c52071ccb11d38

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-29 16:16:50 +0500

      Commit message:


	  
		
 Fix crash when org.Hs.eg.db missing due to network failure at startup

If org.Hs.eg.db failed to install during global.R startup (e.g. network
reset), the app crashed with a hard stop() when convert_ids_to_symbols_simple
or .gexpipe_hs_db was called. Fix:
- Try BiocManager auto-install on demand before giving up
- If network still fails, return gene IDs as-is (no symbol conversion)
  instead of crashing — download step continues with original IDs
- .gexpipe_hs_db returns NULL on failure; callers handle it gracefully

 
    
  
    

      Package: GExPipe

      Commit: abcbfee33481a1b5ddf96a76bcab014374a5aaf5

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 16:42:37 +0500

      Commit message:


	  
		
 PPI: suppress console warnings, show mapping % in app UI

STRINGdb prints "couldn't map X% of identifiers" to the R console
for every map() call (appears 6 times due to version retry loop).
Suppress these with suppressWarnings() and instead show a clean
mapping summary in the app: "65% genes mapped to STRING - 35%
unmapped is normal". Also improve 0-interactions error message to
suggest lowering the score threshold.

 
    
  
    

      Package: GExPipe

      Commit: 407169511d7c8c62c14ba26d5af7d385e944fb61

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 15:42:50 +0500

      Commit message:


	  
		
 Fix GitHub install: set BiocManager repos so Bioc deps install automatically

remotes::install_github() uses CRAN repos by default and cannot find
Bioconductor packages like org.Hs.eg.db, DESeq2, limma etc. from
DESCRIPTION Imports. Setting options(repos = BiocManager::repositories())
before the install call adds all Bioconductor repos so remotes can
resolve and install every dependency without user intervention.
Also added dependencies = TRUE to catch suggested packages.

 
    
  
    

      Package: GExPipe

      Commit: d2fd743945cbd08778d60e1fbccfc656a55a4f39

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 15:31:11 +0500

      Commit message:


	  
		
 Fix RNA-seq download crash when run from installed package

Root cause: get("org.Hs.eg.db", asNamespace("org.Hs.eg.db")) returns
a lazy-loading closure instead of the OrgDb object when the package is
loaded but not attached (i.e. when run via GExPipe::runGExPipe() after
remotes::install_github). This caused "cannot coerce type 'closure' to
vector of type 'character'" in convert_ids_to_symbols_simple and
.gexpipe_hs_db.

Fix: use org.Hs.eg.db::org.Hs.eg.db directly — always returns the
OrgDb object regardless of whether the package is attached or only
namespace-loaded.

 
    
  
    

      Package: GExPipe

      Commit: 5493f3e1de406ba48adc5a5bd4f126c2caa086f5

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 15:20:06 +0500

      Commit message:


	  
		
 PPI: reduce timeout to 120s, show clear error reasons

- STRINGdb timeout: 3600s → 120s (fast fail, not hang for 1 hour)
- On failure: show specific reason (timeout / no internet / alias file
  missing / no genes mapped / no interactions) with a fix hint
- Error shown as notification in the app UI, not raw R error text
- Retry logic (3 attempts) kept for transient network blips

 
    
  
    

      Package: GExPipe

      Commit: 20f238ec0f9f40fdce6f79aab4f7adc8314356e5

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 15:17:12 +0500

      Commit message:


	  
		
 Increase timeouts to 1 hour; fix PPI API reliability

- global.R: raise startup timeout 600s → 3600s (1 hour) so slow
  connections can download large Bioconductor packages without error
- server_ppi.R: raise STRINGdb timeout 180s → 3600s; add 3-attempt
  retry loop with 3s pause between attempts; reorder STRING versions
  to try 12.0 first (most current, most reliable) then 11.5, 11
- vignette: add options(timeout=3600) before install_github() so
  users on slow connections never hit the default 60s timeout

 
    
  
    

      Package: GExPipe

      Commit: f0d9b613767d51a1f906b491956c136aa9ee52c2

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 14:34:07 +0500

      Commit message:


	  
		
 Update vignette: add GitHub install code and isolated library docs

- Replace runGitHub() block with clean 3-line remotes::install_github()
  approach for GitHub users
- Add Bioconductor install section (after acceptance)
- Document isolated GExPipe library location for all 3 OS platforms
- Add helper code to find exact library path on user's system
- Update Quick Start to show expected startup console output
- Clarify first-run (~10-40 min) vs subsequent run (seconds)

 
    
  
    

      Package: GExPipe

      Commit: ac84adaa5f530143ee3fff17c4d95fc01947c920

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-28 07:24:22 +0500

      Commit message:


	  
		
 Fix isolated library: check packages in GExPipe lib only

Previously requireNamespace() found packages in the main R library
and marked them as OK — so nothing was ever installed into the
isolated GExPipe library. Now all checks use lib.loc = .gexpipe_lib
so every package is installed into the isolated library on first run,
regardless of what exists in the user's main library.

 
    
  
    

      Package: GExPipe

      Commit: bf714242e2b33f0fe93d34eff537291f84a937f4

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-27 18:10:41 +0500

      Commit message:


	  
		
 Add minimum version constraints to DESCRIPTION Imports

All version floors based on actual package versions confirmed working
on R 4.5.3 / Bioconductor 3.21. Uses >= constraints so any newer
version is also accepted. Packages without explicit versions
(parallel, cli, glue, lifecycle, rlang, vctrs) are handled by
runtime version checks in global.R.

 
    
  
    

      Package: GExPipe

      Commit: fa8426e4175a733414e99eeebd27c548430e4d7c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-27 17:12:49 +0500

      Commit message:


	  
		
 Remove version pins from DESCRIPTION Imports

Version constraints (rlang >= 1.2.0, cli >= 3.6.0, glue >= 1.7.0,
lifecycle >= 1.0.4, vctrs >= 0.6.5) removed from DESCRIPTION.

Reason: runGitHub() ignores DESCRIPTION entirely, so pins gave no
protection for GitHub users. Version conflict detection and
auto-update is handled by the .gexpipe_min_versions table in
global.R and utils_shiny_app.R, which catches and updates outdated
packages at app startup on every path (runGitHub, installed package,
and gexpipe_setup()). Removing pins from DESCRIPTION prevents
install failures on systems where an older Bioconductor release does
not yet ship the pinned version.

 
    
  
    

      Package: GExPipe

      Commit: 5fd0f2bba9b4f0aa5618c834af87a689615b9672

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-27 12:38:29 +0500

      Commit message:


	  
		
 Sync min version floors with DESCRIPTION requirements

Fixed rlang floor: 1.1.7 → 1.2.0 (DESCRIPTION already declared >= 1.2.0;
1.1.7 was still too low and missed the original runtime error).

Updated DESCRIPTION and both min_versions tables to match exactly:
  rlang     >= 1.2.0  (unchanged in DESCRIPTION, fixed in min_versions)
  cli       >= 3.6.0  (was 3.4.0)
  glue      >= 1.7.0  (was 1.6.0)
  lifecycle >= 1.0.4  (was 1.0.3)
  vctrs     >= 0.6.5  (was 0.6.0)

Rule: DESCRIPTION, global.R .gexpipe_min_versions, and
utils_shiny_app.R .gexpipe_min_versions must always match.

 
    
  
    

      Package: GExPipe

      Commit: 43345bb6f433476b13d12ecbb2d5cb02873018cc

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-27 12:18:36 +0500

      Commit message:


	  
		
 Raise minimum version floors to catch rlang/cli/vctrs conflicts

rlang 1.1.0 floor meant 1.1.6 passed the check and was never updated,
causing 'namespace rlang 1.1.6 is already loaded but >= 1.1.7 required'
errors during GEO download. Updated all floors to current minimums:

  rlang     1.1.0 → 1.1.7
  cli       3.4.0 → 3.6.0
  vctrs     0.6.0 → 0.6.5
  lifecycle 1.0.3 → 1.0.4
  glue      1.6.0 → 1.7.0
  Matrix    1.5.0 → 1.6.0
  Rcpp      1.0.10 → 1.0.12
  withr     (new) 2.5.0
  pillar    (new) 1.9.0

 
    
  
    

      Package: GExPipe

      Commit: 2d158f3e7146187a3a5c975205f9422ff85a26bf

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-25 08:50:04 +0500

      Commit message:


	  
		
 Rewrite STEP 4/5: per-package visible install progress + clean status table

Install logic (global.R):
- Missing packages    → direct BiocManager::install() in parent session with
                        per-package [INSTALL] progress line (guaranteed to work;
                        missing packages have no DLL lock)
- Outdated/conflicted → same direct install with [UPDATE] tag
- DLL-locked (rare)   → lightweight subprocess to pending lib only
- Already OK          → skipped entirely, only library() called
- Subprocess is now used ONLY for the DLL-locked edge case, not for every package

Package status table (STEP 5):
  No.  Package              Version     Status
  [1]  shiny                1.8.1       ✓ Ready
  [2]  GEOquery             2.68.0      ✓ Installed
  ...  54 rows total

Summary block shows:
  Loaded      : 54/54
  Installed   : 26 new packages this run
  Already OK  : 28 packages (skipped)
  Status      : All packages ready — opening app...

On failure: prints exact BiocManager::install(c(...)) snippet to paste,
not just a list of package names.

STEP 4b now re-checks the full .gexpipe_all_required list (not just
.missing_pkgs) so newly-installed packages are counted correctly.

 
    
  
    

      Package: GExPipe

      Commit: 961ec1ec56caf6eec4cb4b67c32ca2e24f5cefc0

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-25 08:24:19 +0500

      Commit message:


	  
		
 Fix mass install failure: dynamic Bioc version + fallback install

Root cause: hardcoded version = "3.22" in every BiocManager::install(pkgs, ...)
call caused ALL Bioconductor + CRAN package installs to fail silently on R < 4.6
(BiocManager rejects Bioc 3.22 on R 4.5 and aborts the entire install batch).

Changes:
- Auto-detect correct Bioconductor release from R version at runtime:
    R >= 4.6 -> 3.22  |  R >= 4.5 -> 3.21  |  R >= 4.4 -> 3.20  |  else -> 3.19
- Remove version = "3.22" from all BiocManager::install(pkgs, ...) calls;
  only the BiocManager configuration upgrade call carries a version
- Capture subprocess stdout+stderr to a temp log file; print last 30 lines
  on non-zero exit so failures are visible instead of silent
- Add direct fallback install loop after subprocess: packages that are still
  missing (never installed = no DLL lock) are retried one-by-one in the
  parent session — catches subprocess crashes cleanly
- STILL MISSING summary now prints a ready-to-paste BiocManager::install()
  snippet so users can recover manually with one copy-paste
- Same fixes applied to global.R, utils_shiny_app.R, and setup.R

 
    
  
    

      Package: GExPipe

      Commit: 7b5157c2fdcc16952bacced9e78ac7208d0dd704

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-25 08:10:55 +0500

      Commit message:


	  
		
 Enforce Bioconductor 3.22 across all install paths

- global.R STEP 1: detect and upgrade BiocManager to Bioc 3.22 at startup
- global.R subprocess: enforce version = "3.22" on all BiocManager::install() calls
- utils_shiny_app.R: same enforcement in parent-session bootstrap and subprocess script
- setup.R: upgrade to Bioc 3.22 before installing required packages

Ensures every package install (interactive, subprocess, gexpipe_setup())
targets the correct Bioconductor release rather than defaulting to whatever
BiocManager::install() resolves without a version constraint.

 
    
  
    

      Package: GExPipe

      Commit: bdda83e06989cc59c7d03a4062570d50b12b50c3

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-25 07:58:19 +0500

      Commit message:


	  
		
 Universal package setup: two-lib design, OS-aware paths, parallel install

Makes the app work without errors on Windows (OneDrive/non-OneDrive),
macOS, Linux, and Google Colab by solving every known install failure:

Library paths (never cloud-synced):
  Windows : %LOCALAPPDATA%\GExPipe\\  (AppData\Local)
  macOS   : ~/Library/Application Support/GExPipe//
  Linux   : $XDG_DATA_HOME/GExPipe//  (~/.local/share fallback)
  All     : old ~/. gexpipe_packages/ kept in .libPaths() for transition

Two-library design (eliminates manual restart requirement):
  main_lib    : GExPipe//          parent loads from here
  pending_lib : GExPipe/-pending/  subprocess writes DLL-locked updates
  On every startup, pending → main before any package loads (no DLL held),
  so the rename always succeeds and updates are active on next run
  automatically without the user doing anything.

Subprocess improvements:
  - safe_pkgs (not DLL-locked) → main lib (usable this run)
  - pending_pkgs (DLL locked)  → pending lib (usable next startup)
  - Ncpus = detectCores()-1 for parallel installation (faster)
  - --no-staged-install --no-lock (no rename step → no OneDrive failures)
  - Per-package retry loop for packages that fail in the batch call
  - wininet fallback when libcurl is locked (Windows only)

Cloud-sync path warning: detects OneDrive/Dropbox/iCloud/etc in path
and prints a warning if the chosen base dir is still cloud-synced.

 </pre>
    </div>
  
    

      Package: GExPipe

      Commit: 976f5e81855ecbbae27eecfe3b63f3c7629b6105

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-25 07:49:11 +0500

      Commit message:


	  
		
 Fix OneDrive file lock + DLL-locked package failures during install

Two root causes identified from user error log:

1. OneDrive sync holds background file locks on Documents folder.
   Library was at ~/. gexpipe_packages/ which resolves to
   OneDrive\Documents\.gexpipe_packages\ on many Windows systems.
   OneDrive locks files while syncing, causing:
     "moving to final location failed" (org.Hs.eg.db)
   Fix: use LOCALAPPDATA (C:\Users\...\AppData\Local\GExPipe\\)
   which Windows never syncs via OneDrive.
   Old Documents-based path kept in .libPaths() as fallback so
   already-installed packages still load during transition.

2. Parent R session loads Rcpp (and other packages) from .gexpipe_lib.
   Windows locks loaded DLLs. Even a fresh subprocess cannot overwrite
   a DLL that is mapped into the parent process, causing:
     "cannot remove earlier installation, is it in use?" (Rcpp)
   Fix: before launching the subprocess, detect which packages in
   .gexpipe_lib are currently loaded in the parent session (DLL held)
   and skip those from the subprocess install list. They update cleanly
   after the user restarts R. A clear console message lists skipped pkgs.

3. Staged installation creates 00LOCK-*/00new/* staging directories and
   then renames to final location — this rename fails under file locks.
   Fix: add INSTALL_opts = c("--no-staged-install", "--no-lock") to
   all BiocManager::install() calls inside both subprocesses, so
   packages are written directly to their final location without a
   staging rename step.

Changes: inst/shinyapp/global.R, R/utils_shiny_app.R

 </pre>
    </div>
  
    

      Package: GExPipe

      Commit: c0ab64e28943c5f5a8b65f593d96f4124131419d

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 23:05:27 +0500

      Commit message:


	  
		
 Backend: auto-detect and bypass DLL locks / version conflicts at startup

Problem: runGExPipe() only triggered the background subprocess when
packages were completely missing. Version-conflicted packages (present
but below minimum required version, and DLL-locked) were silently
ignored and caused runtime errors inside the app.

Changes:

R/runGExPipe.R
- Pre-launch check now detects BOTH missing packages AND packages below
  .gexpipe_min_versions (version conflicts).
- If either condition is found, the background subprocess fires and
  updates the conflicted packages — bypassing DLL locks because the
  subprocess starts with nothing loaded.
- Clear console messages distinguish missing vs. version-conflict cases.

R/utils_shiny_app.R
- After subprocess completes, still-conflicted packages (updated on
  disk but DLL still held by the running session) are stored via:
    options(gexpipe.restart_required = TRUE)
    options(gexpipe.still_conflicted = pkg_names)
- On clean run the options are explicitly cleared (NULL).
- Failed-to-load packages stored as options(gexpipe.failed_pkgs = ...)
  using the correct option name that server_app.R reads.

R/server_app.R
- Fixed stale option name "omniVerse.missingPkgs" -> "gexpipe.failed_pkgs"
  (nothing ever set the old name; notification was never shown).
- Added full-screen Shiny modal when gexpipe.restart_required = TRUE:
  lists each conflicted package + loaded version, gives a clear 3-step
  restart guide (Stop -> Ctrl+Shift+F10 -> run again), and notes the
  analysis pipeline is still usable while the modal is dismissed.
- Missing-package notification now uses tags$div with an icon and a
  hint to run gexpipe_setup() for a clean reinstall log.

 
    
  
    

      Package: GExPipe

      Commit: 1d627071fc265714df084f13658fdad806a04185

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 21:18:40 +0500

      Commit message:


	  
		
 Vignette: restore full 3-step GitHub block for development install

BiocManager::install() from GitHub does not trigger global.R's
background subprocess, so it cannot update packages that are already
loaded (DLL locks) or enforce minimum version requirements across all
54 dependencies.

The runGitHub() 3-step block (wininet + lock cleanup + runGitHub) is
restored as the GitHub install method because global.R runs in a fresh
subprocess with nothing loaded — guaranteeing all dependencies are at
correct versions before the app opens.

Bioconductor stable install block is unchanged (2 lines, primary).

 
    
  
    

      Package: GExPipe

      Commit: 0c55a7191453bb9bbf4f32ded3a9f80f73141cd2

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 19:42:50 +0500

      Commit message:


	  
		
 Vignette: restructure per Bioconductor reviewer guidance

Structure changes:
- Lead with BiocManager::install() as the sole recommended method
- Add pipeline overview table (4 phases × 15 steps) before installation
- GitHub install simplified to one BiocManager call; no 3-step block
  in primary flow
- Windows DLL workaround moved to Troubleshooting subsection only
- Launch reduced to single line: GExPipe::runGExPipe()
- Google Colab updated to use BiocManager install path
- Troubleshooting restructured as a clean table + one subsection for
  the rare persistent DLL lock case
- Removed Option A/B/C framing; single clear path throughout
- number_sections: true added to YAML

Tone: guiding the user, not describing workarounds in the primary flow

 
    
  
    

      Package: GExPipe

      Commit: a247b50860452a92c2e97255189a1563401f197e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 15:19:00 +0500

      Commit message:


	  
		
 Vignette: expert rewrite + remove placeholder screenshots

- Full expert-level rewrite of vignettes/GExPipe.Rmd:
  * Professional Bioconductor-standard prose throughout
  * number_sections: true added to YAML
  * 3-step GitHub launch block uses inline technical comments
    instead of informal blockquotes
  * pak limitation documented precisely (own libcurl binding,
    wininet option has no effect)
  * Launch section reorganised with descriptive headings
  * Troubleshooting table language tightened
  * 15-step walkthrough rewritten in formal academic prose with
    BiocStyle cross-references (sva, pROC, WGCNA, clusterProfiler)
  * Workflow example uses integer suffixes (1L, 2L) for type safety
  * App Screenshots section removed (placeholder images, not real)
  * Session info chunk label corrected to 'sessionInfo'

- inst/extdata/vignette-screenshots/:
  * Deleted five identical placeholder PNGs (all 845 KB, same image)
  * README.md updated with step-by-step instructions for capturing
    and adding real screenshots after the app is running

 
    
  
    

      Package: GExPipe

      Commit: da99c13da3cad5bd7d65f11b07753c9924b3ff87

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 13:08:35 +0500

      Commit message:


	  
		
 Vignette: correct pak curl.dll limitation, add restart requirement

pak uses libcurl directly — options(download.file.method = "wininet")
does not affect it. When curl.dll is locked pak fails the same way as
BiocManager. Updated:
- pak section: add prominent warning + "restart R first" instruction
- pak section: explain the 3-step block as the no-restart alternative
- Troubleshooting table: add pak row with correct fix (restart R),
  clarify that 3-step block never needs a restart

 
    
  
    

      Package: GExPipe

      Commit: cc19ed0a365b6e8619edbbe1f2b02e2475e12b6b

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 09:46:18 +0500

      Commit message:


	  
		
 Vignette: full rewrite — 3-step launch as primary method, Bioconductor-ready

- 3-step block (wininet + lock clean + runGitHub) is now the PRIMARY
  recommended launch method for ALL users, not a troubleshooting note
- Added clear explanation of why each step is needed (curl.dll, 00LOCK)
- Restructured into clean sections: Installation, Launch (A/B/C),
  Troubleshooting table, Advanced, Workflow Example, App Walkthrough
- Bioconductor submission ready:
    * BiocManager::install("GExPipe") as primary install
    * All network-dependent code has eval=FALSE
    * eval=TRUE chunks (PCA, heatmap, sessionInfo) run offline from bundled data
    * sessionInfo() at end as required
    * No stop() or interactive prompts in evaluated chunks
- Step walkthrough condensed (no change to content, shorter format)
- Removed duplicate / redundant code blocks and complex reachability checks

 
    
  
    

      Package: GExPipe

      Commit: 4322d220d03142d89deec7a04606bbc3e8bfceff

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 09:41:45 +0500

      Commit message:


	  
		
 Vignette: add wininet+lock-clean fix for curl DLL download errors

- Replace old subprocess DLL fix with cleaner 3-step block:
    options(download.file.method = "wininet")   # bypass curl.dll
    unlink(00LOCK-* dirs)                        # clear failed install locks
    shiny::runGitHub(...)                        # launch
- Add the same 3-step block directly into the Option 1 launch code
  so users can paste one block and handle both fresh + lock scenarios
- Update troubleshooting table: add curl DLL row, DLL lock row,
  and Rtools row for needs_compilation packages

 
    
  
    

      Package: GExPipe

      Commit: 9c2409fa9bd96c6f73b45705471b9987374eb27f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-24 09:11:18 +0500

      Commit message:


	  
		
 Repo cleanup + fix curl DLL lock breaking all downloads

DLL/download fix (global.R + utils_shiny_app.R):
- Remove 00LOCK-* dirs from ALL .libPaths() entries (not just gexpipe_lib).
  A locked curl.dll leaves 00LOCK-curl in the system library and causes
  every subsequent download to fail with 'cannot download any files'.
- Subprocess now auto-detects when libcurl is unavailable and falls back
  to wininet (Windows-native, no curl.dll dependency) so downloads succeed
  even when curl.dll is locked by RStudio.

Repo cleanup (41 files removed/cleaned):
- Remove 1.1.1-1), 1.2.0, 3.6.6: empty stray version-string files
- Remove GExPipe/GExPipe.Rproj: nested Rproj (root-level one is correct)
- Remove R/shiny_src/ (33 files): stale duplicates of inst/shinyapp/ content,
  never sourced; server_modules_wrappers.R uses inst/shinyapp/ via path alias
- Remove inst/shinyapp/server/server_packages.R + ui/ui_packages.R: packages
  tab was removed from UI; these files are no longer sourced
- Remove inst/pkg_versions.txt: stale version pins (removed from DESCRIPTION)
- Remove gexp_ui_packages() from interface_tabs_wrappers.R: packages tab gone
- Remove server_packages() from server_modules_wrappers.R: packages tab gone

 
    
  
    

      Package: GExPipe

      Commit: 6e707426d2cd26c4f9bed7f5a2f14bb8327d52cd

      Author:  SAFA RAFIQUE <53168745+safarafique@users.noreply.github.com> 

      Date: 2026-04-23 13:35:36 +0500

      Commit message:


	  
		
 Update rlang version requirement to 1.2.0 
    
  
    

      Package: GExPipe

      Commit: 269f60032baa0c774b8ec487ad708b04964ceb0f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 13:12:29 +0500

      Commit message:


	  
		
 Comprehensive cross-system dependency handling: 4-layer protection

Layer 1 — Dedicated library (~/.gexpipe_packages/R-x.y/):
  New/updated packages install there, not into the user's system library.
  This folder has highest .libPaths() priority so updated versions shadow
  old system ones for any package not yet loaded in this session.

Layer 2 — Explicit minimum version table (.gexpipe_min_versions):
  rlang >= 1.1.0, cli >= 3.4.0, vctrs >= 0.6.0, lifecycle >= 1.0.3,
  glue >= 1.6.0, Matrix >= 1.5.0, Rcpp >= 1.0.10.
  Best-across-libPaths version is checked (not just loaded namespace),
  so a good version already sitting in gexpipe_lib is recognised.

Layer 3 — Subprocess with update=TRUE + second old.packages() pass:
  Background Rscript writes into gexpipe_lib (zero DLL locks).
  After main install, a second pass updates any transitive outdated
  deps that were pulled in with wrong versions.

Layer 4 — Force-reload attempt + boxed restart message:
  After subprocess, tries unloadNamespace + loadNamespace from gexpipe_lib
  for each still-conflicted package. If that succeeds the session continues.
  If it fails (e.g. shiny depends on the package), a clear boxed message
  with exact steps is shown and stop() prevents a broken app from opening.

Both global.R (runGitHub path) and R/utils_shiny_app.R (installed path)
implement all four layers.

 
    
  
    

      Package: GExPipe

      Commit: 5f19c00fdb84dd8c91d4d365e5c3b5733974a5ce

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 13:03:45 +0500

      Commit message:


	  
		
 Fix version-conflict handling: pak, version pins, subprocess update=TRUE

- DESCRIPTION: add minimum version pins for the 5 most-conflicted packages
  (rlang >= 1.1.0, cli >= 3.4.0, vctrs >= 0.6.0, lifecycle >= 1.0.3,
   glue >= 1.6.0) so BiocManager/pak refuse to install GExPipe unless
  those deps meet the floor — forcing an upgrade at install time
- DESCRIPTION: add pak to Suggests
- global.R + utils_shiny_app.R: second subprocess BiocManager::install()
  pass now uses update=TRUE, force=TRUE so outdated transitive deps
  (rlang, cli, vctrs) are actually replaced, not skipped
- vignette: add pak as Option 0 (recommended) with full install+launch
  block; add version-conflict row to troubleshooting table; add pak
  to the pre-GitHub install block

 
    
  
    

      Package: GExPipe

      Commit: b108aec408cbbd9dd573b25f6d013bee2de4073c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 12:55:49 +0500

      Commit message:


	  
		
 Auto-detect and update outdated packages via subprocess to fix version conflicts

Both global.R (runGitHub path) and R/utils_shiny_app.R (installed path) now:
- Detect outdated GExPipe deps (utils::old.packages) in addition to missing ones
- Pass both missing + outdated to the background Rscript subprocess
- Subprocess runs a second old.packages() pass after install to resolve any
  remaining transitive version conflicts (e.g. rlang 1.1.7 < required 1.2.0)

 
    
  
    

      Package: GExPipe

      Commit: d0dd40c70ed8b2cc1601ba48c237cabfdc70c194

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 11:58:27 +0500

      Commit message:


	  
		
 vignette: fix install-bioc block and add Windows DLL lock troubleshooting

- install-bioc: add dependencies = TRUE so all 54 packages install when
  GExPipe is eventually accepted on Bioconductor
- Add 'Troubleshooting: Windows packages in use' section with a
  system2(Rscript) subprocess pattern that bypasses DLL locks entirely —
  the most common install failure on Windows

 
    
  
    

      Package: GExPipe

      Commit: 13bc0a412bcef7a7645dcc196b0cb71f6017119e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 11:55:45 +0500

      Commit message:


	  
		
 vignette: update launch docs to match current app behaviour

- Remove Packages tab tip (tab removed from app sidebar)
- Option 1 "What happens": add step for background subprocess install
  and per-package console progress list; note app opens to Step 1
- Option 2 "What happens": add console progress bar example output
  showing [ 1/54] pkg ... check version format; note app opens to Step 1
- install-github block: simplify launch comment, remove Packages tab tip

 
    
  
    

      Package: GExPipe

      Commit: d59d497e8d893f6af328b62dd7fd4872de0d7cea

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 11:12:36 +0500

      Commit message:


	  
		
 Remove Packages status tab from app sidebar

Package status is now shown in the R console progress bar before the
app opens (global.R STEP 4 + gexp_app_attach_packages). The in-app
tab is redundant and removed so the app opens directly to Step 1.

Removed from:
- inst/shinyapp/ui.R: source ui_packages, sidebar menuItem, tabItems entry
- inst/shinyapp/server.R: source server_packages, server_packages() call
- R/interface_app.R: sidebar menuItem, gexp_ui_packages() in tabItems
- R/server_app.R: server_packages() call

 
    
  
    

      Package: GExPipe

      Commit: d18431398877a1c8b72968d51fe09b1a9f6ebed0

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 11:10:07 +0500

      Commit message:


	  
		
 global.R: use background Rscript subprocess for package install

Show live per-package progress bar in R console before app opens.
Both launch paths now print:

  [4/4] Loading 54 libraries...

  [ 1/54] shiny              ... ✓ 1.8.1
  [ 2/54] shinydashboard     ... ✓ 0.7.2
  [ 3/54] Biobase            ... ✓ 2.64.0
  ...
  [54/54] xgboost            ... ✓ 2.1.4

  ✓ Status : All packages ready — opening app...

Changes:
- global.R STEP 4: loop prints [i/n] pkg ... ✓ version per package
- utils_shiny_app.R gexp_app_attach_packages(): same progress block
- Summary line shows loaded/total count + ✓/✗ status per package
- App only opens after all packages finish loading

 
    
  
    

      Package: GExPipe

      Commit: 77d0c281e907f090e5c8095d8b7dabce76c7bb85

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 11:00:16 +0500

      Commit message:


	  
		
 DESCRIPTION: remove version constraints from all Imports and Suggests

Version pins like (>= 1.64.0) cause install failures when Bioconductor
bumps its release numbering (e.g. Bioc 3.19 → 3.21 → 3.22). Without
pins, BiocManager automatically selects the correct version for the
user's R version — R 4.4 gets Bioc 3.19, R 4.5 gets Bioc 3.21, etc.

The R (>= 4.5.0) Depends constraint is kept as the only version pin
since it defines the minimum supported environment. All package version
selection is now delegated to BiocManager at install time.

 
    
  
    

      Package: GExPipe

      Commit: 7af1362a862adbaa8c052b22a1a22b2d7f8c2660

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-23 10:39:19 +0500

      Commit message:


	  
		
 Add missing car package dependency (used for VIF in nomogram step)

car::vif() is called in server_nomogram.R to compute Variance Inflation
Factors for multicollinearity checking (Step 13). The car package was
used directly in code but completely absent from DESCRIPTION — meaning
it was never installed automatically, silently returning NA VIF values.

Added car (>= 3.1.0) to:
- DESCRIPTION Imports
- global.R required list (runGitHub path)
- utils_shiny_app.R core list (installed package path)
- server_packages.R (both copies) Packages tab metadata

Note: arrow was a false positive from the audit — it appears as CSS
.arrow::before in tooltip styles, not the R arrow package.

 
    
  
    

      Package: GExPipe

      Commit: bf56949bca5c11f3b7efab2cb721bcff30f6bc6c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 20:04:18 +0500

      Commit message:


	  
		
 global.R: use background Rscript subprocess for package install

Previously global.R called BiocManager::install() directly in the main
R session. If RStudio had already loaded ggplot2, xgboost, biomaRt etc.
at startup, those DLLs were Windows-locked and silently skipped — causing
the app to open with missing packages and static features.

Fix: mirror the subprocess approach from utils_shiny_app.R. A fresh
Rscript --vanilla process starts with zero packages loaded, so no DLL
is locked and every missing package installs cleanly regardless of what
the parent session has loaded.

 
    
  
    

      Package: GExPipe

      Commit: f5fb25267aa532327a2e26737c22efe608cc6319

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 18:30:07 +0500

      Commit message:


	  
		
 Move feature packages from Suggests to Imports for zero-missing install

Boruta, cicerone, mixOmics, xgboost, SHAPforxgboost, rms, rmda, and
biomaRt were in Suggests — skipped by plain remotes/BiocManager installs
without dependencies = TRUE. This caused Step 10 (ML), Step 13
(nomogram/DCA), guided tour, and Ensembl ID mapping to silently fail.

Changes:
- DESCRIPTION: move all 8 packages from Suggests to Imports so every
  install method (remotes, BiocManager, devtools) installs them
- global.R: merge optional list into required; .gexpipe_all_optional = c()
- utils_shiny_app.R: merge optional into core in .gexpipe_all_pkgs()
- server_packages.R (both copies): reclassify those 8 as "Core" in
  the Packages tab so they show the correct badge colour

 
    
  
    

      Package: GExPipe

      Commit: ffb962fa2f303db0aa66c65e7663a8556dab0f31

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 17:53:10 +0500

      Commit message:


	  
		
 vignette: switch install to BiocManager with dependencies = TRUE

remotes::install_github() without dependencies = TRUE only installs
Imports: packages, leaving Suggests: packages (Boruta, cicerone,
mixOmics, xgboost, rms, rmda, biomaRt) uninstalled. This caused the
ML tab, nomogram, guided tour, and Ensembl ID mapping to silently fail
after install — the app loaded but those features did nothing.

Fix: replace remotes::install_github() with BiocManager::install() +
dependencies = TRUE in both the install-github block and the Option 2
install-then-launch block. BiocManager resolves both CRAN and
Bioconductor repos correctly, ensuring every Suggests: package installs.

 
    
  
    

      Package: GExPipe

      Commit: cb591440da75bf4f7642f4eb536f838060e49f75

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 17:30:15 +0500

      Commit message:


	  
		
 vignette: fix runGitHub calls — add ref = main and subdir = inst/shinyapp

app.R lives at inst/shinyapp/app.R, not the repo root, so runGitHub
without subdir would silently fail to find the app. Fix all three
runGitHub calls (Option 1, Colab R runtime, Colab Python runtime):
  - ref = "main"            → always pulls latest committed code
  - subdir = "inst/shinyapp" → points Shiny to where app.R actually is

Also update the "What happens under the hood" description to match.

 
    
  
    

      Package: GExPipe

      Commit: b3d695d7d3498a3a493e6c30501d890780568458

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 17:23:33 +0500

      Commit message:


	  
		
 vignette: improve install-github comments and sync Option 2 block

- Add explanatory comment for force = TRUE in the install-github block
  (clarifies it reinstalls even when an older version is already present)
- Update launch comment to reference the new Launch section and Colab options
- Add Packages tab tip (green/red status signal for every dependency)
- Add force = TRUE + matching comment to Option 2 install-then-launch block
  for consistency with the install-github block

 
    
  
    

      Package: GExPipe

      Commit: e819bcacbd64c42d219672ccb8db42abb5572304

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 14:40:45 +0500

      Commit message:


	  
		
 Update vignette: add runGitHub option and full Google Colab instructions
 
    
  
    

      Package: GExPipe

      Commit: 66bfa1677baee58d11c3cd9ccf6653515173cabe

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-22 14:05:32 +0500

      Commit message:


	  
		
 Add Packages status tab and fix RNA-seq download crash
 
    
  
    

      Package: GExPipe

      Commit: dcbfa9edcf902c496d28e1650bd65aa5d572e2ba

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 16:37:33 +0500

      Commit message:


	  
		
 Add 40-min timeout and auto-remove 00LOCK dirs before install
 
    
  
    

      Package: GExPipe

      Commit: 7415047597ec51c0f996466db58128f172f3070e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 14:23:18 +0500

      Commit message:


	  
		
 Update vignette: fix typo, update launch section, add R version warning
 
    
  
    

      Package: GExPipe

      Commit: 6bed2e6e82fdc153cb21647fd8ff02d8b2b5ea7e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 14:20:18 +0500

      Commit message:


	  
		
 Fix: gexpipe_setup uses subprocess to prevent session restart errors
 
    
  
    

      Package: GExPipe

      Commit: 14555ebe04012b40781f99fddc8d2ad234baead6

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 14:15:52 +0500

      Commit message:


	  
		
 Fix: initialise still_missing at top of batch install function
 
    
  
    

      Package: GExPipe

      Commit: 5f4dfece2423ec2bf1d7fbc8bba9337a86f2f0db

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 14:09:38 +0500

      Commit message:


	  
		
 Revert source/binary type detection, let BiocManager decide
 
    
  
    

      Package: GExPipe

      Commit: 3ebdba6e9f0ea5296fd0effb556d1d266b970e92

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 13:41:17 +0500

      Commit message:


	  
		
 Add --no-staged-install to prevent corrupt .rdb on Windows
 
    
  
    

      Package: GExPipe

      Commit: bbc14302e726349a78eca991186ec1eb12f852e9

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 13:05:58 +0500

      Commit message:


	  
		
 Update package installer and vignette
 
    
  
    

      Package: GExPipe

      Commit: 31aa0287b10bf4140640b657ed5b110cb98230fd

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 12:15:45 +0500

      Commit message:


	  
		
 Force binary package type on Windows to prevent DLL ABI mismatch
 
    
  
    

      Package: GExPipe

      Commit: b7c637c6492e7e7224ac4685bfc758c5780ef7f3

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 11:36:52 +0500

      Commit message:


	  
		
 Fix subprocess install: mirror parent .libPaths() and always use force=TRUE
 
    
  
    

      Package: GExPipe

      Commit: 33055e47ce79d76770c2c309a8daadadb72a809c

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 11:20:14 +0500

      Commit message:


	  
		
 Fix broken-package detection: use force=TRUE for on-disk but unloadable packages
 
    
  
    

      Package: GExPipe

      Commit: 40f119b0f226c8feb97e627641dc9ab7f40450a4

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 10:57:26 +0500

      Commit message:


	  
		
 Add GExPipe project sub-files
 
    
  
    

      Package: GExPipe

      Commit: b9c24679196623ddbd92bb3695e31ab62c35a879

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 10:47:10 +0500

      Commit message:


	  
		
 Refactor PPI server logic and update UI components
 
    
  
    

      Package: GExPipe

      Commit: 496192ec178b4f053daf8b4599e69b86fa22301e

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 10:43:19 +0500

      Commit message:


	  
		
 Fix Windows DLL-lock error by installing packages in Rscript subprocess
 
    
  
    

      Package: GExPipe

      Commit: 6819b906e766e0bab88459ed9cd67bc8f5eee6a5

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 08:10:02 +0500

      Commit message:


	  
		
 Auto-install all dependencies inside runGExPipe() before app launches
 
    
  
    

      Package: GExPipe

      Commit: ec54c1bcff36b1f5e2693ad67fa93ed5914d33ec

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-21 08:00:59 +0500

      Commit message:


	  
		
 Release v0.99.7: R 4.4/4.5/4.6 support, auto-install, vignette fixes, repo cleanup
 
    
  
    

      Package: GExPipe

      Commit: f0c5ca580c10ac1619052f6fffe4159024f4821f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-20 22:03:50 +0500

      Commit message:


	  
		
 Release v0.99.7: R 4.4/4.5/4.6 support, auto-install, vignette fixes, repo cleanup
 
    
  
    

      Package: GExPipe

      Commit: 11d61338aba007b75a00058be047f8d2dc3c56e9

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 20:10:47 +0500

      Commit message:


	  
		
 Docs: restructure user vignette and polish app title behavior.

Align the main vignette with Bioconductor Shiny guidance using a user-first workflow, explicit install/launch instructions, executable example chunks, and simplified system.file()-based extdata loading. Also set an explicit browser page title and add screenshot folder guidance for documentation assets.

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: 783de89c6b477e1651a5fe862f08117fc0bad2d6

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 17:39:48 +0500

      Commit message:


	  
		
 Fix Shiny step navigation and app path resolution
 
    
  
    

      Package: GExPipe

      Commit: 892793da17f8e3d198ea7217acda1e75bc4fe024

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 12:18:51 +0500

      Commit message:


	  
		
 Docs: Update run instructions in README for clarity and runGitHub
 
    
  
    

      Package: GExPipe

      Commit: 56f8b907e2b2f9e6399c437b114485bfad4a4ff9

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 12:16:13 +0500

      Commit message:


	  
		
 Update version to 0.99.6 and R dependency to 4.6.0
 
    
  
    

      Package: GExPipe

      Commit: 70fd446c7cb71f00dd631131c0950522600d6c60

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 11:51:24 +0500

      Commit message:


	  
		
 Fix: Force source local R files to bypass cached namespace
 
    
  
    

      Package: GExPipe

      Commit: 9bedfa903827714b21df3250d28f14ab0a95e08d

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 11:33:07 +0500

      Commit message:


	  
		
 Update application code
 
    
  
    

      Package: GExPipe

      Commit: ebad309da5b047d2df47fe39bc2d2247284bfdfa

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 11:30:12 +0500

      Commit message:


	  
		
 Fix: Add window.scrollTo to validation next button
 
    
  
    

      Package: GExPipe

      Commit: e237cffacd8059a8d4aaf3cefc0ea51ce5ab5ba9

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 11:01:03 +0500

      Commit message:


	  
		
 Fix: Add window.scrollTo to GSEA next button
 
    
  
    

      Package: GExPipe

      Commit: c922663cfb66dc30cc9bf863e3ba695d78054397

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 10:26:28 +0500

      Commit message:


	  
		
 Improve Next buttons by scrolling to top of page on navigation
 
    
  
    

      Package: GExPipe

      Commit: 972d934e83916740dd1be529ec4cbd86590706dc

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 10:18:49 +0500

      Commit message:


	  
		
 Update placeholder GSE IDs to real examples
 
    
  
    

      Package: GExPipe

      Commit: d5e2f8f1c809be6686a8c25f067b9639b6c85779

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 09:42:21 +0500

      Commit message:


	  
		
 Update R version dependency to 4.5.0
 
    
  
    

      Package: GExPipe

      Commit: 90ce9be237cb0f706edd188802ff998a7c8e2a5f

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 09:16:58 +0500

      Commit message:


	  
		
 Fix CSS application for dynamic dashboard UI
 
    
  
    

      Package: GExPipe

      Commit: 8053aaa83e5f211c3807b598ff8c157aafe17c35

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 09:06:07 +0500

      Commit message:


	  
		
 Fix UI styling and GitHub deployment
 
    
  
    

      Package: GExPipe

      Commit: acead813fac2ac4a3a5c2407c7995ffd0d848d37

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-18 08:58:59 +0500

      Commit message:


	  
		
 Fix UI styling: Add custom CSS block to package UI function
 
    
  
    

      Package: GExPipe

      Commit: aab22252c632209ccf68dcc6f08adcbd4784d206

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-17 21:35:06 +0500

      Commit message:


	  
		
 Initial commit of Gexpipe
 
    
  
    

      Package: GExPipe

      Commit: b8ac3b0196434982935a3d86d552c861b49abbbb

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-02 11:53:39 +0500

      Commit message:


	  
		
 Update selected vignettes
 
    
  
    

      Package: GExPipe

      Commit: 8a73962c97c8c4314b93d9b97246c2bb78020252

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-02 11:27:35 +0500

      Commit message:


	  
		
 Revert version to 0.99.5; align NEWS

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: 14fa6f5711aa58ca752c1971d84acc811527b636

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-02 11:17:27 +0500

      Commit message:


	  
		
 Remove gexpipe-workflow vignette; update references and NEWS

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: 94d01b96a170a6b697c0dd476338f290c4029a50

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-02 11:05:59 +0500

      Commit message:


	  
		
 Vignettes: update GExPipe and shiny-testing-ci; remove architecture vignette; ignore local vignette data exports

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: f316fc0a011d52858b44a979d76642d802f2f984

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-04-02 10:21:01 +0500

      Commit message:


	  
		
 Bump version to 0.99.6; update NEWS for vignette and install docs

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: afeabb46c4cd8cc79bda212cd136dcbd4a970fbb

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 18:42:47 +0500

      Commit message:


	  
		
 Prepare 0.99.5 Bioconductor resubmission.

Bump package version to 0.99.5, update NEWS with reviewer-facing fixes, remove CITATION until a DOI is available, and include current code/style updates to improve SPB/BiocCheck readiness.

Made-with: Cursor
 
    
  
    

      Package: GExPipe

      Commit: 004d0c53e0b040aad0586e6e1e3c790471bb1e30

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 17:13:31 +0500

      Commit message:


	  
		
 Update app navigation and pipeline summary step
 
    
  
    

      Package: GExPipe

      Commit: b812d69b13c459b7c161a12f42f23fa9369c9284

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 16:30:19 +0500

      Commit message:


	  
		
 Address Bioconductor review checks and R 4.6 compatibility
 
    
  
    

      Package: GExPipe

      Commit: 5103c8fa3081dca1d25f63211f14de781eec5900

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 16:27:38 +0500

      Commit message:


	  
		
 Address Bioconductor review checks and R 4.6 compatibility
 
    
  
    

      Package: GExPipe

      Commit: 40c56a8123c44d1f34d4787937f57812c3d21f36

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-29 18:48:11 +0500

      Commit message:


	  
		
 Sync local GExPipe changes for GitHub
 
    
  
    

      Package: GExPipe

      Commit: 942f521d7a88ddf08699b38515115bb192d7e13a

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-27 16:55:49 +0500

      Commit message:


	  
		
 Finalize Bioconductor readiness: runnable vignettes, shiny tests, and check cleanups
 
    
  
    

      Package: GExPipe

      Commit: 992e2a9ce1bfe44009a17a7e5129cd7f31998d45

      Author:  SAFA RAFIQUE <53168745+safarafique@users.noreply.github.com> 

      Date: 2026-03-18 22:45:07 +0500

      Commit message:


	  
		
 Bump version from 0.99.1 to 0.99.2

Removed Additional_repositories from DESCRIPTION
Added ShinyApp to biocViews
Moved core logic to R/ directory: download, normalization, batch correction, differential expression, WGCNA, and helper functions are now in R/ as reusable exported functions (following iSEE-style structure). Shiny server files call these helpers.
Added runGExPipe() launcher as the main entry point
R CMD check passes cleanly: 0 errors, 0 warnings, 0 notes
Fixed LICENSE format to proper DCF stub (MIT + file LICENSE)
Fixed R version dependency to R (>= 4.5.0) 
    
  
    

      Package: ivygapSE

      Commit: a2ce36af2fd73bdebd7af830e681640a6ef4379d

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-06-22 05:39:44 -0400

      Commit message:


	  
		
 update to restore app functionality
 
    
  
    

      Package: ProteinBatcher

      Commit: 20b2985916da69b4fce6fe9ca1f62b613041e8ef

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-06-22 11:38:13 +0200

      Commit message:


	  
		
 Review package changes
 
    
  
    

      Package: TFEA.ChIP

      Commit: 1b6975290751898f98ec0f8081a5ac80fd37a222

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2026-06-22 09:39:34 +0200

      Commit message:


	  
		
 Fix bump v
 
    
  
    

      Package: TFEA.ChIP

      Commit: 6abd5ead9f8785381c03ffbd5bc45a7fdc949fdc

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2026-06-22 09:36:53 +0200

      Commit message:


	  
		
 Fix package CITATION file
 
    
  
    

      Package: netboost

      Commit: 62b63085997d45fc4332a748a814efd51c42e744

      Author:  PascalSchlosser <pascal.schlosser@uniklinik-freiburg.de> 

      Date: 2026-06-21 20:43:51 +0200

      Commit message:


	  
		
 Fix Windows -Wformat WARNING (size_t %zu) and BugReports NOTE; bump to 2.21.3
 
    
  
    

      Package: TSENAT

      Commit: 93ad6b3ecaba0d09e7b676ce7280f217f4e4f4e4

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-21 13:47:25 +0200

      Commit message:


	  
		
 Fix test
 
    
  
    

      Package: TSENAT

      Commit: 3fa8ced9e56aab8d9878b38b82a38980919e9fac

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-21 13:39:36 +0200

      Commit message:


	  
		
 Merge branch 'stable' into devel 
    
  
    

      Package: TSENAT

      Commit: cc24a129dc7a61d6a81c915e90b48150866cd92c

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-21 13:38:42 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: 4cb109b6a0a4dca216d8f4c60dee129a252ef9f9

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-21 01:14:23 +0200

      Commit message:


	  
		
 Devel (#47)

* version bump: 0.99.0 -> 0.99.1

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

* version bump: 0.99.2 -> 0.99.3

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

* version bump: 0.99.3 -> 0.99.4

* Simplify .gitignore: remove problematic patterns and comments

* version bump: 0.99.4 -> 0.99.5

* Remove CITATION file: no doi yet for new package

* version bump: 0.99.5 -> 0.99.6

* Tests fixed

* Fix issues

* Skip tests

* Bump version

* Fix issues

* Bump version

* Fix .gitignore

* Bump version

* Fix tests

* Bump

* Fix issues

* Fix tests

* Fix tests

* Speed up examples

* Fix coding style

* Fix tests

* Add skip_on_bioc

* Bump version

* Fix tests

* Fix build issue

* Bump

* Fix building issue

* Bump version

* Fix test

* Bump version

* Remove space

* Bioconductor submission review

* Bioconductor submission review

* Fix format issue

* Increase test coverage

* Fix punctuation README.md

* Fix codefactor style

* Increase coverage

* Increase coverage

* Fix codefactor issues

* Fix notes and failing test in Mac

* Fix Windows compatibility

* Fix bugs and add tests

* Fix tests

* Add addtional tests

* Fix tests

* Add new tests

* Add addtional tests and fix bug

* Add new tests

* Fix failing tests on Windows and Mac

* Fix codefactor issue

* Fix Windows build errors

* Fix tests

* Fix codefactor

* Increase coverage

* Fix codefactor

* Increase coverage 
    
  
    

      Package: TSENAT

      Commit: 272c972d72b82a1e050115ecf130441e1f9124c6

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 23:03:47 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: e4fcf38ad753e544997b2e427d45614379a76e11

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 22:00:12 +0200

      Commit message:


	  
		
 Fix codefactor
 
    
  
    

      Package: TSENAT

      Commit: d9ce3f0e75f970ad89aebe9346f009b7a964ce0f

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 21:58:23 +0200

      Commit message:


	  
		
 Increase coverage
 
    
  
    

      Package: TSENAT

      Commit: 4b9820692f48ea63aa3c3fe25ade6192f42ad0da

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 20:52:32 +0200

      Commit message:


	  
		
 Fix codefactor
 
    
  
    

      Package: TSENAT

      Commit: ed7cdd00cdb4bfd98e39bdb939e6865499b3dfdf

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 20:47:29 +0200

      Commit message:


	  
		
 Fix tests
 
    
  
    

      Package: TSENAT

      Commit: 759ed9cd3545d81d6657164b0ed1b0ade7f99242

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 18:04:37 +0200

      Commit message:


	  
		
 Merge branch 'stable' into devel 
    
  
    

      Package: TSENAT

      Commit: e1ea3249942d06272e1a53934b881999b8dc64c0

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-20 18:03:20 +0200

      Commit message:


	  
		
 Fix Windows build errors
 
    
  
    

      Package: TSENAT

      Commit: 2dc82d5c3083975dec6003ed03e6c8f5abd712b3

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-19 22:59:59 +0200

      Commit message:


	  
		
 Devel (#46)

* Fix codefactor issue 
    
  
    

      Package: MSstatsConvert

      Commit: dbf8afb0add571ab5d17131825b5c60f35e9867d

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-06-19 17:12:17 -0400

      Commit message:


	  
		
 Bump version to 1.23.2 
    
  
    

      Package: MSstatsConvert

      Commit: 700a25d4be4972dbf30e5fcf2679e590be6f4619

      Author:  Swaraj Patil <patil.swaraj@northeastern.edu> 

      Date: 2026-06-10 13:06:59 -0400

      Commit message:


	  
		
 feat(mzmine): Add SIRIUS annotations and mz_rt fallback to MZMine converter (#138) 
    
  
    

      Package: MSstatsConvert

      Commit: 9f0fee945ef883f794404908d3304bd12375a0d3

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-06-04 17:24:09 -0700

      Commit message:


	  
		
 chore(spectronaut): Remove unnecessary columns from spectronaut example for vignette clarity (#139) 
    
  
    

      Package: phantasusLite

      Commit: 9349f30c9b1ef00ed4c5bd25d449c2d96a1df99e

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-19 12:00:08 -0500

      Commit message:


	  
		
 version bump
 
    
  
    

      Package: phantasusLite

      Commit: 968202b6084494d0b3b0ca155151c1a62a07a393

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-18 18:21:20 -0500

      Commit message:


	  
		
 GEOquery version
 
    
  
    

      Package: phantasusLite

      Commit: 0ec82847dfaf1450ebbf31f982fc641fe34f0d50

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-18 17:54:06 -0500

      Commit message:


	  
		
 force getGEO to return ExpressionSet
 
    
  
    

      Package: phantasusLite

      Commit: e2746cdeee4fac024da6036d6d7a33b066901462

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-18 17:26:51 -0500

      Commit message:


	  
		
 alserglab references
 
    
  
    

      Package: phantasusLite

      Commit: 6b9fefba96c1dce26c03f0af3b744b052c66097d

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-10 12:49:21 -0500

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
    

      Package: phantasusLite

      Commit: f45afaf37be94c89c19088b5c2e8ba65037d2657

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2024-08-28 16:20:25 -0500

      Commit message:


	  
		
 readGct correctly handles case with no column annotations
 
    
  
    

      Package: phantasusLite

      Commit: eb17a1dbae0deb53b75b9904ed76465168b49f5c

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2024-08-28 13:37:26 -0500

      Commit message:


	  
		
 readGct support for duplicate column names
 
    
  
    

      Package: TFEA.ChIP

      Commit: de68f2dbe71a7106e5af4eee57433a00f630c250

      Author:  yosra <yosraberrouayel@gmail.com> 

      Date: 2026-06-19 15:13:49 +0200

      Commit message:


	  
		
 update fx and metadata
 
    
  
    

      Package: scECODA

      Commit: 64cdfaa183996eb76d07ecc014811be39c2a0731

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-06-19 16:59:59 +0200

      Commit message:


	  
		
 plot_boxplot: Add wrap_by_celltype parameter
 
    
  
    

      Package: scECODA

      Commit: 67e4913f91ef8bc6c583f464281cc70049692060

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-06-17 16:54:52 +0200

      Commit message:


	  
		
 * plot_heatmap: Handled error case if user provided no label_col
* Improved robustness: & -> && in plot_pca and plot_barplot
* Updated roxygen documentation format to newest version
 
    
  
    

      Package: scECODA

      Commit: f0a0ef478e2e011636ee5e2bdee3ea1d954b488e

      Author:  halterc <chalterbio@gmail.com> 

      Date: 2026-06-17 16:53:18 +0200

      Commit message:


	  
		
 Update gitignore
 
    
  
    

      Package: universalmotif

      Commit: a4d61cb7dab32e0851d0232608a1cccfba9e35b0

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 12:35:32 +0100

      Commit message:


	  
		
 update version
 
    
  
    

      Package: universalmotif

      Commit: 681cc9a3ac696ce7d41fa082828b9a8dfea82df5

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 12:32:57 +0100

      Commit message:


	  
		
 Remove the "mirrors yamtk" framing from the vignettes

Drop the attribution prose that described the lite functions and the
de novo finder as mirroring the yamtk command-line tool, matching the
earlier removal of the same framing from the R docs. Covers
compare_motifs_lite() ("default surface aligned with yamtk"),
enrich_motifs_lite() (the "mirror yamtk", "yamtk enr default", and
"TSV from yamtk enr one-for-one" lines), and motif_finder() ("defaults
mirror yamtk" and "yamtk-specific stats"). The functions are now
described on their own terms.

The yamtk references in the speed-comparison sections are left in
place: there yamtk is a benchmark baseline alongside motifmatchr, not
an attribution, so removing it would gut the comparison.
 
    
  
    

      Package: universalmotif

      Commit: 2b68e5d6f6926053fa8507e2b11671eb172eb26e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 11:23:46 +0100

      Commit message:


	  
		
 bump version
 
    
  
    

      Package: universalmotif

      Commit: 31d7adf592dbb8ea69ea71930d6a45a9f45c1f4c

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 11:23:17 +0100

      Commit message:


	  
		
 Remove yamtk mentions from the R docs and README

Strip references to the yamtk command-line tool from the roxygen
documentation and internal comments of the lite functions and the de
novo finder, and from the one mention in README. The functions are now
described on their own terms: compare_motifs_lite(),
scan_sequences_lite(), enrich_motifs_lite() and dedup_hits() drop the
"mirrors yamtk" framing and the yamtk @references citation, and
motif_finder() keeps its STREME (Bailey 2021) attribution but no longer
routes it through yamtk. The man pages are regenerated to match.

DESCRIPTION had no yamtk mentions. The references in NEWS, src, tests
and the vignettes are intentionally left untouched.
 
    
  
    

      Package: universalmotif

      Commit: 11ecf4e96f53aff634dc6f9fa2c87f1bfb222744

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 11:13:13 +0100

      Commit message:


	  
		
 Rename the lite comparison C++ symbols to match the _lite convention

Follow-up to the *2 -> *_lite rename: harmonise the internal C++ layer
so it no longer carries the old "2" identity. Rename the dedicated
source file src/compare_motifs2.cpp to compare_motifs_lite.cpp and its
three exported primitives:

  compare_motifs2_align_cpp     -> compare_motifs_lite_align_cpp
  compare_motifs2_pvalue_cpp    -> compare_motifs_lite_pvalue_cpp
  compare_motifs2_consensus_cpp -> compare_motifs_lite_consensus_cpp

Update the R-side callers in compare_motifs_lite(), merge_motifs_lite(),
and view_motifs_lite(), and rename the internal R helper
view_motifs2_align() to view_motifs_lite_align(). RcppExports.cpp and
RcppExports.R are regenerated via Rcpp::compileAttributes() so the
native-symbol registration picks up the new names; the reexports.Rd
cross-reference fix from make prep comes along as a byproduct.

These symbols are internal and never user-visible, so the package API
is unchanged. devtools::test(filter = "lite") passes (FAIL 0, PASS 190).
 
    
  
    

      Package: universalmotif

      Commit: 2961c804fa5262c57a6f64af8799a758014e3569

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 11:06:17 +0100

      Commit message:


	  
		
 Drop dead benchmark-file pointer from the comparison vignette

The speed-comparison table in the motif comparison vignette cited a
benchmark log at benchmarks/compare_motifs2_vignette.log, but that
directory is not tracked, so the reference dangled for anyone reading
the published vignette. Remove the pointer while keeping the note that
the numbers are baked in and the machine they were run on. Also replace
the stale cm2() shorthand with compare_motifs_lite() so the table
matches the surrounding prose.
 
    
  
    

      Package: universalmotif

      Commit: 074cc1f7766e452210befa532d59d52dbfdeb977

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-06-19 11:01:28 +0100

      Commit message:


	  
		
 Rename the lite motif functions from the 2 suffix to _lite

The seven minimalist, yamtk-aligned functions added during this
development cycle were named with a trailing "2" (compare_motifs2()
and so on). That suffix reads as "version 2", which implies the
original functions are superseded, whereas these are deliberately
pared-down counterparts with fewer options and features. Renaming
them to a descriptive _lite suffix is clearer and more findable, and
doing it now, before 1.32.0 ships, costs nothing because the names
have never appeared in a released version:

  compare_motifs2  ->  compare_motifs_lite
  scan_sequences2  ->  scan_sequences_lite
  enrich_motifs2   ->  enrich_motifs_lite
  merge_motifs2    ->  merge_motifs_lite
  merge_similar2   ->  merge_similar_lite
  view_motifs2     ->  view_motifs_lite
  motif_tree2      ->  motif_tree_lite

The original full-featured functions are untouched, so existing user
scripts keep working unchanged. The internal suggest_*2 helpers, the
universalmotif.suggest.*2 options, and the compare_report_from_v2
helper are renamed to match. The C++ symbols (compare_motifs2_*_cpp,
view_motifs2_align) keep their names since they are internal and
invisible to users. Each lite function now shares an @family tag, and
every full-featured counterpart links to its lite variant via
@seealso, so the pair is easy to discover from either direction.

NEWS, README, the vignettes, the tests, and the regenerated man pages
and NAMESPACE are all updated to the new names.
 
    
  
    

      Package: ProteinBatcher

      Commit: 03dcdf186c59aa9532243dcba936cbbe435a4295

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-06-19 11:38:57 +0200

      Commit message:


	  
		
 push new version
 
    
  
    

      Package: ProteinBatcher

      Commit: 80b3211444e5838e73d46e9b6c3332bee7d91113

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-06-19 11:37:53 +0200

      Commit message:


	  
		
 Bioconductor first review round
 
    
  
    

      Package: ProteinBatcher

      Commit: f7ff757ab9bf549c7e4e3f7c96a67e68c78c913e

      Author:  Aitor Moruno Cuenca <amoruno@almirall.com> 

      Date: 2026-06-09 14:35:54 +0200

      Commit message:


	  
		
 Solve error when no interaction is introduced in plotting
 
    
  
    

      Package: damidBind

      Commit: c287f1ca69009f5b5ac796685c6a9f07ed676e23

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:31:10 +0000

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 
    
  
    

      Package: damidBind

      Commit: ff3b37fdcfa8556e3109452a76134aac09add075

      Author:  Marshall lab <85987664+marshall-lab@users.noreply.github.com> 

      Date: 2026-06-19 18:21:44 +1000

      Commit message:


	  
		
 Merge pull request #1 from marshall-lab/metadata_refactor

Metadata refactor 
    
  
    

      Package: damidBind

      Commit: 5e7a139c1b62bc9fad553d8b15f18b6b7dce3393

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:20:20 +0000

      Commit message:


	  
		
 Updated to devel release 1.1.1
 
    
  
    

      Package: damidBind

      Commit: 1bffac4a011710d6b4f76a4468a3af06e8464e13

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:19:58 +0000

      Commit message:


	  
		
 Added the bioRxiv manuscript citation
 
    
  
    

      Package: damidBind

      Commit: 55f15ec10a0410bce22dc4b923992a395f940105

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:19:34 +0000

      Commit message:


	  
		
 Added new diagnostic plots
 
    
  
    

      Package: damidBind

      Commit: 8ecf4ef96716107e6542e69a1caf8b131f072494

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:19:17 +0000

      Commit message:


	  
		
 `plot_volcano()` now takes a new `labels` option, values of `"all"`, `"highlight"`, or a character vector containing one or more group names from the `highlight` list.  Only this group will be labelled on the plot.  The original label configuration options still remain.

`plot_volcano()` supports highlight groups of either loci or gene names, including different categories in the same plot.  The default "auto" behaviour matches a highlight group against whichever definition has the most matches, but use the new `highlight_by` option to enforce matching by either "gene_name" or "id" (i.e. locus).
 
    
  
    

      Package: damidBind

      Commit: cf7bec3cff4fe68cbc11fcc77d0d304ee9a1b43b

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2026-06-19 08:18:36 +0000

      Commit message:


	  
		
 Added genome annotation and input file metadata saving to DamIDResults S4 object, and updated accessors.
 
    
  
    

      Package: wSIR

      Commit: 38118c5eb735490b66db33940da5decea5a18d33

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-19 14:10:26 +1000

      Commit message:


	  
		
 version bump after bioc review edits
 
    
  
    

      Package: wSIR

      Commit: 5ed1d3ade3a97e6a12b06a04458b4ff0b32d8a8a

      Author:  Mwoo-usyd <106008614+Mwoo-usyd@users.noreply.github.com> 

      Date: 2026-06-19 09:07:25 +1000

      Commit message:


	  
		
 Merge pull request #7 from SydneyBioX/bioc_edits

Completed edits for bioconductor review 
    
  
    

      Package: wSIR

      Commit: fe922c9258b3a36291bfa335cdb766766f84b2ad

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-18 18:43:12 +1000

      Commit message:


	  
		
 allow user to specify own bpparam
 
    
  
    

      Package: wSIR

      Commit: f9b69c6b6744ccfa76b362762fd0c5a3359d37cb

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-18 10:45:03 +1000

      Commit message:


	  
		
 change data name
 
    
  
    

      Package: wSIR

      Commit: 7ae006ec789961c8e74b5851722255b1221143e0

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-17 17:22:26 +1000

      Commit message:


	  
		
 finish tidying up for bioc review
 
    
  
    

      Package: wSIR

      Commit: 7d8ea413a88cb92f7e12421fa88afbb0c9983418

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-17 14:34:03 +1000

      Commit message:


	  
		
 some changes for bioc review
 
    
  
    

      Package: wSIR

      Commit: b7fff79fa4ab1a52f7d5a90c109b02b7dd3db418

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-16 14:25:02 +1000

      Commit message:


	  
		
 unit tests
 
    
  
    

      Package: wSIR

      Commit: 707c4cfdbf43c19f9b359c36dce183870c779f7a

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-16 09:55:15 +1000

      Commit message:


	  
		
 add some tests
 
    
  
    

      Package: wSIR

      Commit: 9a65b6b726235673f0153a74706e59d99890f7bd

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-03 14:12:51 +1000

      Commit message:


	  
		
 match up test to changing argument from WSIR to wsir
 
    
  
    

      Package: wSIR

      Commit: 16598cf18c2afaec7caba9afb4bbe5240489e100

      Author:  Maximilian John Woollard <maximilw@maths.usyd.edu.au> 

      Date: 2026-06-03 13:51:31 +1000

      Commit message:


	  
		
 roxygenise
 
    
  
    

      Package: wSIR

      Commit: ce58b74bc55a9df8f10aa8609cf8eb68d887116d

      Author:  Mwoo-usyd <mwoo5086@uni.sydney.edu.au> 

      Date: 2026-06-03 13:13:14 +1000

      Commit message:


	  
		
 changes
 
    
  
    

      Package: wSIR

      Commit: bcdbc15a204c43ed00d1a2ca974b3566a07cdc0f

      Author:  Mwoo-usyd <mwoo5086@uni.sydney.edu.au> 

      Date: 2026-06-03 12:55:40 +1000

      Commit message:


	  
		
 changes for bioc review
 
    
  
    

      Package: wSIR

      Commit: 27ffc79ff435e49ee13207a5139961b857d55906

      Author:  Mwoo-usyd <106008614+Mwoo-usyd@users.noreply.github.com> 

      Date: 2026-06-02 13:47:30 +1000

      Commit message:


	  
		
 Merge pull request #6 from Bisaloo/bioc-review

Misc fixes from Bioconductor review 
    
  
    

      Package: wSIR

      Commit: 4e033f657598a66c1bdff8c84ef0d0f90ac6fb49

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 13:20:22 +0200

      Commit message:


	  
		
 Create umap_df directly

This avoid the cost of conversion from matrix
 
    
  
    

      Package: wSIR

      Commit: 8ca253dcffdc0c8d3e57e15ba0c95f315dcc78ed

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-27 13:19:32 +0200

      Commit message:


	  
		
 Add package level documentation
 
    
  
    

      Package: wSIR

      Commit: b3c673e6d7907a59db09952212374546ded41e47

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-01 18:47:39 +0200

      Commit message:


	  
		
 Do not include .o or .so files in sources
 
    
  
    

      Package: wSIR

      Commit: c40725c0f7be52e9ae69ad1217b6d763f2e70247

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-01 16:53:06 +0200

      Commit message:


	  
		
 Fix typos in vignette
 
    
  
    

      Package: wSIR

      Commit: 29b2871fae1a0021ab9952b1bd381a1d3e7ee5ca

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-04-01 16:52:55 +0200

      Commit message:


	  
		
 Fix code block formatting in README
 
    
  
    

      Package: TSENAT

      Commit: 9023af29fb6e2de8c8dd0155f029164903a14ee5

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-19 02:38:02 +0200

      Commit message:


	  
		
 Fix codefactor issue
 
    
  
    

      Package: TSENAT

      Commit: 6768bb50413c401b8bcb0cd39e3bed0aba939884

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-19 02:12:28 +0200

      Commit message:


	  
		
 Fix failing tests on Windows and Mac
 
    
  
    

      Package: TSENAT

      Commit: 6e452304351b0aa44ae22c6a42047a5f8d08615a

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-17 15:28:20 +0200

      Commit message:


	  
		
 Merge branch 'stable' into devel 
    
  
    

      Package: TSENAT

      Commit: 1fec060a7a4bb33d01f869728d1aec18563380d6

      Author:  gallardoalba <gallardoalbac@gmail.com> 

      Date: 2026-06-17 15:26:27 +0200

      Commit message:


	  
		
 Add new tests
 
    
  
    

      Package: TSENAT

      Commit: e9cd973c8c5ad55dc8b9381b1dc5de39e8df7a6f

      Author:  Cristóbal Gallardo Alba <gallardoalbac@gmail.com> 

      Date: 2026-06-17 15:10:53 +0200

      Commit message:


	  
		
 Devel (#45)

* version bump: 0.99.0 -> 0.99.1

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

* version bump: 0.99.2 -> 0.99.3

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

* version bump: 0.99.3 -> 0.99.4

* Simplify .gitignore: remove problematic patterns and comments

* version bump: 0.99.4 -> 0.99.5

* Remove CITATION file: no doi yet for new package

* version bump: 0.99.5 -> 0.99.6

* Tests fixed

* Fix issues

* Skip tests

* Bump version

* Fix issues

* Bump version

* Fix .gitignore

* Bump version

* Fix tests

* Bump

* Fix issues

* Fix tests

* Fix tests

* Speed up examples

* Fix coding style

* Fix tests

* Add skip_on_bioc

* Bump version

* Fix tests

* Fix build issue

* Bump

* Fix building issue

* Bump version

* Fix test

* Bump version

* Remove space

* Bioconductor submission review

* Bioconductor submission review

* Fix format issue

* Increase test coverage

* Fix punctuation README.md

* Fix codefactor style

* Increase coverage

* Increase coverage

* Fix codefactor issues

* Fix notes and failing test in Mac

* Fix Windows compatibility

* Fix bugs and add tests

* Fix tests

* Add addtional tests

* Fix tests

* Add new tests

* Add addtional tests and fix bug 
    
  
    

      Package: gatom

      Commit: 4bd914ef0a6f5fe2925224602756290ca258027e

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-18 18:23:36 -0500

      Commit message:


	  
		
 KEGGREST version
 
    
  
    

      Package: gatom

      Commit: 72f1b74e2cf49fd37d15ab075314c0f63bbab99c

      Author:  Alexey Sergushichev <alsergbox@gmail.com> 

      Date: 2026-06-18 17:24:06 -0500

      Commit message:


	  
		
 fix for KEGGREST updates
 
    
  
    

      Package: CycleMix

      Commit: 7821a8d38021c30fb985de7b25f8d542319ed0cf

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-06-18 17:49:24 -0400

      Commit message:


	  
		
 bioConductor resubmission
 
    
  
    

      Package: CycleMix

      Commit: 73b416a9b0e6dcf2009a54a539831d476ec93211

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-06-18 17:43:11 -0400

      Commit message:


	  
		
 update vingette
 
    
  
    

      Package: CycleMix

      Commit: d57a3da27ecded9f34c0f7ebf809473cbcd92a16

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-06-18 16:59:47 -0400

      Commit message:


	  
		
 remove class() function calls
 
    
  
    

      Package: CycleMix

      Commit: 75ad0ff7fc7f874f285aa18652521270bfe60025

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-06-18 12:15:00 -0400

      Commit message:


	  
		
 bioc error fix
 
    
  
    

      Package: ENmix

      Commit: 46bcb91c692f1f87584c3ada178c88550d09c5ee

      Author:  xuz1 <xuz@niehs.nih.gov> 

      Date: 2026-06-18 11:05:09 -0400

      Commit message:


	  
		
 bugfix

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

      Package: MeLSI

      Commit: 19902ee27eb55b11d471d7afb62c7e53eccba723

      Author:  Nathan Bresette <nathanbresette04@gmail.com> 

      Date: 2026-06-17 16:23:49 -0500

      Commit message:


	  
		
 MeLSI 1.1.7: C++ weak-learner optimizer (~4.6x, ~2x end-to-end)

Port optimize_weak_learner_robust to a C++ kernel (melsi_opt_weak_learner).
The gradient loop draws its within/between-class pairs with R's own
R_unif_index, so it consumes the global RNG stream identically to the
sample()-based R loop. End-to-end F-statistics reproduce 1.1.6 to ~1e-15
with no p-value changes. Profiling showed this loop was ~83% of runtime.
 
    
  
    

      Package: MeLSI

      Commit: 57f8d9525e450b5e3e3fd3de51b5acd9025d56c6

      Author:  Nathan Bresette <nathanbresette04@gmail.com> 

      Date: 2026-06-17 14:49:30 -0500

      Commit message:


	  
		
 Validate label length to prevent native out-of-bounds in F kernel

melsi() now errors clearly when length(y) != nrow(X), and .melsi_F_scaled
guards the C boundary, instead of the kernel reading past the label vector
(which segfaulted under R CMD check).
 
    
  
    

      Package: MeLSI

      Commit: c91bc5b9ece4ded235ea1fdca0abd8c64d270a6b

      Author:  Nathan Bresette <nathanbresette04@gmail.com> 

      Date: 2026-06-17 14:44:15 -0500

      Commit message:


	  
		
 Fused Rcpp PERMANOVA F kernel: plain-double accumulators, v1.1.6

Use double (not long double) accumulators with restrict pointers so the inner
loop vectorises at -O2; ~4x faster F-stat, ~1.3-2.2x end-to-end, composes with
BPPARAM. Statistically equivalent (no observed p-value flips; ~1e-12 relative
difference), not bit-identical.
 
    
  
    

      Package: MeLSI

      Commit: 79a16d015a81be19e292f1b36ccb7a4078b1d296

      Author:  Nathan Bresette <nathanbresette04@gmail.com> 

      Date: 2026-06-17 11:07:31 -0500

      Commit message:


	  
		
 WIP: fused Rcpp PERMANOVA F kernel wired into hot paths

Add src/melsi_fstat.cpp (single-pass squared-distance accumulation, long
double totals) and route the five F-only hot-path sites (F_null x2, early
stopping x2, ensemble weak-learner) plus F_observed through it. Distance
matrix still computed where needed for PCoA output.
 
    
  
    

      Package: SynExtend

      Commit: 8077d0c9fb004ff1eab0212ce190c48f2587cc01

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-06-18 13:00:17 +0100

      Commit message:


	  
		
 incomplete final line...
 
    
  
    

      Package: SynExtend

      Commit: 3d2b3d47e18a4a77c32be88973e54e9b8c555461

      Author:  npcooley <npcooley@gmail.com> 

      Date: 2026-06-18 12:52:45 +0100

      Commit message:


	  
		
 db access fixes
 
    
  
    

      Package: scifer

      Commit: 0f46ed0586ad97170de03b7271f48fd52135587b

      Author:  Rodrigo Arcoverde Cerveira <rodrigo.arcoverde@pixelgen.com> 

      Date: 2026-06-18 13:45:20 +0200

      Commit message:


	  
		
 Fix igblast() parse crash and harden test (v1.15.1)

igblast() crashed with the cryptic error 'argument of length 0' on the
Bioconductor build machines when the igblast output contained no AIRR
header line: grep() returned integer(0) and 'integer(0):length(res)'
errored. The wrapper now detects the missing header, returns NULL, and
echoes the captured igblast/conda output so the real failure is
diagnosable from the build log.

The 'returns a data.frame object' test now skips (instead of erroring)
when igblast/conda is unavailable in the test environment, while still
verifying the data.frame contract when igblast actually runs.

Also guard a division-by-zero in igblastwrap.py when zero sequences are
processed.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
 
    
  
    

      Package: Pedixplorer

      Commit: a11495594644d91f594a1719b2e081a31abe99a2

      Author:  Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> 

      Date: 2026-06-18 12:17:16 +0200

      Commit message:


	  
		
 Update website (#43)

* Update website

* Update readme

* Update readme
 
    
  
    

      Package: Pedixplorer

      Commit: 3d8417bf8f098313c524b6c0bdb9eb949753dbcb

      Author:  Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> 

      Date: 2026-06-18 10:32:44 +0200

      Commit message:


	  
		
 Fix licence (#42)

* Update documentation

* Update description

* Set back options

* Update GA
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: d94070748ac479d580d53419345e0f27890a319c

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-06-18 07:59:56 +0200

      Commit message:


	  
		
 Update DESCRIPTION and NEWS
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: f1b352b9ad7b221c46fbfdb65a892cff5cbae236

      Author:  Philippine Louail <philippine.louail@outlook.com> 

      Date: 2026-06-17 18:12:46 +0200

      Commit message:


	  
		
 Merge pull request #22 from rformassspectrometry/phili

pass fileName to backendInitialize() 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 15da030c20073db62fdc8de751df2b3bfa4cee41

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-06-17 16:51:53 +0200

      Commit message:


	  
		
 fix test to stricter
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 93bc1acb13de330e8ea23e7d51bca353286f06fa

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-06-17 16:48:39 +0200

      Commit message:


	  
		
 switch to exported for online download too
 
    
  
    

      Package: MsBackendMetaboLights

      Commit: 2ca4fab785ac928e9fa7a0e06813257b5198d1cc

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-06-17 16:23:37 +0200

      Commit message:


	  
		
 pass fileName to backendInitialize()
 
    
  
    

      Package: gDRstyle

      Commit: 09959b9a4ef3f329b31b0c129627df17255b3ea5

      Author:  darsoo <daro.scig@gmail.com> 

      Date: 2026-06-18 08:04:43 +0200

      Commit message:


	  
		
 Merge pull request #100 from gdrplatform/GDR-3433_2

fix: allow License NOTE for packages with file LICENSE 
    
  
    

      Package: gDRstyle

      Commit: 6ab473e8ad0a4e5035cc52a96d5d7bab47ee1da9

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-06-17 22:45:46 +0200

      Commit message:


	  
		
 ci: trigger build
 
    
  
    

      Package: gDRstyle

      Commit: ded973ee016d2404b203a5511f5c0ea593ea1371

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-06-17 21:43:11 +0200

      Commit message:


	  
		
 fix: check specific license text instead of generic restriction message
 
    
  
    

      Package: gDRstyle

      Commit: cade983d79e005485f111e7e6a960dd12a744786

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-06-17 21:42:44 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.5
 
    
  
  


</div>

</div>