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GIT Logs

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

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Package: gesel
Commit: 51cb1b77add18d2a54741883c7f897a487789b76
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-10-31 13:26:49 +1100
Commit message:

 Protect against overflow in num_genes= for validateDatabaseFiles.

Also bump version and date for a new release.

Package: gesel
Commit: 8bd621e0e07832c33e8200074f07e53e47601666
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-10-31 13:11:01 +1100
Commit message:

 Rename 'genes' to 'overlaps' in searchOverlappingSets results.

This avoids confusion with the argument of the same name.

Package: gesel
Commit: d9d07d8ef7da7d3392437fd80432d51b7235b71e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-10-30 01:07:08 +1100
Commit message:

 searchOverlappingGenes directly returns a dataframe, for simplicity.

We move the 'present' count into an attribute. Most people probably won't
be using it so we don't really need to put it in a convenient place.

Also fleshed out the tests for this function.

Package: gesel
Commit: 44fbaa1ca1b584659d1d03eda09008c9138eafd8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-10-29 23:59:21 +1100
Commit message:

 More explanatory comments in the test files.

Also renamed test file to match the new function name, and fleshed out
searchGenes() to actually test the default types=.

Package: MetaboDynamics
Commit: 6ad6c3abc1f82e35a9fcef21f480beb7f4b4cdc6
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-10-30 18:10:57 +0100
Commit message:

 version bump

Package: MetaboDynamics
Commit: 0aaf84188e8f438cc01254bcbfec013f6120fd4b
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-10-30 18:09:55 +0100
Commit message:

 fit_dynamics_model argument 'raw_plus_counts' changed to 'raw_plus_cell_counts'

Package: MetaboDynamics
Commit: bb40670c820738542f80755cb63dfe5fe25df8cc
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-10-30 17:05:31 +0100
Commit message:

 small nomenclatur changes

Package: curatedMetagenomicData
Commit: 8894f1a45b9705a754629e745e5e7e87c2398ac6
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-30 12:20:06 -0400
Commit message:

 bump version to 3.21.2

Package: curatedMetagenomicData
Commit: c89178c241d391c6ca3a8aaf143dd2297a059156
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-30 12:17:45 -0400
Commit message:

 docs: add R CMD check status badge to README

Package: curatedMetagenomicData
Commit: afd13adf72a4cda3c60ce60e7d5f20ef04bd5f8e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 19:58:28 +0200
Commit message:

 Merge pull request #343 from waldronlab/fix/ncbi-rownames-316

fix: give rownames = "NCBI" bare identifiers (#316)

Package: curatedMetagenomicData
Commit: d7848a6aa0901b3a7bf8cb51a27250178d2a5865
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 13:56:11 -0400
Commit message:

 docs: update the taxonomy section for the behaviour this PR changes

#342 merged first, so devel now documents the rank prefix that this PR
removes, and says the species-group rows are not filtered out when this
PR drops them.

Corrected on all three counts:

- "NCBI" row names are bare identifiers now, so they work as a join key
  rather than being something to avoid.
- "short" and "NCBI" return fewer rows than "long", for two distinct
  reasons: clades NCBI resolves no further than genus are dropped, and
  "NCBI" additionally sums clades that share an identifier. Both report
  themselves, and "long" stays lossless.
- "short" is the species name again, since the rows that made it
  sometimes a genus are no longer there.

man/ regenerated with roxygen2 8.0.0 and verified byte-identical.
DESCRIPTION and NAMESPACE reverted: regenerating also swaps RoxygenNote
for Config/roxygen2/version and reflows an Authors@R line, neither of
which belongs in this change.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 90609b42175b5509521f4112472928c8d018cca5
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 13:55:11 -0400
Commit message:

 Merge branch 'devel' into fix/ncbi-rownames-316

Package: curatedMetagenomicData
Commit: cd7a01346b53f4a6fc911229d69b32ef6863b154
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 19:54:14 +0200
Commit message:

 docs: explain how the three rownames vocabularies differ (#342)

* docs: explain how the three rownames vocabularies differ

Reported in #341: merging an external MetaPhlAn3 profile with
curatedMetagenomicData by species name silently drops taxa that NCBI has
reclassified since mpa_v30_CHOCOPhlAn_201901 was built. MetaPhlAn3
reports Bacteroides_dorei, rownames = "short" gives Phocaeicola_dorei,
and the rows never match.

Nothing is wrong with the data. "short" and "NCBI" are resolved against
NCBI in data-raw/rowData.R, so they follow current taxonomy, while "long"
keeps the MetaPhlAn clade string verbatim. The documentation did not say
so: it described "short" only as "(species name)", which is exactly the
assumption that fails.

Adds a Taxonomic names section to curatedMetagenomicData(), points the
rownames parameter at it in both functions, and says the same thing in
the vignette. Covers which option to join on, why the failure is silent,
and how to build a crosswalk from a returned object.

The scope is wider than the reported example: about 10% of species
(1,394 of 13,117) sit under a different genus in the two schemes, the
largest case being the 2020 Lactobacillus split.

man/ edited by hand to match: RoxygenNote is 7.3.2 and the installed
roxygen2 is 8.0.0, so regenerating would churn every man page.

* docs: correct the crosswalk and NCBI join advice

rowData() holds either names or identifiers, never both: the function
assigns rowDataLong for "long" and "short" and rowDataNCBI for "NCBI".
So the claim that a single returned object yields a three-way crosswalk
was false, and is removed.

The replacement advice is better anyway. To join on NCBI Taxonomy ID,
use the integer rowData() column rather than the row names, which avoids
the rank-prefixed labels reported in #316 entirely.

Also:

- returnSamples pointed at a "Taxonomic names" section that exists only
  on the curatedMetagenomicData help page. It now links there.
- Exact MetaPhlAn matching is qualified by database version rather than
  claimed unconditionally.
- "all-zero rows" was merge-strategy dependent. The guaranteed behaviour
  is a failed match, which is what the text now says.

* docs: correct the taxonomy snapshot, the rate, and the crosswalk

Three rounds of Copilot review plus a subagent review, all verified
against the data before acting.

The snapshot point (Copilot's second round, which I had not seen when I
pushed 53f95a3): rowDataLong and rowDataNCBI are generated offline by
data-raw/rowData.R and shipped in sysdata.rda. Nothing queries NCBI at
retrieval time. Calling them "current NCBI taxonomy" would have gone
stale the moment NCBI moved, so they are now described as a snapshot
taken when the packaged taxonomy is built.

The rate was overstated. 1,394 of 13,117 (10.6%) counts rows that are
never returned: only 10,363 of 13,128 rows are tips of phylogeneticTree
and reach a returned object. Among those it is 769 of 10,352, about 7%.
Roughly half of the affected rows are also phages, which MetaPhlAn names
after the host rather than by NCBI's virus genus, so attributing the
whole figure to reclassification was wrong too.

The crosswalk claim was an overcorrection. A "long" object does give a
clade-string to NCBI-name mapping on its own, because its row names and
its rowData() names are different vocabularies. What one object cannot
give is the integer identifiers alongside the names.

Also: species identifiers are stable across genus reclassification but
genus identifiers are not (Bacteroides 816, Phocaeicola 909656), so the
advice names the species column specifically. "long" returns slightly
more rows than the other options, which is now stated.

man/ still hand-edited, but \code{species:} is now \verb{species:} to
match what roxygen emits for a backtick span containing a colon. Both
.Rd files are now byte-identical to roxygen2 8.0.0 output, so
regenerating is a no-op for them.

* docs: correct the rank filtering and the "short" label description

Copilot's fourth round, verified before acting and correct on both points.

taxonomyRankEmpty() is called without a rank, so it defaults to
taxonomyRanks(x)[1], which is superkingdom given this object's column
order. No row has an empty superkingdom, so it flags zero rows and drops
nothing. The claim added in 4d72be6 that "long" returns more rows than
the other options was wrong, and is removed. I took it from a review
without checking it.

"short" is also not always the species name. getTaxonomyLabels() uses the
lowest available rank, which is genus for the MetaPhlAn species groups
and complexes that NCBI resolves no further. Those rows survive the
filter, and their presence is exactly why "NCBI" row names carry a rank
prefix, so the two facts are now stated together.

Both man pages remain byte-identical to roxygen2 8.0.0 output.

* docs: say where the integer taxonomy column comes from

Copilot's fifth round: the ID-join advice was not actionable from the
objects the vignette actually builds. Both examples request
rownames = "short", whose rowData() holds character names, so a reader
following the paragraph would look for an integer species column and not
find one.

Says plainly that the integer column exists only when the resource was
requested with rownames = "NCBI".

---------

Co-authored-by: Claude Opus 5 <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: d4c74bb2f6747a82d3069a9d1190f805aeddf9fc
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 13:46:37 -0400
Commit message:

 test: assert the merge behaviour, not just the label syntax

Copilot on #343: the rewritten test checked only that row names look like
bare integers, so it would pass even if duplicate-ID rows were averaged
rather than summed, or if agglomeration left rowTree inconsistent. Those
are the actual changes in this PR.

Adds assertions that cover them:

- column totals identical between "NCBI" and "short". Both drop the same
  taxa and only "NCBI" merges, so any aggregation other than a sum shows
  up as a difference.
- "NCBI" returns fewer rows than "short", which is the point: identifiers
  collapse where names do not.
- row count matches rowLinks(), so the tree stays consistent with the rows.
- the drop warning and the merge message both fire, with "long" asserted
  not to warn at all.

"long" still emits the unrelated "dropping rows without rowTree matches"
message, so that last one checks for no warning rather than for silence.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: a01638aaa254a50500c3cc279a955fa846620746
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 13:40:32 -0400
Commit message:

 fix: give rownames = "NCBI" bare identifiers (#316)

Two defects, propping each other up.

taxonomyRankEmpty() was called without a rank, so it defaulted to
taxonomyRanks(x)[1], which here is superkingdom and is never empty. It
flagged zero rows, so the filter never removed anything, and the block was
duplicated verbatim. Eleven rows are MetaPhlAn species groups and
complexes that NCBI resolves no further than genus, so the rows disagreed
on their lowest rank and getTaxonomyLabels() prefixed every label with its
rank, which is what #316 reports.

Naming the rank drops those eleven, which removes the prefixes. That then
exposed the second defect: without the prefix the labels are bare
integers, and NCBI has merged species that MetaPhlAn still reports
separately, so duplicates reach make.unique(), which requires character
and errors.

Those duplicates are a real signal rather than noise. NCBI has lumped taxa
that CHOCOPhlAn_201901 keeps apart: Rhodobacter_sphaeroides and
R_megalophilus are both Cereibacter sphaeroides now, Xanthomonas_hortorum,
_gardneri and _cynarae are one species. The rows are partitioned reads of
one organism, so they are summed via agglomerateByVariable(), which keeps
the rowTree consistent. Summing, not averaging: these values are
compositional, and with counts = TRUE they are read counts.

Both changes report themselves. The drop warns, lists what went and says
rownames = "long" keeps everything. The merge messages which clades went
into which identifier.

The test for this behaviour stripped rank prefixes and uniquifying
suffixes before asserting, so it passed while every user got tagged row
names. It now asserts bare, unique, integer-coercible row names.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 23c8bc3e584a56730d5b27314e05b041467c95c0
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-10-06 19:01:08 +0200
Commit message:

 Merge pull request #340 from waldronlab/fix/description-suggests

fix: drop OmicsMLRepoR from Suggests while it is uninstallable

Package: curatedMetagenomicData
Commit: 3a7a563f8cc92a49df3630270dfee7e82d064b2f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 23:04:40 -0400
Commit message:

 fix: drop OmicsMLRepoR from Suggests while it is uninstallable

R CMD check refuses to run at all when a Suggests package cannot be
installed:

  checking package dependencies ... ERROR
  Package suggested but not available: 'OmicsMLRepoR'

That is stricter than vignette building, so #339's guard did not help
here -- the requirement is on DESCRIPTION, not on usage. The whole check
aborted in 2.3 seconds without evaluating anything else.

OmicsMLRepoR is uninstallable on Bioconductor 3.24 because it depends on
rols, removed in that release (shbrief/OmicsMLRepoR#60). Declaring a
package that cannot be installed is inaccurate as well as fatal.

Also drops library(OmicsMLRepoR) from the vignette, which would otherwise
become an unstated vignette dependency and a WARNING. The one function
used is already called namespaced, inside a chunk that is only evaluated
when the package is present, so nothing is attached and nothing breaks.

Restore the Suggests entry once OmicsMLRepoR builds on devel again.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 661de6271741b3dcb436e950ae9b7cb65e918a25
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-19 04:54:35 +0200
Commit message:

 Merge pull request #338 from waldronlab/ci/bioconductor-workflows

ci: replace rworkflows with the Bioconductor reusable workflow

Package: curatedMetagenomicData
Commit: 2c23e8e9435ba1aaf9cac3549b3f179122fc90a9
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-19 04:53:51 +0200
Commit message:

 Merge pull request #339 from waldronlab/fix/vignette-suggests-guard

fix(vignette): don't require Suggests packages to build

Package: curatedMetagenomicData
Commit: f4b9dc9ed924f230b562407888ec2ea8afca83d7
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 22:46:38 -0400
Commit message:

 fix(vignette): guard DT as well

Copilot caught that the first fix was incomplete. DT is also in Suggests
and was loaded unconditionally at line 101, well before the Example
Analysis guard, so a build without DT still failed -- just earlier and
for a different reason.

Loads DT only when present, and falls back to printing the tibble when
it isn't, so the sample metadata table still renders either way.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 4a74ab15957df0b3c263a63eb179717358197421
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 22:27:19 -0400
Commit message:

 fix(vignette): don't require Suggests packages to build

The example analysis calls library(OmicsMLRepoR) and then builds
everything downstream from OmicsMLRepoR::getMetadata("cMD"), but
OmicsMLRepoR is only in Suggests. R CMD check is allowed to run without
Suggests installed, so the vignette must build without them.

Right now it can't: rols was removed in Bioconductor 3.24, OmicsMLRepoR
depends on it and so fails to install on all three Bioc devel builders,
and the package therefore isn't installable in the devel container. That
takes down R CMD build, which is why CI has been failing since January.

Computes availability once, sets eval for the example analysis chunks
accordingly, and resets before Type Conversion so Session Info still
runs. When the packages are missing the analysis is shown but not
evaluated, with a note naming what's absent.

This is worth doing on its own terms -- unconditional use of a Suggests
package in a vignette is a bug regardless of the rols situation.

Upstream: shbrief/OmicsMLRepoR#60

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: b05d26f54f0bd7a210123bad5496272e7fdc2c1a
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 22:16:21 -0400
Commit message:

 ci: re-enable pkgdown and add workflow_dispatch

Reverts the previous commit's enable_pkgdown: false. The reusable
workflow does build and deploy pkgdown, just only on RELEASE_* branches,
and for a public docs site that is the right source — it should show the
released version rather than unreleased devel.

Adds workflow_dispatch so the site can be rebuilt on demand instead of
waiting for a push to a release branch. set-matrix treats dispatch as a
non-PR event, so GITHUB_REF_NAME is the dispatched branch and a RELEASE_*
dispatch sets is_release_branch.

Restores pages: write and id-token: write, which the deploy job needs.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: b419ac2405ea39e64d0d3df1e0daab684929f3c0
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 22:14:18 -0400
Commit message:

 ci: drop enable_pkgdown, which never fires on devel

Copilot caught that bioccheck.yml gates the pkgdown build, upload and
deploy on is_release_branch == 'true', and set-matrix only sets that for
RELEASE_* refs. On devel all three are skipped, so enable_pkgdown: true
was a no-op that also asked for pages: write and id-token: write it never
used. Permissions are now just contents: read.

The docs site is a separate problem: gh-pages was last deployed
2026-01-21, from the only successful rworkflows run, on a
fix-failed-actions branch rather than devel. It has been stale for eight
months and restoring it needs its own change rather than riding along
with a CI swap meant to clear existing breakage.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 8ab62d808cbd894f79886d592ce0b0c2c3e1e0db
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-09-18 22:07:10 -0400
Commit message:

 ci: replace rworkflows with the Bioconductor reusable workflow

rworkflows has been failing on devel since at least 2026-07-30, on all
three of its OS jobs, so the check has given no signal for months.

Switches to bioconductor/workflows, which runs the official Bioconductor
R CMD check and BiocCheck in the bioconductor_docker container. This
drops the third-party neurogenomics/rworkflows@master dependency and its
blanket `permissions: write-all`, and narrows permissions to the three
the reusable workflow actually needs.

error_on is 'warning', matching the Bioconductor default rather than the
laxer setting that would turn the check green sooner. The build will very
likely be red at first; that reflects the package's real state.

pkgdown and Codecov are both enabled: the site at
waldronlab.io/curatedMetagenomicData is live and Pages is already on
build_type=workflow, and CODECOV_TOKEN is present in the repo.

macOS and Windows coverage is dropped deliberately. bioccheck.yml is
Linux-only, and the Bioconductor build system already checks the other
platforms; r-universe-org/workflows remains available if we want them back.

Refs #315

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Package: curatedMetagenomicData
Commit: 116ac707bf8e7bc0a589ec3c4a91b73966123084
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-08-05 15:48:11 +0200
Commit message:

 Merge branch 'devel' of github.com:waldronlab/curatedMetagenomicData into devel

Package: curatedMetagenomicData
Commit: 825855d168929c07b95d29ada6810b678025155e
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-08-05 15:47:30 +0200
Commit message:

 docs: add details to our-pipeline.Rmd

Package: curatedMetagenomicData
Commit: f3ed9f1f13fafc60a602cac7688f04d5e31e24e1
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-08-05 15:45:25 +0200
Commit message:

 docs: add useful detail to our-pipeline.Rmd

Package: curatedMetagenomicData
Commit: afbb9279ec30b57ce73fac82d4615dcdec29a797
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-07-30 10:18:19 +0200
Commit message:

 Merge pull request #337 from ltsyk/fix/docs-typos-0730000223

docs: fix typo (seperate->separate (x2))

Package: curatedMetagenomicData
Commit: 81267999c87d1633de95ae2871aca7506e6bf186
Author: ltsyk <ltsyk@users.noreply.github.com>
Date: 2026-07-30 08:02:29 +0800
Commit message:

 docs: fix typos in project documentation

Fix documentation typos: seperate->separate (x2)

Package: curatedMetagenomicData
Commit: e4bf8f1491df1ab3649f8d022da8c26f142c35f8
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-06-18 10:48:39 +0200
Commit message:

 merge DESCRIPTION

Package: curatedMetagenomicData
Commit: df1ab8eb937d4e7dcaa93a225562f856e7b41d62
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-03-26 16:36:31 -0400
Commit message:

 Merge pull request #324 from waldronlab/funding/add-fnd-authors-r-23616328932

Package: curatedMetagenomicData
Commit: 3581b3740192c31d1629cfa2e83339810db090bf
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-26 20:34:50 +0000
Commit message:

 Add missing fnd entries to Authors@R in DESCRIPTION

Package: curatedMetagenomicData
Commit: 655390214ef61928d710bb372eaeb9a4e3d39b3f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-20 15:20:38 +0100
Commit message:

 Move all workflow functionality to rworkflows.yml,
add copilot-instructions.md

Package: curatedMetagenomicData
Commit: 93a90e17f8fd246306dcf04ecdb0f008f23785db
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-20 14:20:00 +0100
Commit message:

 Remove duplicate biocViews fields in DESCRIPTION,
bump version

Package: curatedMetagenomicData
Commit: f319f416ddb00083dfd2fa56edc8c2174c5aa816
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-20 13:54:12 +0100
Commit message:

 Merge branch 'devel' of github.com:waldronlab/curatedMetagenomicData into devel

Package: curatedMetagenomicData
Commit: 280cc4fdd045a14b2e9037f843c98d2e6b973a22
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-20 13:53:32 +0100
Commit message:

 Remove duplicate biocViews in DESCRIPTION

Package: curatedMetagenomicData
Commit: 4ca3fec142451db382d9583098396136f6de8246
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-19 18:39:22 +0100
Commit message:

 Uncommitted changes from Tuomas Borman PR #314

Package: curatedMetagenomicData
Commit: d17c18a272eedb28ee53514638acbe9555a08afe
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-01-19 18:39:22 +0100
Commit message:

 Uncommitted changes from Tuomas Borman PR #314

Package: StatescopeR
Commit: 0535cf1c7cfd60124f2385d24478bafd57fa6d46
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2026-10-30 17:14:26 +0100
Commit message:

 Added Ecotype discovery and retrieval

Package: BiocFileCache
Commit: 85ab72ff95efcf0f8780f36da324e83279191e9b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-10-30 10:28:05 -0400
Commit message:

 If incomplete file or missing file do not proceed

Package: DESeq2
Commit: 4ba3e3a159da872566d825609a119a7615069663
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-10-30 10:15:37 -0400
Commit message:

 add note about random effects

Package: BiocBookDemo
Commit: a19d57bcc3ae2dc2e9bb0070444faff4909b1544
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-10-30 13:52:41 +0100
Commit message:

 bump to 1.11.9

Package: BiocBookDemo
Commit: c1f3e7295942c714bddc062031cb235a061bd814
Author: Jacques Serizay <jacquesserizay@gmail.com>
Date: 2026-10-30 13:52:25 +0100
Commit message:

 doc: a chapter on serving the book to AI assistants (#5)

Chapter 5, before the comparison with rebook, describes the AI-related
features of a BiocBook:
- llms.txt, and the block BiocBook adds to it, shown live: the chapter
  computes it while it renders, with BiocBook::enrich_llms_txt(), from
  the book's own DESCRIPTION and requirements.yml;
- the Markdown copy of every page, and the links to it ("View as
  Markdown", ); quarto's conditional content keeps
  content out of the copies, or puts a note for assistants in them only,
  with a live example of each;
- one llms.txt per Bioconductor release, and the index of versions;
- how a BiocBook builds these files (llms profile, post-render.R,
  .nojekyll), and how to use them with an assistant.
Chapter 3's section on llms.txt now points to it, and the index lists it
among the main features of BiocBooks.


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

-----

Package: Spectra
Commit: 48cacffc417be870d29d7829a4616dbf32994a31
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-10-30 13:50:35 +0100
Commit message:

 Merge pull request #391 from rformassspectrometry/jomain

Add new filterNoisePeaks function

Package: Spectra
Commit: 2c10e8185e55a7fc61da9297a9724816d09a3c5b
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-30 08:52:46 +0100
Commit message:

 feat: address Gabriele's comments

Package: Spectra
Commit: 8a5031968f101d83847a716b690103f3a87e1756
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-28 14:04:26 +0100
Commit message:

 tests: update test after fix in upstream code

Package: Spectra
Commit: c8828c8125c6bbaa7691087134415621c56bfb27
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-28 11:24:10 +0100
Commit message:

 ci: split GHA

Package: Spectra
Commit: c0c2ac95313165866fce25336c6d413da85c4a8f
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-10-28 11:12:10 +0100
Commit message:

 feat: add new filterNoisePeaks function

- Add a new `filterNoisePeaks()` function to clean spectra removing potential
  background/noise peaks. The currently supported method is from Dalla Valle et
  al. Anal. Chem. (2025).
- Issue #390

Package: OHCA
Commit: 22198dd014340afe5385be8a1b28223f4524b8c6
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-10-30 12:56:50 +0100
Commit message:

 bump to 1.9.4

Package: OHCA
Commit: dcc6ebf228d2148426e3bafc55b23a783dfbe789
Author: Jacques Serizay <jacquesserizay@gmail.com>
Date: 2026-10-30 12:53:19 +0100
Commit message:

 ci: the book's GitHub Pages site holds a .nojekyll (#10)

BiocBook >= 1.11.7 names the Markdown copy of each page .md, next
to .html, and links every page to it. Unless the site holds a
.nojekyll file, GitHub Pages runs Jekyll on it, which renders every .md
file into an HTML page of the same name: .md would give a second
.html. As in template 1.1.3, the "Index the llms.txt" step writes
.nojekyll, which the next step deploys at the root of the site (docs/ on
gh-pages).


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

----- </pre>
    </div>
  
    
      Package: BiocBookDemo

      Commit: d71894fceb81605a9ef8466970aabcb94beb7d7f

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 12:55:38 +0100

      Commit message:


	  
		 bump to 1.11.8
 
    
  
    
      Package: BiocBookDemo

      Commit: fd8a2d0c657b67fdd9b4f4f454a895238c480a7b

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 12:52:39 +0100

      Commit message:


	  
		 ci: the book's GitHub Pages site holds a .nojekyll (#4)

BiocBook >= 1.11.7 names the Markdown copy of each page .md, next
to .html, and links every page to it. Unless the site holds a
.nojekyll file, GitHub Pages runs Jekyll on it, which renders every .md
file into an HTML page of the same name: .md would give a second
.html. As in template 1.1.3, the "Index the llms.txt" step writes
.nojekyll, which the next step deploys at the root of the site (docs/ on
gh-pages).

Chapter 3 describes the Markdown copies as .md, the links to them,
and .nojekyll.


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

----- </pre>
    </div>
  
    
      Package: BiocBook

      Commit: 504d3a665857a3f217b37c7ec69f1fbbc453c472

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 12:55:09 +0100

      Commit message:


	  
		 bump to 1.11.7
 
    
  
    
      Package: BiocBook

      Commit: 228e55313c03bce0c83679f5ee79f127c73ef7d3

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 12:52:17 +0100

      Commit message:


	  
		 feat: Markdown copies of the pages are .md, and every page links to its own (#14)

quarto (>= 1.11, with llms-txt on) writes the Markdown copy of each page
as .llms.md. enrich_llms_txt() renames it .md, so that a
page's Markdown lives at its URL with .md in place of .html (e.g.
pages/Chapter-2.md for pages/Chapter-2.html), and rewrites the relative
links of llms.txt, and those between the copies, to follow. It then links
every HTML page to its copy: in its , with
, for AI assistants, and under
its title, with a "View as Markdown" link, for readers. Pages that already
link to their copy are left alone, so a second run changes nothing.

Rebuilt the template from js2264/BiocBook.template 706bd2e (template
1.1.3), whose biocbook workflow writes .nojekyll at the root of the
book's GitHub Pages site: otherwise, GitHub Pages runs Jekyll, which
renders .md into a second .html. ?BiocBook-llms and NEWS say
how to add it to books created from an earlier template.


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

----- </pre>
    </div>
  
    
      Package: RmzTabM

      Commit: 39d8d51f84593f5ad4ab2b69f99d3dfbb6c7d664

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2026-10-30 12:05:22 +0100

      Commit message:


	  
		 Merge pull request #57 from rformassspectrometry/gabri_export

fix: issue with new version validator 
    
  
    
      Package: RmzTabM

      Commit: 70f421cdf5fcf1cfaf922933c72fe46b71e23ae8

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-10-29 14:29:43 +0100

      Commit message:


	  
		 Merge branch 'main' into gabri_export
 
    
  
    
      Package: RmzTabM

      Commit: 9b14f78023c680a36ce811ee2333e70323dde5e0

      Author:  Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com> 

      Date: 2026-10-29 14:28:26 +0100

      Commit message:


	  
		 fix: Validation errors with new (?) validator
Fixes #56 and issue in .NAtonull()
 
    
  
    
      Package: OHCA

      Commit: 01f088c3d1e2cc82ce482d6a4b618fa3acae3e52

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:20:46 +0100

      Commit message:


	  
		 bump to 1.9.3
 
    
  
    
      Package: OHCA

      Commit: f60d51a31b51c62f28e41a2a4db74a53442086ba

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:18:56 +0100

      Commit message:


	  
		 fix: python chapter takes its packages from PyPI (#9)

* fix: python chapter takes its packages from PyPI

OHCA 1.9.2 still fails on nebbiolo2 at `import cooler`:
  libssl.so.3: version `OPENSSL_3.2.0' not found (required by
  .../envs/OHCA/lib/python3.12/site-packages/h5py/../../.././libcurl.so.4)
Loading R's curl package first did not help there. The chapter's packages
now come from PyPI, in the `pip:` section of requirements.yml, which
BiocBook >= 1.11.5 installs. Their wheels carry their own compiled
libraries (h5py's HDF5 does not link libcurl), so they cannot pick up the
OpenSSL or harfbuzz R has already loaded, and matplotlib no longer needs to
be held below 3.11. conda provides python only.

The hidden chunk loading curl goes, and curl leaves Imports. With R's
system OpenSSL loaded first, the conda environment fails to import cooler,
the pip one imports cooler, cooltools and matplotlib 3.11.2, and the
chapter's insulation and eigenvectors are unchanged (within 2e-15).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: drop the workflow telemetry step, whose action no longer exists

catchpoint/workflow-telemetry-action no longer exists, so every biocbook
run failed at "Set up job", before building anything:
  Unable to resolve action `catchpoint/workflow-telemetry-action`, not found
The step only recorded the runner's CPU, memory and step timings, which
nothing uses. Same change as BiocBook template 1.1.2.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 
    
  
    
      Package: BiocBookDemo

      Commit: 5e524a11b94e45ef9ee4b31221ca0a823a236693

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:18:16 +0100

      Commit message:


	  
		 bump to 1.11.7
 
    
  
    
      Package: BiocBookDemo

      Commit: 3976b0a14225b1137a6128916e5585ec23fd37b9

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:18:06 +0100

      Commit message:


	  
		 doc: python chapter takes numpy from PyPI, and samtools from bioconda (#3)

* doc: python chapter takes numpy from PyPI, and samtools from bioconda

The demo declared numpy, matplotlib 3.8 and deeptools as conda packages,
the pattern BiocBook 1.11.5 now advises against: python chunks run inside
the R session, and conda builds of the packages they import link libraries
R may already have loaded, in an older version (on the Bioconductor
builders, h5py and matplotlib >= 3.11 then fail to import). PyPI wheels
carry their own.

requirements.yml now keeps conda for python and a command-line tool
(samtools 1.24, from bioconda), and takes numpy 2.5.4 from PyPI under
`pip:`. The python chapter explains why, and its bioconda example runs
samtools from a bash chunk and from python's subprocess, rather than
printing deeptools' version: setup_python() puts the environment's tools on
the PATH. deeptools, and matplotlib with it, are no longer needed.

Suggests asks for BiocBook (>= 1.11.5), which installs the `pip:` section.
The landing page no longer says the environment is named `BiocBook`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* ci: drop the workflow telemetry step, whose action no longer exists

catchpoint/workflow-telemetry-action no longer exists, so every biocbook
run failed at "Set up job", before building anything:
  Unable to resolve action `catchpoint/workflow-telemetry-action`, not found
The step only recorded the runner's CPU, memory and step timings, which
nothing uses. Same change as BiocBook template 1.1.2.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 
    
  
    
      Package: BiocBookDemo

      Commit: d25558268a48d99b20a6b6aa4b34d0411194865c

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:15:48 +0100

      Commit message:


	  
		 bump to 1.11.6
 
    
  
    
      Package: BiocBook

      Commit: 3c3747d71e30199a76e472f6f359067eda8256ad

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:14:36 +0100

      Commit message:


	  
		 bump to 1.11.6
 
    
  
    
      Package: BiocBook

      Commit: f8b9b1ec2603c66dbb03dcd4674f5ecaeeca22c0

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 11:13:54 +0100

      Commit message:


	  
		 fix: new books' biocbook workflow no longer uses a deleted action (#13)

Rebuilt from js2264/BiocBook.template 3ac23c6 (template 1.1.2).
catchpoint/workflow-telemetry-action no longer exists, so every run of a
book's biocbook workflow failed at "Set up job", before building anything:
  Unable to resolve action `catchpoint/workflow-telemetry-action`, not found
The template drops that step, which only recorded the runner's CPU, memory
and step timings. NEWS says how to fix books created from an earlier
template.


Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

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

------- 
    
  
    
      Package: omXplore

      Commit: e96807c24114322d472b1e7dfe508064af8bcd18

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-30 11:08:05 +0100

      Commit message:


	  
		 Update
 
    
  
    
      Package: omXplore

      Commit: 419af813640294ddd16292213219e17bf6b6e0d1

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-30 10:43:14 +0100

      Commit message:


	  
		 Fix cc issue
 
    
  
    
      Package: omXplore

      Commit: 210fb3b1b3bb160ec661d468cf5bed6ea0031619

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-30 10:24:54 +0100

      Commit message:


	  
		 Fix cc issues
 
    
  
    
      Package: omXplore

      Commit: 0cd152d0dcf1ee95be3add2fae4dfe49a60da38e

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-18 13:43:42 +0200

      Commit message:


	  
		 Fix PCA bug
 
    
  
    
      Package: omXplore

      Commit: 92aa46210a0bf887bf79bb46bf9c3170a98647ad

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 13:48:37 +0200

      Commit message:


	  
		 Fix import issue
 
    
  
    
      Package: omXplore

      Commit: eebe607efb4dc9e25ec62e7c17b81e96bbf02f75

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 13:10:34 +0200

      Commit message:


	  
		 Fix example bug
 
    
  
    
      Package: omXplore

      Commit: 9bdec8338d2eb2c46aebcae678a12b54ee996180

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 12:58:55 +0200

      Commit message:


	  
		 Minor fix
 
    
  
    
      Package: omXplore

      Commit: 1ed20c4f5a5b11920fbe8578becfb1a7247a095f

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 12:29:17 +0200

      Commit message:


	  
		 Minor fix
 
    
  
    
      Package: omXplore

      Commit: 4c0064dd43d79b9b6ea6c1e777e321971b794813

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 11:59:11 +0200

      Commit message:


	  
		 Minor fix
 
    
  
    
      Package: omXplore

      Commit: ed44fb98c9f1d743b0c8d66de9e1d17721ec5022

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 11:41:57 +0200

      Commit message:


	  
		 Plot fixes
 
    
  
    
      Package: omXplore

      Commit: 8b3964eeb79b59fa4eb9ab9b8aa3bbff10633c2b

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-08-06 16:51:02 +0200

      Commit message:


	  
		 Multiple corrections
 
    
  
    
      Package: lcmsPlot

      Commit: 7295ef087aa1e02c1dad975114c4df07ddb08692

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-30 10:07:14 +0000

      Commit message:


	  
		 feat(plot): label absolute intensity axes in scientific notation

The intensity axes of chromatograms (TIC, BPC, EICs) and of the total
ion current are labelled in scientific notation, so intensities read
the same in every panel of a figure. Previously ggplot2 picked plain or
scientific labels per panel depending on its range. Relative and
transformed intensities, and stacked chromatograms, keep their axes.

Bump the version to 1.1.25 and add the CI and Bioconductor links to
codemeta.json.
 
    
  
    
      Package: lcmsPlot

      Commit: b76259f799a906e133a3f0b42ebaee6e95865da6

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-30 10:07:14 +0000

      Commit message:


	  
		 test(baseline): drop the rt_diff baseline scenario

The rt_diff baseline still failed on the aarch64 Bioconductor builder
(taishan) after diff was left out of the comparison: Obiwarp's adjusted
retention times differ between aarch64 and x86_64, so no recorded
reference holds on every builder.

The scenario and its fixture are removed. test-dataset-rt-diff.R still
checks that diff is the shift between rt_raw and rt_adj on the data
itself, which does not depend on the platform.
 
    
  
    
      Package: BiocBook

      Commit: 07bf9c44b12cc7bbc4b83166e951d255399dd583

      Author:  Jacques <jacquesserizay@gmail.com> 

      Date: 2026-10-30 09:34:34 +0100

      Commit message:


	  
		 bump to 1.11.5
 
    
  
    
      Package: BiocBook

      Commit: f09f9d09a865425bd82fcaedbd5a57cfdd8cf25d

      Author:  Jacques Serizay <jacquesserizay@gmail.com> 

      Date: 2026-10-30 09:31:36 +0100

      Commit message:


	  
		 feat: setup_python() installs the pip: section of requirements.yml, template 1.1.1 (#12)

* feat: setup_python() installs the pip: section of requirements.yml

python chunks run inside the R process, which holds a single copy of each
shared library name. conda packages link libssl, libcurl or harfbuzz under
their usual names, so once R has loaded the system's copies they can pick up
an older one: on the Bioconductor builders, h5py (and so cooler) fails with
`OPENSSL_3.2.0 not found`, and matplotlib >= 3.11 with
`undefined symbol: hb_ft_font_get_ft_face`.

Wheels from PyPI carry their compiled dependencies under names of their
own, so setup_python() now installs a `pip:` section with the environment's
own pip, once the conda packages are in place, rather than refusing it.
conda keeps python itself and command-line tools, which setup_python() now
puts on the PATH from the first chunk on. An environment whose build fails
half way is removed rather than re-used, and llms.txt lists the PyPI
packages after the conda ones.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

* feat: new books start from template 1.1.1

Rebuilt from js2264/BiocBook.template 72ae753. Its requirements.yml declares
the python packages a book imports under `pip:`, which setup_python() now
installs from PyPI, and keeps conda for python itself and for command-line
tools, rather than telling authors to pin matplotlib below 3.11.

The example it ships, uncommented (samtools 1.24 from bioconda; numpy 2.5.4
and matplotlib 3.11.2 from PyPI), builds with setup_python(): samtools is
on the PATH before python starts, and matplotlib imports and draws once R
has loaded the system's OpenSSL.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FLbRhpc2hEajWKBL7zXM8Q

--------- 
    
  
    
      Package: crisprDesign

      Commit: 81f5530955e18ee7f84c8cd17bdf9013c08ce6c4

      Author:  Jean-Philippe Fortin <fortin946@gmail.com> 

      Date: 2026-10-29 19:19:00 -0700

      Commit message:


	  
		 Changed standard_chr_only default
 
    
  
    
      Package: DuckDBSpatial

      Commit: e0a2eb18e54154408b5a24d533a76d52a9f0d257

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-29 18:56:39 -0700

      Commit message:


	  
		 Add append = TRUE support to writeGeoParquet()

A user asked for a way to add rows to an existing GeoParquet file
incrementally. Build it on nanoparquet::append_parquet(), then update
the file's geo metadata in place: union the geometry_types, extend the
bbox (omitting it if either side's extent is unknown), and require a
matching CRS rather than silently embedding mismatched coordinates
under one CRS label.

Also fixes two latent bugs in the existing metadata serialization,
found while making the CRS check round-trip correctly:
- jsonlite::toJSON()'s default digits = 4 silently truncated numeric
  precision anywhere in the geo metadata, including the CRS's own
  ellipsoid parameters, on every writeGeoParquet() call. Use
  digits = NA throughout.
- sf::st_crs() silently returns an NA CRS, with no warning, when given
  toJSON()'s "json"-classed return value directly instead of a plain
  character string.

append_parquet() reads the existing file's WKB column back as a
blob::blob() vector to validate the combined schema, so the appended
geometry column needs that same representation; add blob to Suggests.
 
    
  
    
      Package: sesame

      Commit: 4a67752093ff2bb0819999dfd9abe70cf0fb7aca

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-29 21:33:41 -0400

      Commit message:


	  
		 1.31.10: startup message points at knowYourCG for CpG-set enrichment
 
    
  
    
      Package: sesameData

      Commit: 119df217cea4da8cb18173226fa85e6152d13e51

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-29 21:21:19 -0400

      Commit message:


	  
		 1.31.3: the 1.31.1 objects come from ExperimentHub

ExperimentHub assigned ids on 2026-10-20 (Bioc 3.24) to the eight objects
added in 1.31.1, until now served from Zenodo record 23263026:
HM450/EPIC/EPICv2/MSA.address = EH10648-EH10651,
KYCG.{HM450,EPIC,EPICv2,MSA}.Mask.20261008 = EH10652-EH10655.
df_master (R/sysdata.rda) records them, so sesameDataGet() reads them
from the hub and sesameDataCache() caches them with the rest. Each hub
file is byte-identical to its Zenodo copy.
 
    
  
    
      Package: grayleafspotr

      Commit: 37200214f333d39434973305efa1935f72166efd

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-30 01:11:56 +0000

      Commit message:


	  
		 Merge 0.99.15 citation correction into devel
 
    
  
    
      Package: grayleafspotr

      Commit: 9242d5dad175f46cf37ba802b4e8b6012be4fb61

      Author:  rotsl <wot25kir.nbi@gmail.com> 

      Date: 2026-10-30 01:11:36 +0000

      Commit message:


	  
		 Remove custom citation and add DOI badge (0.99.15)
 
    
  
    
      Package: mixOmics

      Commit: b6d7f153fa89c985336e42f050599a29df7da4d5

      Author:  Kim-Anh Lê Cao <mixomicsdeveloper@gmail.com> 

      Date: 2026-10-30 11:58:06 +1100

      Commit message:


	  
		 build: bump package version to 6.37.1
 
    
  
    
      Package: mixOmics

      Commit: 3fc71132a1aa1ea7f5e14ddf3a07391d19149477

      Author:  Kim-Anh Lê Cao <mixomicsdeveloper@gmail.com> 

      Date: 2026-10-30 11:54:52 +1100

      Commit message:


	  
		 Merge remote-tracking branch 'bioc/devel' into HEAD
 
    
  
    
      Package: mixOmics

      Commit: 1c7f420460df6354f9764f48f79c06ff69e461a6

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 16:03:14 +1100

      Commit message:


	  
		 Update URL, BugReports and Date in DESCRIPTION (#417)

## Summary

- **URL:** change to `https://mixomics.org`, the address that
`http://www.mixOmics.org` redirects to.
- **BugReports:** change to `mixOmics-org`.
- **Date:** change to`2026-04-28`, when Bioconductor 3.23 published
6.36.0 and devel moved to 6.37.0. It was `2021-07-15`, the date of
6.18.0.
- **Packaged:** removed. `R CMD build` writes this field, and R official
handbook suggest for no `Packaged` field in the sources.

No package code changes. 
    
  
    
      Package: mixOmics

      Commit: 0fbbdc2ec4ddf3f165400c9c24ad9cb7fcbd6d37

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 16:02:56 +1100

      Commit message:


	  
		 Correct the author names in citation() and add the DOI (#416)

## Summary

`citation("mixOmics")` printed the authors as "F R, B G, A S, K-A LC
(2017)": the author string was read with given and family names swapped,
and the BibTeX entry carried the same names into reference managers. The
entry also had no DOI, which BiocCheck reports as a warning on every
check.

`inst/CITATION` now uses `bibentry()` and `person()` with:

- the full author names, with "Lê Cao" kept as one family name in
BibTeX;
- the DOI `10.1371/journal.pcbi.1005752`;
- the journal name as registered with Crossref, PLOS Computational
Biology;
- a text version in the PLOS citation format, so the last author reads
"Lê Cao K-A".

Accented letters are written as `\u` escapes, so the file stays plain
ASCII.

## Testing

After `devtools::load_all()`, `citation("mixOmics")` prints (follows the
PLOS citation format):

```
Rohart F, Gautier B, Singh A, Lê Cao K-A (2017) mixOmics: An R
package for 'omics feature selection and multiple data integration.
PLoS Comput Biol 13(11): e1005752.
https://doi.org/10.1371/journal.pcbi.1005752
```

BiocCheck in the R-CMD-check of this pull request no longer reports the
missing DOI. 
    
  
    
      Package: mixOmics

      Commit: a0148e0b7889d70f326912507a333b821c0eefeb

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 16:02:39 +1100

      Commit message:


	  
		 Clean up the buildignore folder (#415)

## Summary

`buildignore/` holds development scripts that stay out of the package.
Its remaining scripts date from 2019 to 2021, and no file refers to
them.

- Remove the five scripts in `buildignore/devel/`: a 2019 Q2 debugging
script, an empty stub, and old `plot.perf` examples that are copies of
each other and of the examples #414 attaches to `?plot.perf.pls`. The
`perf()` and `plot.tune()` examples and the perf tests cover their
content.
- Add `buildignore/README.md`, which describes what the folder is for.
- `.Rbuildignore` excludes the folder by name (`^buildignore$`) in place
of `ignore`, which matched every path containing "ignore". The other
paths it matched (`.Rbuildignore`, `.gitignore`, `.github/.gitignore`,
`renv/.gitignore`) are excluded by their own rules.

No package code changes. 
    
  
    
      Package: mixOmics

      Commit: 868f018db42e27a3bd68b023d2e31404fe0d217e

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 16:02:22 +1100

      Commit message:


	  
		 Add examples to the plot.perf.pls help page (#414)

## Summary

The help page of `plot()` for `perf()` results of (s)PLS models
(`?plot.perf.pls`) had no examples. The examples written for it in 2021
were never attached.

- Rename `examples/perf.pls-examples.R` to
`examples/plot.perf.pls-examples.R` and attach it with `@example`.
- Fix the examples:
  - `y` is taken from `Y` after `Y` is defined;
  - progress bars are off;
- `keepY` gives one value per component, `rep(10, 4)`; the previous
`c(10, 4)` was completed by `spls()` to `10, 4, 21, 21`.
- The details now read "See ?perf for more examples."

## Testing

- The examples extracted from `man/plot.perf.pls.Rd` run in about 1 s
with no errors or warnings.
- roxygen2 7.3.3 regenerates only `man/plot.perf.pls.Rd`. 
    
  
    
      Package: mixOmics

      Commit: ecddc808707a1e3c49bd56f14752022f56d9fe97

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 16:02:01 +1100

      Commit message:


	  
		 Remove the Travis CI configuration (#413)

## Summary

- Remove `.travis.yml`. CI runs on GitHub Actions; the Travis
configuration was last updated in 2020 and lists branches and a
Bioconductor release (`RELEASE_3_11`) that are no longer in use.
- Remove its entry from `.Rbuildignore`.

No package code changes. 
    
  
    
      Package: mixOmics

      Commit: d760350e1bfd28149553bf78cb3130075b5e66fd

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-23 15:57:59 +1100

      Commit message:


	  
		 feat(ci): remove the weekly README workflow and render README.md in pull requests (#412)

## Summary

README.md is now rendered by CI in the pull request, on the same setup
for every contributor.

- **Removed:** the weekly Update README workflow, which ran only on the
`aljabadi/mixOmics` fork and was skipped on every scheduled run here,
and the `updateREADME` exclusion in R-CMD-check that served it.
- **Added:** the Render README workflow. On a pull request that changes
`inst/README.Rmd`, `inst/README-WhatsNew.Rmd` or `DESCRIPTION` (the
license badge follows its `License` field), it renders README.md and
commits it to the pull request branch.
- The commit is created through the GraphQL API, so GitHub signs it as
`github-actions[bot]` (Verified), and it carries a `Signed-off-by`
trailer.
- pandoc follows the default of `r-lib/actions/setup-pandoc`, which
dependabot updates.
- **Pull requests from forks:** the token is read-only, so the job fails
when README.md differs and uploads the rendered README.md as the
`rendered-readme` artifact for the author to commit.
- **Manual run:** on a branch, the workflow renders and commits; on
master, it checks only and fails when README.md differs.

## Testing

This pull request changes `inst/README.Rmd`, so the workflow runs here.
Expected result: a `docs(readme): render README.md from inst/README.Rmd`
commit from `github-actions[bot]`, shown as Verified, that changes two
lines of README.md:

- the header comment, from the edit in `inst/README.Rmd`;
- the line break after `*username*: rstudio`, which pandoc 3.8.3 writes
as two trailing spaces instead of a backslash; GitHub displays both the
same.

## Notes

- A commit pushed with `GITHUB_TOKEN` starts the pull request workflows
in an approval-required state, so after the bot commit a maintainer
selects **Approve workflows to run** in the merge box. README.md is
excluded from the package build. 
    
  
    
      Package: mixOmics

      Commit: ca710aa2ff85e27f83eb4c10096d71d7b27e6525

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-22 08:57:29 +1100

      Commit message:


	  
		 Speed up the weighted vote in predict() for multi-block models (#410)

## Summary

`predict()` on multi-block models (`block.pls`, `block.spls`,
`block.plsda`, `block.splsda`) computed `WeightedPredict` by calling
`aggregate()` once for every sample and response, which took most of the
run time. The weighted vote is now computed for all samples and
responses at once, so that `predict()` on these models runs 3 to 67
times faster in the benchmarks below, and `perf()` and
`tune.block.plsda()` about 2 times faster, with results identical to the
previous code.

## Changes

- `R/predict.R`: the weighted vote moves into a new internal function,
`.weighted_predict()`, with the same rules as before: blocks that give
the same prediction add up their weights and the prediction with the
largest total weight is kept; predictions that agree to 15 significant
digits count as the same; a tie gives NA; blocks that give NA are left
out of the vote. The weights are added with `rowSums()`, which uses the
precision of `sum()`, so the totals and their ties match the previous
code on every platform, including x86_64, where `sum()` adds in extended
precision. The largest total is taken with `pmax()`.

## Results

Median times on `breast.TCGA`, R 4.5.3 on Apple Silicon, with the
scenarios and script from #383:

| Scenario | master | this PR | Speedup |
| --- | --- | --- | --- |
| `predict()` — `block.splsda` (2 blocks, 3 classes) | 162.50 ms | 48.00
ms | 3.39× |
| `perf()` 5-fold × 5 repeat — `block.splsda` | 2.25 s | 1.10 s | 2.05×
|
| `predict()` — `block.spls` (2 blocks, Y dim = 142) | 3645.50 ms |
54.50 ms | 66.89× |
| `tune.block.splsda()` — 4 keepX combos × 5-fold × 5 repeat | 2.52 s |
2.53 s | 1.00× |
| `tune.block.plsda()` — 5-fold × 5 repeat | 2.32 s | 1.09 s | 2.13× |

`tune.block.splsda()` does not compute `WeightedPredict`, so its time is
unchanged.

The output of `predict()` in these scenarios is `identical()` to master.
The vote alone is `identical()` to the previous code on 22 constructed
cases and 2000 random cases (ties, NA and NaN predictions, NA weights,
values that differ beyond 15 significant digits), on both arm64 and
x86_64.

## Tests

- `test-predict.R`, through `predict()`: for the four block models,
`WeightedPredict` equals the prediction of the block with the largest
weight; with equal block weights it is all NA.
- `test-predict.R`, `.weighted_predict()` on constructed arrays: blocks
with the same prediction add up their weights; a tie gives NA, and a tie
in every cell gives a logical NA matrix; predictions that agree to 15
significant digits count as the same and keep the value of the first
block; NA and NaN predictions are left out of the vote; an NA weight of
a block that takes part in the vote gives NA; every block giving NA
stops with an error. A random case compares the result with a vote
computed with `sum()` in each cell; on x86_64 it also checks that the
totals use the precision of `sum()`.

## Notes

- Thanks to @RestlessTail for the profiling in #236 and #369 that found
this bottleneck, and to @frohart for pointing out the handling of ties
in #369, which this version keeps. This PR supersedes #370.
- #236 stays open: the repeated computation of W* described there is not
changed here.
- `AveragedPredict` still averages cell by cell with `apply()` and is
now the largest part of the run time for a large Y. `rowMeans()` would
be faster, but it differs from `mean()` in the last bit for some cells,
so it is left for a separate issue.

Closes #383
Closes #369 
    
  
    
      Package: mixOmics

      Commit: 61a5f91b156f4c7634edc672822e78456c35738c

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-21 16:20:08 +1100

      Commit message:


	  
		 chore(description): update date and drop packaged field

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: db7ed7941029b7a317ef03a7ac9932789c245eb0

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-21 16:19:53 +1100

      Commit message:


	  
		 chore(description): update project URLs

Point URL to https://mixomics.org and BugReports to the
mixOmics-org GitHub organization.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 52e379243a386098a06f7db97339b77577f1a750

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-21 15:18:09 +1100

      Commit message:


	  
		 fix(citation): correct the author names and add the DOI

citation("mixOmics") printed the authors as "F R, B G, A S, K-A LC":
the author string was read with given and family names swapped, and
the BibTeX entry carried the same names. The entry also had no DOI,
which BiocCheck reports as a warning, and used the old-style
citEntry().

The entry now uses bibentry() and person() with the full author names,
the DOI and the journal name as registered with Crossref. Its text
version follows the PLOS citation format, so the last author reads
"Lê Cao K-A".

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 125139af3f69b61e6073e4a9f686777c768f38c2

      Author:  github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> 

      Date: 2026-10-21 03:24:38 +0000

      Commit message:


	  
		 docs(readme): render README.md from inst/README.Rmd

Signed-off-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> 
    
  
    
      Package: mixOmics

      Commit: c549f12353bf91e3254d046f48f39c7fd04012bd

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-21 14:16:12 +1100

      Commit message:


	  
		 docs(plot.perf.pls): add examples

The help page of plot() for perf() results of (s)PLS models had no
examples. Attach the examples written for it, renamed to
examples/plot.perf.pls-examples.R, and fix them: y is taken from Y
after Y is defined, progress bars are off, and keepY gives one value
per component.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 1d952af9d0cdbd024e2e0c9d53612704dab930d9

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-21 12:21:34 +1100

      Commit message:


	  
		 chore: clean up the buildignore folder

Remove the five scripts left in buildignore/devel: a 2019 Q2 debugging
script, an empty stub and old plot.perf examples, which are copies of
each other and of examples/perf.pls-examples.R. Their examples are
covered by the perf() and plot.tune() examples and the perf tests.

Add a README that describes the folder: development scripts that belong
to a version of the code, deleted or turned into tests once their work
is merged; deleted scripts remain in the git history. .Rbuildignore now
excludes the folder by name, in place of the pattern that matched every
path containing "ignore".

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 2a938808529741afbe65ff7cc0d40b52085b330d

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-20 17:44:19 +1100

      Commit message:


	  
		 feat(ci): render README.md in pull requests

A pull request that changes inst/README.Rmd, inst/README-WhatsNew.Rmd or
DESCRIPTION now renders README.md on the runner and commits it to the
pull request branch, so that every README.md is rendered on the same
setup. pandoc follows the default of r-lib/actions/setup-pandoc, which
dependabot updates.

The commit is created through the GraphQL API, so GitHub signs it as
github-actions[bot] and it carries a Signed-off-by trailer.

A pull request from a fork receives a read-only token, so for a fork the
job fails when README.md differs and uploads the rendered README.md for
the author to commit.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 46802b21eb0bb18e8f5285725125507a4182f568

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-20 17:43:36 +1100

      Commit message:


	  
		 chore(ci): remove the weekly README workflow

The Update README workflow ran only on the aljabadi/mixOmics fork, so
every scheduled run here was skipped. Remove it together with the
updateREADME exclusion in R-CMD-check, which only served this workflow.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 415874d366bf8dc064471554ac25bf4f2d8bb602

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-20 13:45:56 +1100

      Commit message:


	  
		 chore(ci): remove Travis CI configuration

CI runs on GitHub Actions. The Travis configuration was last updated
in 2020, so remove it together with its .Rbuildignore entry.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 086400413f4f63255644e57b3e09c0c21ee21857

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-19 14:50:09 +1100

      Commit message:


	  
		 Merge branch 'master' into issue-383
 
    
  
    
      Package: mixOmics

      Commit: 8731bc90dfa72922e58f6d323ac16a2162e2871f

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-19 14:49:28 +1100

      Commit message:


	  
		 test(predict): test .weighted_predict() on constructed arrays

Cover the paths that predict() rarely reaches with real data: blocks
with the same prediction adding up their weights, ties, predictions
that agree to 15 significant digits, NA and NaN predictions, NA
weights, and the error when every block gives NA. A random case
compares the result with a vote computed with sum() in each cell; on
x86_64 it also checks that the totals use the precision of sum().

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: e82d5fbb7a9c0b22a73ded084ec4a2af9438efe7

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-19 14:46:18 +1100

      Commit message:


	  
		 perf(predict): move the weighted vote into .weighted_predict()

Move the block vote for WeightedPredict into an internal helper that
takes the array of block predictions and the block weights, so that
the tests can call it on constructed arrays.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 9f9fd66b69105fdb618b54588b638b567e85c0d6

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-15 11:21:52 +1100

      Commit message:


	  
		 fix(ci): log in to Docker Hub with a personal access token (#409)

## Summary

- **CI:** Docker Hub login uses a personal access token: the username
comes from the `DOCKERHUB_USERNAME` repository variable and the token
from the `DOCKERHUB_TOKEN` secret.
- **README:** `docker pull` and `docker run` use the `github` tag.

## After merge

- Check that the Docker job passes on master.
- Delete the old `DOCKER_USERNAME` and `DOCKER_PASSWORD` secrets. 
    
  
    
      Package: mixOmics

      Commit: 23e2fea74ab13fed96e9d5596e8c697fa4ebfc56

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-15 10:37:44 +1100

      Commit message:


	  
		 Accept folds supplied as a list in perf() and perf.assess() for DIABLO models (#408)

## Summary

`perf()` and `perf.assess()` on DIABLO objects (`block.plsda`,
`block.splsda`) accepted only a number of folds. A list of folds, as
documented in `?perf` and already accepted for `pls`/`spls`, failed with
`Invalid number of folds.` inside a `BiocParallel errors` message. Both
functions now accept `folds` as a list of integer vectors, one per test
fold, so that all samples from one subject, site or batch can be kept in
the same test fold.

## Changes

- New internal `.check_folds()` in `R/utils-argument_checkers.R`. It
replaces the list checks duplicated in `perf.mixo_pls()` and
`perf.assess.mixo_pls()`, and adds checks that each element is an
integer vector, no fold is empty, and every index is a whole number
between 1 and n. For DIABLO it also checks that every class is present
in the training set of every fold.
- `R/perf.diablo.R`, `R/perf.assess.diablo.R`: the list is validated
before the repeats are sent to `bplapply()`, so errors reach the user
directly. Each element is used as one test fold instead of calling
`stratified.subsampling()`. With a list, `nrepeat > 1` gives a warning
and is set to 1.

One change from the issue: a class absent from a training set stops with
an error instead of a warning. Without this check the run fails later
inside `bplapply()` with `length of 'dimnames' [2] not equal to array
extent`: `block.splsda()` drops the missing level, so `predict()`
returns one column fewer than the aggregation expects.

## Tests

- `test-perf.and.perf.assess.diablo.R`: a list runs for `perf()` and
`perf.assess()` with one fold per list element and one repeat; every
sample is predicted once; `nrepeat > 1` warns and runs once; invalid
lists (repeated or missing sample, index above n, non-integer index,
single fold, empty fold, list of lists, class absent from a training
set) give clear errors.
- `test-perf.and.perf.assess.mixo.plsR.R`: a list on `spls` runs for
both functions, the seed leaves the result unchanged, and a repeated
sample gives an error.

## Notes
- plsda/splsda and the `tune.*` functions are separate issues, as listed
in #400.

Closes #400 
    
  
    
      Package: mixOmics

      Commit: 853ff55a078cf54ba3f4c892cac62f0af24a79c7

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-10-15 10:36:50 +1100

      Commit message:


	  
		 Fix plotVar() points outside the correlation circle when components are not orthogonal (#407)

## Summary

`plotVar()` plots `cor(variable, component)` on perpendicular axes,
which is only valid when the two plotted components are orthogonal. When
they are not, points can fall outside the unit circle, and points that
stay inside can still be in the wrong position. This happens for the Y
block of `block.pls()` / `block.spls()` (regression, classic and
invariant modes), for `rcc()` with ridge regularisation, and when a
block has missing values.

## Cause and fix

The components are now orthogonalised symmetrically once, before the
correlations are computed (`.cor_orthogonalised()` in `R/plotVar.R`).
With `V` the centred, unit-length components and `G = V'V`, the new axes
are `V G^(-1/2)`. This is the closest orthonormal basis to the original
components, so the result does not depend on the order of `comp`.

- If the components are already orthogonal, `G` is the identity and the
coordinates are unchanged.
- Otherwise `plotVar()` prints a message naming the block and appends
"(orthogonalised)" to the default axis labels. The message is only shown
when `|cor| >= 0.01`.
- Missing values are not treated separately. The components have no
missing values and are orthogonal on the full sample, so they are
orthogonalised once for all variables and every point shares the same
axes. The earlier per-variable orthogonalisation on each variable's
observed samples gave each variable its own axes. A point can therefore
still end up slightly outside the circle when a variable is already very
close to the boundary and has many missing values. The overshoot is
small.
- `comp` containing the same component twice now raises an error.
- Points are not rescaled or clipped.
- The new behaviour is described in `?plotVar`.

On the `liver.toxicity` example from #405, the two Y variables at radius
1.10 and 1.11 are now at 0.91 and 0.91. For `multidrug`, which has 3.8%
missing values, the maximum radius is 0.90.

## Tests

Added to `test-plotVar.R`:

- coordinates are unchanged when the components are already orthogonal,
with no message
- duplicate `comp` is rejected
- correlated components: all points are inside the circle, the radii
match the explained variance, swapping `comp` swaps `x` and `y`, and the
axis labels are updated
- missing values: coordinates match the single full-sample
orthogonalisation

Closes #405 
    
  
    
      Package: mixOmics

      Commit: 8de785228a6682f79a06bc465e3c83eafd149bed

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-14 21:20:20 +1100

      Commit message:


	  
		 docs(readme): pull the Docker image by its github tag

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 96963b36b3496f93f690279a5659513aa2fcd1de

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-14 21:13:01 +1100

      Commit message:


	  
		 ci: log in to Docker Hub with a personal access token

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 164907c3f59b5e6d7c3c72d2980a75ec707f322e

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:47:19 +1000

      Commit message:


	  
		 test(plotVar): cover unchanged and orthogonalised coordinates

Check that plotVar leaves coordinates unchanged for (s)plsda and
canonical (s)pls. Check that it orthogonalises correlated components
for rcc and for 3d-style block.pls. Also check that
.cor_orthogonalised returns NA for collinear components.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: bdb72f83920c8765712cb5229e34183ebb7745f2

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:34:44 +1000

      Commit message:


	  
		 test(perf): cover folds supplied as a list

Add tests for perf() and perf.assess() on DIABLO and sPLS models when
folds is a list of sample indices. They check that each sample is
predicted once, that results are reproducible, that nrepeat > 1 warns
and runs once, and that invalid folds give clear errors.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 080840a28c4a1624c38e440591ea265b3913970e

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:34:24 +1000

      Commit message:


	  
		 docs(perf): document list input for folds argument

Clarify that `folds` accepts either a number of folds or a list of
test-fold row indices for pls, spls and DIABLO objects. For DIABLO,
supplying a list fixes the folds and sets `nrepeat` to 1.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: cd9f6092a725f217eb1ed52eb9158a2cd19471a9

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:34:01 +1000

      Commit message:


	  
		 feat(perf.assess): support list folds for DIABLO objects

Validate folds supplied as a list once in `perf.assess.sgccda` before
the repeats are dispatched, so errors and warnings reach the user
directly. Because the folds are then fixed, `nrepeat` is set to 1 with a
warning.

Reuse the shared `.check_folds` helper in the `pls` and `spls` method
instead of its inline checks. Update the docs for `folds` accordingly.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 0478fa0db38f9924f65943ac21985b6fecc191dc

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:33:22 +1000

      Commit message:


	  
		 feat(perf): accept folds as a list for DIABLO objects

Validate user-supplied folds with the shared `.check_folds` helper in
both `perf.mixo_pls` and `perf.sgccda`. For DIABLO objects, a warning is
issued and `nrepeat` is set to 1 when folds are given as a list, since
the folds are fixed.

Update the documentation of `folds` accordingly.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: b0097a9ae2d628a6143cd39bb25fbd612719c8a2

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 16:32:45 +1000

      Commit message:


	  
		 feat(utils): add validator for list-based cross-validation folds

Add an internal `.check_folds()` helper that validates user-supplied
folds for M-fold cross-validation. It rejects non-list input, an invalid
number of folds, empty folds, out-of-range or non-integer indices, and
missing or repeated samples.

When class labels are given, it also errors if a class is absent from
the training set of any fold.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: c4e7cea9fd4ee898d2db93f03b1d731639e6c880

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-02 14:17:36 +1000

      Commit message:


	  
		 build(deps): bump the actions-minor-patch group with 4 updates (#406)

Bumps the actions-minor-patch group with 4 updates:
[r-lib/actions/setup-r](https://github.com/r-lib/actions),
[r-lib/actions/setup-r-dependencies](https://github.com/r-lib/actions),
[docker/build-push-action](https://github.com/docker/build-push-action)
and [codecov/codecov-action](https://github.com/codecov/codecov-action).

Updates `r-lib/actions/setup-r` from 2.13.0 to 2.14.0

Changelog
Sourced from r-lib/actions/setup-r's
changelog.

'v2.14.0` (2026-09-21)


[setup-r]: use-public-rspm: true now sets
up P3M (https://p3m.dev)
on macOS as well, for all repositories.


[setup-r] now installs flang 23 on R 4.7.0 (current
R-devel) and
later, as this is what CRAN uses now (#1107,
@andrjohns).


[check-r-package] now uses the correct check directory
when showing
the testthat output (#1109,
@NotAFlightRisk).


v2.13.0 (2026-08-28)


[setup-r] now retries r-hub.io HTTP failures (#1088,
@nbenn).


[setup-r] now sets the correct RTOOLS environment
variables on
aarch64 Windows (@vjymisal0, #1104).


[setup-r] keep repositories if they are set by the
build.
E.g. aarch64 Windows builds now set them (@jeroen, #1101).


[setup-r] now retries transient failures when resolving
the R
version from api.r-hub.io, rather than failing the job on
the first
timeout or server error (@nbenn, #1086).


[setup-r-dependencies] now switches back to classic
sudo, if
available, on Linux. This fixes installing pak on Ubuntu 26.04 runners
(@jeroen, #1096).


v2.12.1 (2026-06-23)


[setup-r] now avoids a warning about an
url.parse() deprecation
(#1074).


[setup-r-dependencies] now uses
quarto-dev/quarto-actions v2.2.0
(@jdblischak,
#1076).


Examples: test-coverage.yaml now uses
codecov/codecov-action v7
(@shikokuchuo, #1081).


New example claude-investigate.yaml workflow (@DavisVaughan,
#1084).


v2.12.0 (2026-04-29)


All node.js actions use node 24 now. Relatedly, all example workflows
use recent versions of actions that use node 24.


[setup-r] now uses use-public-rspm: true by
default on Linux and
Windows. macOS binaries require further opt-in with
use-public-rspm: always.




... (truncated)


Commits

f9a764f
Update NEWS before release (#1111)
3a1a90f
[setup-r] use-public-rspm: true is TRUE for all repos on
macOS (#1110)
0e37acd
setup-r: Add installation for flang on mac r-devel (#1108)
196dc04
[check-r-package] Use the resolved check-dir when showing testthat
output (#1...
8efa420
Fix typo (#1106)
See full diff in compare
view





Updates `r-lib/actions/setup-r-dependencies` from 2.13.0 to 2.14.0

Changelog
Sourced from r-lib/actions/setup-r-dependencies's
changelog.

'v2.14.0` (2026-09-21)


[setup-r]: use-public-rspm: true now sets
up P3M (https://p3m.dev)
on macOS as well, for all repositories.


[setup-r] now installs flang 23 on R 4.7.0 (current
R-devel) and
later, as this is what CRAN uses now (#1107,
@andrjohns).


[check-r-package] now uses the correct check directory
when showing
the testthat output (#1109,
@NotAFlightRisk).


v2.13.0 (2026-08-28)


[setup-r] now retries r-hub.io HTTP failures (#1088,
@nbenn).


[setup-r] now sets the correct RTOOLS environment
variables on
aarch64 Windows (@vjymisal0, #1104).


[setup-r] keep repositories if they are set by the
build.
E.g. aarch64 Windows builds now set them (@jeroen, #1101).


[setup-r] now retries transient failures when resolving
the R
version from api.r-hub.io, rather than failing the job on
the first
timeout or server error (@nbenn, #1086).


[setup-r-dependencies] now switches back to classic
sudo, if
available, on Linux. This fixes installing pak on Ubuntu 26.04 runners
(@jeroen, #1096).


v2.12.1 (2026-06-23)


[setup-r] now avoids a warning about an
url.parse() deprecation
(#1074).


[setup-r-dependencies] now uses
quarto-dev/quarto-actions v2.2.0
(@jdblischak,
#1076).


Examples: test-coverage.yaml now uses
codecov/codecov-action v7
(@shikokuchuo, #1081).


New example claude-investigate.yaml workflow (@DavisVaughan,
#1084).


v2.12.0 (2026-04-29)


All node.js actions use node 24 now. Relatedly, all example workflows
use recent versions of actions that use node 24.


[setup-r] now uses use-public-rspm: true by
default on Linux and
Windows. macOS binaries require further opt-in with
use-public-rspm: always.




... (truncated)


Commits

f9a764f
Update NEWS before release (#1111)
3a1a90f
[setup-r] use-public-rspm: true is TRUE for all repos on
macOS (#1110)
0e37acd
setup-r: Add installation for flang on mac r-devel (#1108)
196dc04
[check-r-package] Use the resolved check-dir when showing testthat
output (#1...
8efa420
Fix typo (#1106)
See full diff in compare
view





Updates `docker/build-push-action` from 7.3.0 to 7.4.0

Release notes
Sourced from docker/build-push-action's
releases.

v7.4.0

Use the shared error helper for Buildx commands by @crazy-max in docker/build-push-action#1620
Prevent workflow command injection in metadata logs by @crazy-max in docker/build-push-action#1617
Bump @docker/actions-toolkit from 0.92.0 to 0.100.0 in
docker/build-push-action#1614
docker/build-push-action#1618
docker/build-push-action#1621
Bump @humanfs/node from 0.16.7 to 0.16.8 in docker/build-push-action#1609
Bump brace-expansion from 1.1.13 to 1.1.18 in docker/build-push-action#1592
Bump csv-parse from 7.0.0 to 7.0.2 in docker/build-push-action#1613
Bump js-yaml from 4.3.0 to 4.3.2 in docker/build-push-action#1605
docker/build-push-action#1615
Bump nanoid from 3.3.16 to 3.3.18 in docker/build-push-action#1611
Bump postcss from 8.5.10 to 8.5.25 in docker/build-push-action#1590
Bump postcss-selector-parser from 7.1.1 to 7.1.5 in docker/build-push-action#1606
Bump sigstore from 4.1.0 to 4.1.1 in docker/build-push-action#1577
Bump undici from 6.27.0 to 6.28.0 in docker/build-push-action#1594

Full Changelog: https://github.com/docker/build-push-action/compare/v7.3.0...v7.4.0



Commits

c3c9e26
Merge pull request #1621
from docker/dependabot/npm_and_yarn/docker/actions-t...
459b674
[dependabot skip] chore: update generated content
4dedcb2
chore(deps): Bump @docker/actions-toolkit from 0.99.0 to
0.100.0
379bf63
Merge pull request #1620
from crazy-max/buildx-error-message
9877975
chore: update generated content
7ed0556
use the shared Buildx error summary helper
91670ba
Merge pull request #1618
from docker/dependabot/npm_and_yarn/docker/actions-t...
80dbc86
[dependabot skip] chore: update generated content
50cac3a
chore(deps): Bump @docker/actions-toolkit from 0.98.0 to
0.99.0
03b4d6c
Merge pull request #1617
from crazy-max/fix-metadata-workflow-commands
Additional commits viewable in compare
view





Updates `codecov/codecov-action` from 7.0.0 to 7.1.1

Release notes
Sourced from codecov/codecov-action's
releases.

v7.1.1
What's Changed

chore(release): 7.1.1 by @thomasrockhu-codecov
in codecov/codecov-action#1973

Full Changelog: https://github.com/codecov/codecov-action/compare/v7.1.0...v7.1.1
v7.1.0
What's Changed

chore(release): 7.1.0 by @thomasrockhu-codecov
in codecov/codecov-action#1971

Full Changelog: https://github.com/codecov/codecov-action/compare/v7.0.0...v7.1.0



Commits

303a32d
chore(release): 7.1.1 (#1973)
0b35c9e
chore(release): 7.1.0 (#1971)
See full diff in compare
view






Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---


Dependabot commands and options



You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: bb11f8e019a5584ff7ac623d329b706dd72e76ce

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-10-01 23:11:05 +0000

      Commit message:


	  
		 build(deps): bump the actions-minor-patch group with 4 updates

Bumps the actions-minor-patch group with 4 updates: [r-lib/actions/setup-r](https://github.com/r-lib/actions), [r-lib/actions/setup-r-dependencies](https://github.com/r-lib/actions), [docker/build-push-action](https://github.com/docker/build-push-action) and [codecov/codecov-action](https://github.com/codecov/codecov-action).


Updates `r-lib/actions/setup-r` from 2.13.0 to 2.14.0
- [Release notes](https://github.com/r-lib/actions/releases)
- [Changelog](https://github.com/r-lib/actions/blob/v2-branch/NEWS.md)
- [Commits](https://github.com/r-lib/actions/compare/465b7d8e732ca3921382b1674c59bada9cbf3399...f9a764fea8d5c63df6ef9a5c7795bf7deb5d7e05)

Updates `r-lib/actions/setup-r-dependencies` from 2.13.0 to 2.14.0
- [Release notes](https://github.com/r-lib/actions/releases)
- [Changelog](https://github.com/r-lib/actions/blob/v2-branch/NEWS.md)
- [Commits](https://github.com/r-lib/actions/compare/465b7d8e732ca3921382b1674c59bada9cbf3399...f9a764fea8d5c63df6ef9a5c7795bf7deb5d7e05)

Updates `docker/build-push-action` from 7.3.0 to 7.4.0
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](https://github.com/docker/build-push-action/compare/53b7df96c91f9c12dcc8a07bcb9ccacbed38856a...c3c9e263c25d99ce0380d002d59b67737d91b0dc)

Updates `codecov/codecov-action` from 7.0.0 to 7.1.1
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/fb8b3582c8e4def4969c97caa2f19720cb33a72f...303a32d7a59b442fa8d48b6a1cc6825c09c847a5)

---
updated-dependencies:
- dependency-name: r-lib/actions/setup-r
  dependency-version: 2.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
- dependency-name: r-lib/actions/setup-r-dependencies
  dependency-version: 2.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
- dependency-name: docker/build-push-action
  dependency-version: 7.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
- dependency-name: codecov/codecov-action
  dependency-version: 7.1.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: 76514b668e2d90da28c5c50680e39d9d44f10f94

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-01 17:10:22 +1000

      Commit message:


	  
		 test(plotVar): update missing-value orthogonalisation test

Check that plotVar orthogonalises the components on all samples when
data has missing values. Variables are compared against the orthonormal
basis closest to the components, instead of per-variable regression on
observed samples.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 5e5250d4ef677ae8f93dcabdfe542f03b9aa7751

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-01 17:09:38 +1000

      Commit message:


	  
		 docs(plotVar): drop missing-values note from orthogonalisation

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 2e1945599a9c12e7ac4118ac02e0eafd24e9a385

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-10-01 17:09:17 +1000

      Commit message:


	  
		 refactor(plotVar): simplify component orthogonalisation

Compute correlations with `use = "pairwise"` instead of
orthogonalising the components separately on the observed samples of
each variable. Drop the `missing` and `cor.components` attributes and
shorten the message shown when the components are orthogonalised.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 90a92cac750da449ad52145122d9603847c51c8e

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:25:12 +1000

      Commit message:


	  
		 test(plotVar): cover orthogonalised component coordinates

Add tests for the orthogonal case, duplicate components, correlated
block components that must stay inside the correlation circle, and
missing values.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 96a98822654a393ae59cf3f43b31ab51db44f3eb

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:24:49 +1000

      Commit message:


	  
		 feat(plotVar): add orthogonalised variable correlations

Add an internal helper, `.cor_orthogonalised`, that computes
correlations between variables and symmetrically orthogonalised
components, so the correlation circle reads correctly when components
are not orthogonal (cross-block deflation, regularised covariance, or
missing values).

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 4468cac21d73319974795baa29ae40b1424645e2

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:24:22 +1000

      Commit message:


	  
		 feat(plotVar): flag orthogonalised components in axis labels

Append "(orthogonalised)" to the default component axis labels when any
of the underlying coordinates were orthogonalised.

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 17a40210daf2ac053e67747b5d0ed7a23fa00e80

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:20:56 +1000

      Commit message:


	  
		 fix(plotVar): report orthogonalised coordinates when changes

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 8b1a16500bc104d9d4da15fe84e628e3d4d7fbd6

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:19:55 +1000

      Commit message:


	  
		 fix(plotVar): apply symmetric orthogonalise correlations

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 9631d87ef25b6cd7cb7f6c6372a8402892a20719

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:17:29 +1000

      Commit message:


	  
		 fix(plotVar): reject duplicate components

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 2fc1f7bb4b074060f64d34534f44eb4ee7ed21cc

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-30 15:17:00 +1000

      Commit message:


	  
		 docs(plotVar): explain component orthogonalisation

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: ef3e760526623d9e91e945e4b50be48d764efc40

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-09-11 09:18:17 +1000

      Commit message:


	  
		 Fix circosPlot() error when a block has a single selected variable (#404)

# PR addressing Issue #402

Closes #402

## Summary

`circosPlot()` failed with `subscript out of bounds` when a block had a
single selected variable on the chosen component (e.g. `comp = 1` with
`keepX = list(mrna = c(10, 10), mirna = c(1, 10), protein = c(10,
10))`). This reproduces the error reported on the [user
forum](https://mixomics-users.discourse.group/t/circus-plot-cannot-choose-only-one-component/1424).

## Cause and fix

In `R/circosPlot.R`, `cor(x[, keep], y[, comp], use = "pairwise")`
dropped `x[, keep]` to a vector when only one variable was selected,
losing its column name, so the later indexing by `colnames(simMat)`
failed. The fix adds `drop = FALSE` to both subsets so the correlation
matrix keeps its dimensions and names.

## Tests

Added a test in `test-circsPlot.R` that fits the `breast.TCGA` model
from the issue, calls `circosPlot(comp = 1)`, and checks that the
returned similarity matrix has one row and column per selected variable
(21) with all feature names preserved in block order. Existing
`circosPlot` tests are unchanged. 
    
  
    
      Package: mixOmics

      Commit: f6ca7c24c173cf91e3ba5794935475cb007a3389

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-09 10:27:21 +1000

      Commit message:


	  
		 test(circosPlot): cover single-variable block selection

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 9ae2f68b98b8d730bfc134e6f99062277205dbbc

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-09 10:27:05 +1000

      Commit message:


	  
		 fix(circos): preserve matrix dimensions for correlations

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 9bd0d13bc76834cee220d866f0e5053b9f67cd9c

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-09-03 15:46:32 +1000

      Commit message:


	  
		 docs: fix the documented default for comp in network() and cimDiablo() (#401)

## What this PR does

This is a docs only change. Nothing in the code behaviour changes.

The help pages for `network()` and `cimDiablo()` said that `comp`
defaults to 1. That is not what the code does. Both functions set `comp
= NULL` and then fall back to all components, which is `1:ncomp`. This
PR fixes the help text so it matches the code.

It also notes that `comp` in `cimDiablo()` can be a vector of integers,
not just a single integer.

While I was here I updated the README so the GitHub links point to the
new `mixOmics-org` organisation instead of `mixOmicsTeam`. The logo now
comes from the org profile repo, and the website link is a proper https
link.

## Files changed

- `R/network.R` and `man/network.Rd`: the comp default is now documented
as `1:ncomp`
- `R/cimDiablo.R` and `man/cimDiablo.Rd`: same fix, plus a note that
comp can be a vector
- `README.md`: GitHub org links, logo URL, and website link

## How to check

Open the help page for `network` or `cimDiablo` and read the `comp`
entry. Then look at the source. In `network.R` the fallback is around
line 309 and in `cimDiablo.R` it is around line 106. Both set comp to
`1:ncomp` when nothing is passed in.

No tests needed since only comments, help files, and the README changed. 
    
  
    
      Package: mixOmics

      Commit: 6ff67abc0a5b55926ab75ed2cc5b106bcf18d422

      Author:  Kim-Anh Lê Cao <kimanh@mixomics.org> 

      Date: 2026-09-03 15:44:04 +1000

      Commit message:


	  
		 build(deps): bump docker/build-push-action from 1.1.2 to 7.3.0 (#390)

Bumps
[docker/build-push-action](https://github.com/docker/build-push-action)
from 1.1.2 to 7.3.0.

Release notes
Sourced from docker/build-push-action's
releases.

v7.3.0

Preserve names in esbuild bundle by @crazy-max in docker/build-push-action#1567
Bump @docker/actions-toolkit from 0.90.0 to 0.92.0 in
docker/build-push-action#1545
docker/build-push-action#1572
Bump @sigstore/core from 3.1.0 to 3.2.1 in docker/build-push-action#1568
Bump js-yaml from 4.1.1 to 4.3.0 in docker/build-push-action#1566
Bump tmp from 0.2.5 to 0.2.7 in docker/build-push-action#1547
Bump undici from 6.24.1 to 6.27.0 in docker/build-push-action#1564
Bump vite from 7.3.2 to 7.3.6 in docker/build-push-action#1563

Full Changelog: https://github.com/docker/build-push-action/compare/v7.2.0...v7.3.0
v7.2.0

Bump @actions/core from 3.0.0 to 3.0.1 in docker/build-push-action#1525
Bump @docker/actions-toolkit from 0.87.0 to 0.90.0 in
docker/build-push-action#1517
Bump brace-expansion from 2.0.2 to 5.0.6 in docker/build-push-action#1534
Bump fast-xml-builder from 1.1.4 to 1.2.0 in docker/build-push-action#1529
Bump fast-xml-parser from 5.5.7 to 5.8.0 in docker/build-push-action#1521
Bump postcss from 8.5.6 to 8.5.10 in docker/build-push-action#1526
Bump tar from 6.2.1 to 7.5.15 in docker/build-push-action#1533

Full Changelog: https://github.com/docker/build-push-action/compare/v7.1.0...v7.2.0
v7.1.0

Git context query
format support by @crazy-max in docker/build-push-action#1505
Bump @docker/actions-toolkit from 0.79.0 to 0.87.0 by
@crazy-max in
docker/build-push-action#1505
Bump brace-expansion from 1.1.12 to 1.1.13 in docker/build-push-action#1500
Bump fast-xml-parser from 5.4.2 to 5.5.7 in docker/build-push-action#1489
Bump flatted from 3.3.3 to 3.4.2 in docker/build-push-action#1491
Bump glob from 10.3.12 to 10.5.0 in docker/build-push-action#1490
Bump handlebars from 4.7.8 to 4.7.9 in docker/build-push-action#1497
Bump lodash from 4.17.23 to 4.18.1 in docker/build-push-action#1510
Bump picomatch from 4.0.3 to 4.0.4 in docker/build-push-action#1496
Bump undici from 6.23.0 to 6.24.1 in docker/build-push-action#1486
Bump vite from 7.3.1 to 7.3.2 in docker/build-push-action#1509

Full Changelog: https://github.com/docker/build-push-action/compare/v7.0.0...v7.1.0
v7.0.0

Node 24 as default runtime (requires Actions
Runner v2.327.1 or later) by @crazy-max in docker/build-push-action#1470
Remove deprecated DOCKER_BUILD_NO_SUMMARY and
DOCKER_BUILD_EXPORT_RETENTION_DAYS envs by @crazy-max in docker/build-push-action#1473
Remove legacy export-build tool support for build summary by @crazy-max in docker/build-push-action#1474
Switch to ESM and update config/test wiring by @crazy-max in docker/build-push-action#1466
Bump @actions/core from 1.11.1 to 3.0.0 in docker/build-push-action#1454
Bump @docker/actions-toolkit from 0.62.1 to 0.79.0 in
docker/build-push-action#1453
docker/build-push-action#1472
docker/build-push-action#1479
Bump minimatch from 3.1.2 to 3.1.5 in docker/build-push-action#1463

Full Changelog: https://github.com/docker/build-push-action/compare/v6.19.2...v7.0.0
v6.19.2

Preserve port in GIT_AUTH_TOKEN host by @crazy-max in docker/build-push-action#1458



... (truncated)


Commits

53b7df9
Merge pull request #1572
from docker/dependabot/npm_and_yarn/docker/actions-t...
154298c
[dependabot skip] chore: update generated content
cb1238b
chore(deps): Bump @docker/actions-toolkit from 0.91.0 to
0.92.0
24f845d
Merge pull request #1566
from docker/dependabot/npm_and_yarn/js-yaml-4.2.0
9c69730
[dependabot skip] chore: update generated content
bc3a3a5
Merge pull request #1574
from docker/dependabot/github_actions/aws-actions/co...
a82c504
chore(deps): Bump js-yaml from 4.1.1 to 4.3.0
0285a75
Merge pull request #1573
from docker/dependabot/github_actions/actions/cache-...
c6ad2a3
Merge pull request #1575
from docker/dependabot/github_actions/actions/checko...
d37484f
Merge pull request #1564
from docker/dependabot/npm_and_yarn/undici-6.27.0
Additional commits viewable in compare
view



 
    
  
    
      Package: mixOmics

      Commit: f1f230ad1370e8c4b39ea97be0eb36005931b5eb

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 14:16:20 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/docker/build-push-action-7.3.0

Signed-off-by: Derek Lei <derek.lei@mixomics.org> 
    
  
    
      Package: mixOmics

      Commit: 873414591ee4990907c3dac7d680aa78b7255d04

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 14:00:10 +1000

      Commit message:


	  
		 Merge remote-tracking branch 'origin/master' into
dependabot/github_actions/docker/build-push-action-7.3.0

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 4e9a1dfdd269b61cc878394bc37dac5f3fdc4fa7

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 13:39:08 +1000

      Commit message:


	  
		 docs(cimDiablo): update comp argument description

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 95cb038beb4034a3edea023691284971701ff46b

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 13:38:38 +1000

      Commit message:


	  
		 docs(cimDiablo): update comp parameter docs

Signed-off-by: Derek Lei <derek.lei@mixomics.org>
 
    
  
    
      Package: mixOmics

      Commit: 7fb4a0656e79ecac58e425535367271c2791fa93

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 12:28:08 +1000

      Commit message:


	  
		 docs: update GitHub org references to mixOmics-org
 
    
  
    
      Package: mixOmics

      Commit: 511471a557a2807229ab3cad476557da343dc776

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 12:27:44 +1000

      Commit message:


	  
		 docs(network): fix documented default for comp
 
    
  
    
      Package: mixOmics

      Commit: a299c74f11527dcd7867eedbb4157a28da944ecd

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-09-01 12:27:29 +1000

      Commit message:


	  
		 docs(network): correct comp default to 1:ncomp
 
    
  
    
      Package: mixOmics

      Commit: b58f0726dfc964a8648f51878bd4d2904c03d13d

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-31 21:35:04 +1000

      Commit message:


	  
		 build(deps): bump the actions-major group with 2 updates (#397)

Bumps the actions-major group with 2 updates:
[docker/build-push-action](https://github.com/docker/build-push-action)
and
[peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request).

Updates `docker/build-push-action` from 1.1.2 to 7.3.0

Release notes
Sourced from docker/build-push-action's
releases.

v7.3.0

Preserve names in esbuild bundle by @crazy-max in docker/build-push-action#1567
Bump @docker/actions-toolkit from 0.90.0 to 0.92.0 in
docker/build-push-action#1545
docker/build-push-action#1572
Bump @sigstore/core from 3.1.0 to 3.2.1 in docker/build-push-action#1568
Bump js-yaml from 4.1.1 to 4.3.0 in docker/build-push-action#1566
Bump tmp from 0.2.5 to 0.2.7 in docker/build-push-action#1547
Bump undici from 6.24.1 to 6.27.0 in docker/build-push-action#1564
Bump vite from 7.3.2 to 7.3.6 in docker/build-push-action#1563

Full Changelog: https://github.com/docker/build-push-action/compare/v7.2.0...v7.3.0
v7.2.0

Bump @actions/core from 3.0.0 to 3.0.1 in docker/build-push-action#1525
Bump @docker/actions-toolkit from 0.87.0 to 0.90.0 in
docker/build-push-action#1517
Bump brace-expansion from 2.0.2 to 5.0.6 in docker/build-push-action#1534
Bump fast-xml-builder from 1.1.4 to 1.2.0 in docker/build-push-action#1529
Bump fast-xml-parser from 5.5.7 to 5.8.0 in docker/build-push-action#1521
Bump postcss from 8.5.6 to 8.5.10 in docker/build-push-action#1526
Bump tar from 6.2.1 to 7.5.15 in docker/build-push-action#1533

Full Changelog: https://github.com/docker/build-push-action/compare/v7.1.0...v7.2.0
v7.1.0

Git context query
format support by @crazy-max in docker/build-push-action#1505
Bump @docker/actions-toolkit from 0.79.0 to 0.87.0 by
@crazy-max in
docker/build-push-action#1505
Bump brace-expansion from 1.1.12 to 1.1.13 in docker/build-push-action#1500
Bump fast-xml-parser from 5.4.2 to 5.5.7 in docker/build-push-action#1489
Bump flatted from 3.3.3 to 3.4.2 in docker/build-push-action#1491
Bump glob from 10.3.12 to 10.5.0 in docker/build-push-action#1490
Bump handlebars from 4.7.8 to 4.7.9 in docker/build-push-action#1497
Bump lodash from 4.17.23 to 4.18.1 in docker/build-push-action#1510
Bump picomatch from 4.0.3 to 4.0.4 in docker/build-push-action#1496
Bump undici from 6.23.0 to 6.24.1 in docker/build-push-action#1486
Bump vite from 7.3.1 to 7.3.2 in docker/build-push-action#1509

Full Changelog: https://github.com/docker/build-push-action/compare/v7.0.0...v7.1.0
v7.0.0

Node 24 as default runtime (requires Actions
Runner v2.327.1 or later) by @crazy-max in docker/build-push-action#1470
Remove deprecated DOCKER_BUILD_NO_SUMMARY and
DOCKER_BUILD_EXPORT_RETENTION_DAYS envs by @crazy-max in docker/build-push-action#1473
Remove legacy export-build tool support for build summary by @crazy-max in docker/build-push-action#1474
Switch to ESM and update config/test wiring by @crazy-max in docker/build-push-action#1466
Bump @actions/core from 1.11.1 to 3.0.0 in docker/build-push-action#1454
Bump @docker/actions-toolkit from 0.62.1 to 0.79.0 in
docker/build-push-action#1453
docker/build-push-action#1472
docker/build-push-action#1479
Bump minimatch from 3.1.2 to 3.1.5 in docker/build-push-action#1463

Full Changelog: https://github.com/docker/build-push-action/compare/v6.19.2...v7.0.0
v6.19.2

Preserve port in GIT_AUTH_TOKEN host by @crazy-max in docker/build-push-action#1458



... (truncated)


Commits

53b7df9
Merge pull request #1572
from docker/dependabot/npm_and_yarn/docker/actions-t...
154298c
[dependabot skip] chore: update generated content
cb1238b
chore(deps): Bump @docker/actions-toolkit from 0.91.0 to
0.92.0
24f845d
Merge pull request #1566
from docker/dependabot/npm_and_yarn/js-yaml-4.2.0
9c69730
[dependabot skip] chore: update generated content
bc3a3a5
Merge pull request #1574
from docker/dependabot/github_actions/aws-actions/co...
a82c504
chore(deps): Bump js-yaml from 4.1.1 to 4.3.0
0285a75
Merge pull request #1573
from docker/dependabot/github_actions/actions/cache-...
c6ad2a3
Merge pull request #1575
from docker/dependabot/github_actions/actions/checko...
d37484f
Merge pull request #1564
from docker/dependabot/npm_and_yarn/undici-6.27.0
Additional commits viewable in compare
view





Updates `peter-evans/create-pull-request` from 3 to 8

Release notes
Sourced from peter-evans/create-pull-request's
releases.

Create Pull Request v8.0.0
What's new in v8

Requires Actions
Runner v2.327.1 or later if you are using a self-hosted runner for
Node 24 support.

What's Changed

chore: Update checkout action version to v6 by @yonas in peter-evans/create-pull-request#4258
Update actions/checkout references to @v6 in docs by @Copilot in peter-evans/create-pull-request#4259
feat: v8 by @peter-evans in
peter-evans/create-pull-request#4260

New Contributors

@yonas made
their first contribution in peter-evans/create-pull-request#4258
@Copilot made
their first contribution in peter-evans/create-pull-request#4259

Full Changelog: https://github.com/peter-evans/create-pull-request/compare/v7.0.11...v8.0.0
Create Pull Request v7.0.11
What's Changed

fix: restrict remote prune to self-hosted runners by @peter-evans in
peter-evans/create-pull-request#4250

Full Changelog: https://github.com/peter-evans/create-pull-request/compare/v7.0.10...v7.0.11
Create Pull Request v7.0.10
⚙️ Fixes an issue where updating a pull request failed when targeting
a forked repository with the same owner as its parent.
What's Changed

build(deps): bump the github-actions group with 2 updates by @dependabot[bot]
in peter-evans/create-pull-request#4235
build(deps-dev): bump prettier from 3.6.2 to 3.7.3 in the npm group
by @dependabot[bot]
in peter-evans/create-pull-request#4240
fix: provider list pulls fallback for multi fork same owner by @peter-evans in
peter-evans/create-pull-request#4245

New Contributors

@obnyis made
their first contribution in peter-evans/create-pull-request#4064

Full Changelog: https://github.com/peter-evans/create-pull-request/compare/v7.0.9...v7.0.10
Create Pull Request v7.0.9
⚙️ Fixes an incompatibility
with the recently released actions/checkout@v6.
What's Changed

~70 dependency updates by @dependabot
docs: fix workaround description about ready_for_review
by @ybiquitous
in peter-evans/create-pull-request#3939
Docs: add-paths default behavior by @joeflack4 in peter-evans/create-pull-request#3928
docs: update to create-github-app-token v2 by @Goooler in peter-evans/create-pull-request#4063
Fix compatibility with actions/checkout@v6 by @ericsciple in peter-evans/create-pull-request#4230

New Contributors

@joeflack4
made their first contribution in peter-evans/create-pull-request#3928
@Goooler made
their first contribution in peter-evans/create-pull-request#4063
@ericsciple made
their first contribution in peter-evans/create-pull-request#4230



... (truncated)


Commits

5f6978f
fix: retry post-creation API calls on 422 eventual consistency errors
(#4356)
d32e88d
build(deps-dev): bump the npm group with 3 updates (#4349)
8170bcc
build(deps-dev): bump handlebars from 4.7.8 to 4.7.9 (#4344)
0041819
build(deps): bump picomatch (#4339)
b993918
build(deps-dev): bump flatted from 3.3.1 to 3.4.2 (#4334)
36d7c84
build(deps-dev): bump undici from 6.23.0 to 6.24.0 (#4328)
a45d1fb
build(deps): bump @tootallnate/once and
jest-environment-jsdom (#4323)
3499eb6
build(deps): bump the github-actions group with 2 updates (#4316)
3f3b473
build(deps): bump minimatch (#4311)
6699836
build(deps-dev): bump the npm group with 2 updates (#4305)
Additional commits viewable in compare
view






Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---


Dependabot commands and options



You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot show  ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore  major version` will close this
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remove the ignore condition of the specified dependency and ignore
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: 5d486a7850bba2e048c2c67cf795f5e441dae35c

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-31 21:34:29 +1000

      Commit message:


	  
		 build(deps): bump the actions-minor-patch group with 2 updates (#396)

Bumps the actions-minor-patch group with 2 updates:
[r-lib/actions/setup-r](https://github.com/r-lib/actions) and
[r-lib/actions/setup-r-dependencies](https://github.com/r-lib/actions).

Updates `r-lib/actions/setup-r` from 2.12.1 to 2.13.0

Changelog
Sourced from r-lib/actions/setup-r's
changelog.

v2.13.0 (2026-08028)


[setup-r] now retries r-hub.io HTTP failures (#1088,
@nbenn).


[setup-r] now sets the correct RTOOLS environment
variables on
aarch64 Windows (@vjymisal0, #1104).


[setup-r] keep repositories if they are set by the
build.
E.g. aarch64 Windows builds now set them (@jeroen, #1101).


[setup-r] now retries transient failures when resolving
the R
version from api.r-hub.io, rather than failing the job on
the first
timeout or server error (@nbenn, #1086).


[setup-r-dependencies] now switches back to classic
sudo, if
available, on Linux. This fixes installing pak on Ubuntu 26.04 runners
(@jeroen, #1096).


v2.12.1 (2026-06-23)


[setup-r] now avoids a warning about an
url.parse() deprecation
(#1074).


[setup-r-dependencies] now uses
quarto-dev/quarto-actions v2.2.0
(@jdblischak,
#1076).


Examples: test-coverage.yaml now uses
codecov/codecov-action v7
(@shikokuchuo, #1081).


New example claude-investigate.yaml workflow (@DavisVaughan,
#1084).


v2.12.0 (2026-04-29)


All node.js actions use node 24 now. Relatedly, all example workflows
use recent versions of actions that use node 24.


[setup-r] now uses use-public-rspm: true by
default on Linux and
Windows. macOS binaries require further opt-in with
use-public-rspm: always.


It is now possible to require actions to be pinned to a full-length
commit SHA in repositories using r-lib/actions (#1070).


[setup-pandoc][setup-r-dependencies] now default to
Pandoc
version 3.8.3.


[setup-r-dependencies] now includes the R architecture
in the
cache key, so caches for macos-15 (Apple Silicon) and
macos-15-intel (Rosetta/x86_64) no longer collide (#1035).




... (truncated)


Commits

465b7d8
NEWS for 2.13.0 (#1105)
d06a540
[setup-r] retry transient r-hub.io request failures (#1088)
ed9aa85
fix(setup-r): export correct RTOOLS HOME env vars on Windows ARM64 and
x64 (#...
c86f32c
setup-r-dependencies: set JAVA_HOME on Windows runners from Java 21 env
vars ...
2a66450
setup-r-dependencies: switch back to classic sudo on runners with
sudo-rs (#1...
5cc1f0d
Fix minor typo (#1098)
33d09fb
fix: Remove stray ::group:: (#1103)
aae88a2
Special-case CRAN mirror for Windows ARM64 (#1101)
b7484da
[setup-r] Support installing RTools without installing R (#1093)
See full diff in compare
view





Updates `r-lib/actions/setup-r-dependencies` from 2.12.1 to 2.13.0

Changelog
Sourced from r-lib/actions/setup-r-dependencies's
changelog.

v2.13.0 (2026-08028)


[setup-r] now retries r-hub.io HTTP failures (#1088,
@nbenn).


[setup-r] now sets the correct RTOOLS environment
variables on
aarch64 Windows (@vjymisal0, #1104).


[setup-r] keep repositories if they are set by the
build.
E.g. aarch64 Windows builds now set them (@jeroen, #1101).


[setup-r] now retries transient failures when resolving
the R
version from api.r-hub.io, rather than failing the job on
the first
timeout or server error (@nbenn, #1086).


[setup-r-dependencies] now switches back to classic
sudo, if
available, on Linux. This fixes installing pak on Ubuntu 26.04 runners
(@jeroen, #1096).


v2.12.1 (2026-06-23)


[setup-r] now avoids a warning about an
url.parse() deprecation
(#1074).


[setup-r-dependencies] now uses
quarto-dev/quarto-actions v2.2.0
(@jdblischak,
#1076).


Examples: test-coverage.yaml now uses
codecov/codecov-action v7
(@shikokuchuo, #1081).


New example claude-investigate.yaml workflow (@DavisVaughan,
#1084).


v2.12.0 (2026-04-29)


All node.js actions use node 24 now. Relatedly, all example workflows
use recent versions of actions that use node 24.


[setup-r] now uses use-public-rspm: true by
default on Linux and
Windows. macOS binaries require further opt-in with
use-public-rspm: always.


It is now possible to require actions to be pinned to a full-length
commit SHA in repositories using r-lib/actions (#1070).


[setup-pandoc][setup-r-dependencies] now default to
Pandoc
version 3.8.3.


[setup-r-dependencies] now includes the R architecture
in the
cache key, so caches for macos-15 (Apple Silicon) and
macos-15-intel (Rosetta/x86_64) no longer collide (#1035).




... (truncated)


Commits

465b7d8
NEWS for 2.13.0 (#1105)
d06a540
[setup-r] retry transient r-hub.io request failures (#1088)
ed9aa85
fix(setup-r): export correct RTOOLS HOME env vars on Windows ARM64 and
x64 (#...
c86f32c
setup-r-dependencies: set JAVA_HOME on Windows runners from Java 21 env
vars ...
2a66450
setup-r-dependencies: switch back to classic sudo on runners with
sudo-rs (#1...
5cc1f0d
Fix minor typo (#1098)
33d09fb
fix: Remove stray ::group:: (#1103)
aae88a2
Special-case CRAN mirror for Windows ARM64 (#1101)
b7484da
[setup-r] Support installing RTools without installing R (#1093)
See full diff in compare
view






Dependabot will resolve any conflicts with this PR as long as you don't
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: dcae038489018917cb47d1b51cf50854eb8818bc

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-31 10:40:39 +0000

      Commit message:


	  
		 build(deps): bump the actions-major group with 2 updates

Bumps the actions-major group with 2 updates: [docker/build-push-action](https://github.com/docker/build-push-action) and [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request).


Updates `docker/build-push-action` from 1.1.2 to 7.3.0
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](https://github.com/docker/build-push-action/compare/3e7a4f6646880c6f63758d73ac32392d323eaf8f...53b7df96c91f9c12dcc8a07bcb9ccacbed38856a)

Updates `peter-evans/create-pull-request` from 3 to 8
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/v3...v8)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.3.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-major
- dependency-name: peter-evans/create-pull-request
  dependency-version: '8'
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: actions-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: 8173d479ba563cfa7f7b450fa5794d15dd67a7eb

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-31 10:40:13 +0000

      Commit message:


	  
		 build(deps): bump the actions-minor-patch group with 2 updates

Bumps the actions-minor-patch group with 2 updates: [r-lib/actions/setup-r](https://github.com/r-lib/actions) and [r-lib/actions/setup-r-dependencies](https://github.com/r-lib/actions).


Updates `r-lib/actions/setup-r` from 2.12.1 to 2.13.0
- [Release notes](https://github.com/r-lib/actions/releases)
- [Changelog](https://github.com/r-lib/actions/blob/v2-branch/NEWS.md)
- [Commits](https://github.com/r-lib/actions/compare/d3c5be51b12e724e68f33216ca3c148b66d5f0b6...465b7d8e732ca3921382b1674c59bada9cbf3399)

Updates `r-lib/actions/setup-r-dependencies` from 2.12.1 to 2.13.0
- [Release notes](https://github.com/r-lib/actions/releases)
- [Changelog](https://github.com/r-lib/actions/blob/v2-branch/NEWS.md)
- [Commits](https://github.com/r-lib/actions/compare/d3c5be51b12e724e68f33216ca3c148b66d5f0b6...465b7d8e732ca3921382b1674c59bada9cbf3399)

---
updated-dependencies:
- dependency-name: r-lib/actions/setup-r
  dependency-version: 2.13.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
- dependency-name: r-lib/actions/setup-r-dependencies
  dependency-version: 2.13.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions-minor-patch
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: bb1ffc27dbbe0895d0ad56cd895fcc212c564ed6

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-31 20:38:57 +1000

      Commit message:


	  
		 ci(dependabot): group monthly GitHub Actions updates by semantic versioning level (#395)

This PR configures Dependabot to group monthly GitHub Actions updates by
semantic versioning level: ‎⁠minor⁠ and ‎⁠patch⁠ updates are combined
into one group, while ‎⁠major⁠ updates are grouped separately, making it
easier to review changes and reducing the number of duplicate CI runs.

The ‎⁠`skip-ci⁠` flag has been added in the commit, so this PR will not
trigger CI checks. It is recommended to merge this PR soon so the new
grouping takes effect before the next month and prevents scattered CI
runs and multiple separate PRs. 
    
  
    
      Package: mixOmics

      Commit: 21beec1419b9ce84f9a0e8549aec3b4a7491f3d1

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-29 12:21:43 +1000

      Commit message:


	  
		 ci(dependabot): group monthly GitHub Actions updates by semver level [skip ci]
 
    
  
    
      Package: mixOmics

      Commit: 1d02a97a68182c69b37852ee26f15440acc44338

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 17:21:55 +1000

      Commit message:


	  
		 ci: restrict GITHUB_TOKEN permissions to contents read
 
    
  
    
      Package: mixOmics

      Commit: 9843b7812e3242ec1f3ad531ed0ea7aac6c78ba6

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 17:12:29 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/docker/build-push-action-7.3.0 
    
  
    
      Package: mixOmics

      Commit: 86e3b8ed767d1873c13804cf9362337f509159ca

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 17:07:08 +1000

      Commit message:


	  
		 ci: move docker push to a dedicated job
 
    
  
    
      Package: mixOmics

      Commit: 664aff1465041edaaeff358595dbbad1465a9a23

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 17:05:27 +1000

      Commit message:


	  
		 fix(ci): use GITHUB_EVENT_NAME in shell condition
 
    
  
    
      Package: mixOmics

      Commit: 7dfcc10bfbf0026edec9cca1be07438bdf4e434c

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-28 14:48:38 +1000

      Commit message:


	  
		 build(deps): bump codecov/codecov-action from 4 to 7 (#392)

Bumps
[codecov/codecov-action](https://github.com/codecov/codecov-action) from
4 to 7.

Release notes
Sourced from codecov/codecov-action's
releases.

v7.0.0
⚠️ Due to migration issues with keybase, we are unable to update our
keys under the codecovsecurity account. We have deleted the
account and are using codecovsecops with the original gpg
key
What's Changed

ci: remove Enforce License Compliance workflow by @thomasrockhu-codecov
in codecov/codecov-action#1950
chore(release): 7.0.0 by @thomasrockhu-codecov
in codecov/codecov-action#1957

Full Changelog: https://github.com/codecov/codecov-action/compare/v6.0.1...v7.0.0
v6.0.2
This is a copy of the v7.0.0 release to make updates
easier
What's Changed

ci: remove Enforce License Compliance workflow by @thomasrockhu-codecov
in codecov/codecov-action#1950
chore(release): 7.0.0 by @thomasrockhu-codecov
in codecov/codecov-action#1957

Full Changelog: https://github.com/codecov/codecov-action/compare/v6.0.1...v6.0.2
v6.0.1
What's Changed

fix: prevent template injection in run: steps (VULN-1652) by @thomasrockhu-codecov
in codecov/codecov-action#1947
chore(release): 6.0.1 by @thomasrockhu-codecov
in codecov/codecov-action#1949

Full Changelog: https://github.com/codecov/codecov-action/compare/v6.0.0...v6.0.1
v6.0.0
⚠️ This version introduces support for node24 which make cause
breaking changes for systems that do not currently support node24.
⚠️
What's Changed

Revert "Revert "build(deps): bump actions/github-script
from 7.0.1 to 8.0.0"" by @thomasrockhu-codecov
in codecov/codecov-action#1929
Th/6.0.0 by @thomasrockhu-codecov
in codecov/codecov-action#1928

Full Changelog: https://github.com/codecov/codecov-action/compare/v5.5.4...v6.0.0
v5.5.5
This release only contains the keybase.io change as described here.
Full Changelog: https://github.com/codecov/codecov-action/compare/v5.5.4...v5.5.5
v5.5.4
This is a mirror of v5.5.2. v6 will be
released which requires node24
What's Changed

Revert "build(deps): bump actions/github-script from 7.0.1 to
8.0.0" by @thomasrockhu-codecov
in codecov/codecov-action#1926
chore(release): 5.5.4 by @thomasrockhu-codecov
in codecov/codecov-action#1927



... (truncated)


Changelog
Sourced from codecov/codecov-action's
changelog.

v5.5.2
What's Changed
Full Changelog: https://github.com/codecov/codecov-action/compare/v5.5.1..v5.5.2
v5.5.1
What's Changed

fix: overwrite pr number on fork by @thomasrockhu-codecov
in codecov/codecov-action#1871
build(deps): bump actions/checkout from 4.2.2 to 5.0.0 by
@app/dependabot in codecov/codecov-action#1868
build(deps): bump github/codeql-action from 3.29.9 to 3.29.11 by
@app/dependabot in codecov/codecov-action#1867
fix: update to use local app/ dir by @thomasrockhu-codecov
in codecov/codecov-action#1872
docs: fix typo in README by @datalater in codecov/codecov-action#1866
Document a codecov-cli version reference example by @webknjaz in codecov/codecov-action#1774
build(deps): bump github/codeql-action from 3.28.18 to 3.29.9 by
@app/dependabot in codecov/codecov-action#1861
build(deps): bump ossf/scorecard-action from 2.4.1 to 2.4.2 by
@app/dependabot in codecov/codecov-action#1833

Full Changelog: https://github.com/codecov/codecov-action/compare/v5.5.0..v5.5.1
v5.5.0
What's Changed

feat: upgrade wrapper to 0.2.4 by @jviall in codecov/codecov-action#1864
Pin actions/github-script by Git SHA by @martincostello
in codecov/codecov-action#1859
fix: check reqs exist by @joseph-sentry
in codecov/codecov-action#1835
fix: Typo in README by @spalmurray in codecov/codecov-action#1838
docs: Refine OIDC docs by @spalmurray in codecov/codecov-action#1837
build(deps): bump github/codeql-action from 3.28.17 to 3.28.18 by
@app/dependabot in codecov/codecov-action#1829

Full Changelog: https://github.com/codecov/codecov-action/compare/v5.4.3..v5.5.0
v5.4.3
What's Changed

build(deps): bump github/codeql-action from 3.28.13 to 3.28.17 by
@app/dependabot in codecov/codecov-action#1822
fix: OIDC on forks by @joseph-sentry
in codecov/codecov-action#1823

Full Changelog: https://github.com/codecov/codecov-action/compare/v5.4.2..v5.4.3
v5.4.2


... (truncated)


Commits

fb8b358
chore(release): 7.0.0 (#1957)
ca0a928
ci: remove Enforce License Compliance workflow (#1950)
e79a696
chore(release): 6.0.1 (#1949)
51e6422
fix: prevent template injection in run: steps (VULN-1652) (#1947)
57e3a13
Th/6.0.0 (#1928)
f67d33d
Revert "Revert "build(deps): bump actions/github-script from
7.0.1 to 8.0.0""...
75cd116
chore(release): 5.5.4 (#1927)
87d39f4
Revert "build(deps): bump actions/github-script from 7.0.1 to
8.0.0" (#1926)
1af5884
chore(release): bump to 5.5.3 (#1922)
c143300
build(deps): bump actions/github-script from 7.0.1 to 8.0.0 (#1874)
Additional commits viewable in compare
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[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=codecov/codecov-action&package-manager=github_actions&previous-version=4&new-version=7)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---


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You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
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Dependabot creating any more for this major version (unless you reopen
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: 78b3aadb1349dc12cc84c6c8e2e5fedd7f93ed0c

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 13:22:44 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/codecov/codecov-action-7 
    
  
    
      Package: mixOmics

      Commit: a3dea72826ce9410bd9d6c4ac4826f03c39e8c70

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 12:09:44 +1000

      Commit message:


	  
		 build(deps): bump actions/cache from 4.3.0 to 6.1.0 (#391)

Bumps [actions/cache](https://github.com/actions/cache) from 4.3.0 to
6.1.0.

Release notes
Sourced from actions/cache's
releases.

v6.1.0
What's Changed

Bump @actions/cache to v6.1.0 - handle read-only cache
access by @jasongin in actions/cache#1768

Full Changelog: https://github.com/actions/cache/compare/v6...v6.1.0
v6.0.0
What's Changed

Update packages, migrate to ESM by @Samirat in actions/cache#1760

Full Changelog: https://github.com/actions/cache/compare/v5...v6.0.0
v5.1.0
What's Changed

Bump @actions/cache to v5.1.0 - handle read-only cache
access by @jasongin in actions/cache#1775

Full Changelog: https://github.com/actions/cache/compare/v5...v5.1.0
v5.0.5
What's Changed

Update ts-http-runtime dependency by @yacaovsnc in actions/cache#1747

Full Changelog: https://github.com/actions/cache/compare/v5...v5.0.5
v5.0.4
What's Changed

Add release instructions and update maintainer docs by @Link- in actions/cache#1696
Potential fix for code scanning alert no. 52: Workflow does not
contain permissions by @Link- in actions/cache#1697
Fix workflow permissions and cleanup workflow names / formatting by
@Link- in actions/cache#1699
docs: Update examples to use the latest version by @XZTDean in actions/cache#1690
Fix proxy integration tests by @Link- in actions/cache#1701
Fix cache key in examples.md for bun.lock by @RyPeck in actions/cache#1722
Update dependencies & patch security vulnerabilities by @Link- in actions/cache#1738

New Contributors

@XZTDean made
their first contribution in actions/cache#1690
@RyPeck made
their first contribution in actions/cache#1722

Full Changelog: https://github.com/actions/cache/compare/v5...v5.0.4
v5.0.3
What's Changed

Bump @actions/cache to v5.0.5 (Resolves: https://github.com/actions/cache/security/dependabot/33)
Bump @actions/core to v2.0.3



... (truncated)


Changelog
Sourced from actions/cache's
changelog.

Releases
How to prepare a release

[!NOTE]
Relevant for maintainers with write access only.


Switch to a new branch from main.
Run npm test to ensure all tests are passing.
Update the version in https://github.com/actions/cache/blob/main/package.json.
Run npm run build to update the compiled files.
Update this https://github.com/actions/cache/blob/main/RELEASES.md
with the new version and changes in the ## Changelog
section.
Run licensed cache to update the license report.
Run licensed status and resolve any warnings by
updating the https://github.com/actions/cache/blob/main/.licensed.yml
file with the exceptions.
Commit your changes and push your branch upstream.
Open a pull request against main and get it reviewed
and merged.
Draft a new release https://github.com/actions/cache/releases
use the same version number used in package.json

Create a new tag with the version number.
Auto generate release notes and update them to match the changes you
made in RELEASES.md.
Toggle the set as the latest release option.
Publish the release.


Navigate to https://github.com/actions/cache/actions/workflows/release-new-action-version.yml

There should be a workflow run queued with the same version
number.
Approve the run to publish the new version and update the major tags
for this action.



Changelog
6.1.0

Bump @actions/cache to v6.1.0 to pick up actions/toolkit#2435
Handle cache write error due to read-only token
Switch redundant "Cache save failed" warning to debug log
in save-only

6.0.0

Updated @actions/cache to ^6.0.1,
@actions/core to ^3.0.1, @actions/exec to
^3.0.0, @actions/io to ^3.0.2
Migrated to ESM module system
Upgraded Jest to v30 and test infrastructure to be ESM
compatible

5.0.4

Bump minimatch to v3.1.5 (fixes ReDoS via globstar
patterns)
Bump undici to v6.24.1 (WebSocket decompression bomb
protection, header validation fixes)
Bump fast-xml-parser to v5.5.6

5.0.3

Bump @actions/cache to v5.0.5 (Resolves: https://github.com/actions/cache/security/dependabot/33)
Bump @actions/core to v2.0.3

5.0.2


... (truncated)


Commits

55cc834
Merge pull request #1768
from jasongin/readonly-cache
d8cd72f
Bump @actions/cache to v6.1.0 - handle cache write error
due to RO token
2c8a9bd
Merge pull request #1760
from actions/samirat/esm_migration_and_package_update
e9b91fd
Prettier fixes
e4884b8
Rebuild dist
10baf01
Fixed licenses
e39b386
Fix test mock return order
b692820
PR feedback
6074912
Rebuild dist bundles as ESM to match type:module
5a912e8
Fix lint and jest issues
Additional commits viewable in compare
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[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/cache&package-manager=github_actions&previous-version=4.3.0&new-version=6.1.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---


Dependabot commands and options



You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot show  ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: 19edea1eea4b3593bf2537a02a6d87e7309a27c7

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 11:52:45 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/codecov/codecov-action-7 
    
  
    
      Package: mixOmics

      Commit: 66446ab9bb826cb3b9d75a0e7b0ed914cbab89a4

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 11:51:46 +1000

      Commit message:


	  
		 ci: pin codecov-action and update input names
 
    
  
    
      Package: mixOmics

      Commit: 40838944a48a431fb9dffc912c65db45f911e459

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 11:30:28 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/cache-6.1.0 
    
  
    
      Package: mixOmics

      Commit: 109d57eb50412e384b97a81ac23cd6d473b2060b

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 11:29:24 +1000

      Commit message:


	  
		 build(deps): bump actions/upload-artifact from 4 to 7 (#389)

Bumps
[actions/upload-artifact](https://github.com/actions/upload-artifact)
from 4 to 7.

Release notes
Sourced from actions/upload-artifact's
releases.

v7.0.0
v7 What's new
Direct Uploads
Adds support for uploading single files directly (unzipped). Callers
can set the new archive parameter to false to
skip zipping the file during upload. Right now, we only support single
files. The action will fail if the glob passed resolves to multiple
files. The name parameter is also ignored with this
setting. Instead, the name of the artifact will be the name of the
uploaded file.
ESM
To support new versions of the @actions/* packages,
we've upgraded the package to ESM.
What's Changed

Add proxy integration test by @Link- in actions/upload-artifact#754
Upgrade the module to ESM and bump dependencies by @danwkennedy in
actions/upload-artifact#762
Support direct file uploads by @danwkennedy in
actions/upload-artifact#764

New Contributors

@Link- made
their first contribution in actions/upload-artifact#754

Full Changelog: https://github.com/actions/upload-artifact/compare/v6...v7.0.0
v6.0.0
v6 - What's new

[!IMPORTANT]
actions/upload-artifact@v6 now runs on Node.js 24 (runs.using:
node24) and requires a minimum Actions Runner version of 2.327.1.
If you are using self-hosted runners, ensure they are updated before
upgrading.

Node.js 24
This release updates the runtime to Node.js 24. v5 had preliminary
support for Node.js 24, however this action was by default still running
on Node.js 20. Now this action by default will run on Node.js 24.
What's Changed

Upload Artifact Node 24 support by @salmanmkc in actions/upload-artifact#719
fix: update @actions/artifact for Node.js 24 punycode
deprecation by @salmanmkc in actions/upload-artifact#744
prepare release v6.0.0 for Node.js 24 support by @salmanmkc in actions/upload-artifact#745

Full Changelog: https://github.com/actions/upload-artifact/compare/v5.0.0...v6.0.0
v5.0.0
What's Changed
BREAKING CHANGE: this update supports Node
v24.x. This is not a breaking change per-se but we're
treating it as such.

Update README.md by @GhadimiR in actions/upload-artifact#681
Update README.md by @nebuk89 in actions/upload-artifact#712
Readme: spell out the first use of GHES by @danwkennedy in
actions/upload-artifact#727
Update GHES guidance to include reference to Node 20 version by @patrikpolyak
in actions/upload-artifact#725
Bump @actions/artifact to v4.0.0
Prepare v5.0.0 by @danwkennedy in
actions/upload-artifact#734



... (truncated)


Commits

043fb46
Merge pull request #797
from actions/yacaovsnc/update-dependency
634250c
Include changes in typespec/ts-http-runtime 0.3.5
e454baa
Readme: bump all the example versions to v7 (#796)
74fad66
Update the readme with direct upload details (#795)
bbbca2d
Support direct file uploads (#764)
589182c
Upgrade the module to ESM and bump dependencies (#762)
47309c9
Merge pull request #754
from actions/Link-/add-proxy-integration-tests
02a8460
Add proxy integration test
b7c566a
Merge pull request #745
from actions/upload-artifact-v6-release
e516bc8
docs: correct description of Node.js 24 support in README
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Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
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[//]: # (dependabot-automerge-end)

---


Dependabot commands and options



You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
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</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: c66b029f4bf361a1628ca01e3cab1309a7383a85

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 10:42:57 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/upload-artifact-7 
    
  
    
      Package: mixOmics

      Commit: 8880939f398d0f8b0b9af43dd9bef4c04a57d258

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-28 10:37:39 +1000

      Commit message:


	  
		 build(deps): bump actions/checkout from 2 to 7 (#393)

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to
7.

Release notes
Sourced from actions/checkout's
releases.

v7.0.0
What's Changed

block checking out fork pr for pull_request_target and workflow_run
by @aiqiaoy in actions/checkout#2454
Bump actions/publish-immutable-action from 0.0.3 to 0.0.4 in the
minor-actions-dependencies group across 1 directory by @dependabot[bot]
in actions/checkout#2458
Bump flatted from 3.3.1 to 3.4.2 by @dependabot[bot]
in actions/checkout#2460
Bump js-yaml from 4.1.0 to 4.2.0 by @dependabot[bot]
in actions/checkout#2461
Bump @actions/core and
@actions/tool-cache and Remove uuid by @dependabot[bot]
in actions/checkout#2459
upgrade module to esm and update dependencies by @aiqiaoy in actions/checkout#2463
Bump the minor-npm-dependencies group across 1 directory with 3
updates by @dependabot[bot]
in actions/checkout#2462
getting ready for checkout v7 release by @aiqiaoy in actions/checkout#2464
update error wording by @aiqiaoy in actions/checkout#2467

New Contributors

@aiqiaoy made
their first contribution in actions/checkout#2454

Full Changelog: https://github.com/actions/checkout/compare/v6.0.3...v7.0.0
v6.1.0
What's Changed

[BREAKING] backport
allow-unsafe-pr-checkout to v6 by @aiqiaoy in actions/checkout#2500
backport fixes to releases-v6 by @aiqiaoy in actions/checkout#2527

https://github.blog/changelog/2026-06-18-safer-pull_request_target-defaults-for-github-actions-checkout/
for more details about this breaking change
Full Changelog: https://github.com/actions/checkout/compare/v6.0.3...v6.1.0
v6.0.3
What's Changed

Update changelog by @ericsciple in actions/checkout#2357
fix: expand merge commit SHA regex and add SHA-256 test cases by @yaananth in actions/checkout#2414
Fix checkout init for SHA-256 repositories by @yaananth in actions/checkout#2439
Update changelog for v6.0.3 by @yaananth in actions/checkout#2446

New Contributors

@yaananth
made their first contribution in actions/checkout#2414

Full Changelog: https://github.com/actions/checkout/compare/v6...v6.0.3
v6.0.2
What's Changed

Add orchestration_id to git user-agent when ACTIONS_ORCHESTRATION_ID
is set by @TingluoHuang
in actions/checkout#2355
Fix tag handling: preserve annotations and explicit fetch-tags by @ericsciple in actions/checkout#2356

Full Changelog: https://github.com/actions/checkout/compare/v6.0.1...v6.0.2
v6.0.1
What's Changed

Update all references from v5 and v4 to v6 by @ericsciple in actions/checkout#2314
Add worktree support for persist-credentials includeIf by @ericsciple in actions/checkout#2327
Clarify v6 README by @ericsciple in actions/checkout#2328



... (truncated)


Commits

3d3c42e
prep v7.0.1 release (#2531)
2880268
escape values passed to --unset (#2530)
12cd223
trim only ascii whitespace for branch (#2521)
62661c4
skip running unsafe pr check if input is default (#2518)
e8d4307
Bump the minor-actions-dependencies group with 2 updates (#2499)
631c942
eslint 9 (#2474)
4f1f4ae
Bump actions/upload-artifact from 4 to 7 (#2476)
ba09753
Bump actions/checkout from 6 to 7 (#2488)
b9e0990
Bump docker/login-action from 3.3.0 to 4.2.0 (#2479)
e8cb398
Bump docker/build-push-action from 6.5.0 to 7.2.0 (#2478)
Additional commits viewable in compare
view






[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/checkout&package-manager=github_actions&previous-version=2&new-version=7)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

Dependabot will resolve any conflicts with this PR as long as you don't
alter it yourself. You can also trigger a rebase manually by commenting
`@dependabot rebase`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---


Dependabot commands and options



You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot show  ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop
Dependabot creating any more for this minor version (unless you reopen
the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop
Dependabot creating any more for this dependency (unless you reopen the
PR or upgrade to it yourself)


</details> </pre>
    </div>
  
    
      Package: mixOmics

      Commit: 229565af1586aab4c328c1711a42e1f6c7a75da6

      Author:  Kim-Anh Lê Cao <kimanh.lecao@unimelb.edu.au> 

      Date: 2026-08-27 21:14:23 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/codecov/codecov-action-7 
    
  
    
      Package: mixOmics

      Commit: 54db59c2f8c8ec3a088c2d5148a8af7141a3558a

      Author:  Kim-Anh Lê Cao <kimanh.lecao@unimelb.edu.au> 

      Date: 2026-08-27 21:14:12 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/cache-6.1.0 
    
  
    
      Package: mixOmics

      Commit: 085240dd7dee148c19196b3502b411d13c63833b

      Author:  Kim-Anh Lê Cao <kimanh.lecao@unimelb.edu.au> 

      Date: 2026-08-27 21:14:02 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/docker/build-push-action-7.3.0 
    
  
    
      Package: mixOmics

      Commit: 90140327b4d1087e51a0e9135bc6b61c946f2fcd

      Author:  Kim-Anh Lê Cao <kimanh.lecao@unimelb.edu.au> 

      Date: 2026-08-27 21:13:52 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/upload-artifact-7 
    
  
    
      Package: mixOmics

      Commit: ae5d9cbcaaaaae3dce08a8cde78b555373ffa115

      Author:  Kim-Anh Lê Cao <kimanh.lecao@unimelb.edu.au> 

      Date: 2026-08-27 21:13:34 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/checkout-7 
    
  
    
      Package: mixOmics

      Commit: 6a8af57e57d3a6d80e0b286ca848a6e6495a8ab1

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 18:56:54 +1000

      Commit message:


	  
		 Fix codecov badge reference in README (#394) 
    
  
    
      Package: mixOmics

      Commit: 91c7726988d25be3907eafd88401eb46b029467a

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 17:11:57 +1000

      Commit message:


	  
		 Merge branch 'master' into fix/docs-readme 
    
  
    
      Package: mixOmics

      Commit: 2463a7e0216c3f05d44d6f2e57a15980407f9bee

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 17:03:23 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/checkout-7 
    
  
    
      Package: mixOmics

      Commit: b8c0b8b93f1365dc74fb542ea07d281825286e91

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 17:01:14 +1000

      Commit message:


	  
		 ci: add workflow_dispatch trigger to Code Coverage (#388) 
    
  
    
      Package: mixOmics

      Commit: 640f0877d91202078fb2ec4987d09bd21ed3f484

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 16:29:04 +1000

      Commit message:


	  
		 Fix codecov badge reference in README

Signed-off-by: Mike Rennie <mike@mixomics.org> 
    
  
    
      Package: mixOmics

      Commit: 9f823341bd969d77808a01c170091ef098ec3c6f

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 16:20:02 +1000

      Commit message:


	  
		 Merge branch 'master' into dependabot/github_actions/actions/checkout-7 
    
  
    
      Package: mixOmics

      Commit: 872c3547a2dbac96c4ab6c1ca0acc89eed428a4c

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 16:18:40 +1000

      Commit message:


	  
		 Merge branch 'master' into fix/ci-workflow-dispatch 
    
  
    
      Package: mixOmics

      Commit: 7db9449b0e9ca005a54016855dea742045215d18

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 16:17:53 +1000

      Commit message:


	  
		 fix(mint.block): fix returned model objects and enable predict() (#386)

This PR continues @david-hirst's work in #368, which was opened from his
fork. All of his original commits are preserved here unchanged, and #368
will close automatically once this PR is merged.

## Changes

- **Model object structure**: `mint.block.*` objects now match the
structure of `block.*` objects (`X` + `indY` instead of a wrong `Y`,
plus `design` and `weights`), so `predict()` now works for all four
functions, incl. weighted predictions for DA.
- **keepX/keepY**: now return the actual values (previously an internal
per-component structure / `NULL`). Same bug also fixed in the non-MINT
`block.spls`.
- **Class vectors**: DA classes now include
`block.plsda`/`block.splsda`, so e.g. `selectVar()` correctly excludes
the outcome block.
- **Documentation**: `@return` sections now describe the real
components; both examples fixed (they called the wrong functions).

## Tests

Extended the mint.block tests with the new behaviour and added a
regression test for `block.spls`; 105 assertions passing locally on the
merged tree. Note: some assertions from #382 codified the old buggy
`keepX`/`keepY` and are deliberately replaced. 
    
  
    
      Package: mixOmics

      Commit: c2a21c3c026d7cb9641e192f203cfcd41cd1317c

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-27 06:11:29 +0000

      Commit message:


	  
		 build(deps): bump actions/checkout from 2 to 7

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 7.
- [Release notes](https://github.com/actions/checkout/releases)
- [Commits](https://github.com/actions/checkout/compare/v2...v7)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: 5af6e4fa4d5bc4eb2cba26e98757f1253a535251

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-27 06:11:25 +0000

      Commit message:


	  
		 build(deps): bump codecov/codecov-action from 4 to 7

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 7.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v4...v7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: 813584a8bc7971d0baa3f15847e37c9f81cdb41f

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-27 06:11:21 +0000

      Commit message:


	  
		 build(deps): bump actions/cache from 4.3.0 to 6.1.0

Bumps [actions/cache](https://github.com/actions/cache) from 4.3.0 to 6.1.0.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/0057852bfaa89a56745cba8c7296529d2fc39830...55cc8345863c7cc4c66a329aec7e433d2d1c52a9)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-version: 6.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: 9135366dbeb5ee37ba061ea8d9179d171a92e940

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-27 06:11:14 +0000

      Commit message:


	  
		 build(deps): bump docker/build-push-action from 1.1.2 to 7.3.0

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 1.1.2 to 7.3.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](https://github.com/docker/build-push-action/compare/3e7a4f6646880c6f63758d73ac32392d323eaf8f...53b7df96c91f9c12dcc8a07bcb9ccacbed38856a)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-version: 7.3.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: dc0a4cb21b35f81fa6d06547c29ed1a3214ed10a

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2026-08-27 06:11:03 +0000

      Commit message:


	  
		 build(deps): bump actions/upload-artifact from 4 to 7

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 7.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v4...v7)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '7'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com> 
    
  
    
      Package: mixOmics

      Commit: fda4f22cae985e6c6daf6c5856a484eb924ee49f

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 16:10:51 +1000

      Commit message:


	  
		 Merge branch 'master' into fix/pr-368 
    
  
    
      Package: mixOmics

      Commit: 6473d223d5f611498c4363db64dacbbbbead2d76

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 16:10:27 +1000

      Commit message:


	  
		 ci: replace third-party actions and pin versions in R-CMD-check (#385)

## Why

This PR fixes the `R-CMD-check.yml` workflow, which has been broken
after the migration to `mixOmics-org`: the new Actions security policy,
and several reference from old name.

## Changes

- **Third-party actions replaced**: the policy only allows actions from
trusted sources, so personal third-party actions like
`fkirc/skip-duplicate-actions` and `rlespinasse/github-slug-action` have
been removed. Both are replaced with native steps that do the same job.
Behaviour is unchanged.
- **Actions pinned to commit SHAs**, and a **Dependabot** config keep
version updated.
- **Org rename**: updated from `mixOmicsTeam` to `mixOmics-org`
- **Concurrency**: added workflow-level concurrency.

## Note: action required from an org admin

The two `r-lib/actions` steps (`setup-r`, `setup-r-dependencies`) live
in subdirectories of a monorepo, which the GitHub Marketplace cannot
list. An org admin needs to add `r-lib/actions/*` under **Org Settings →
Actions → General → "Allow specified actions and reusable workflows"**.
Once this entry is added, CI in this repository can run normally again. 
    
  
    
      Package: mixOmics

      Commit: 13e55d8243f379793f8c543b898a42670a4f169a

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 15:58:41 +1000

      Commit message:


	  
		 Merge branch 'master' into fix/pr-368 
    
  
    
      Package: mixOmics

      Commit: 505993b2658e2dbd831bfe1275066a42992db34e

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 15:53:34 +1000

      Commit message:


	  
		 Merge branch 'master' into fix/ci-actions-policy 
    
  
    
      Package: mixOmics

      Commit: feb02f698d63d7762db0c678373ad92b841a146b

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 15:18:26 +1000

      Commit message:


	  
		 ci: add workflow_dispatch trigger to Code Coverage
 
    
  
    
      Package: mixOmics

      Commit: 105b2d1b4e78738dac2c1e03f9bb223437e32080

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-27 13:58:46 +1000

      Commit message:


	  
		 Fix links and badges in README.Rmd (#387)

Updated github links and badges in README from 'mixOmicsTeam' to
'mixOmics-org'. bioconductor and codecov links untouched until updated
on their platforms. 
    
  
    
      Package: mixOmics

      Commit: 81d816d687d8d574e1f0eeffa2bfb517e42d170b

      Author:  Mike Rennie <mike@mixomics.org> 

      Date: 2026-08-27 09:45:40 +1000

      Commit message:


	  
		 Fix links and badges in README.Rmd

Updated github links and badges in README from 'mixOmicsTeam' to 'mixOmics-org'. bioconductor and codecov links untouched until updated on their platforms.

Signed-off-by: Mike Rennie <mike@mixomics.org> 
    
  
    
      Package: mixOmics

      Commit: 4dd9dafb3c04d02d1df9736a853a8d90eddc7daa

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 17:34:15 +1000

      Commit message:


	  
		 ci: replace disallowed third-party actions with native steps and pin all
actions to commit SHAs
 
    
  
    
      Package: mixOmics

      Commit: 62781d6e8d63844f488b7aef38875f06d7aae734

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 17:09:43 +1000

      Commit message:


	  
		 ci: add dependabot config for GitHub Actions
 
    
  
    
      Package: mixOmics

      Commit: f20b816a0d152a03116e6fbf0fdef9919b063df0

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 17:09:22 +1000

      Commit message:


	  
		 ci: pin actions to commit SHAs and update repo org
 
    
  
    
      Package: mixOmics

      Commit: 6c39e3907ea63c48310ed0b0b3ca68cdbc79849d

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 15:12:05 +1000

      Commit message:


	  
		 Merge remote-tracking branch 'origin/master' into fix/pr-368
 
    
  
    
      Package: mixOmics

      Commit: e0f44c0b6323bb3b76814aa015843a1c94721c80

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:34:10 +1000

      Commit message:


	  
		 chore: update RoxygenNote to 7.3.3
 
    
  
    
      Package: mixOmics

      Commit: dc45785caf70d1e3990c37790e2d3d5eb71ce977

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:34:05 +1000

      Commit message:


	  
		 test: add mint.block.splsda structure and predict tests
 
    
  
    
      Package: mixOmics

      Commit: 2048377d9e7d2f700439cc08f8e7c5a095e9415c

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:33:53 +1000

      Commit message:


	  
		 test: expand mint.block.spls test coverage
 
    
  
    
      Package: mixOmics

      Commit: fbe86a96b2785bf980e73e183d7c6890b34156c0

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:33:43 +1000

      Commit message:


	  
		 test(mint.block.pls): expand coverage for block structure and errors
 
    
  
    
      Package: mixOmics

      Commit: 89763aeff6d051e60cf4bec345d02afe2f2b0de7

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:33:26 +1000

      Commit message:


	  
		 test(block.spls): add regression test for keepX/keepY extraction
 
    
  
    
      Package: mixOmics

      Commit: d4de902137d89dfe33e42eba4d4a60490e08690b

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:33:16 +1000

      Commit message:


	  
		 docs(mint): update block PLS documentation for response matrices and
outputs
 
    
  
    
      Package: mixOmics

      Commit: 1d9b5d768aca771c43d37c99aaa1b36c44c2dcd3

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:32:56 +1000

      Commit message:


	  
		 feat(mint.block.splsda): document return value and fix keepX/keepY
extraction
 
    
  
    
      Package: mixOmics

      Commit: 83776db9b94785f21a48935d7d92dc4d046c714c

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:32:38 +1000

      Commit message:


	  
		 fix(mint.block.spls): correct keepX and keepY extraction
 
    
  
    
      Package: mixOmics

      Commit: c9d1cf4a147ccdb2c7f983c112a3e1b4e3e35fd6

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:32:23 +1000

      Commit message:


	  
		 docs(mint.block.plsda): document returned components accurately
 
    
  
    
      Package: mixOmics

      Commit: 275bba6db808fd87dc19c9df2ce3965aab38f79a

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:32:01 +1000

      Commit message:


	  
		 docs(mint.block.pls): update documentation and examples
 
    
  
    
      Package: mixOmics

      Commit: c2f79d49df1e6f48e9818aed0131823ee53bb0cd

      Author:  Derek Lei <derek.lei@mixomics.org> 

      Date: 2026-08-26 11:31:15 +1000

      Commit message:


	  
		 fix(block.spls): correct keepX and keepY extraction in output
 
    
  
    
      Package: mixOmics

      Commit: 2f1c60bfd7b8bb8702dd0d38da53b1755ed68d78

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-25 15:35:48 +1000

      Commit message:


	  
		 docs(readme): note Version 6.36.0 under April 2026
 
    
  
    
      Package: mixOmics

      Commit: 129ebfb8637101bacbc9080a6ffae7c2864cbee8

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-22 11:25:23 +1000

      Commit message:


	  
		 docs(readme): update whats new for May 2026 changes
 
    
  
    
      Package: mixOmics

      Commit: 5f4fcba6f2dc4570b076e37b57f190fc83cffd8d

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-22 10:57:53 +1000

      Commit message:


	  
		 Merge pull request #384 from mixOmicsTeam/issue-377

PR addressing Issue # 377 
    
  
    
      Package: mixOmics

      Commit: 25441ab3b139ac8505fa47c4a85dc53f58351217

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-20 16:44:58 +1000

      Commit message:


	  
		 test(plotLoadings-graphics): add sgccda vector xlim regression test
 
    
  
    
      Package: mixOmics

      Commit: fe7a341fe0af2af062a76975a9183b6f45091812

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-20 16:43:07 +1000

      Commit message:


	  
		 fix(plotLoadings-graphics): preserve xlim indexing for contribution
plots
 
    
  
    
      Package: mixOmics

      Commit: 4295eb82cd9d0cb33d53fe4f477c30279ed77371

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-20 15:46:09 +1000

      Commit message:


	  
		 test: add WeightedPredict tests for block models
 
    
  
    
      Package: mixOmics

      Commit: e3ed0f7ec4e4f4e46e3433ddef217d9bcdaa9af7

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-20 11:39:34 +1000

      Commit message:


	  
		 perf(predict): vectorize WeightedPredict computation for multi-block
models
 
    
  
    
      Package: mixOmics

      Commit: 8573687463f43764ddcdbcc4d2491849d02fae72

      Author:  Kim-Anh Lê Cao <38733836+kimanh-lecao@users.noreply.github.com> 

      Date: 2026-05-11 10:22:01 +1000

      Commit message:


	  
		 Merge pull request #382 from mixOmicsTeam/issue-381

PR addressing Issue #381 
    
  
    
      Package: mixOmics

      Commit: e0537c78185448c49f1b150f444bcdb2d42acd9e

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 15:02:53 +1000

      Commit message:


	  
		 test(wrapper.sgcca): add tests for wrapper.sgcca
 
    
  
    
      Package: mixOmics

      Commit: b6a56761e6673c3c58176c309722c1df7b678495

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 14:45:32 +1000

      Commit message:


	  
		 fix: use x$X for blocks in print.rgcca
 
    
  
    
      Package: mixOmics

      Commit: 300a063b7f5f28f419adc7435a22f0a37f4932a6

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 11:50:43 +1000

      Commit message:


	  
		 test: rewrite mint.block tests
 
    
  
    
      Package: mixOmics

      Commit: 7f0380729dbdab5bcc62bfcdaadc27e107b51f3d

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 11:18:36 +1000

      Commit message:


	  
		 test: add summary tests for PLS, sPLS, RCC and PCA
 
    
  
    
      Package: mixOmics

      Commit: c85a1da304fc8c13b0fa79e1853023bd71afc899

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 11:13:04 +1000

      Commit message:


	  
		 Fix(summary.pca): use prop_expl_var$X
 
    
  
    
      Package: mixOmics

      Commit: d3878bec47603dcd3ba416529fb88b0571879946

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 11:12:02 +1000

      Commit message:


	  
		 fix: check for mixo_pls class
 
    
  
    
      Package: mixOmics

      Commit: fb51e39a3f46576179327727e6dc70a29d5d0aa9

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-08 11:10:14 +1000

      Commit message:


	  
		 Refactor: use method field for type checks
 
    
  
    
      Package: mixOmics

      Commit: 68f43c4b0c1f8dbbcd154f2105ceee47211f7476

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-07 17:34:05 +1000

      Commit message:


	  
		 Fix(Dockerfile): set upgrade to FALSE in R install
 
    
  
    
      Package: mixOmics

      Commit: d788dd272cf3cd997245e206b12456f98c6bbdc2

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-07 16:38:49 +1000

      Commit message:


	  
		 Build(Dockerfile): add remotes/devtools install guard
 
    
  
    
      Package: mixOmics

      Commit: d22a8a15629755f07c5c2688bbf8056ce679183f

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-07 10:52:20 +1000

      Commit message:


	  
		 ci: track bioc devel on non-release branches
 
    
  
    
      Package: mixOmics

      Commit: cad84223f13798ba4c47dd87c8207d6f8d05a1e9

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-07 10:49:09 +1000

      Commit message:


	  
		 build: bump x.y.z version to odd y for Bioc 3.24 devel cycle
 
    
  
    
      Package: mixOmics

      Commit: 0563f27998c15ef3f4a09a4df23a966e831662b5

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-05 12:01:57 +1000

      Commit message:


	  
		 test(vip): add tests for vip across models
 
    
  
    
      Package: mixOmics

      Commit: 51feb43226ff2a48261efbd981c3497e464b022f

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-05 11:47:47 +1000

      Commit message:


	  
		 Test: add zero-variance predictor test
 
    
  
    
      Package: mixOmics

      Commit: 6fafe74a19c685423b626fc17bfce82297da8e7a

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-04 16:22:05 +1000

      Commit message:


	  
		 test(sipca): add tests for exp and logcosh
 
    
  
    
      Package: mixOmics

      Commit: f761fa03fad3c7ee2c0a271da765e760275cf6f5

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-04 16:19:05 +1000

      Commit message:


	  
		 test(ipca): add exp and parallel mode tests
 
    
  
    
      Package: mixOmics

      Commit: 952efad63cd7e2d880d17732e70c79b9aad3e9f2

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-01 12:40:35 +1000

      Commit message:


	  
		 fix(unmap): correct dimnames and group labels
 
    
  
    
      Package: mixOmics

      Commit: 3aa6519a2c41af86229f11aa6480a28b2dfea187

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-05-01 12:39:45 +1000

      Commit message:


	  
		 test: Add unit tests for unmap and map
 
    
  
    
      Package: mixOmics

      Commit: d732983ad52fdd7fb2496a7ca8ac1bec501a63ab

      Author:  Derek Lei <leiderek12@gmail.com> 

      Date: 2026-04-22 01:43:28 +1000

      Commit message:


	  
		 build: Bump mixOmics version to 6.35.2
 
    
  
    
      Package: mixOmics

      Commit: 97c8cacf8c16e9ca03cf05b50bb5cab6c83016ab

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2026-02-12 13:59:19 +1100

      Commit message:


	  
		 return design matrix with mint block (s)pls model fits
 
    
  
    
      Package: mixOmics

      Commit: f2814c18b3297053d18108c2de8978bd7a071624

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2025-11-28 09:53:00 +1100

      Commit message:


	  
		 add in block.(s)plsda to class list
 
    
  
    
      Package: mixOmics

      Commit: db6ab30ec5d2ec319db330cac8ba503b2e130c55

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2025-10-01 16:51:25 +1000

      Commit message:


	  
		 Fix keepX and keepY values returned for mint.block.splsda
 
    
  
    
      Package: mixOmics

      Commit: 1f1ca475833d79592d54c7197b1df6cff4834bf0

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2025-08-07 10:18:08 +1000

      Commit message:


	  
		 Treatment of mint block objects by the predict function
 
    
  
    
      Package: mixOmics

      Commit: 9f52a1041dc5a9336f20c6f349f83d4733eb6b58

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2025-08-01 17:11:43 +1000

      Commit message:


	  
		 changes to mint.block.spls function
 
    
  
    
      Package: mixOmics

      Commit: 68acc77275fc316a432a5151d5e8454c3740d672

      Author:  david-hirst <hirstdp@gmail.com> 

      Date: 2025-08-01 15:22:08 +1000

      Commit message:


	  
		 changes to mint.block.pls function
 
    
  
    
      Package: OmnipathR

      Commit: be33ccd2088aeae44d02953fb287daac731ff7f8

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-30 00:42:36 +0000

      Commit message:


	  
		 Bump version: 4.1.2 → 4.1.3
 
    
  
    
      Package: OmnipathR

      Commit: 974c81207d9ddb0c34d01b30834e5181d7c1fd1e

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-10-29 23:21:14 +0000

      Commit message:


	  
		 UniProt: HTTP/1.1 and build-server fallback, faster examples

Over HTTP/2, rest.uniprot.org sometimes resets slow transfers ("HTTP/2
stream 1 was not closed cleanly"). This stopped the checks on taishan
and nebbiolo1. The hosts in the new option `omnipathr.http1_hosts` use
HTTP/1.1.

On build servers, a failed UniProt query gives a warning and an empty
table, and later queries in the session skip UniProt, as with BioMart.

`kinasephos` and the deprecated NicheNet network functions do not
download in the checks of OmnipathR.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
 
    
  
    
      Package: plyxp

      Commit: 273c0b7e8a91597be0c41870e834a786b650dac9

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 18:47:16 -0400

      Commit message:


	  
		 version bump
 
    
  
    
      Package: plyxp

      Commit: 0e409cbda04f6a451d97bbd0add48e2379d59fd2

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 18:46:55 -0400

      Commit message:


	  
		 updating the news for this version
 
    
  
    
      Package: plyxp

      Commit: 1575a740a36b0ae8960cd54c0250ad006791b85d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 18:30:53 -0400

      Commit message:


	  
		 speed up some splitting
 
    
  
    
      Package: plyxp

      Commit: bf537d3883422da91061da83a6053cc25b0f13ad

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 18:30:48 -0400

      Commit message:


	  
		 some thing I missed to include
 
    
  
    
      Package: plyxp

      Commit: 592b3402071d2db7210428b2fff371ec59834ca1

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 17:47:55 -0400

      Commit message:


	  
		 Update vctrs-S4-group.R
 
    
  
    
      Package: plyxp

      Commit: 25ffa7623291eb7636481fb062f0a620a20f98bd

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 16:16:01 -0400

      Commit message:


	  
		 Revert "Merge branch 'mikelove-devel' into devel-DF-group_data"

This reverts commit 3269e8b2b81f3574ea9f980f66477fb8cead01ef.
 
    
  
    
      Package: plyxp

      Commit: 1898b65d6394f36b893347ff5772fc5bea6ef35e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-29 16:12:07 -0400

      Commit message:


	  
		 Merge branch 'devel' into devel-DF-group_data
 
    
  
    
      Package: plyxp

      Commit: be2240330903a22630cfb576d269871d4eb3b1be

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-28 22:30:26 -0400

      Commit message:


	  
		 optim on missing expression
 
    
  
    
      Package: plyxp

      Commit: 7a12fafb4e4fde54352f49765aa6bbfba04e1d3d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-28 21:31:08 -0400

      Commit message:


	  
		 refactoring standard code to check functions
 
    
  
    
      Package: plyxp

      Commit: 3269e8b2b81f3574ea9f980f66477fb8cead01ef

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-27 11:16:44 -0400

      Commit message:


	  
		 Merge branch 'mikelove-devel' into devel-DF-group_data
 
    
  
    
      Package: plyxp

      Commit: 405a297486205d6eef327fc65e7296224bd0be55

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-27 11:12:36 -0400

      Commit message:


	  
		 Merge branch 'devel' into devel-DF-group_data
 
    
  
    
      Package: plyxp

      Commit: 45d99c57a4a5b5d5c3adab5b02ba3953ccc47f88

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 13:47:17 -0400

      Commit message:


	  
		 minimal changes to tests due to code changes.
 
    
  
    
      Package: plyxp

      Commit: 6f9fd2faed112004a579861f48521566408c1518

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2026-10-20 13:44:25 -0400

      Commit message:


	  
		 minimal changes to make the package work with DF group_data
 
    
  
    
      Package: scRNAseqApp

      Commit: 8cbbe63d44a8a6e7e1429dec99db601be6ed265e

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-10-29 15:09:44 -0400

      Commit message:


	  
		 add plots for multiple grouped paired genes.
 
    
  
    
      Package: LACE

      Commit: ccf646a99559ea41d030c318f3924ff7f2b33fda

      Author:  DavideMaspero <d.maspero@campus.unimib.it> 

      Date: 2026-10-29 20:09:59 +0100

      Commit message:


	  
		 Update DESCRIPTION
 
    
  
    
      Package: VERSO

      Commit: 63be67133da6ad537ba54efdf877a1631dcba837

      Author:  DavideMaspero <d.maspero@campus.unimib.it> 

      Date: 2026-10-29 20:08:01 +0100

      Commit message:


	  
		 Update DESCRIPTION
 
    
  
    
      Package: prolfqua

      Commit: cd755445d69dee0908ba076cfcc39ad20f5c2f3c

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 18:50:32 +0100

      Commit message:


	  
		 Merge fgcz/prolfqua main into prolfqua_bioc; version 0.99.5
 
    
  
    
      Package: prolfqua

      Commit: 6b89e986b31550a09bcd929b8637875982bd424d

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:58:49 +0100

      Commit message:


	  
		 Intro: documentation list first, method list updated; imputation heatmaps share one row order
 
    
  
    
      Package: prolfqua

      Commit: eae1e3168cb59d2f75bde210424c3b8bdef02e9b

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:48:27 +0100

      Commit message:


	  
		 Rename articles to say what they cover; redirect old URLs

- ContrastFacades -> ComparingMethods, ContrastFacade2Factor -> TwoFactorDesigns,
  Contrasts_from_factors -> ContrastsFromFactors
- Clearer titles for CreatingConfigurations and SimulateData
- pkgdown redirects for the old URLs; links in vignettes, README, NEWS updated
 
    
  
    
      Package: prolfqua

      Commit: 383c577199955d37560745cf3bbd09eba958f984

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:44:59 +0100

      Commit message:


	  
		 Imputation article renamed ModelBasedImputation; heatmaps and PCA before and after imputation
 
    
  
    
      Package: prolfqua

      Commit: a0b74c070d309f9fefae9915b80be7c63f581534

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:42:18 +0100

      Commit message:


	  
		 Rename imputation article to LODImputation, redirect old URL; pkgdown url and GitHub link point to fgcz
 
    
  
    
      Package: prolfqua

      Commit: 20892bb85702b9786750e0355b59f79d553c8d53

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:32:37 +0100

      Commit message:


	  
		 Vignettes use build_contrast_analysis(); rewrite imputation article, add low-level API article

- Comparing2Groups and SimulateData fit contrasts with lm_impute / lm facades
- Drop DEqMS_Moderation, Modelling2Factors, limpa_example articles
- TestingMissingInference rewritten: 'Absent, not unknown: proteins missing
  in a whole group' (LOD estimate, lm_impute refit, impute_from_model)
- New LowLevelAPI article: strategy -> model -> contrasts by hand, equal to
  the lm facade
 
    
  
    
      Package: prolfqua

      Commit: 73d3a7aff80206a54ad062228ad047c79907fdf9

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:14:44 +0100

      Commit message:


	  
		 Drop the Limma Backend article; facades cover limma, limma_voom and limpa
 
    
  
    
      Package: prolfqua

      Commit: 0fe3361a9b4e39e82aaed331bd404b8799669448

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:13:15 +0100

      Commit message:


	  
		 Vignettes prolfqua and ModellingMethods: author Witold E. Wolski only
 
    
  
    
      Package: prolfqua

      Commit: c7c61066e5d8c71c88952f09dc2ff46e36cd7f18

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 13:09:45 +0100

      Commit message:


	  
		 Intro vignette quick start uses lm_impute; fix JPR citation fields in CITATION and README
 
    
  
    
      Package: prolfqua

      Commit: 9e4b6b575603026a7bc23ffbf4e669b225a1b98d

      Author:  Christian Panse <cp@fgcz.ethz.ch> 

      Date: 2026-10-27 13:37:42 +0100

      Commit message:


	  
		 add logo to vignette
 
    
  
    
      Package: prolfqua

      Commit: 9a1e2785d54072f2466a1ecddf154f6481215cec

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 12:37:53 +0100

      Commit message:


	  
		 Vignettes cite the JPR 2023 article instead of the bioRxiv preprint
 
    
  
    
      Package: prolfqua

      Commit: 261884eb0bb18ac7e9a114f5f1e95081b62a3904

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 11:38:20 +0100

      Commit message:


	  
		 Ship three vignettes; move eleven tutorials to pkgdown articles

- New fast vignette ModellingMethods: every build_contrast_analysis() method
  on 20 simulated proteins, one summary line per method (~3 s).
- Eleven heavy vignettes moved to vignettes/articles/ (excluded from R CMD
  build via .Rbuildignore); pkgdown still renders them under the same
  articles/.html URLs.
- Package ships prolfqua, Comparing2Groups, ModellingMethods, which keeps the
  Bioconductor build short.
 </pre>
    </div>
  
    
      Package: prolfqua

      Commit: 03fe23b6220e1d7a59c406bfb81601442baec960

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 10:03:45 +0100

      Commit message:


	  
		 README: state this is the stripped-down Bioconductor version; all vignettes live in fgcz/prolfqua
 
    
  
    
      Package: prolfqua

      Commit: 9a23e8ccdcc3be879e63c7b7afb14cd0d14b3993

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 10:03:22 +0100

      Commit message:


	  
		 Merge remote-tracking branch 'bioc/devel'
 
    
  
    
      Package: prolfqua

      Commit: 2980c1be0d22bc21dc1ae4d82eb83a3b0ef18156

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-26 12:34:48 +0100

      Commit message:


	  
		 Add hurdle contrasts and the binomial_firth_nested detection model

- ContrastsHurdleFacade combines a fitted intensity facade with a fitted
  detection facade (firth_nested, binomial_nested, binomial_firth_nested)
  by Fisher's method, as msqrob2's hypothesisTestHurdle; fully detected
  proteins keep their intensity p-value.
- binomial_firth_nested (ContrastsBinomialFirthNestedFacade,
  StrategyBinomialFirth): binomial_nested with Firth's bias reduction in
  place of the fixed pseudo-count. Dispersion and df come from the samples,
  so p-values do not sharpen with the number of peptides as in firth_nested.
- hurdle_nested (ContrastsHurdleNestedFacade): peptide input, median polish,
  lm_impute + binomial_firth_nested, combined; registered, so prolfquapp can
  use it as a model.
 
    
  
    
      Package: prolfqua

      Commit: 9538ce0c8aabe13fb0e6395d919762c4844e5a72

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-21 10:55:22 +0200

      Commit message:


	  
		 DESCRIPTION: record roxygen2 8.1.1 (Config/roxygen2/version)
 
    
  
    
      Package: prolfqua

      Commit: e4ecc9a4b175114535018e96d7cba576188a3c05

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-14 14:34:05 +0200

      Commit message:


	  
		 Merge fgcz/prolfqua main (CI: r-universe Bioconductor build, R 4.6) into the Bioconductor fork
 
    
  
    
      Package: prolfqua

      Commit: 2e2483ab264d487ce7bdadd5a17cc23b2b23bd0a

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-09 09:35:48 +0200

      Commit message:


	  
		 CI: add the r-universe Bioconductor build and R 4.6 to R CMD check

r-universe.yml runs the same build and BiocCheck as BiocStaging, as the
Bioconductor precheck recommends (Bioconductor/BiocContributions#171).
 
    
  
    
      Package: DRIMSeq

      Commit: d7a601b2e9a568e89c3e2ed0fe1207b3456ff075

      Author:  Mark Robinson <mark.robinson@mls.uzh.ch> 

      Date: 2026-10-29 18:56:34 +0100

      Commit message:


	  
		 fix unexported data loader
 
    
  
    
      Package: DuckDBSpatial

      Commit: 5c4e99d743b86fc2ada74a49fd39079adae82779

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-29 09:59:10 -0700

      Commit message:


	  
		 Fix st_as_sfc() binder error on already-GEOMETRY-typed columns

st_as_sfc.DuckDBTable unconditionally applied ST_GeomFromText (or the
WKB/GeoJSON variant) to every column, assuming it was always stored as
text needing conversion. A column already read back as native GEOMETRY
(e.g. via readGeoParquet(), which can tag it with a CRS like
GEOMETRY('OGC:CRS84')) fails that call at the DuckDB binder, since
ST_GeomFromText only accepts VARCHAR. Check each column's type via
coltypes() first and leave already-GEOMETRY columns untouched.
 
    
  
    
      Package: TiDEomics

      Commit: 8f1ba5a51afcdb9f2c3ea2c641c0673d2ef5fb99

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-10-29 15:25:09 +0000

      Commit message:


	  
		 Update README

Regenerated README.md
 
    
  
    
      Package: regioneR

      Commit: 4337700a8f1dbd850ae4ed463e774ca237df013e

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 16:20:34 +0100

      Commit message:


	  
		 Version Bump
 
    
  
    
      Package: regioneR

      Commit: 1c2a7bf1c28be6ecbac0f8f2f72648a5c9e0cf45

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 16:20:18 +0100

      Commit message:


	  
		 Added ORCID for all authors
 
    
  
    
      Package: regioneR

      Commit: aaead84657c6c6c5b64bb026e3494824e15bf92e

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 16:16:47 +0100

      Commit message:


	  
		 Applyed a couple of minor code improvements
 
    
  
    
      Package: regioneR

      Commit: d250e2565af9932a08376cb6768f02dc3afb848c

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 16:14:48 +0100

      Commit message:


	  
		 updated stale Rd file
 
    
  
    
      Package: regioneR

      Commit: a35298b811af2d6e2a4787530127fdae87a6ad5c

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 16:03:54 +0100

      Commit message:


	  
		 Added URL and BuGReports to DESCRIPTION
 
    
  
    
      Package: regioneR

      Commit: 2703400873bd1e3ac2e7a5b4daf583e6d83c4454

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 15:39:02 +0100

      Commit message:


	  
		 removed stale tests
 
    
  
    
      Package: regioneR

      Commit: 5460b7425f2443471cd987e4c6567218f9a6aae3

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 15:29:40 +0100

      Commit message:


	  
		 updated multiple small problems reported by BiocCheck (documentation, etc...)
 
    
  
    
      Package: TiDEomics

      Commit: 8a73a651d81a986b70cc707c675dc794fa659a84

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-10-29 12:54:11 +0000

      Commit message:


	  
		 v0.99.7, improve DE result naming and scatter plot

Increase version to 0.99.7. Improve column naming in `DE_timecourse()` results. Make `y=x` line optional for `plot_scatter()`. Update tests and NEWS.
 
    
  
    
      Package: biomaRt

      Commit: c041de8929457c305faccde1a02001b2d34c7dc5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-29 15:00:03 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: biomaRt

      Commit: dfeaf8696d90ec8d1752f584d6555123ae6f1ae6

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-29 14:59:43 +0100

      Commit message:


	  
		 Fix date for e116

Co-authored-by: David Laehnemann <1379875+dlaehnemann@users.noreply.github.com>
 
    
  
    
      Package: biomaRt

      Commit: 2083db2f7a4f9a88b2349632edad8303bef98fd4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-29 14:42:01 +0100

      Commit message:


	  
		 Try avoid hitting upstream server in .constructEnsemblURL()
 
    
  
    
      Package: knowYourCG

      Commit: 0a4c2f9a99483c31dc87d55ff33680bdcc36c93b

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-29 07:53:06 -0400

      Commit message:


	  
		 Vignettes and README point to the kycg command line and the web app
 
    
  
    
      Package: knowYourCG

      Commit: b285807f978abdcc12609ec288b3b7f85638d148

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-28 10:41:28 -0400

      Commit message:


	  
		 library(knowYourCG) names the paper to cite; version 1.9.7
 
    
  
    
      Package: universalmotif

      Commit: 2e1fb8f241844ba3f93a45204194bd3b80f813fc

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-10-29 11:54:38 +0000

      Commit message:


	  
		 bump version
 
    
  
    
      Package: universalmotif

      Commit: f2cefc3f1ed31a709bf2d7e27ee0ec528b96c995

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-10-29 11:54:38 +0000

      Commit message:


	  
		 Fix scan P-values next to gapped motifs and refuse unknown mask ranges

scan_sequences() expanded gapped motifs into one per combination of gap
sizes, and with RC split them by strand, but then looked up each hit's
motif by its original index in those lists, so motifs scanned after a
gapped one, or with respect.strand, got P-values from the wrong motif.
P-values and q-values now come from the motifs as given. mask_ranges()
ignored ranges on sequences not in seqs, which hid typos in sequence
names; it now stops with an error.
 
    
  
    
      Package: regioneR

      Commit: f9504082faae0879f3cefcbca61f2a16daf3a4a1

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 12:32:06 +0100

      Commit message:


	  
		 Version Bump
 
    
  
    
      Package: regioneR

      Commit: a90ddd9439b1fcbe8446b5567143405b9e65e3fb

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 12:30:59 +0100

      Commit message:


	  
		 Fixed DESCRIPTION - Authors and GenomicRanges
 
    
  
    
      Package: regioneR

      Commit: 27460888ed56331478a17daece0f9f1a86e54043

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 12:19:33 +0100

      Commit message:


	  
		 Updated toDataframe to future proof it. Updated related tests
 
    
  
    
      Package: regioneR

      Commit: 3d65fa4e502f4a407d51bfa0f1985d7d9685c48a

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 12:11:48 +0100

      Commit message:


	  
		 removed Maintainer field from DESCRIPTION
 
    
  
    
      Package: regioneR

      Commit: fa3ecf0a249ab5eb1a062e097ad41c598232d3af

      Author:  Bernat <bernatgel@gmail.com> 

      Date: 2026-10-29 11:43:28 +0100

      Commit message:


	  
		 Updated authors field in DESCRIPTION
 
    
  
    
      Package: exploreSE

      Commit: 7c3b2e73b4f0d5920f25b36b494d3398ad485080

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-29 12:02:47 +0100

      Commit message:


	  
		 added landing page, edited the context gene matching
 
    
  
    
      Package: exploreSE

      Commit: d7b6196cff4c99c055b22398256e03f4cfb4d424

      Author:  Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com> 

      Date: 2026-10-23 15:31:30 +0200

      Commit message:


	  
		 added more example context, added an about page
 
    
  
    
      Package: MetaboDynamics

      Commit: ee624945f57e88b5484a1ee3a90971ccf4d5bf08

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-29 12:00:13 +0100

      Commit message:


	  
		 version bump
 
    
  
    
      Package: MetaboDynamics

      Commit: 71bb645992e1b95ee75edeedea770903af68626d

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-10-29 11:59:24 +0100

      Commit message:


	  
		 notation changes of model in vignette
 
    
  
    
      Package: lcmsPlot

      Commit: 655c0d145f5c39f62793217b4af41b6dbff8fad1

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 16:43:45 +0000

      Commit message:


	  
		 docs(readme): add build and licence badges

Add README badges for R CMD check, the Bioconductor devel build, and
the GPL-3 licence.

Refs #68
 
    
  
    
      Package: lcmsPlot

      Commit: 75ada3959c60d14d7f9a767c5d80d187c6dd76e4

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 16:40:44 +0000

      Commit message:


	  
		 docs(formats): document the supported input formats and versions

Add a ?lcmsPlot-formats help page listing every supported input with
the versions it supports, the way to read it, and the packages it needs
beyond the imports, and link it from lcmsPlot(). The README table gains
a Versions column, and the Interoperability section of the vignette
shows the same table.

The vignette also gets a section on saving figures with lp_save() and
exporting the plotted data with lp_export_data(), and the README
overview mentions both.

Refs #68
 
    
  
    
      Package: lcmsPlot

      Commit: 6787c4e58185e625720afed6be67645e1be11095

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 16:36:27 +0000

      Commit message:


	  
		 feat(report): record the provenance of reports

lp_report() now closes with a provenance section, the last page of a
PDF report, listing the versions of lcmsPlot, R and Bioconductor, the
pipeline layers with their arguments, and the input files. The full
record, with every loaded package version, is written next to the
report as .provenance.json and, in HTML reports, embedded as a
JSON script element alongside a generator meta tag. PDF reports carry
their title in the document metadata.

provenance = FALSE leaves all of this out, and checksums = TRUE adds the
MD5 of every input file.

Refs #68
 </pre>
    </div>
  
    
      Package: lcmsPlot

      Commit: 0c01611e13d6132d6ef821c55dbeca88e5bb2c66

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 16:29:52 +0000

      Commit message:


	  
		 feat(export): save figures with provenance and export the plotted data

Add lp_save(), which saves the plot of a pipeline with ggsave() and
writes a .provenance.json next to it: the versions of lcmsPlot, R,
Bioconductor and every loaded package, the pipeline layers with their
arguments (from the history slot), and the input files with their size
and modification time, plus MD5 checksums with checksums = TRUE. The
sidecar is named after the full file name so the PDF and PNG of a figure
each keep their own.

Add lp_export_data(), which writes the plotted datasets as CSV or TSV in
the tidy form the plot is drawn from, with the detected peaks, the
samples, and a columns data dictionary (type, unit, description).
lp_save(data = TRUE) calls it into _data/.

The per-dataset loop of .render_plot() moves into .plot_datasets() so
that plotting and the export share it.

Refs #68
 </pre>
    </div>
  
    
      Package: lcmsPlot

      Commit: ad51eebe75d29bdbd576db756abd53eeb32afa60

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 16:24:04 +0000

      Commit message:


	  
		 chore(meta): add codemeta.json and extend biocViews

Add a codemeta.json generated from DESCRIPTION with codemetar, so
software registries can harvest the package metadata, and note in
CONTRIBUTING that it is regenerated with every version bump.

Extend biocViews with Software, Lipidomics, Visualization and
ShinyApps, which are all in the biocViews vocabulary.

Refs #68
 
    
  
    
      Package: universalmotif

      Commit: aa72ba5c0ece1d687636d2932a36f520a2d3d967

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-10-29 10:30:16 +0000

      Commit message:


	  
		 bump version
 
    
  
    
      Package: universalmotif

      Commit: d2420b1a129062a0617ad73a6b9a06061a927f61

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-10-29 10:30:16 +0000

      Commit message:


	  
		 Use 201 bins for compare_motifs_lite() P-values

Column correlations of real motifs pile up near 1 and -1, where 51 bins
resolve them poorly. Over all pairs of JASPAR vertebrate motifs, 51 bins
lost 6% of the comparisons significant at q 0.05 against a 2001-bin
reference, and 201 bins a third as many, at about three times the cost of
the P-values.
 
    
  
    
      Package: DaparToolshed

      Commit: 9974d52e5f4264b8df447e83a461ee43a7093ff5

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-29 11:22:30 +0100

      Commit message:


	  
		 Update
 
    
  
    
      Package: DaparToolshed

      Commit: b9a6cef0267ae85c8618713db8f2f87df6ec2d63

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-29 10:31:26 +0100

      Commit message:


	  
		 Fix cc issue
 
    
  
    
      Package: DaparToolshed

      Commit: 1eaaa4049c5fa9872498a1ed1f9e50a2337101bd

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-29 10:06:40 +0100

      Commit message:


	  
		 Fix dependency issue
 
    
  
    
      Package: DaparToolshed

      Commit: 491b172ae167ceeb88c302a70c11e1fae0680aa3

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-29 09:58:09 +0100

      Commit message:


	  
		 Update
 
    
  
    
      Package: DaparToolshed

      Commit: d969950235d0e78c0fc7c6c3cde4df78b571de97

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-10-29 09:49:10 +0100

      Commit message:


	  
		 Correct cc bug
 
    
  
    
      Package: DaparToolshed

      Commit: c98fe5edf908f9c5cd358811eaa0d75a9e3a64f1

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-21 17:24:59 +0200

      Commit message:


	  
		 Fix bug in import
 
    
  
    
      Package: DaparToolshed

      Commit: bb1a2ff24eee545aa732456f456c8f9377af63a9

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-18 12:13:24 +0200

      Commit message:


	  
		 Fix history bug
 
    
  
    
      Package: DaparToolshed

      Commit: 729ca872bd036b4f7a3f5208f2de919330ac6e53

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-18 11:27:37 +0200

      Commit message:


	  
		 Fix history bug
 
    
  
    
      Package: DaparToolshed

      Commit: 72b7a5e9fd076777a3a07ab5c1e040fb3d32ff2c

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-09-14 10:17:34 +0200

      Commit message:


	  
		 Update version number
 
    
  
    
      Package: DaparToolshed

      Commit: 303ae061f8dfd052e47c9bc4469d843a6a2d4f76

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-08-06 16:46:42 +0200

      Commit message:


	  
		 Minor bug fixes
 
    
  
    
      Package: DaparToolshed

      Commit: fdf1b55c598cc6f061d0622efe025bcf3de2d1a8

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-07-16 09:21:41 +0200

      Commit message:


	  
		 version bump in devel
 
    
  
    
      Package: DaparToolshed

      Commit: 5d07a0efc24b17a2f9d40a80c617a9ebd408370c

      Author:  Manon Gaudin <144104844+PomKokca@users.noreply.github.com> 

      Date: 2026-07-10 14:54:51 +0200

      Commit message:


	  
		 Merge branch 'master' into devel 
    
  
    
      Package: DaparToolshed

      Commit: 0c48c86b5f25042c27cab587e8768e2301b7331a

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-05-07 10:59:26 +0200

      Commit message:


	  
		 Minor fix
 
    
  
    
      Package: DaparToolshed

      Commit: 144222b004a4a48b361f9623e1b333bcf4aa274d

      Author:  PomKokca <manong2085@orange.fr> 

      Date: 2026-05-06 16:06:53 +0200

      Commit message:


	  
		 Minor fix
 
    
  
    
      Package: prolfqua

      Commit: 8c4e28d1774e96f5d4dd1e3ff7e27126a11e8058

      Author:  Witold Wolski <wewolski@gmail.com> 

      Date: 2026-10-29 09:49:52 +0100

      Commit message:


	  
		 README: drop trailing blank line (Bioconductor push-access test)
 
    
  
    
      Package: SpatialFeatureExperiment

      Commit: baf697bf521f7babfe790da01eb895668ab6463b

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-29 16:46:59 +0800

      Commit message:


	  
		 Deal with ramifications of changing to withDimnames = FALSE in defaults
 
    
  
    
      Package: SpatialFeatureExperiment

      Commit: 1cbb150548f42870749bd985b627c7a120e83bdb

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-28 22:09:15 +0800

      Commit message:


	  
		 Allow parquet file name or DuckDBColumn in colGeometry setter
 
    
  
    
      Package: SpatialFeatureExperiment

      Commit: d3e4688b4b24f03d9ac1e5b115eb88452c7afada

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-28 22:07:58 +0800

      Commit message:


	  
		 Allow parquet file name or DuckDBColumn for colGeometries in SFE constructor
 
    
  
    
      Package: SpatialFeatureExperiment

      Commit: b3ca303d8b9956ded0be2785d0b4ba9aaf444b6a

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-27 22:07:01 +0800

      Commit message:


	  
		 Begin the DuckDB transformation. Deprecate using non-spatial data frames in *Geometry<-
 
    
  
    
      Package: SpatialFeatureExperiment

      Commit: 8270398c252da1f250b5b81334659545563dbc8a

      Author:  Lambda Moses <lambda.calc29@gmail.com> 

      Date: 2026-10-27 16:36:46 +0800

      Commit message:


	  
		 Simplify containsOutOfMemoryData. Code is a liability.
 
    
  
    
      Package: gDRimport

      Commit: f83acc120961a5001fdd0b6e0c1457bdac6ff8a6

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-10-29 09:42:34 +0100

      Commit message:


	  
		 Merge pull request #133 from gdrplatform/GDR-3761

fix: read DepMap OncRef compound lists and numeric doses in the level 6 PRISM converter 
    
  
    
      Package: gDRimport

      Commit: 6c702d4347ad7d7196d47db2565776824571ccf5

      Author:  Arkadiusz Gladki <gladki.arkadiusz@gmail.com> 

      Date: 2026-10-28 12:56:43 +0100

      Commit message:


	  
		 fix: read DepMap OncRef compound lists and numeric doses in the level 6 PRISM converter
 
    
  
    
      Package: BreastSubtypeR

      Commit: 4566e305fe54ae90d8dd02d142a1653352b67bd4

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-28 20:42:34 +0100

      Commit message:


	  
		 Merge pull request #217 from JohanHartmanGroupBioteam/release/prepare-1.5.11

Prepare BreastSubtypeR 1.5.11 release metadata 
    
  
    
      Package: BreastSubtypeR

      Commit: fac1c9415a3455e0a79d1c558c86d5b68e1452a4

      Author:  Manos Sifakis <sifakis_manos@yahoo.com> 

      Date: 2026-10-28 18:54:37 +0000

      Commit message:


	  
		 Prepare version 1.5.11 release metadata and validation filenames
 
    
  
    
      Package: BreastSubtypeR

      Commit: d0c1267c71ccbac9f2199f95ff64116cbbc86b08

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-28 18:51:29 +0100

      Commit message:


	  
		 Merge pull request #216 from JohanHartmanGroupBioteam/codex/mapping-opt-in-target-knn-20261028

Make Mapping imputation opt-in with target-only gene-level KNN 
    
  
    
      Package: BreastSubtypeR

      Commit: bf4bb3f0ecf235ee362088f54b10afb0016bcbf1

      Author:  Manos Sifakis <sifakis_manos@yahoo.com> 

      Date: 2026-10-28 14:01:28 +0000

      Commit message:


	  
		 Preserve missing values by default and add opt-in target-only gene KNN
 
    
  
    
      Package: BreastSubtypeR

      Commit: f65b1bff312c5ccf453f248ab8d1f4dc336c5057

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-27 01:05:08 +0100

      Commit message:


	  
		 Merge pull request #215 from JohanHartmanGroupBioteam/fix/212-zero-evaluable-rules

Return NA for AIMS/SSPBC subtype samples with no evaluable rules 
    
  
    
      Package: BreastSubtypeR

      Commit: 5bef871854aa08c824346f522662b4dc54e65515

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-27 00:41:24 +0100

      Commit message:


	  
		 Validate rule predictor matches and resolve SSPBC subtype aliases
 
    
  
    
      Package: BreastSubtypeR

      Commit: e791aadb353bc185448787db612853b7dc4facac

      Author:  Emmanouil Sifakis <emmanouil.sifakis@ki.se> 

      Date: 2026-10-26 23:40:19 +0100

      Commit message:


	  
		 Return missing subtype calls when no rules are evaluable
 
    
  
    
      Package: MSnbase

      Commit: 55c17d2c64ed952898a76724d8cdce16f9690fc8

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-29 09:23:54 +0100

      Commit message:


	  
		 remove notes
 
    
  
    
      Package: MSnbase

      Commit: 93411b09842bc6064f1fb32b6951adcccfb6020d

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-29 09:14:38 +0100

      Commit message:


	  
		 testing/fixing: TEST VERIFICATIONS
 
    
  
    
      Package: MSnbase

      Commit: 8b16f90484469fbf2693c1543878dcf40fabbde2

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-28 23:36:26 +0100

      Commit message:


	  
		 testing/fixing: TEST VERIFICATIONS
 
    
  
    
      Package: MSnbase

      Commit: 0d60652fe001e69edb58a57d9d0dd0ea9c122e2e

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-28 18:27:32 +0100

      Commit message:


	  
		 testing/fixing: TEST VERIFICATIONS
 
    
  
    
      Package: MSnbase

      Commit: 124c3df81f63f81db8cec80db93c29a0b6e9735d

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-28 18:11:58 +0100

      Commit message:


	  
		 testing/fixing: TEST VERIFICATIONS
 
    
  
    
      Package: MSnbase

      Commit: 20c1bfe773b9b8e08fcaea313c0c82f577ce3832

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-05 10:17:54 +0200

      Commit message:


	  
		 more fixing
 
    
  
    
      Package: MSnbase

      Commit: 149c0449e2be9bbe939e0b9b911076f5d749caae

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-04 19:58:38 +0200

      Commit message:


	  
		 remove failing plot from example
 
    
  
    
      Package: MSnbase

      Commit: 42a19a2fb4f729ae784ff4c252b5618919ff39ad

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-04 19:54:57 +0200

      Commit message:


	  
		 install PSMatch and PTMods from Bioc
 
    
  
    
      Package: MSnbase

      Commit: 032a11bae55c3e5a16b96d5c1bff0d0e3670d992

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-04 19:51:10 +0200

      Commit message:


	  
		 drop msdata
 
    
  
    
      Package: MSnbase

      Commit: 8689d43fd3679b1c9ba6a0565a5cc70f569748b9

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-10-02 07:03:24 +0200

      Commit message:


	  
		 more fixing and MsDataHub
 
    
  
    
      Package: SCArray

      Commit: 8af405e7c978011a8dbf8ff1ea2ef88b57843d6d

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-10-28 23:34:31 -0500

      Commit message:


	  
		 fix overflow in row and col products
 
    
  
    
      Package: scrapbook

      Commit: e1eb810bf789bd81dd8a81c94cb1063cfa533759

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-29 15:12:43 +1100

      Commit message:


	  
		 Minor wording fix for blocked variance section.

Also bumped version for a new build.
 
    
  
    
      Package: gdsfmt

      Commit: 2b41d2358ed078251411708c030bbb8068491492

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-10-28 22:45:57 -0500

      Commit message:


	  
		 new rle nodes
 
    
  
    
      Package: hoodscanR

      Commit: 441f5f07b1be397e114634131cbf0a4cfc6ea9b9

      Author:  Ning Liu <ning.liu@adelaide.edu.au> 

      Date: 2026-10-29 10:17:56 +1030

      Commit message:


	  
		 Use published hoodscanR paper as preferred citation
 
    
  
    
      Package: standR

      Commit: 95b4f7ca2c18f70695244ebb4e213a6db37910c6

      Author:  Ning Liu <ning.liu@adelaide.edu.au> 

      Date: 2026-10-29 10:11:39 +1030

      Commit message:


	  
		  fix issue with unit test using annotationhub
 
    
  
    
      Package: peakPantheR

      Commit: b6f757182fd1f6a7fe35adf8ddd1cf1a7ffa1c45

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-10-29 00:01:05 +0100

      Commit message:


	  
		 Merge remote-tracking branch 'upstream/devel-origin' into devel
 
    
  
    
      Package: peakPantheR

      Commit: 1d249d8b057aea6e17b1c59762c1cc209f3e6128

      Author:  Arnaud Wolfer <adwolfer@gmail.com> 

      Date: 2026-10-28 23:58:46 +0100

      Commit message:


	  
		 updated unittests
 
    
  
    
      Package: arrayQualityMetrics

      Commit: 0119fd74725eba19718282b146ac341b57385dbd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 21:52:57 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: arrayQualityMetrics

      Commit: ccc07a306d01ed18839091129b4afeddc1412d42

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 21:52:49 +0100

      Commit message:


	  
		 Mention data.frame fix in NEWS
 
    
  
    
      Package: arrayQualityMetrics

      Commit: 6c45dfbd724a46618625fc56a6366a49fc1a90f2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 21:49:52 +0100

      Commit message:


	  
		 Fix data.frame check
 
    
  
    
      Package: arrayQualityMetrics

      Commit: 34a7b46f47d1c02a3b92c978a921571ca3c5ae02

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 21:49:41 +0100

      Commit message:


	  
		 Use canCoerce()
 
    
  
    
      Package: StatescopeR

      Commit: d3e94dd2338caffc5ba5ad6d44e46a575e08df9c

      Author:  MSteketee <m.f.b.steketee@amsterdamumc.nl> 

      Date: 2026-10-28 20:24:02 +0100

      Commit message:


	  
		 Added State Retrieval to retrieve discovered states in external data sets
 
    
  
    
      Package: Banksy

      Commit: 70175fbfe10d5ee38efeaba86575bc55965c1ed3

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-10-28 11:55:08 -0700

      Commit message:


	  
		 bump version to 1.9.6
 
    
  
    
      Package: Banksy

      Commit: ea1653a6bb045e8c298959880eced108fef6243c

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-10-28 11:55:08 -0700

      Commit message:


	  
		 fix irlba dispatch for the lazy operator
 
    
  
    
      Package: Banksy

      Commit: 77dcbf4e5b545ccdcb4487f1c4060c23606d6cff

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 16:13:57 -0700

      Commit message:


	  
		 rebuild pkgdown site
 
    
  
    
      Package: Banksy

      Commit: a91507e94a32ecc0d9ce70f3bdaab893fc06d3f9

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 16:13:57 -0700

      Commit message:


	  
		 bump version to 1.9.5
 
    
  
    
      Package: Banksy

      Commit: a46a7837451a0e23c3415973751d22eb0fae578b

      Author:  Joseph Lee <jxlee@tillicum-login01.hyak.local> 

      Date: 2026-09-29 16:13:57 -0700

      Commit message:


	  
		 link upstream seurat-wrappers docs
 
    
  
    
      Package: curatedTCGAData

      Commit: dab8efa4f63042445bd35dfac928fa78eae41f73

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

      Date: 2026-10-28 13:27:15 -0400

      Commit message:


	  
		 version bump 1.35.1
 
    
  
    
      Package: curatedTCGAData

      Commit: b082a40f1f252d3e310467b7fd15236220f50901

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2026-10-28 17:13:18 +0100

      Commit message:


	  
		 Clarify CNASNP and CNVSNP descriptions

CNVSNP is derived from Firehose segmented_scna_minus_germline_cnv_hg19,
i.e. somatic copy number segments from SNP arrays with germline CNVs
removed, not germline CNVs. CNASNP (segmented_scna_hg19) is not filtered
for germline CNVs. Update the assay description table accordingly.

Co-authored-by: Vanna Marina Giusti <vannamarina.giusti@studenti.unipd.it>
 
    
  
    
      Package: curatedTCGAData

      Commit: 5c423dfe2210f65ca85ca78ef3fd0bf25e1e3621

      Author:  meichuanyi <35057768+meichuanyi@users.noreply.github.com> 

      Date: 2026-06-26 02:34:06 +0800

      Commit message:


	  
		 docs: fix typo availble -> available in NEWS 
    
  
    
      Package: DuckDBGRanges

      Commit: 4bf0a2c0b7c059a192739c9a958b4bcf45036e6a

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-28 10:17:28 -0700

      Commit message:


	  
		 Fix deprecated lambda arrow syntax for DuckDB 2.0

DuckDB 2.0 disables the arrow-style SQL lambda syntax (x -> expr) by
default ahead of its removal in 2.1, breaking DuckDBGRangesList's
start/end/width/strand imputation and its .row_idx-based end column
construction with a "Binder Error: Deprecated lambda arrow (->)
detected" at query materialization. Convert all four list_transform()
call sites to the new lambda x: expr syntax.
 
    
  
    
      Package: RTCGAToolbox

      Commit: 8a5f48fc680618791d0ae552dbaadb6c62b01434

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

      Date: 2026-10-28 13:05:23 -0400

      Commit message:


	  
		 version bump 2.43.1
 
    
  
    
      Package: RTCGAToolbox

      Commit: edacb6ba4ee20562e18aa9ca85edb820ef94b80f

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2026-10-28 17:04:27 +0100

      Commit message:


	  
		 Clarify CNASNP and CNVSNP documentation

CNVSNP retrieves Firehose segmented_scna_minus_germline_cnv_hg19, i.e.
somatic copy number segments from SNP arrays with germline CNVs removed,
not germline CNVs. CNASNP retrieves segmented_scna_hg19, which is not
filtered for germline CNVs. Update @param, @slot and data type
descriptions accordingly and regenerate man pages.

Co-authored-by: Vanna Marina Giusti <vannamarina.giusti@studenti.unipd.it>
 
    
  
    
      Package: spicyR

      Commit: a68ec3bfbf83a83ea3b9a6196c78cf9ee425f8c2

      Author:  EllisPatrick <ellis.patrick@sydney.edu.au> 

      Date: 2026-10-29 03:42:42 +1100

      Commit message:


	  
		 1.99.47: radiusPlot()'s example compares two stages of diabetesData (Bioconductor check error)

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013sjhuCgL8kii1snyas2Aj8
 
    
  
    
      Package: carnation

      Commit: 1f53b15a81275739f901c2b704e16d0c14ae8769

      Author:  Apratim Mitra <16709900+mitraak@users.noreply.github.com> 

      Date: 2026-10-28 12:00:42 -0400

      Commit message:


	  
		 Merge pull request #48 from NICHD-BSPC/v1.1.3

V1.1.3

minor bug fixes

- fix a bug where setting multiple facet variables and reloading the dataset was breaking the app. Turns out a condition needed to be wrapped with any() or all()
- handle duplicate symbols when building internal mapping
- move DEGreport to Depends to stop r-universe build warning 
    
  
    
      Package: carnation

      Commit: e1777dc6df7d33f4bedd9048463bef899789a4df

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-28 11:00:32 -0400

      Commit message:


	  
		 version bump
 
    
  
    
      Package: carnation

      Commit: bd8d328141f3029c3c1908de6b65566899fd4627

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-28 10:34:14 -0400

      Commit message:


	  
		 mv DEGreport to Depends
 
    
  
    
      Package: carnation

      Commit: 43995f58c0efe0a6dddba393388a79ba4adc5dcf

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-28 10:30:15 -0400

      Commit message:


	  
		 handle non-unique symbols in mapping
 
    
  
    
      Package: carnation

      Commit: 20658638ba4d0756323cb699f45d69e2daad2385

      Author:  Apratim Mitra <apratim.mitra@nih.gov> 

      Date: 2026-10-28 10:29:58 -0400

      Commit message:


	  
		 fix multi-facet error frm gene plt
 
    
  
    
      Package: gesel

      Commit: ae2af9df0c17ba909fd8bf0350985453a0d9bd51

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-29 02:50:40 +1100

      Commit message:


	  
		 Document that end <= start is okay in read/downloadDatabaseRanges.

Explicitly add tests for this behavior for readDatabaseRanges.
 
    
  
    
      Package: gesel

      Commit: 58d8dcf6994b24b80dbb82d08fb494a1a84e04fb

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-29 02:37:43 +1100

      Commit message:


	  
		 Shift start/size for collections to the fetchAllCollections tests.

These are no longer needed in the prepareDatabaseFiles() call.
 
    
  
    
      Package: gesel

      Commit: 39126a687726e28b01ad4909ceb589f3f37b5d9f

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-29 02:30:16 +1100

      Commit message:


	  
		 Use different prefixes for the test genes with varying casing.

This enables more thorough tests for the correct handling of ignore.case= in
createGeneIdentifierMap. We also rename those tests for the new function name.

This also distinguishes the gene prefixes from the collection prefixes, which
were previously (confusingly) similar. Updated all other affected test suites.
 
    
  
    
      Package: PostChicago

      Commit: 9cba9c2cfa1fa8c1220d6cb8a1b55aac2c06fcc4

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:17:07 +0100

      Commit message:


	  
		 Add citation and bump version from 0.99.4 to 0.99.5
 
    
  
    
      Package: PostChicago

      Commit: 91dfe8e4001dfb2aed7ead3ca547112be8a08696

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:01:48 +0100

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: PostChicago

      Commit: cfa383e9c755a05a4037b71bd2f420341541729d

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:01:31 +0100

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: PostChicago

      Commit: a89629df33552e9f48d1fd15cdb3fd7817dda6cc

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:01:05 +0100

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: PostChicago

      Commit: f2b71b9e3e2cf64002131c63d3da8217554c2024

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:00:31 +0100

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: PostChicago

      Commit: 599782c32fb5ded5cf04ca70af663e14cfce86f7

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-10-28 14:00:04 +0100

      Commit message:


	  
		 Add files via upload 
    
  
    
      Package: PostChicago

      Commit: d30c9d23e4c76c8e803bdc53eca5f55f32d9902a

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:57:04 +0100

      Commit message:


	  
		 Update NEWS.md 
    
  
    
      Package: PostChicago

      Commit: 1bc30b37aee67f88c2597d5ddf237e9b63ab1cf4

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:55:52 +0100

      Commit message:


	  
		 Delete NAMESPACE 
    
  
    
      Package: PostChicago

      Commit: 1540ee3c44ed904822f672aed6fd0b2a1d68f1e6

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:55:41 +0100

      Commit message:


	  
		 Delete DESCRIPTION 
    
  
    
      Package: PostChicago

      Commit: f64c97c3198851bb73033810efb518472cf80eff

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:55:26 +0100

      Commit message:


	  
		 Delete vignettes directory 
    
  
    
      Package: PostChicago

      Commit: c2217e58cabd08aa2c48c467c0d4fbe663bb2eae

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:55:14 +0100

      Commit message:


	  
		 Delete man directory 
    
  
    
      Package: PostChicago

      Commit: 2c5316fd2bccdda1153a712f70239d9d614f2a4c

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:55:00 +0100

      Commit message:


	  
		 Delete inst/extdata directory 
    
  
    
      Package: PostChicago

      Commit: b5a78a18debe0194adefebf90c42c13d01b28635

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-10-28 13:54:45 +0100

      Commit message:


	  
		 Delete R directory 
    
  
    
      Package: rhdf5filters

      Commit: 14f682342eb83ab757a39e700133c7037a81ccff

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 12:32:55 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: rhdf5filters

      Commit: 93b6ae472b8dbffca187f0ed5ac48b75accafe3f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 12:33:41 +0100

      Commit message:


	  
		 Mention WASM compilation in NEWS
 
    
  
    
      Package: rhdf5filters

      Commit: edd21f8e3aa6a1a5908aa01cbc1bf9a57131b2f5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 11:58:48 +0100

      Commit message:


	  
		 Run autoreconf
 
    
  
    
      Package: rhdf5filters

      Commit: 4097178409749e083797bf201805b239b48e9d9a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 11:58:42 +0100

      Commit message:


	  
		 Try fixing cross-compilation
 
    
  
    
      Package: Rarr

      Commit: fbeb1d5aa3c3baf6924a4bfa755e85cca50df512

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 12:42:09 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: Rarr

      Commit: a38a18550fdf6fb38cd8cb6dee25659f751f42dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 12:42:01 +0100

      Commit message:


	  
		 Document cross-compilation fix in NEWS
 
    
  
    
      Package: Rarr

      Commit: cf0ca2a08636fbf2281c89d5d7f5ba09628b5731

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-28 12:41:46 +0100

      Commit message:


	  
		 Fix cross-compilation
 
    
  
    
      Package: Rarr

      Commit: 388be44f2c1db790ecd41127f75bbaacc3fdc141

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-27 18:05:35 +0100

      Commit message:


	  
		 Remove stale if
 
    
  
    
      Package: Rarr

      Commit: d0f5639f4343e6a5decae8dfa7b27891472f0d09

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-27 10:16:38 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: Rarr

      Commit: cb44bff516cd177f8b7a5acef9d623d6971058d6

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-27 10:15:03 +0100

      Commit message:


	  
		 Mention read_zarr_attributes() breaking change in return value
 
    
  
    
      Package: Rarr

      Commit: cb22c73b8dd66b152d2f727269c4d3768e186471

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-27 10:13:20 +0100

      Commit message:


	  
		 Return empty attributes as NULL

To avoid writing an unnamed list when consolidating metadata
 
    
  
    
      Package: Rarr

      Commit: 4fd770ff866e5ca31c9b7884781cd5e1e156fbfd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 16:09:48 +0100

      Commit message:


	  
		 Skip partial read when full read
 
    
  
    
      Package: Rarr

      Commit: 0cf0e8bf0d8714a65ca736a97eee3aad55ffcc8e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 16:09:01 +0100

      Commit message:


	  
		 Expand sharded codec tests for partial reads
 
    
  
    
      Package: Rarr

      Commit: d561b1ea3ff002a1c0a492e93fadee9e18135864

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 16:04:49 +0100

      Commit message:


	  
		 Skip reading unused inner chunks in sharding codec
 
    
  
    
      Package: Rarr

      Commit: 0e0156fe6a5229e0439b3085e4f687b3ff7b859d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 15:25:22 +0100

      Commit message:


	  
		 Avoid expensive decoding of discarded VLen-UTF8
 
    
  
    
      Package: Rarr

      Commit: 3f59c435c4741f006e2e03c420d3fd612d43877b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 11:22:04 +0100

      Commit message:


	  
		 Bump version
 
    
  
    
      Package: Rarr

      Commit: 6f59a6b10bab9926963fbf7bf49452742a3f0694

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-10-26 11:21:39 +0100

      Commit message:


	  
		 Add fast shortcircuit to .truncate_overflow
 
    
  
    
      Package: lcmsPlot

      Commit: c5976b6b18768f5cd821776af714a14d7e687306

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 10:43:32 +0000

      Commit message:


	  
		 test(baseline): compare the rt_diff shift through its retention times

The rt_diff baseline failed on the aarch64 Bioconductor builder: Obiwarp's
adjusted retention times differ there by up to ~5e-4 s. That is well within
the relative tolerance for rt_adj (~3000 s), but not for diff, the small
difference rt_adj - rt_raw, which is often below a second.

The baseline now leaves diff out, as rt_raw and rt_adj are still compared
against the recorded values, and a new test checks that diff is the shift
between the two columns on the data itself.
 
    
  
    
      Package: lcmsPlot

      Commit: 2fbbea6270e3d0d42d2cf6d320751686cb7cbc19

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-28 10:31:36 +0000

      Commit message:


	  
		 feat(report): write per-feature HTML and PDF reports with lp_report

Add lp_report(), which turns a plot pipeline into a report of its
features: each page draws the pipeline restricted to a feature, with a
table of its annotations and of its detected peak in every sample. Pages
are made per value of `by` (feature_id, name, or any annotation column),
and the data is extracted once for the whole report, then narrowed with
subset_features(), so large reports do not read the raw files again.

The HTML report is one self-contained file with the plots embedded and a
searchable, sortable index linking to each page; the PDF report is one
multi-page file with the index first and a page size option. `sections`
toggles the annotation and peak tables and can add the MS2 spectra by
precursor, `features_per_page` and `ncol` tile several features on a page,
and `theme` styles the report ("plain", "clean", or "journal"). Features
with no data are listed as empty, and a page that fails to render is
marked as an error rather than stopping the report.

PDF reports need gridExtra and gtable, added to Suggests. A QC trend
section is left for when #56 lands.

Closes #61.
 
    
  
    
      Package: lcmsPlot

      Commit: 9b4e30844690430b7d705aec68557c4a869b0f56

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-10-26 19:49:16 +0000

      Commit message:


	  
		 feat(app): refresh the Shiny app interface

Fix the unbalanced font sizes (Bootstrap 3's 10px root font shrank the
Tailwind text), drop the icons, and restyle the app after a TailAdmin-like
dashboard with the bundled Outfit font. Add loading indicators, button
busy states and empty-state messages. Bump the version to 1.1.22.
 
    
  
    
      Package: metaseqR2

      Commit: 99ac5dc3b487be022c28833f95ac0285fa588c62

      Author:  Panagiotis Moulos <pmoulos@gmail.com> 

      Date: 2026-10-28 09:29:00 +0000

      Commit message:


	  
		 Fixed issues related to TxDb, logger and EDASeq::SeqExpressionSet
 
    
  
    
      Package: metaseqR2

      Commit: fcaee1876ea4d9a2d9e8235acf60ab4cd1273f2d

      Author:  Panagiotis Moulos <pmoulos@gmail.com> 

      Date: 2026-10-27 10:45:00 +0000

      Commit message:


	  
		 Merge remote-tracking branch 'upstream/devel' into devel
 
    
  
    
      Package: metaseqR2

      Commit: b9d9c6ae30d5057abeb4e404bd7e0e6ffc439919

      Author:  Panagiotis Moulos <pmoulos@gmail.com> 

      Date: 2026-10-27 09:58:16 +0000

      Commit message:


	  
		 Removed survcomp dependency
 
    
  
    
      Package: gesel

      Commit: 0d7a042ace691873291c9fe813b835be49e65782

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 16:50:08 +1100

      Commit message:


	  
		 Strip out GH actions as we have our checks on BioC now.

Also added a link to the BioC landing page.
 
    
  
    
      Package: gesel

      Commit: 389925ed002cb321002dfde664cba5d7bd742d84

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 16:40:58 +1100

      Commit message:


	  
		 Tidied up docstrings and examples for validate, prepare functions.
 
    
  
    
      Package: knowYourCG

      Commit: 34ace46cb4722c363dc76ed5b9ab24ac61ba3800

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-27 22:20:19 -0400

      Commit message:


	  
		 coverage badge: 83.5% with the 1.9.6 tests, as the light CI measures it
 
    
  
    
      Package: knowYourCG

      Commit: 8ac59fe1696d782b4487a6d25bd94c41ebde6c40

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-27 22:08:18 -0400

      Commit message:


	  
		 version: 1.9.6
 
    
  
    
      Package: knowYourCG

      Commit: 6e4d905eb097b951177e81fdb4f301af9673a441

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-27 22:08:18 -0400

      Commit message:


	  
		 Warn on a query outside the universe and on databases dropped while loading; testEnrichmentSEA reports nQ as the query and nD as the database
 
    
  
    
      Package: knowYourCG

      Commit: e3f50a59ac16bad8474ad7574c90e5347cb63628

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-27 22:03:59 -0400

      Commit message:


	  
		 vignettes: drop sesameDataCache("HM450.address"); sesameData 1.31.2 lists the record with no ExperimentHub id yet, so the cache call stops while sesameDataGet falls back to Zenodo (devel buildsrc ERROR on visualization ky21)
 
    
  
    
      Package: knowYourCG

      Commit: 8f3f2bbc5f25f0e76fb0db192d1ebbf2e4025532

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-27 21:58:38 -0400

      Commit message:


	  
		 coverage badge: 82.6%, as the light CI measures it (bedToCg's conversion test skips without bedtools and yame)
 
    
  
    
      Package: knowYourCG

      Commit: 4129b90d70f374762f248e933ae1f78946fe62c7

      Author:  Wanding Zhou <zhouw3@email.chop.edu> 

      Date: 2026-10-26 09:25:23 -0400

      Commit message:


	  
		 coverage workflow: install the package and cache the six hub records the tests read
 
    
  
    
      Package: GExPipe

      Commit: 33a771ef56a451033b13a9b89960b4aa30746c16

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

      Date: 2026-10-28 04:49:15 +0500

      Commit message:


	  
		 Sync with GitHub main: GExPipe 0.99.118
 
    
  
    
      Package: GExPipe

      Commit: ddd5cafbf45b46916577d9a5154d103c4b57c411

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

      Date: 2026-10-28 03:25:41 +0500

      Commit message:


	  
		 Sync with GitHub main: GExPipe 0.99.117
 
    
  
    
      Package: TiDEomics

      Commit: 5a15b0c166428d09c651cb05ae26a90fa50bc66c

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-10-27 20:21:36 +0000

      Commit message:


	  
		 Update README

Increase diagram width in README.
 
    
  
    
      Package: TiDEomics

      Commit: 749598877e0c19c1a013a8f6e1605e4bf431940f

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-10-27 16:02:26 +0000

      Commit message:


	  
		 Update documentation

Fix `enrichGO_list()` to omit the universe argument when no background is supplied. Update vignettes, README, DESCRIPTION, and NEWS. Update diagram in README.
 
    
  
    
      Package: TiDEomics

      Commit: 3824463f18cbb9f6e88dc75127d227f4e278d37a

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-17 01:02:28 +0100

      Commit message:


	  
		 v0.99.6, update NEWS

Increase version to 0.99.6. Improve `decomp_variance()` reporting. Update NEWS to include the new multi-dataset/multi-omics support, other changes, and bug fixes. Improve plotting.
 
    
  
    
      Package: TiDEomics

      Commit: 5c5eb8c0cd7b63d0d96116e13aca7020cc2305fb

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-17 00:27:28 +0100

      Commit message:


	  
		 Add multi-dataset vignette

Update main vignette with addition of `DE_timecourse()`. Add a new vignette `TiDEomics_multi.Rmd` to demonstrate the multi-dataset / multi-omics workflow, including dataset combination, visualisation, consensus WGCNA, and feature-level comparisons.
 
    
  
    
      Package: TiDEomics

      Commit: 7f8a72a80e8201aeefb7055f6da714ee8e42a003

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-13 23:20:46 +0100

      Commit message:


	  
		 Improve wording, fix single module plotting

Improve cophenetic distance correlations wording in `plot_cor_matrix()`. Fix `plot_modules_h()` to handle single module selection, with other minor improvements.
 
    
  
    
      Package: TiDEomics

      Commit: 86ac87af22e22a2d8044436b4d520efada223d01

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-08 14:29:45 +0100

      Commit message:


	  
		 Rename plot_upset to plot_upset_h and unify with plot_upset_v

Rename `plot_upset()` to `plot_upset_h()`. Unify `plot_upset_h/v()` styling and behaviours. Add enrichment term ordering and colour controls to `plot_upset_v()`, and enrichment term wrapping to `plot_upset_h()` . Update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 98c74f9457b9ca9aab0267a39f8c83df1ee763be

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-07 19:12:42 +0100

      Commit message:


	  
		 Add custom feature colours to plot_modules_h

Update `plot_modules_h()` with a new `feature_colours` argument for colouring named feature sets. Legends are changed to show only used enrichment colours per category. Update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: acd9174105d61c1f84147e20b178e5387d7ae443

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-06 16:51:27 +0100

      Commit message:


	  
		 Update summarise_module_metrics to support consensus WGCNA

Add support for `run_consensus_WGCNA()` output in `summarise_module_metrics()`, returns a list (consensus + per-dataset) of metrics tables. Add output of kME 25 and 75 quantiles. Refactor consensus WGCNA kME calculation in `extract_consensus_hubs()` into `.consensus_kme_scores()`, used also by `summarise_module_metrics()`. Update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 91c97998c17df81f10aa551484da7231d306334f

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-03 19:32:08 +0100

      Commit message:


	  
		 Expand functionality of plot_modules_h

Add parameters to `plot_modules_h()` to allow selected visualisation of modules, wrapping of long enrichment terms, and two legend positions, with new and modified internal helpers and tests. Improve plot styling in `plot_modules_h()` and `plot_cor_matrix()`.
 
    
  
    
      Package: TiDEomics

      Commit: 095be1e6863efd83d2ae41ca914cb6b8cf72e8c9

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-09-03 11:26:27 +0100

      Commit message:


	  
		 Add temporal DE function with omnibus F-tests

Add `DE_timecourse()` for per-group or joint group x time limma models, with time as factor or numeric, reporting F statistics. Improve documentation for existing `DE_between_time/group()` functions. Add related tests.
 
    
  
    
      Package: TiDEomics

      Commit: afebce41f2656288e32d5faf607590c329cccba7

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-28 18:59:06 +0100

      Commit message:


	  
		 Update enrichGO_rank, prepare_tide, plots, vignette

Add optional GO term simplification to `enrichGO_rank()`. Change filtering mode `below_quantile` to `quantile` in `prepare_tide()` to avoid inaccurate description. Add `plot_cophenetic` parameter to `plot_cor_matrix()`. Improve styling of PCA and UMAP plots. Update documentation, vignette and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 55df991fbc2271b07debb916d4e3a1515ebeb2fc

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-28 16:46:13 +0100

      Commit message:


	  
		 Improve plot_modules_h display controls

Add new arguments to `plot_modules_h()`: `group_annotation` (`name`/`colour`/`both`/`none`), `profile_scale` (`dataset`/`shared`/`free`), and `return_legends`. Minor changes to `theme_custom()` and `plot_variance()`.
 
    
  
    
      Package: TiDEomics

      Commit: 56cf1917c4c9629b296142e0094d59b865e215cf

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-26 17:23:33 +0100

      Commit message:


	  
		 Add plot_upset_v with aligned enrichment dotplot

Add new function `plot_upset_v()` to generate a ComplexHeatmap UpSet plot vertically aligned with a clusterProfiler dotplot-style enrichment annotation.
 
    
  
    
      Package: TiDEomics

      Commit: fb9fd0fd2dad92b08796f1ab006be807a87e746d

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-26 17:06:10 +0100

      Commit message:


	  
		 Improve enrichR_list and plots

Add feature count extraction for `enrichR_list()`. Update `theme_custom()` with font family parameter. Improve `plot_modules_h()` font and colours, add SVG output, remove duplicated heatmap colour legend. Update docs and tests accordingly.
 
    
  
    
      Package: TiDEomics

      Commit: 514a8c412cd7d16313a67ac0ae56c7c4c99006cf

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-25 12:04:17 +0100

      Commit message:


	  
		 Refactor extract_consensus_hubs

Refactor `extract_consensus_hubs()` to use `WGCNA::consensusKME()`, handle unsigned networks separately, and return a data frame instead of per-dataset character vectors. Update `plot_modules_h()` to accept data frame format `mark_features` and generalise "Hub features" to "Features", with other improvements. Update docs and tests accordingly.
 
    
  
    
      Package: TiDEomics

      Commit: fc3c585d0165b7d2f99b20052dd836f234d78cb5

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-25 11:37:32 +0100

      Commit message:


	  
		 Add combine_tide for multiple prepare_tide outputs

Add `combine_tide()` to combine multiple `prepare_tide()` outputs for multi-dataset or multi-omics workflows, with tests and docs.
 
    
  
    
      Package: TiDEomics

      Commit: 12768834010a206a9559f2059c2393bc59d1878d

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-16 02:22:26 +0100

      Commit message:


	  
		 Add plot_scatter, plot_upset, Net_FC property

Add functions `plot_scatter()` (compare two values per feature) and `plot_upset()` (UpSet plot with optional per-intersection enrichment textboxes) with tests. Add Net_FC and improve `calc/summarise_feature_property()`. Add output of residual-filter cutoff in `prepare_tide()`.
 
    
  
    
      Package: TiDEomics

      Commit: 56034f47f25174b1666bc0f7638e482cd36216cb

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-10 01:47:13 +0100

      Commit message:


	  
		 Update simulated example data

Update the example Exp2 to have 5 different features (with suffix `_Exp2`) from Exp1, and regenerate example .rda objects. Update `run_consensus_WGCNA()` example and tests to run on shared features.
 
    
  
    
      Package: TiDEomics

      Commit: 5871dfa56a2ba9e9922c5c5a02b8f3ec5fa12a39

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-09 16:20:09 +0100

      Commit message:


	  
		 Add multi-dataset support to plot_modules_h/v

Extend `plot_modules_h/v()` to accept a named list of SummarizedExperiment objects, and allow per-dataset ylabel and optional display names. Introduce `.warn_unshared_features()` to restrict plotting to features present in all datasets and emit warnings or errors.  Fix issue in `run_WGCNA()`. Update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: a751f19085fe0e7ad00b9fb884d6306269bac29a

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-07 22:40:17 +0100

      Commit message:


	  
		 Add WGCNA custom power estimate

`prepare_WGCNA()` now computes a custom_powerEstimate in addition to WGCNA's default powerEstimate. Update docs, namespace, and vignette.
 
    
  
    
      Package: TiDEomics

      Commit: 9617ec598f1da3d3c551c72855e23d18be844661

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-07 17:48:57 +0100

      Commit message:


	  
		 Improve WGCNA, simplify examples and tests

Strengthen WGCNA-related functions `run_WGCNA()`, `plot_WGCNA()`, `extract_hubs()`, and `run_consensus_WGCNA()`, unifying single and multi-dataset WGCNA behaviours. Remove redundant code in examples and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 6b215d001a01a0729912807570121b9b5bd5a053

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-07 02:42:20 +0100

      Commit message:


	  
		 Add consensus WGCNA and hub extraction

Add `run_consensus_WGCNA()` for multi-dataset consensus modules with input validation, shared-feature handling, and optional plotting. Add `extract_consensus_hubs()` for consensus and dataset-specific hub features. Add new example data & script, update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 780d18b26d16dc8c756784af2462a692bb64ac8c

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-07 00:23:47 +0100

      Commit message:


	  
		 Allow NULL feature_threshold in prepare_tide

Fix `prepare_tide()` to accept `feature_threshold = NULL` for treating non-NA values as expressed. Update tests and docs. Also update multi-dataset plotting functions to use `example_obj_2` in examples.
 
    
  
    
      Package: TiDEomics

      Commit: e11ed8b75ab26b7b75a0740f9ba919a154285694

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-06 15:40:33 +0100

      Commit message:


	  
		 Add multi-dataset support to plot_cor_matrix

Extend `plot_cor_matrix()` to accept a named list of SummarizedExperiment objects, with optional `shared_only` feature intersection, custom dataset display names, shared colour scaling, and pairwise cophenetic correlation. Also fixed minor issue in `plot_umap()`, and updated tests and docs.
 
    
  
    
      Package: TiDEomics

      Commit: d3c33c912572adff36205d5539e095fef828b6ff

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-06 00:25:11 +0100

      Commit message:


	  
		 Add multi-dataset support to PCA and UMAP plots

Extend `plot_pca/umap()` to accept a named list of SummarizedExperiment objects with a new `.as_se_list()` helper and new parameters `shared_only` and `names`. Update docs and tests.
 
    
  
    
      Package: TiDEomics

      Commit: 64dc9f0ec4ee6ccff401093315cd04ae69629e8b

      Author:  Tianen He <tianen.he@ndm.ox.ac.uk> 

      Date: 2026-08-05 17:31:50 +0100

      Commit message:


	  
		 Add multi-dataset support to plot_trend

Extend plot_trend to accept a named list of SummarizedExperiment objects (multi-dataset / multi-omics). Introduce parameters multi_layout, ncol and independent_y and add an internal helper .plot_trend_multi. Adjust point/errorbar size. Update global variables, import, docs and tests.
 
    
  
    
      Package: CycleMix

      Commit: 1036599e965631e512c6f5e25830dff53906fc51

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-10-27 12:29:30 -0400

      Commit message:


	  
		 fix documentation
 
    
  
    
      Package: CycleMix

      Commit: 9eb3e24b353b3719efdd85c3552a394d6e659c4e

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

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

      Commit message:


	  
		 fix duplicate genes in Quiescence Set
 
    
  
    
      Package: CycleMix

      Commit: a231864e22f111288c9eea8ab3f13ff7b9555ced

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-10-27 12:05:34 -0400

      Commit message:


	  
		 Added tests and swap to orthogene orthologs
 
    
  
    
      Package: CycleMix

      Commit: 6f97a7708436cc5be7d48f09993ed8b71e4de911

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-09-01 23:31:32 -0400

      Commit message:


	  
		 fixed dealing with zeros when regressing counts
 
    
  
    
      Package: CycleMix

      Commit: 37a5e332f4715576cd2e2c3f71a3ad31f9c3a2ac

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-09-01 19:43:12 -0400

      Commit message:


	  
		 fix glm_discrete for nb regression
 
    
  
    
      Package: CycleMix

      Commit: 59932160cf58b86a0597a8430c4e93944473fc8a

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-09-01 16:42:09 -0400

      Commit message:


	  
		 update data storage
 
    
  
    
      Package: ClustIRR

      Commit: 267ec5b9d05aa8815d9505fbdbcc458f63837635

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-10-27 18:24:00 +0100

      Commit message:


	  
		 minor changes in attach_clonotypes and bump
 
    
  
    
      Package: ClustIRR

      Commit: bc0c5015fc2ffbf66df7e214e1d86eea83734cdd

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-10-27 18:20:29 +0100

      Commit message:


	  
		 Update attach_clonotypes documentation to include community_k and list return shape 
    
  
    
      Package: ClustIRR

      Commit: eb15f95d96654054bd55cbe0d53bccf33fcbdf96

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-10-27 18:14:35 +0100

      Commit message:


	  
		 Add optional random community subset to attach_clonotypes and validate community_k 
    
  
    
      Package: gesel

      Commit: 23e93340b0df72054506bd6f6efd57bcad8a8e4e

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 02:47:31 +1100

      Commit message:


	  
		 Bumped version and date, reoxygenated.
 
    
  
    
      Package: gesel

      Commit: dd88aea9d395966c0e86d38d27afa85009933fdd

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 02:28:45 +1100

      Commit message:


	  
		 Split the validation functions into their own files.

Also make sure that the integer casts are safe for the number of genes.
 
    
  
    
      Package: gesel

      Commit: 9ba979bb8d271b6eb79b7b35c5acec82b0a6f20a

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 01:55:16 +1100

      Commit message:


	  
		 Cleaned up docstrings for the prepare*Files functions.
 
    
  
    
      Package: gesel

      Commit: 1da8df35bc4014d753b97d8a5a5d828bce90e39d

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-10-28 01:52:44 +1100

      Commit message:


	  
		 Deprecate mapGenesByName in favor of its new name.
 
    
  
    
      Package: prolfqua

      Commit: 200ac6dc5208017a13f122ee1d6843e657fae039

      Author:  Christian Panse <cp@fgcz.ethz.ch> 

      Date: 2026-10-27 16:51:04 +0100

      Commit message:


	  
		 version bump 0.99.4
 
    
  
    
      Package: gDRtestData

      Commit: be2717ab23a8b8f7c35455b838ac033649a30a9e

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-10-27 16:43:56 +0100

      Commit message:


	  
		 Merge pull request #87 from gdrplatform/GDR-3741

chore: regenerate the reference datasets for the corrected fit types 
    
  
    
      Package: gDRtestData

      Commit: d5f5dda651c1ccea33aa75ec160c2d05d3a70a1b

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

      Date: 2026-10-26 08:57:10 +0100

      Commit message:


	  
		 chore: regenerate the reference datasets with gDRcore 1.11.26
 
    
  
    
      Package: gDRtestData

      Commit: b778c9a932a3dde96892d9d9f3031c4ee9b9aa08

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

      Date: 2026-10-24 08:45:24 +0200

      Commit message:


	  
		 chore: regenerate the reference datasets for the corrected fit types
 
    
  
    
      Package: gDRutils

      Commit: 6adb1e74f92cc1102ea2bf8d7f43ea893955b495

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-10-27 16:43:49 +0100

      Commit message:


	  
		 Merge pull request #210 from gdrplatform/GDR-3741

fix: give the same fit types in both fit paths 
    
  
    
      Package: gDRutils

      Commit: 32d694a36bad80d9139f89cb5e07e770d0a65cba

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

      Date: 2026-10-26 11:10:33 +0100

      Commit message:


	  
		 fix: cap the response before deciding the fit type
 
    
  
    
      Package: gDRutils

      Commit: 48594987839095c33f37405c67536f24f72e783c

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

      Date: 2026-10-26 10:59:45 +0100

      Commit message:


	  
		 test: start the provenance tests from data without a provenance
 
    
  
    
      Package: gDRutils

      Commit: 61083b5acfce24217c08fbb517422e9d007c9496

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

      Date: 2026-10-24 08:35:00 +0200

      Commit message:


	  
		 fix: label a solver failure in fit_curves as an invalid fit
 
    
  
    
      Package: gDRutils

      Commit: f00744e40682c39034ae6070ca347fedcec00392

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

      Date: 2026-10-24 08:35:00 +0200

      Commit message:


	  
		 fix: label too few points and flat responses as logisticFit does
 
    
  
    
      Package: DuckDBSpatial

      Commit: 9431ea93b75ee7542b4f459e9426a7188ff392ef

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-27 08:02:22 -0700

      Commit message:


	  
		 Warn in readGeoParquet() when no geometry column is found

Lambda noticed that reading an ordinary, non-spatial parquet file
(e.g. iris.parquet) through readGeoParquet() silently returned
non-spatial data with no indication anything was off. Add a geom=
parameter and check it with hasGeometry() after the read, warning
(not erroring) when the expected GEOMETRY-typed column isn't present,
since the read itself is still valid for plain tabular data.
 
    
  
    
      Package: DuckDBSpatial

      Commit: 9b2f1a32b68d0850d622dda1b00de800352678ef

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-10-27 07:04:56 -0700

      Commit message:


	  
		 feat: add hasGeometry to detect whether a table has a geometry column (0.99.10)

st_geometry_type(x) on a DuckDBTable with no geometry column didn't
error -- it silently built a query applying ST_GeometryType to every
column, including plain numeric/character ones, and only failed once
that query was actually materialized, not when printed or built.
Reported by a user hitting exactly this on a DuckDBTable backed by plain
tabular data.

Not unique to st_geometry_type(): essentially every unary geometry
accessor/predicate in DuckDBTable-spatial.R (st_is_valid, st_area,
st_centroid, st_buffer, ...) is built on the same sql_call(x, "ST_*"),
which applies its SQL function to all of x's columns with no upfront
check that any of them are actually geometry-typed. Rather than retrofit
validation into ~20 existing functions, added the one primitive needed
to guard any of them.

hasGeometry(x, geom = "geometry") checks whether x has a column named
geom that is genuinely GEOMETRY-typed, returning FALSE (not an error) if
it's missing or a different type. Built entirely on the already-exported
DuckDBDataFrame::coltypes(), which already reports "geometry" as a
distinct type value -- no change to DuckDBDataFrame was needed.

Added a regression test covering a real geometry column, a wrong-type
column, a missing column, a table with no geometry column at all, and
non-DuckDBTable input. Full test suite: 0 failures.
 
    
  
    
      Package: STRINGdb

      Commit: 171afc34c87d2d8652c7cae34f07141dfbaeff34

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-10-27 15:04:19 +0100

      Commit message:


	  
		 Bump version to 2.25.2 for refused pictures and the new API options
 
    
  
    
      Package: STRINGdb

      Commit: bf6ff44205975bd54a9d507df9f248574181f461

      Author:  Damian <damian.szk@gmail.com> 

      Date: 2026-10-27 15:04:09 +0100

      Commit message:


	  
		 Stop on refused pictures; add enrichment filters and clustering options

get_png and get_enrichment_figure stop with STRING's explanation when STRING
refuses the request (HTTP 4xx), for example a PNG of more than 150,000
interactions, instead of reading STRING's JSON error answer as a PNG or
returning it as the SVG. get_enrichment_figure also stops on server errors
(HTTP 5xx), as the other methods do.

New options, sent only to STRING version 12.5 or later; older versions such
as 12.0 ignore them, so there they are not used, with a warning:
- get_enrichment and get_enrichment_figure: max_fdr, min_gene_count,
  min_strength, min_signal and merge_similarity filter the terms like the
  enrichment table of the STRING website.
- get_enrichment_figure: graph_type ("dotplot" or "barplot") and sort_by.
- get_png: network_clustering_algorithm ("kmeans", "mcl" or "leiden"),
  network_clustering_parameter, cluster_aware_layout,
  network_clustering_edge_visibility, show_cluster_names and
  cluster_name_size, as the Clusters tab of the website.

Calls without these options send the same requests as before. The help of
get_png and plot_network describes the simplified pictures of networks of
more than 1,000 proteins and the PNG limit; the usage of get_enrichment shows
its real defaults. New unit tests, offline and live (also against 12.0).
 
    
  
    
      Package: immReferent

      Commit: 0975f73b73e5c22103b458861ae8dc5ba252d41f

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-10-27 08:40:15 -0400

      Commit message:


	  
		 modify github actions to devel branch
 
    
  
    
      Package: prolfqua

      Commit: af085e0a4795cfecb5d800ffa46ba6f4eb954739

      Author:  Christian Panse <cp@fgcz.ethz.ch> 

      Date: 2026-10-27 13:37:42 +0100

      Commit message:


	  
		 add logo to vignette
 
    
  
    
      Package: escape

      Commit: da5564071eefbf53f04e901710cf4c29bb62e4e2

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 05:49:11 -0500

      Commit message:


	  
		 Merge pull request #181 from BorchLab/spe-plaid-support

Add SpatialExperiment support, fix SCE normalization, and add optional plaid backend 
    
  
    
      Package: escape

      Commit: 61e2d56413968ed7e8eafd7e233b6e7bfccc6de4

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 04:49:53 -0500

      Commit message:


	  
		 Documentation update
 
    
  
    
      Package: escape

      Commit: 8f9848a303a472242f6b398b7062973181ebf4a1

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 04:49:38 -0500

      Commit message:


	  
		 Update escape.Rmd
 
    
  
    
      Package: escape

      Commit: 7e699d06955a7822208529a96c0550254e3f1c89

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 04:49:30 -0500

      Commit message:


	  
		 Update github actions
 
    
  
    
      Package: escape

      Commit: 5a65356091a79bb36d2853c659eef74ff0aa0a27

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 04:49:14 -0500

      Commit message:


	  
		 Add plaid

per issue #167
 
    
  
    
      Package: escape

      Commit: 01c44a9048047dcee87c019e3291489d14a1ce3c

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 04:48:49 -0500

      Commit message:


	  
		 Spatal Support

Per issue #180
 
    
  
    
      Package: immApex

      Commit: 2ec70dc84621f83dc4a31bf957b04697ba409835

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 07:06:27 -0500

      Commit message:


	  
		 Merge pull request #22 from Qile0317/fix-property-matrix-aa-reorder

Fix AA-identity/property-value mismatch in sequenceEncoder()/sequenceDecoder() property mode 
    
  
    
      Package: immApex

      Commit: 8d3d4969006d813a158a7c07a631d42d54d24fcc

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 06:49:21 -0500

      Commit message:


	  
		 Update documentation
 
    
  
    
      Package: immApex

      Commit: 28ea99281b3b3485329a6bd94006aecf99efeddd

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 06:49:14 -0500

      Commit message:


	  
		 Update unit tests
 
    
  
    
      Package: immApex

      Commit: 75ebc31de2424ee41f5827dbb506837c2c7e337f

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 06:49:03 -0500

      Commit message:


	  
		 Update sequenceEncoder.R

Updating using the use of sequence.dictionary
 
    
  
    
      Package: immApex

      Commit: d07687f866beb3695caa184b68a2f662fd013c91

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 06:48:28 -0500

      Commit message:


	  
		 Update sequenceDecoder.R

Correcting documentation
 
    
  
    
      Package: immApex

      Commit: ea862eb0eb73cf58616be471c9b7dd1a8876a033

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-22 06:47:28 -0500

      Commit message:


	  
		 remove duplicate aa definition
 
    
  
    
      Package: immApex

      Commit: 57e14f4e9a7f105d82ab3f000f0123295742b64a

      Author:  Qile0317 <qile0317@gmail.com> 

      Date: 2026-08-19 23:44:23 -0700

      Commit message:


	  
		 Fix AA-identity/property-value mismatch in property mode

.aa.property.matrix() returned property scales in whatever column order
Peptides::AAdata happened to store them in (alphabetical for MSWHIM/ProtFP,
E/Q-swapped for crucianiProperties), not the canonical amino-acid order that
sequenceEncoder()'s C++ backend and sequenceDecoder()'s distance-based caller
both assume positionally. calculateProperty() already reordered by name after
calling this helper; sequenceEncoder()/sequenceDecoder() did not, so e.g.
encoding "R" under MSWHIM silently returned Cysteine's values.

Centralizes the canonical-AA reorder inside .aa.property.matrix() itself so
every caller gets it by construction, fixing both call sites at once. Verified
against Peptides' own independent public scoring functions (mswhimScores(),
crucianiProperties(), protFP()), not just immApex internals.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
 
    
  
    
      Package: immLynx

      Commit: 0b5b5b44ee5664e888f456b82844767df7930b72

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-10-27 08:29:31 -0400

      Commit message:


	  
		 fixing version to 1.1.3
 
    
  
    
      Package: immLynx

      Commit: 9bdfd82eb8739e0ffc92f9902a23793400b6873f

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-10-27 08:21:16 -0400

      Commit message:


	  
		 version bump 1.3.2

Bumping version to add CITATION info
 
    
  
    
      Package: immLynx

      Commit: 627ced4825f70d4c18fc7828eedabbae8eeda534

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-10-16 11:27:17 -0500

      Commit message:


	  
		 adding citations
 
    
  
    
      Package: immLynx

      Commit: 87c1e5fa441af1eef7d2c04fd638d91ea59e8344

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-10 08:34:00 -0500

      Commit message:


	  
		 Merge pull request #18 from BorchLab/scxpand

Expanding support for python modules 
    
  
    
      Package: immLynx

      Commit: 5d0b29f11e5a15a2d47192a59a0f195d0aa31fa2

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-10 07:24:38 -0500

      Commit message:


	  
		 update unit tests
 
    
  
    
      Package: immLynx

      Commit: 483de9ae0b16c256b95b4b9a4669bb7ceba3a6b9

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-10 07:05:53 -0500

      Commit message:


	  
		 Add full Seurat Support
 
    
  
    
      Package: immLynx

      Commit: 22bbf36d6b7110303f82d320ae00e10a6a3b42fa

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:47:15 -0500

      Commit message:


	  
		 update vignettes
 
    
  
    
      Package: immLynx

      Commit: 3c751161e721320db4970a80c72968b54eeb9dcd

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:47:05 -0500

      Commit message:


	  
		 update unit tests
 
    
  
    
      Package: immLynx

      Commit: 40204bbc42b40c11b7c703f835d7ae5b1cd01b2e

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:46:53 -0500

      Commit message:


	  
		 Create dot-deeptcrFeaturesToCells.Rd
 
    
  
    
      Package: immLynx

      Commit: 4419d906850f52a99c43ab7892aaec0aae881c56

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:46:50 -0500

      Commit message:


	  
		 Update DESCRIPTION
 
    
  
    
      Package: immLynx

      Commit: 1169043397f2d4bd164f5932bf01d1029aa02993

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:46:41 -0500

      Commit message:


	  
		 update documentation
 
    
  
    
      Package: immLynx

      Commit: e2e81a80fd899cd47ee4d8d8c91e3dcc56945323

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:46:14 -0500

      Commit message:


	  
		 Update exportToScanpy.R
 
    
  
    
      Package: immLynx

      Commit: a613bc5bbcb3872f0e7490fc7bf74caefd0f43a2

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:46:00 -0500

      Commit message:


	  
		 XT support (symdel)

#6
 
    
  
    
      Package: immLynx

      Commit: e1f354e7ecd2bb08608eab826f6e6c5ce0af147c

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:45:22 -0500

      Commit message:


	  
		 deeptcr addition

#8
 
    
  
    
      Package: immLynx

      Commit: 2e153946398be78f0df0b97c29f3741b1fb71c30

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-08-09 07:41:41 -0500

      Commit message:


	  
		 Add scXpand
 
    
  
    
      Package: immLynx

      Commit: 85385c809b748a43d0a208f564b4d18a6dc64bae

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-05-14 12:27:00 -0500

      Commit message:


	  
		 fixing github actions
 
    
  
    
      Package: immLynx

      Commit: 413d5dbc5ce7653dec735bf69eebd17bde524695

      Author:  theHumanBorch <ncborch@gmail.com> 

      Date: 2026-05-14 11:11:34 -0500

      Commit message:


	  
		 v1.1.2

Cleaning README
 
    
  
  


</div>

</div>

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6.1.0

`v2.13.0` (2026-08-28)

`v2.12.1` (2026-06-23)

`v2.12.0` (2026-04-29)

`v2.13.0` (2026-08-28)

`v2.12.1` (2026-06-23)

`v2.12.0` (2026-04-29)

`v2.13.0` (2026-08028)

`v2.12.1` (2026-06-23)

`v2.12.0` (2026-04-29)

`v2.13.0` (2026-08028)

`v2.12.1` (2026-06-23)

`v2.12.0` (2026-04-29)