From f8890e45b31282cd7cca614321422a17509773b3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Jun 2026 17:17:08 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/lorenzwalthert/precommit: v0.3.2 → v0.4.3.9023](https://github.com/lorenzwalthert/precommit/compare/v0.3.2...v0.4.3.9023) - [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v6.0.0) - [github.com/pre-commit-ci/pre-commit-ci-config: v1.5.1 → v1.6.1](https://github.com/pre-commit-ci/pre-commit-ci-config/compare/v1.5.1...v1.6.1) - [github.com/pre-commit/mirrors-prettier: v2.7.1 → v4.0.0-alpha.8](https://github.com/pre-commit/mirrors-prettier/compare/v2.7.1...v4.0.0-alpha.8) --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) mode change 100755 => 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml old mode 100755 new mode 100644 index 51e0780..a3a12fb --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # R specific hooks: https://github.com/lorenzwalthert/precommit repos: - repo: https://github.com/lorenzwalthert/precommit - rev: v0.3.2 + rev: v0.4.3.9023 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] @@ -13,12 +13,12 @@ repos: - id: deps-in-desc args: [--allow_private_imports] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.3.0 + rev: v6.0.0 hooks: - id: end-of-file-fixer exclude: '\.Rd' - repo: https://github.com/pre-commit-ci/pre-commit-ci-config - rev: v1.5.1 + rev: v1.6.1 hooks: # Only reuiqred when https://pre-commit.ci is used for config validation - id: check-pre-commit-ci-config @@ -32,7 +32,7 @@ repos: exclude: "(inst/extdata|data)/.*" # `exclude: ` to allow committing specific files - repo: https://github.com/pre-commit/mirrors-prettier - rev: v2.7.1 + rev: v4.0.0-alpha.8 hooks: - id: prettier From 1cbd78bc11184f665925551c2ad848b7694be4c7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 1 Jun 2026 17:18:25 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- LICENSE | 2 +- R/DeconvExplorer.R | 2 -- tests/testthat/setup_tests_DeconvExplorer.R | 1 - tests/testthat/test-signatures.R | 1 - 4 files changed, 1 insertion(+), 5 deletions(-) diff --git a/LICENSE b/LICENSE index e72bfdd..f288702 100755 --- a/LICENSE +++ b/LICENSE @@ -671,4 +671,4 @@ into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read -. \ No newline at end of file +. diff --git a/R/DeconvExplorer.R b/R/DeconvExplorer.R index 9206fb8..0d3573e 100755 --- a/R/DeconvExplorer.R +++ b/R/DeconvExplorer.R @@ -127,7 +127,6 @@ DeconvExplorer <- function(deconvexp_bulk = NULL, width = 12, fileInput("userSignatureUpload", "Upload Signature"), div(style = "margin-top: -25px"), - p("You can upload a previsouly generated signature matrix of a deconvolution method and analyse it with DeconvExplorer. Multiple uploads are possible."), fluidRow( column(4, shinyWidgets::actionBttn("selectSigExploration", "Explore the signature", icon = icon("arrow-right"), color = "success", style = "simple")), @@ -208,7 +207,6 @@ DeconvExplorer <- function(deconvexp_bulk = NULL, column( width = 5, conditionalPanel( - # all methods that take another signature as input condition = "input.deconvMethod == 'cibersortx' || input.deconvMethod == 'dwls' || diff --git a/tests/testthat/setup_tests_DeconvExplorer.R b/tests/testthat/setup_tests_DeconvExplorer.R index f2db2b9..9d972e5 100755 --- a/tests/testthat/setup_tests_DeconvExplorer.R +++ b/tests/testthat/setup_tests_DeconvExplorer.R @@ -7,7 +7,6 @@ suppressPackageStartupMessages({ message("- Done!") - message("--- Generating objects for the testing setup...") data("RefData", package = "omnideconv") RefData <- as.data.frame(RefData) diff --git a/tests/testthat/test-signatures.R b/tests/testthat/test-signatures.R index a08428e..a970cc2 100755 --- a/tests/testthat/test-signatures.R +++ b/tests/testthat/test-signatures.R @@ -9,7 +9,6 @@ test_that("Signature refinement operations are correct", { expect_true("B.cells" %in% colnames(signature_renamed)) - signature_nozeros <- removePercentZeros( signature_mat = signature_list$bisque, max_percentage_zeroes = 0.5