[pre-commit.ci] pre-commit autoupdate

.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: v0.4.3.9020
     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: <regex>` 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
 

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
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

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' ||

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)

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