From 1bb2ea532dbb296a9018ade4aa0c36d1c43645fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mateusz=20Ko=C5=82oma=C5=84ski?=
 <63905560+m-kolomanski@users.noreply.github.com>
Date: Thu, 31 Oct 2024 07:56:06 +0100
Subject: [PATCH 01/10] Enhancement: implemented relevant CI workflows from
 admiralci

---
 .github/workflows/admiral.yml | 61 +++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 .github/workflows/admiral.yml

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
new file mode 100644
index 00000000..909aa151
--- /dev/null
+++ b/.github/workflows/admiral.yml
@@ -0,0 +1,61 @@
+# Source: https://github.com/pharmaverse/admiralci
+# Stripped down version of admiralci checks. Good for
+# the developement process. When package is ready to
+# be published, revisit and add release-related
+# workflows.
+name: admiral CI/CD Workflows
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - "*"
+
+concurrency:
+  group: admiral-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  R_VERSION: "release"
+
+jobs:
+  get_r_version:
+    name: Get R version
+    runs-on: ubuntu-latest
+    outputs:
+      r-version: ${{ steps.get_r_version.outputs.R_VERSION }}
+    steps:
+      - name: Get R Version for Downstream Container Jobs
+        id: get_r_version
+        run: echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT
+        shell: bash
+  spellcheck:
+    name: Spelling
+    uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  linter:
+    name: Lint
+    uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
+    needs: get_r_version
+    if: github.event_name == 'pull_request'
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  man-pages:
+    name: Man Pages
+    uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
+    if: github.event_name == 'pull_request'
+    needs: get_r_version
+    with:
+      r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  check:
+    name: Check
+    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    with:
+      error-on: warning # TODO: find a way to ignore specific notes
+    if: github.event_name == 'pull_request'

From cbcfee61a7f115da34465e74f824fb769f56fcb1 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:15:00 +0100
Subject: [PATCH 02/10] fix: removed error-on: warning from R CMD CHECK

---
 .github/workflows/admiral.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
index 909aa151..42e29b2e 100644
--- a/.github/workflows/admiral.yml
+++ b/.github/workflows/admiral.yml
@@ -12,7 +12,7 @@ on:
       - main
   pull_request:
     branches:
-      - "*"
+      - main
 
 concurrency:
   group: admiral-${{ github.event.pull_request.number || github.ref }}
@@ -56,6 +56,5 @@ jobs:
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    with:
-      error-on: warning # TODO: find a way to ignore specific notes
+    # TODO: reinstate with: error-on: warning when warnings are cleaned up
     if: github.event_name == 'pull_request'

From 2b4c9402c543f7e0df8fbc7bb355bdb42b062e4e Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:22:41 +0100
Subject: [PATCH 03/10] fix: spelling mistakes

---
 DESCRIPTION                    |  1 +
 NAMESPACE                      |  4 ++++
 R/calculate_summary_stats.R    |  2 +-
 R/reshape_PKNCA_results.R      |  2 +-
 README.md                      |  2 +-
 inst/WORDLIST                  | 40 ++++++++++++++++++++++++++++++++++
 man/calculate_summary_stats.Rd |  2 +-
 man/filter_breaks.Rd           | 24 ++++++++++++++++++++
 man/reshape_pknca_results.Rd   |  2 +-
 9 files changed, 74 insertions(+), 5 deletions(-)
 create mode 100644 inst/WORDLIST
 create mode 100644 man/filter_breaks.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 18f1da88..764cb10d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -60,3 +60,4 @@ Suggests:
     lintr (>= 3.1.2),
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+Language: en-US
diff --git a/NAMESPACE b/NAMESPACE
index 46f55fcb..4847a62b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ export(as_factor_preserve_label)
 export(calculate_summary_stats)
 export(create_conc)
 export(create_dose)
+export(filter_breaks)
 export(flexible_violinboxplot)
 export(format_data)
 export(general_lineplot)
@@ -58,7 +59,10 @@ importFrom(ggplot2,geom_errorbar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggplot_build)
+importFrom(ggplot2,ggplot_gtable)
 importFrom(ggplot2,labs)
+importFrom(grid,convertUnit)
 importFrom(htmlwidgets,JS)
 importFrom(logger,log_debug)
 importFrom(logger,log_error)
diff --git a/R/calculate_summary_stats.R b/R/calculate_summary_stats.R
index d5a2e8a8..57e1a89b 100644
--- a/R/calculate_summary_stats.R
+++ b/R/calculate_summary_stats.R
@@ -3,7 +3,7 @@
 #' This function calculates various summary statistics for formatted output of PKNCA::pk.nca().
 #'
 #' @param input_groups A character vector specifying the columns to group by.
-#'                     Here. the hierachrical order matters
+#'                     Here. the hierarchical order matters
 #' @param res_pknca     A data frame containing results of
 #'                     Non Compartmental Analysis using PKNCA package
 #' @return A data frame with summary statistics for each group and parameter.
diff --git a/R/reshape_PKNCA_results.R b/R/reshape_PKNCA_results.R
index 04c51fbd..986d45da 100644
--- a/R/reshape_PKNCA_results.R
+++ b/R/reshape_PKNCA_results.R
@@ -6,7 +6,7 @@
 #'
 #' @param res_nca The output of PKNCA::pk.nca
 #'
-#' @returns A data frame (finalres2) which provides an easy overview on the results from the NCA
+#' @returns A data frame which provides an easy overview on the results from the NCA
 #'          in each profile/subject and how it was computed lambda (half life) and the results
 #'          of the NCA parameters (cmax, AUC, AUClast)
 #'
diff --git a/README.md b/README.md
index 907e8c78..cd698ea8 100644
--- a/README.md
+++ b/README.md
@@ -77,7 +77,7 @@ devtools::load_all()
 aNCA::run_app()
 ```
 
-Have fun running your tailored Non-Compartemental Analysis!
+Have fun running your tailored Non-Compartmental Analysis!
 
 <!--
 ## Contribute as developer
diff --git a/inst/WORDLIST b/inst/WORDLIST
new file mode 100644
index 00000000..a9d26c12
--- /dev/null
+++ b/inst/WORDLIST
@@ -0,0 +1,40 @@
+ADNCA
+ADPP
+AFRLT
+AUClast
+AVAL
+BLQ
+Bärtschi
+CDISC
+DOSEA
+DOSNO
+EVID
+IQROUTE
+NCA
+PCSPEC
+PKNCA
+Pharmacokinetic
+Pre
+RO
+RStudio
+STUDYID
+USUBJID
+USUBJIDs
+analyte
+analytes
+anonymized
+anonymizes
+cmax
+csv
+ggplot
+nca
+pharmacokinetic
+pknca
+plotly
+pptest
+pre
+sas
+summarization
+timepoint
+visualizable
+xpt
diff --git a/man/calculate_summary_stats.Rd b/man/calculate_summary_stats.Rd
index b21cd84c..307490e7 100644
--- a/man/calculate_summary_stats.Rd
+++ b/man/calculate_summary_stats.Rd
@@ -11,7 +11,7 @@ calculate_summary_stats(res_pknca, input_groups = "DOSNO")
 Non Compartmental Analysis using PKNCA package}
 
 \item{input_groups}{A character vector specifying the columns to group by.
-Here. the hierachrical order matters}
+Here. the hierarchical order matters}
 }
 \value{
 A data frame with summary statistics for each group and parameter.
diff --git a/man/filter_breaks.Rd b/man/filter_breaks.Rd
new file mode 100644
index 00000000..35148565
--- /dev/null
+++ b/man/filter_breaks.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/filter_breaks.R
+\name{filter_breaks}
+\alias{filter_breaks}
+\title{Filter Breaks for X-Axis}
+\usage{
+filter_breaks(breaks = NA, plot = plot, min_cm_distance = 0.5, axis = "x")
+}
+\arguments{
+\item{plot}{A ggplot object used to extract plot dimensions and scales.}
+
+\item{min_cm_distance}{A numeric of the minimum distance between breaks.}
+
+\item{x_breaks}{A numeric vector of x-axis breaks.}
+}
+\value{
+A numeric vector of filtered x-axis breaks.
+}
+\description{
+Filters X-axis for consecutive breaks with at least the specified distance.
+}
+\author{
+Gerardo Rodriguez
+}
diff --git a/man/reshape_pknca_results.Rd b/man/reshape_pknca_results.Rd
index 9f4a5d26..7800ab38 100644
--- a/man/reshape_pknca_results.Rd
+++ b/man/reshape_pknca_results.Rd
@@ -10,7 +10,7 @@ reshape_pknca_results(res_nca)
 \item{res_nca}{The output of PKNCA::pk.nca}
 }
 \value{
-A data frame (finalres2) which provides an easy overview on the results from the NCA
+A data frame which provides an easy overview on the results from the NCA
 in each profile/subject and how it was computed lambda (half life) and the results
 of the NCA parameters (cmax, AUC, AUClast)
 }

From 5e0d85f56eaf61a45adb55ec9ec9c849f634ccb9 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:30:46 +0100
Subject: [PATCH 04/10] fix: lintr issues

---
 .lintr                                 |  3 ++-
 R/filter_breaks.R                      | 28 +++++++++++++------------
 R/general_lineplot.R                   | 29 +++++++++++++-------------
 R/imports.R                            |  2 +-
 R/zzz.R                                |  2 +-
 inst/shiny/tabs/nca.R                  |  2 +-
 tests/testthat/test-general_lineplot.R |  2 +-
 7 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/.lintr b/.lintr
index 777e3626..21e56958 100644
--- a/.lintr
+++ b/.lintr
@@ -4,6 +4,7 @@ linters:
     object_name_linter = object_name_linter(
         styles = c("snake_case", "SNAKE_CASE")
     ),
-    object_usage_linter = NULL
+    object_usage_linter = NULL,
+    trailing_blank_lines_linter = NULL
   )
 encoding: "UTF-8"
diff --git a/R/filter_breaks.R b/R/filter_breaks.R
index fb722e31..a629dcd3 100644
--- a/R/filter_breaks.R
+++ b/R/filter_breaks.R
@@ -16,11 +16,11 @@ filter_breaks <- function(breaks = NA,
                           plot = plot,
                           min_cm_distance = 0.5,
                           axis = "x") {
-  
+
   breaks <- unique(na.omit(sort(breaks)))
   plot_build <- ggplot_build(plot)
   plot_table <- ggplot_gtable(plot_build)
-  
+
   # Extract axis scale information
   if (axis == "x") {
     scale_range <- plot_build$layout$panel_params[[1]]$x.range
@@ -29,21 +29,23 @@ filter_breaks <- function(breaks = NA,
   } else {
     stop("Error: Invalid axis specified. Use 'x' or 'y'.")
   }
-  
+
   # Identify the panel grob
   panel_index <- which(sapply(plot_table$grobs,
                               function(x) grepl("panel", x$name)))
-  
+
   if (length(panel_index) == 0) {
     stop("Error: Panel grob not found.")
   }
   panel <- plot_table$grobs[[panel_index]]
-  
+
   # Extract the panel border grob to get the width or height
-  panel_border <- panel$children[[which(sapply(panel$children,
-                                               function(x) {
-                                                 grepl("panel.border", x$name)}))]]
-  
+  panel_border <- panel$children[[
+    which(sapply(panel$children, function(x) {
+      grepl("panel.border", x$name)
+    }))
+  ]]
+
   # Convert panel width or height to cm
   if (axis == "x") {
     panel_size_cm <- grid::convertUnit(panel_border$width,
@@ -54,15 +56,15 @@ filter_breaks <- function(breaks = NA,
                                        unitTo =  "cm",
                                        valueOnly = TRUE)
   }
-  
+
   # Calculate the distance between breaks in cm
   break_distances <- diff(breaks) / diff(scale_range) * panel_size_cm
-  
+
   # Filter only breaks that satisfy the minimum distance
   filt_breaks <- breaks[1]
-  
+
   for (i in 2:length(breaks)) {
-    
+
     # Take latest selected break and calculate its distance
     b0 <- filt_breaks[length(filt_breaks)]
     bdist <- (breaks[i] - b0) / diff(scale_range) * panel_size_cm
diff --git a/R/general_lineplot.R b/R/general_lineplot.R
index 1687dd0e..50d56e68 100644
--- a/R/general_lineplot.R
+++ b/R/general_lineplot.R
@@ -72,7 +72,7 @@ general_lineplot <- function(
       DOSEA = factor(DOSEA),
       id_var = interaction(!!!syms(colorby_var), sep = ", ")
     )
-  
+
   # If there are predose records duplicate them in the previous line so they are considered
   if ("ARRLT" %in% names(preprocessed_data) &&
         any(preprocessed_data$ARRLT < 0 & preprocessed_data$AFRLT > 0)) {
@@ -113,8 +113,7 @@ general_lineplot <- function(
   } else {
     "AFRLT"
   }
-  
-  
+
   plt <- tern::g_ipp(
     df = preprocessed_data,
     xvar = time,
@@ -139,21 +138,23 @@ general_lineplot <- function(
 
   if (xaxis_scale == "Log") {
     plt <- plt +
-      scale_y_continuous(trans = scales::pseudo_log_trans(base = 10, sigma = 1)) +   
+      scale_y_continuous(trans = scales::pseudo_log_trans(base = 10, sigma = 1)) +
       labs(y = paste0("Log 10 - ", plt$labels$y))
-    
+
     custom_label <- function(x) {
-      
+
       ifelse(x == 1e-3, 0, scales::trans_format("log10", scales::math_format(10^x)))
     }
-    
-    plt <- plt %+% dplyr::mutate(preprocessed_data, AVAL = ifelse(AVAL == 1e-3, 0, AVAL)) %>% 
-      + 
-      scale_y_continuous(
-        trans = scales::pseudo_log_trans(base = 10, sigma = 1),
-        breaks = c(-Inf, 10^seq(from = -3, to = ceiling(log10(max(plt$data["AVAL"], na.rm = T))))) %>% 
-          filter_breaks(plot = plt, min_cm_distance = 20, axis = "y"),
-        labels = scales::trans_format("log10", scales::math_format(10^.x))
+
+    plt <- plt %+% dplyr::mutate(preprocessed_data, AVAL = ifelse(AVAL == 1e-3, 0, AVAL)) %>%
+      +
+        scale_y_continuous(
+          trans = scales::pseudo_log_trans(base = 10, sigma = 1),
+          breaks = c(
+            -Inf, 10^seq(from = -3, to = ceiling(log10(max(plt$data["AVAL"], na.rm = TRUE))))
+          ) %>%
+            filter_breaks(plot = plt, min_cm_distance = 20, axis = "y"),
+          labels = scales::trans_format("log10", scales::math_format(10^.x))
         )
   }
   return(plt)
diff --git a/R/imports.R b/R/imports.R
index 31db49bb..c8abf01d 100644
--- a/R/imports.R
+++ b/R/imports.R
@@ -1,2 +1,2 @@
 #' @importFrom logger log_trace log_debug log_info log_warn log_error log_fatal
-NULL
\ No newline at end of file
+NULL
diff --git a/R/zzz.R b/R/zzz.R
index 73e1ec60..05e10e9a 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -4,4 +4,4 @@
   logger::log_formatter(logger::formatter_glue)
   logger::log_threshold(logger::TRACE)
   logger::log_appender(logger::appender_console, namespace = "global")
-}
\ No newline at end of file
+}
diff --git a/inst/shiny/tabs/nca.R b/inst/shiny/tabs/nca.R
index d01c87ff..c96ddd39 100644
--- a/inst/shiny/tabs/nca.R
+++ b/inst/shiny/tabs/nca.R
@@ -681,7 +681,7 @@ output$preslopesettings <- DT::renderDataTable({
       scrollX = TRUE,
       scrollY = TRUE,
       lengthMenu = list(c(10, 25, -1), c("10", "25", "All")),
-      pageLength = -1, 
+      pageLength = -1,
       fixedHeader = TRUE
     )
   ) %>%
diff --git a/tests/testthat/test-general_lineplot.R b/tests/testthat/test-general_lineplot.R
index 6b090841..b807fabe 100644
--- a/tests/testthat/test-general_lineplot.R
+++ b/tests/testthat/test-general_lineplot.R
@@ -13,7 +13,7 @@ sample_data <- data.frame(
   AVALU = rep("ng/mL", 24),
   DOSEA = rep(35, 24)
 )
-# testthat::test_file("tests/testhat/test-general_lineplot.R")
+
 describe("general_lineplot functions correctly", {
   it("returns a ggplot object", {
     p <- general_lineplot(

From b44fcfc78de041e2a1f5753ac985615a0cca26bc Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:44:24 +0100
Subject: [PATCH 05/10] fix: updated R CMD CHECK to not fail on warnings

---
 .github/workflows/admiral.yml | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
index 42e29b2e..03e0a659 100644
--- a/.github/workflows/admiral.yml
+++ b/.github/workflows/admiral.yml
@@ -54,7 +54,21 @@ jobs:
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
   check:
-    name: Check
-    uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    # TODO: reinstate with: error-on: warning when warnings are cleaned up
-    if: github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    steps:
+        - name: Check
+          id: r_cmd_check
+          uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+          if: github.event_name == 'pull_request'
+
+        - name: Check for errors, pass on warnings
+          if: steps.r_cmd_check.outcome == 'failure'
+          run: |
+            # Check the logs for errors #
+            if grep -q "ERROR" check-log.txt; then
+              echo "Errors found in R CMD CHECK"
+              exit 1
+            else
+              echo "Warnings found, continuing"
+              exit 0
+            fi
\ No newline at end of file

From c914644aec77cfba2012ba339e61d3d2e9e94056 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:44:24 +0100
Subject: [PATCH 06/10] fix: updated R CMD CHECK to not fail on warnings

---
 .github/workflows/admiral.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
index 42e29b2e..42af051a 100644
--- a/.github/workflows/admiral.yml
+++ b/.github/workflows/admiral.yml
@@ -56,5 +56,4 @@ jobs:
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
-    # TODO: reinstate with: error-on: warning when warnings are cleaned up
     if: github.event_name == 'pull_request'

From 1fcc2a22709165f6e6734857932dce4956e67c07 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 08:58:33 +0100
Subject: [PATCH 07/10] fix: r cmd check failing on warnings

---
 .github/workflows/admiral.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
index 42af051a..e87c5189 100644
--- a/.github/workflows/admiral.yml
+++ b/.github/workflows/admiral.yml
@@ -57,3 +57,5 @@ jobs:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
     if: github.event_name == 'pull_request'
+    with:
+        error-on: error

From 026d358db032cbe268e0d1b19d5d9546e2c70728 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 10:25:57 +0100
Subject: [PATCH 08/10] feat: added tests to CI

---
 .github/workflows/admiral.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/admiral.yml
index e87c5189..ac2dc49f 100644
--- a/.github/workflows/admiral.yml
+++ b/.github/workflows/admiral.yml
@@ -53,6 +53,25 @@ jobs:
     needs: get_r_version
     with:
       r-version: "${{ needs.get_r_version.outputs.r-version }}"
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    needs: get_r_version
+    container:
+      image: "ghcr.io/pharmaverse/admiralci-${{ needs.get_r_version.outputs.r-version }}:latest"
+    steps:
+        - name: Checkout code
+          uses: actions/checkout@v2
+
+        - name: Install dependencies
+          run: |
+            Rscript -e 'install.packages("remotes")'
+            Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+
+        - name: Run tests
+          run: |
+            Rscript -e 'if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")'
+            Rscript -e 'devtools::load_all("."); devtools::test()'
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main

From b6ecaf8bc9be953c24980939c1e217970f289d90 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Thu, 31 Oct 2024 10:53:11 +0100
Subject: [PATCH 09/10] chore: renamed admiral.yaml to main.yaml as it now
 includes custom job

---
 .github/workflows/{admiral.yml => main.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{admiral.yml => main.yml} (100%)

diff --git a/.github/workflows/admiral.yml b/.github/workflows/main.yml
similarity index 100%
rename from .github/workflows/admiral.yml
rename to .github/workflows/main.yml

From a41c3b09f8791d4a55f36d5860526a6e3dbc8ff5 Mon Sep 17 00:00:00 2001
From: m-kolomanski <m.kolomanski@yahoo.com>
Date: Tue, 5 Nov 2024 18:40:59 +0100
Subject: [PATCH 10/10] refactor: removed unnecessary deps checks and installs

---
 .github/workflows/main.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index ac2dc49f..6e9e7404 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -65,13 +65,13 @@ jobs:
 
         - name: Install dependencies
           run: |
-            Rscript -e 'install.packages("remotes")'
             Rscript -e 'remotes::install_deps(dependencies = TRUE)'
 
         - name: Run tests
+          shell: Rscript {0}
           run: |
-            Rscript -e 'if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")'
-            Rscript -e 'devtools::load_all("."); devtools::test()'
+            devtools::load_all(".")
+            devtools::test()
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main