From 475e6857be8c7ee934517376968484ad8020eea6 Mon Sep 17 00:00:00 2001
From: Maarten van Kessel <m.vankessel@mi-erasmusmc.nl>
Date: Fri, 29 Nov 2024 13:18:34 +0100
Subject: [PATCH 1/8] cran hotfix

---
 DESCRIPTION                             | 2 +-
 extras/PackageMaintenance.R             | 2 +-
 tests/testthat/test-checkDependencies.R | 8 +++-----
 3 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3dc9380..b9794ee 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PaRe
 Type: Package
 Title: A Way to Perform Code Review or QA on Other Packages
-Version: 0.1.14
+Version: 0.1.15
 Language: en-US
 Authors@R:
     person("Maarten", "van Kessel", email = "m.l.vankessel@erasmusmc.nl",
diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
index 5ab84e8..140cfc8 100644
--- a/extras/PackageMaintenance.R
+++ b/extras/PackageMaintenance.R
@@ -1,6 +1,6 @@
 # Copyright 2024 DARWIN EU®
 #
-# This file is part of TreatmentPatterns
+# This file is part of PaRe
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/tests/testthat/test-checkDependencies.R b/tests/testthat/test-checkDependencies.R
index ec858bd..fe7a752 100644
--- a/tests/testthat/test-checkDependencies.R
+++ b/tests/testthat/test-checkDependencies.R
@@ -15,11 +15,8 @@ test_that("void", {
 })
 
 test_that("minimal", {
-  skip_if(
-    utils::packageVersion(pkg = "base") > package_version("4.4.0")
-  )
+  skip_if_offline()
   repo <- makeRepo()
-  testthat::skip_if(!R6::is.R6(repo))
 
   expect_message(
     suppressWarnings(checkDependencies(repo = repo)),
@@ -30,8 +27,9 @@ test_that("minimal", {
 
 
 test_that("parallel", {
+  skip_if_offline()
+
   repo <- makeRepo()
-  testthat::skip_if(!R6::is.R6(repo))
 
   expect_message(
     suppressWarnings(checkDependencies(repo = repo, nThreads = 2)),

From 92610472fed267d36c1e1d2ce5a421c6379a5565 Mon Sep 17 00:00:00 2001
From: Maarten van Kessel <m.vankessel@mi-erasmusmc.nl>
Date: Fri, 29 Nov 2024 14:49:54 +0100
Subject: [PATCH 2/8] Updated test suite for CRAN

---
 DESCRIPTION                              |  1 +
 tests/testthat/helper-checkSuggests.R    |  3 ++-
 tests/testthat/helper-makeRepo.R         | 18 ------------------
 tests/testthat/setup.R                   | 17 +++++++++++++++++
 tests/testthat/test-addPareArticle.R     |  5 ++---
 tests/testthat/test-checkDependencies.R  |  7 +++----
 tests/testthat/test-getApplyCall.R       | 10 ++++------
 tests/testthat/test-getDlplyCall.R       | 10 ++++------
 tests/testthat/test-getDoCall.R          | 10 ++++------
 tests/testthat/test-getDoCallFromLines.R |  3 ---
 tests/testthat/test-getFunCall.R         |  7 ++++---
 tests/testthat/test-getMultiLineFun.R    |  7 ++++---
 12 files changed, 45 insertions(+), 53 deletions(-)
 delete mode 100644 tests/testthat/helper-makeRepo.R
 create mode 100644 tests/testthat/setup.R

diff --git a/DESCRIPTION b/DESCRIPTION
index b9794ee..dfaa7c4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -44,6 +44,7 @@ Suggests:
     withr,
     cowplot,
     knitr,
+    curl,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
diff --git a/tests/testthat/helper-checkSuggests.R b/tests/testthat/helper-checkSuggests.R
index 7811f79..0cea7ec 100644
--- a/tests/testthat/helper-checkSuggests.R
+++ b/tests/testthat/helper-checkSuggests.R
@@ -3,6 +3,7 @@ checkSuggests <- function() {
     c("ggplot2", "plotly", "ggraph", "DT", "magick", "withr", "cowplot", "knitr", "testthat"),
     require,
     character.only = TRUE,
-    quietly = TRUE
+    quietly = TRUE,
+    warn.conflicts = FALSE
   ))))
 }
diff --git a/tests/testthat/helper-makeRepo.R b/tests/testthat/helper-makeRepo.R
deleted file mode 100644
index a4f696e..0000000
--- a/tests/testthat/helper-makeRepo.R
+++ /dev/null
@@ -1,18 +0,0 @@
-makeRepo <- function() {
-  repo <- tryCatch({
-    tmpDir <- tempdir()
-    pathToRepo <- file.path(tmpDir, "glue")
-
-    if (!dir.exists(pathToRepo)) {
-      git2r::clone(
-        url = "https://github.com/tidyverse/glue",
-        local_path = pathToRepo
-      )
-    }
-
-    PaRe::Repository$new(path = pathToRepo)
-  }, error = function(e) {
-    FALSE
-  })
-  return(repo)
-}
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
new file mode 100644
index 0000000..690e33c
--- /dev/null
+++ b/tests/testthat/setup.R
@@ -0,0 +1,17 @@
+library(PaRe)
+library(testthat)
+library(git2r)
+
+path <- file.path(tempdir(), "glue")
+
+if (!is.null(curl::nslookup("captive.apple.com", error = FALSE))) {
+  clone(
+    url = "https://github.com/tidyverse/glue",
+    local_path = path
+  )
+}
+
+withr::defer({
+  unlink(path, recursive = TRUE, force = TRUE)},
+  teardown_env()
+)
diff --git a/tests/testthat/test-addPareArticle.R b/tests/testthat/test-addPareArticle.R
index 0e47cf0..1268b0a 100644
--- a/tests/testthat/test-addPareArticle.R
+++ b/tests/testthat/test-addPareArticle.R
@@ -1,13 +1,12 @@
 test_that("minimal", {
   skip_if_not(checkSuggests())
+  skip_if_offline()
 
-  repo <- makeRepo()
-  testthat::skip_if(!R6::is.R6(repo))
+  repo <- Repository$new(path)
 
   suppressWarnings(addPareArticle(repo))
 
   path <- file.path(repo$getPath(), "vignettes", "articles", "PareReport.Rmd")
 
   expect_true(file.exists(path))
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-checkDependencies.R b/tests/testthat/test-checkDependencies.R
index fe7a752..b22e2cc 100644
--- a/tests/testthat/test-checkDependencies.R
+++ b/tests/testthat/test-checkDependencies.R
@@ -16,24 +16,23 @@ test_that("void", {
 
 test_that("minimal", {
   skip_if_offline()
-  repo <- makeRepo()
+
+  repo <- Repository$new(path)
 
   expect_message(
     suppressWarnings(checkDependencies(repo = repo)),
     "All dependencies are approved."
   )
-  unlink(repo$getPath(), recursive = TRUE)
 })
 
 
 test_that("parallel", {
   skip_if_offline()
 
-  repo <- makeRepo()
+  repo <- Repository$new(path)
 
   expect_message(
     suppressWarnings(checkDependencies(repo = repo, nThreads = 2)),
     "All dependencies are approved."
   )
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-getApplyCall.R b/tests/testthat/test-getApplyCall.R
index 7420746..ca0cc68 100644
--- a/tests/testthat/test-getApplyCall.R
+++ b/tests/testthat/test-getApplyCall.R
@@ -1,9 +1,8 @@
-library(PaRe)
-library(testthat)
-
 test_that("minimal", {
-  repo <- makeRepo()
-  testthat::skip_if_not(all(class(repo) == c("Repository", "R6")))
+  skip_if_offline()
+
+  repo <- Repository$new(path)
+
   files <- repo$getRFiles()
   glueIdx <- sapply(files, function(file) {
     file$getName() == "glue.R"
@@ -20,5 +19,4 @@ test_that("minimal", {
   fun <- funs[glueIdx][[1]]
 
   expect_null(PaRe:::getApplyCall(fun, defFuns))
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-getDlplyCall.R b/tests/testthat/test-getDlplyCall.R
index a9fcf23..dc853af 100644
--- a/tests/testthat/test-getDlplyCall.R
+++ b/tests/testthat/test-getDlplyCall.R
@@ -1,6 +1,3 @@
-library(PaRe)
-library(testthat)
-
 # if dlply calls > 0
 #   lapply
 #     if dlply call %in% defined functions
@@ -10,8 +7,10 @@ library(testthat)
 # 2: if1 if2
 
 test_that("minimal", {
-  repo <- makeRepo()
-  testthat::skip_if_not(all(class(repo) == c("Repository", "R6")))
+  skip_if_offline()
+
+  repo <- Repository$new(path)
+
   files <- repo$getRFiles()
   glueIdx <- sapply(files, function(file) {
     file$getName() == "glue.R"
@@ -28,5 +27,4 @@ test_that("minimal", {
   fun <- funs[glueIdx][[1]]
 
   expect_null(PaRe:::getDlplyCall(fun, defFuns))
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-getDoCall.R b/tests/testthat/test-getDoCall.R
index 5b1f89f..9c162f8 100644
--- a/tests/testthat/test-getDoCall.R
+++ b/tests/testthat/test-getDoCall.R
@@ -1,9 +1,8 @@
-library(PaRe)
-library(testthat)
-
 test_that("minimal", {
-  repo <- makeRepo()
-  testthat::skip_if_not(all(class(repo) == c("Repository", "R6")))
+  skip_if_offline()
+
+  repo <- Repository$new(path)
+
   files <- repo$getRFiles()
   glueIdx <- sapply(files, function(file) {
     file$getName() == "glue.R"
@@ -20,5 +19,4 @@ test_that("minimal", {
   fun <- funs[glueIdx][[1]]
 
   expect_null(PaRe:::getDoCall(fun, defFuns))
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-getDoCallFromLines.R b/tests/testthat/test-getDoCallFromLines.R
index 9406b3e..dde7171 100644
--- a/tests/testthat/test-getDoCallFromLines.R
+++ b/tests/testthat/test-getDoCallFromLines.R
@@ -1,6 +1,3 @@
-library(PaRe)
-library(testthat)
-
 test_that("minimal", {
   lines <- c(
     "do.call(mean, list(c(1, 2, 3)))",
diff --git a/tests/testthat/test-getFunCall.R b/tests/testthat/test-getFunCall.R
index f67d488..431212a 100644
--- a/tests/testthat/test-getFunCall.R
+++ b/tests/testthat/test-getFunCall.R
@@ -1,6 +1,8 @@
 test_that("minimal", {
-  repo <- makeRepo()
-  testthat::skip_if_not(all(class(repo) == c("Repository", "R6")))
+  skip_if_offline()
+
+  repo <- Repository$new(path)
+
   files <- repo$getRFiles()
   glueIdx <- sapply(files, function(file) {
     file$getName() == "glue.R"
@@ -19,5 +21,4 @@ test_that("minimal", {
   df <- bind_rows(PaRe:::getFunCall(fun, defFuns))
   expect_true(nrow(df) == 1)
   expect_true(ncol(df) == 2)
-  unlink(repo$getPath(), recursive = TRUE)
 })
diff --git a/tests/testthat/test-getMultiLineFun.R b/tests/testthat/test-getMultiLineFun.R
index 20467fb..7144186 100644
--- a/tests/testthat/test-getMultiLineFun.R
+++ b/tests/testthat/test-getMultiLineFun.R
@@ -15,8 +15,10 @@
 # 10: while con1 con2 if1 if2
 
 test_that("regular use", {
-  repo <- makeRepo()
-  testthat::skip_if_not(all(class(repo) == c("Repository", "R6")))
+  skip_if_offline()
+
+  repo <- Repository$new(path)
+
   files <- repo$getRFiles()
   glueIdx <- sapply(files, function(file) {
     file$getName() == "glue.R"
@@ -33,7 +35,6 @@ test_that("regular use", {
   fun <- funs[glueIdx][[1]]
 
   expect_true(length(PaRe:::getMultiLineFun(line = 1, lines = fun$getLines())) == 1)
-  unlink(repo$getPath(), recursive = TRUE)
 })
 
 test_that("No closing bracket", {

From 815814579e6ae25b42e67641920bfd8b0bdc09d6 Mon Sep 17 00:00:00 2001
From: Maarten van Kessel <m.vankessel@mi-erasmusmc.nl>
Date: Fri, 29 Nov 2024 16:00:01 +0100
Subject: [PATCH 3/8] Updated tests

---
 CRAN-SUBMISSION                         |  6 +++---
 tests/testthat/setup.R                  | 16 ++++++++++++----
 tests/testthat/test-addPareArticle.R    |  1 +
 tests/testthat/test-checkDependencies.R |  2 ++
 tests/testthat/test-getApplyCall.R      |  1 +
 tests/testthat/test-getDlplyCall.R      |  1 +
 tests/testthat/test-getDoCall.R         |  1 +
 tests/testthat/test-getFunCall.R        |  1 +
 tests/testthat/test-getMultiLineFun.R   |  1 +
 9 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
index d6e7e62..a323ba4 100644
--- a/CRAN-SUBMISSION
+++ b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.1.14
-Date: 2024-11-28 15:02:25 UTC
-SHA: 6b421989f4c43662982bbe2723d109a843f5e982
+Version: 0.1.15
+Date: 2024-11-29 14:23:55 UTC
+SHA: 92610472fed267d36c1e1d2ce5a421c6379a5565
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 690e33c..484effe 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -3,12 +3,20 @@ library(testthat)
 library(git2r)
 
 path <- file.path(tempdir(), "glue")
+repoCloned <- NULL
 
 if (!is.null(curl::nslookup("captive.apple.com", error = FALSE))) {
-  clone(
-    url = "https://github.com/tidyverse/glue",
-    local_path = path
-  )
+  tryCatch({
+    clone(
+      url = "https://github.com/tidyverse/glue",
+      local_path = path
+    )
+    repoCloned <- TRUE
+  }, error = function(e) {
+    repoCloned <- FALSE
+  })
+} else {
+  repoCloned <- FALSE
 }
 
 withr::defer({
diff --git a/tests/testthat/test-addPareArticle.R b/tests/testthat/test-addPareArticle.R
index 1268b0a..f45ab02 100644
--- a/tests/testthat/test-addPareArticle.R
+++ b/tests/testthat/test-addPareArticle.R
@@ -1,6 +1,7 @@
 test_that("minimal", {
   skip_if_not(checkSuggests())
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-checkDependencies.R b/tests/testthat/test-checkDependencies.R
index b22e2cc..f66fce9 100644
--- a/tests/testthat/test-checkDependencies.R
+++ b/tests/testthat/test-checkDependencies.R
@@ -16,6 +16,7 @@ test_that("void", {
 
 test_that("minimal", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
@@ -28,6 +29,7 @@ test_that("minimal", {
 
 test_that("parallel", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-getApplyCall.R b/tests/testthat/test-getApplyCall.R
index ca0cc68..f4c8316 100644
--- a/tests/testthat/test-getApplyCall.R
+++ b/tests/testthat/test-getApplyCall.R
@@ -1,5 +1,6 @@
 test_that("minimal", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-getDlplyCall.R b/tests/testthat/test-getDlplyCall.R
index dc853af..7236fb8 100644
--- a/tests/testthat/test-getDlplyCall.R
+++ b/tests/testthat/test-getDlplyCall.R
@@ -8,6 +8,7 @@
 
 test_that("minimal", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-getDoCall.R b/tests/testthat/test-getDoCall.R
index 9c162f8..fc1ee8c 100644
--- a/tests/testthat/test-getDoCall.R
+++ b/tests/testthat/test-getDoCall.R
@@ -1,5 +1,6 @@
 test_that("minimal", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-getFunCall.R b/tests/testthat/test-getFunCall.R
index 431212a..1af42fc 100644
--- a/tests/testthat/test-getFunCall.R
+++ b/tests/testthat/test-getFunCall.R
@@ -1,5 +1,6 @@
 test_that("minimal", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 
diff --git a/tests/testthat/test-getMultiLineFun.R b/tests/testthat/test-getMultiLineFun.R
index 7144186..0ad1a08 100644
--- a/tests/testthat/test-getMultiLineFun.R
+++ b/tests/testthat/test-getMultiLineFun.R
@@ -16,6 +16,7 @@
 
 test_that("regular use", {
   skip_if_offline()
+  skip_if_not(repoCloned)
 
   repo <- Repository$new(path)
 

From f43e8d8939d53cd9ecc1959489185f9419528598 Mon Sep 17 00:00:00 2001
From: Maarten van Kessel <m.vankessel@mi-erasmusmc.nl>
Date: Tue, 3 Dec 2024 09:18:32 +0100
Subject: [PATCH 4/8] CRAN sub

---
 CRAN-SUBMISSION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
index a323ba4..f428b04 100644
--- a/CRAN-SUBMISSION
+++ b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 0.1.15
-Date: 2024-11-29 14:23:55 UTC
-SHA: 92610472fed267d36c1e1d2ce5a421c6379a5565
+Date: 2024-11-29 15:15:17 UTC
+SHA: 815814579e6ae25b42e67641920bfd8b0bdc09d6

From 3c8d59c3dbb5e8229f41d2e461dc2b0b20fe4a3b Mon Sep 17 00:00:00 2001
From: Maarten van Kessel <m.vankessel@mi-erasmusmc.nl>
Date: Tue, 3 Dec 2024 13:21:44 +0100
Subject: [PATCH 5/8] report fix

---
 inst/rmd/report.Rmd | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/inst/rmd/report.Rmd b/inst/rmd/report.Rmd
index d1a68ea..b812e43 100644
--- a/inst/rmd/report.Rmd
+++ b/inst/rmd/report.Rmd
@@ -180,11 +180,8 @@ DT::datatable(data.frame(
   meanDegree = round(mean(igraph::degree(graphData)), 2),
   meanDistance = round(mean(igraph::distances(graphData)), 2)
   ),
-              rownames= FALSE)
-}, error = function(e) {
-  message("Could not get graph data with error:")
-  message(sprintf("\t%s", e))
-})
+  rownames = FALSE
+)
 ```
 
 ### Function use per dependency

From f4177d9f6fb4bd343b5720434e3a2c6981035474 Mon Sep 17 00:00:00 2001
From: mvankessel-EMC <m.vankessel@mi-erasmusmc.nl>
Date: Wed, 4 Feb 2026 11:55:43 +0100
Subject: [PATCH 6/8] summarise -> reframe

---
 R/lint.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/lint.R b/R/lint.R
index 5a693f7..425ef18 100644
--- a/R/lint.R
+++ b/R/lint.R
@@ -151,7 +151,7 @@ lintScore <- function(repo, messages) {
   pct <- messages %>%
     dplyr::group_by(.data$type) %>%
     dplyr::tally() %>%
-    dplyr::summarise(.data$type, pct = round(.data$n / nLines * 100, 2))
+    dplyr::reframe(.data$type, pct = round(.data$n / nLines * 100, 2))
 
   if (nrow(pct) == 0) {
     message(glue::glue("{nrow(pct)} Lintr messages found"))

From 4391dd09a7693cd49b45af4d65a92edee88c7ec4 Mon Sep 17 00:00:00 2001
From: mvankessel-EMC <m.vankessel@mi-erasmusmc.nl>
Date: Wed, 4 Feb 2026 13:34:31 +0100
Subject: [PATCH 7/8] release prep

---
 DESCRIPTION                       |   2 +-
 NEWS.md                           |   8 ++
 R/getDefaultPermittedPackages.R   |  44 +++++---
 tests/testthat/setup.R            |  27 +++--
 vignettes/Documentation.Rmd       |   9 +-
 vignettes/articles/PareReport.Rmd | 174 ++++++++++++++++++------------
 6 files changed, 162 insertions(+), 102 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index dfaa7c4..0398366 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PaRe
 Type: Package
 Title: A Way to Perform Code Review or QA on Other Packages
-Version: 0.1.15
+Version: 0.1.16
 Language: en-US
 Authors@R:
     person("Maarten", "van Kessel", email = "m.l.vankessel@erasmusmc.nl",
diff --git a/NEWS.md b/NEWS.md
index e343d7d..1bb4788 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,11 @@
+PaRe 0.1.16
+==========
+1. Use `dplyr::reframe()` instead of `dplyr::summarise()`
+
+PaRe 0.1.15
+==========
+1. Updated internal test setup
+
 PaRe 0.1.14
 ==========
 1. Changed tests so R-CMD-Check passes on depends-only environment
diff --git a/R/getDefaultPermittedPackages.R b/R/getDefaultPermittedPackages.R
index 3355f07..0db08e9 100644
--- a/R/getDefaultPermittedPackages.R
+++ b/R/getDefaultPermittedPackages.R
@@ -18,28 +18,38 @@ getParDeps <- function(pkgs, nThreads) {
   deps <- if (nThreads > 1) {
     cl <- parallel::makeCluster(nThreads)
     on.exit(parallel::stopCluster(cl = cl))
-    parallel::clusterEvalQ(cl = cl, expr = {library("pak", character.only = TRUE)})
+    parallel::clusterEvalQ(cl = cl, expr = {
+      library("pak", character.only = TRUE)
+    })
 
     parallel::parLapply(cl = cl, X = pkgs, fun = function(pkg) {
-      tryCatch({
-        res <- pak::pkg_deps(pkg = pkg)
-        return(res)
-      }, error = function(e) {
-        return(NULL)
-      }, warning = function(w) {
-        return(res)
-      })
+      tryCatch(
+        {
+          res <- pak::pkg_deps(pkg = pkg)
+          return(res)
+        },
+        error = function(e) {
+          return(NULL)
+        },
+        warning = function(w) {
+          return(res)
+        }
+      )
     })
   } else {
     lapply(X = pkgs, function(pkg) {
-      tryCatch({
-        res <- pak::pkg_deps(pkg = pkg)
-        return(res)
-      }, error = function(e) {
-        return(NULL)
-      }, warning = function(w) {
-        return(res)
-      })
+      tryCatch(
+        {
+          res <- pak::pkg_deps(pkg = pkg)
+          return(res)
+        },
+        error = function(e) {
+          return(NULL)
+        },
+        warning = function(w) {
+          return(res)
+        }
+      )
     })
   }
 
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 484effe..1df6163 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -6,20 +6,25 @@ path <- file.path(tempdir(), "glue")
 repoCloned <- NULL
 
 if (!is.null(curl::nslookup("captive.apple.com", error = FALSE))) {
-  tryCatch({
-    clone(
-      url = "https://github.com/tidyverse/glue",
-      local_path = path
-    )
-    repoCloned <- TRUE
-  }, error = function(e) {
-    repoCloned <- FALSE
-  })
+  tryCatch(
+    {
+      clone(
+        url = "https://github.com/tidyverse/glue",
+        local_path = path
+      )
+      repoCloned <- TRUE
+    },
+    error = function(e) {
+      repoCloned <- FALSE
+    }
+  )
 } else {
   repoCloned <- FALSE
 }
 
-withr::defer({
-  unlink(path, recursive = TRUE, force = TRUE)},
+withr::defer(
+  {
+    unlink(path, recursive = TRUE, force = TRUE)
+  },
   teardown_env()
 )
diff --git a/vignettes/Documentation.Rmd b/vignettes/Documentation.Rmd
index b036c16..50c5fdd 100644
--- a/vignettes/Documentation.Rmd
+++ b/vignettes/Documentation.Rmd
@@ -234,10 +234,11 @@ PaRe::pkgDiagram(repo = repo) %>%
 if (fetchedRepo) {
   if (all(c(
     require("DiagrammeRsvg", character.only = TRUE),
-    require("magick", character.only = TRUE)))) {
-      PaRe::pkgDiagram(repo = repo) %>%
-        DiagrammeRsvg::export_svg() %>%
-        magick::image_read_svg()
+    require("magick", character.only = TRUE)
+  ))) {
+    PaRe::pkgDiagram(repo = repo) %>%
+      DiagrammeRsvg::export_svg() %>%
+      magick::image_read_svg()
   }
 }
 ```
diff --git a/vignettes/articles/PareReport.Rmd b/vignettes/articles/PareReport.Rmd
index 8a486c8..1fbd03d 100644
--- a/vignettes/articles/PareReport.Rmd
+++ b/vignettes/articles/PareReport.Rmd
@@ -43,66 +43,91 @@ defFuns <- defFuns %>%
 ```
 
 ```{r summaryDefFunStats, echo=FALSE}
-DT::datatable(data.frame(
-  min = c(min(defFuns$nArgs, na.rm = TRUE), 
-          min(defFuns$size, na.rm = TRUE), 
-          min(defFuns$cycloComp, na.rm = TRUE)),
-  median = c(median(defFuns$nArgs, na.rm = TRUE), 
-             median(defFuns$size, na.rm = TRUE), 
-             median(defFuns$cycloComp, na.rm = TRUE)),
-  max = c(max(defFuns$nArgs, na.rm = TRUE), 
-          max(defFuns$size, na.rm = TRUE), 
-          max(defFuns$cycloComp, na.rm = TRUE)),
-  row.names = c("Number of arguments",
-                "Lines of code",
-                "Cyclomatic complexity")), 
-  options = list(dom = 't'))
+DT::datatable(
+  data.frame(
+    min = c(
+      min(defFuns$nArgs, na.rm = TRUE),
+      min(defFuns$size, na.rm = TRUE),
+      min(defFuns$cycloComp, na.rm = TRUE)
+    ),
+    median = c(
+      median(defFuns$nArgs, na.rm = TRUE),
+      median(defFuns$size, na.rm = TRUE),
+      median(defFuns$cycloComp, na.rm = TRUE)
+    ),
+    max = c(
+      max(defFuns$nArgs, na.rm = TRUE),
+      max(defFuns$size, na.rm = TRUE),
+      max(defFuns$cycloComp, na.rm = TRUE)
+    ),
+    row.names = c(
+      "Number of arguments",
+      "Lines of code",
+      "Cyclomatic complexity"
+    )
+  ),
+  options = list(dom = "t")
+)
 ```
 
 ```{r echo=FALSE}
-gg_nArgs <- defFuns %>% 
-  ggplot2::ggplot()+
-  ggplot2::geom_histogram(ggplot2::aes(nArgs), binwidth = 1,
-                 colour = "black",
-                 fill = "grey")+
-  ggplot2::theme_minimal()+
+gg_nArgs <- defFuns %>%
+  ggplot2::ggplot() +
+  ggplot2::geom_histogram(ggplot2::aes(nArgs),
+    binwidth = 1,
+    colour = "black",
+    fill = "grey"
+  ) +
+  ggplot2::theme_minimal() +
   ggplot2::xlab("Number of arguments")
 
-gg_size <- defFuns %>% 
-  ggplot2::ggplot()+
-  ggplot2::geom_histogram(ggplot2::aes(size), binwidth = 1,
-                 colour = "black",
-                 fill = "grey")+
-  ggplot2::theme_minimal()+
+gg_size <- defFuns %>%
+  ggplot2::ggplot() +
+  ggplot2::geom_histogram(ggplot2::aes(size),
+    binwidth = 1,
+    colour = "black",
+    fill = "grey"
+  ) +
+  ggplot2::theme_minimal() +
   ggplot2::xlab("Lines of code")
 
-gg_cycloComp <- defFuns %>% 
-  ggplot2::ggplot()+
-  ggplot2::geom_histogram(ggplot2::aes(cycloComp), binwidth = 1,
-                 colour = "black",
-                 fill = "grey")+
-  ggplot2::theme_minimal()+
+gg_cycloComp <- defFuns %>%
+  ggplot2::ggplot() +
+  ggplot2::geom_histogram(ggplot2::aes(cycloComp),
+    binwidth = 1,
+    colour = "black",
+    fill = "grey"
+  ) +
+  ggplot2::theme_minimal() +
   ggplot2::xlab("Cyclomatic complexity")
 
 cowplot::plot_grid(gg_nArgs, gg_size, gg_cycloComp, nrow = 3)
 ```
 
 ```{r, warning=FALSE, message=FALSE, echo=FALSE}
-p <- defFuns %>% 
-  ggplot2::ggplot(ggplot2::aes(group = name))+
-  ggplot2::geom_point(ggplot2::aes(size, cycloComp, 
-                          colour = nArgs),
-                      size = 3)+
-  ggplot2::scale_colour_gradient(name = "Number of\nargruments",
-                               low = "blue", high = "red")  +
+p <- defFuns %>%
+  ggplot2::ggplot(ggplot2::aes(group = name)) +
+  ggplot2::geom_point(
+    ggplot2::aes(size, cycloComp,
+      colour = nArgs
+    ),
+    size = 3
+  ) +
+  ggplot2::scale_colour_gradient(
+    name = "Number of\nargruments",
+    low = "blue", high = "red"
+  ) +
   ggplot2::theme_minimal() +
   ggplot2::xlab("Lines of code") +
   ggplot2::ylab("Cyclomatic complexity") +
   ggplot2::theme(legend.position = "top")
 
-  plotly::ggplotly(p,
-                  tooltip = c("group", "colour",
-                              "x", "y"))
+plotly::ggplotly(p,
+  tooltip = c(
+    "group", "colour",
+    "x", "y"
+  )
+)
 ```
 
 ## Function details
@@ -114,15 +139,17 @@ lineBreaks <- c(100, 200)
 
 DT::datatable(
   defFuns %>%
-    dplyr::mutate(file_start = paste0(.data$fileName, " (from line: ", lineStart, ")")) %>% 
-    dplyr::select("name", "nArgs", "size","cycloComp", "file_start") %>% 
+    dplyr::mutate(file_start = paste0(.data$fileName, " (from line: ", lineStart, ")")) %>%
+    dplyr::select("name", "nArgs", "size", "cycloComp", "file_start") %>%
     dplyr::rename(
       "Function" = "name",
       "Number of arguments" = "nArgs",
       "Lines of code" = "size",
       "Cyclomatic complexity" = "cycloComp",
-      "Location" = "file_start"),
-  rownames = FALSE) %>%
+      "Location" = "file_start"
+    ),
+  rownames = FALSE
+) %>%
   DT::formatStyle("Number of arguments", backgroundColor = DT::styleInterval(argBreaks, colours)) %>%
   DT::formatStyle("Cyclomatic complexity", backgroundColor = DT::styleInterval(complexBreaks, colours)) %>%
   DT::formatStyle("Lines of code", backgroundColor = DT::styleInterval(lineBreaks, colours))
@@ -132,7 +159,8 @@ DT::datatable(
 ```{r countLines, echo=FALSE}
 DT::datatable(
   PaRe::countPackageLines(repo),
-  rownames = "# lines of code")
+  rownames = "# lines of code"
+)
 ```
 
 ## Style adherence, syntax errors and possible semantic issues
@@ -140,19 +168,21 @@ DT::datatable(
 ```{r lintScores, message=FALSE, warning=FALSE, echo=FALSE}
 lintMsgs <- PaRe::lintRepo(repo)
 
-DT::datatable(PaRe::lintScore(repo, lintMsgs) %>% 
-                dplyr::rename("Percentage of lines assessed" = "pct"),
-              rownames = FALSE)
+DT::datatable(
+  PaRe::lintScore(repo, lintMsgs) %>%
+    dplyr::rename("Percentage of lines assessed" = "pct"),
+  rownames = FALSE
+)
 ```
 
 ### Warnings
 ```{r lintMessages warnings, message=FALSE, warning=FALSE, echo=FALSE}
 DT::datatable(
   lintMsgs %>%
-    dplyr::filter(type == "warning") %>% 
-  dplyr::group_by(message) %>%
-  dplyr::tally(sort = TRUE),
-              rownames= FALSE
+    dplyr::filter(type == "warning") %>%
+    dplyr::group_by(message) %>%
+    dplyr::tally(sort = TRUE),
+  rownames = FALSE
 )
 ```
 
@@ -160,10 +190,10 @@ DT::datatable(
 ```{r lintMessages style, message=FALSE, warning=FALSE, echo=FALSE}
 DT::datatable(
   lintMsgs %>%
-    dplyr::filter(type == "style") %>% 
-  dplyr::group_by(message) %>%
-  dplyr::tally(sort = TRUE),
-              rownames= FALSE
+    dplyr::filter(type == "style") %>%
+    dplyr::group_by(message) %>%
+    dplyr::tally(sort = TRUE),
+  rownames = FALSE
 )
 ```
 
@@ -181,13 +211,15 @@ DT::datatable(PaRe::checkDependencies(repo = repo, nThreads = 10))
 ```{r dependencyGraphStats, message=FALSE, warning=FALSE, echo=FALSE}
 graphData <- PaRe::getGraphData(repo = repo, nThreads = 10)
 
-DT::datatable(data.frame(
-  countVertices = length(igraph::V(graphData)),
-  countEdges = length(igraph::E(graphData)),
-  meanDegree = round(mean(igraph::degree(graphData)), 2),
-  meanDistance = round(mean(igraph::distances(graphData)), 2)
+DT::datatable(
+  data.frame(
+    countVertices = length(igraph::V(graphData)),
+    countEdges = length(igraph::E(graphData)),
+    meanDegree = round(mean(igraph::degree(graphData)), 2),
+    meanDistance = round(mean(igraph::distances(graphData)), 2)
   ),
-              rownames= FALSE)
+  rownames = FALSE
+)
 ```
 
 ### Function use per dependency
@@ -196,11 +228,12 @@ funsUsed <- PaRe::getFunctionUse(repo = repo)
 
 DT::datatable(
   funsUsed,
-  rownames = FALSE)
+  rownames = FALSE
+)
 ```
 
 ```{r plotFunctionUse, dpi=100, fig.height=25, out.width="100%", message=FALSE, warning=FALSE, echo=FALSE}
-function_sub <- funsUsed %>% 
+function_sub <- funsUsed %>%
   dplyr::filter(!pkg %in% c("base"))
 
 fun_counts <- function_sub %>%
@@ -212,16 +245,19 @@ nonPkgFuns <- fun_counts[!fun_counts$fun %in% defFuns$fun, ]
 
 ggplot2::ggplot(
   data = nonPkgFuns,
-  mapping = ggplot2::aes(x = .data$fun, y = .data$n, fill = .data$pkg)) +
+  mapping = ggplot2::aes(x = .data$fun, y = .data$n, fill = .data$pkg)
+) +
   ggplot2::geom_col() +
   ggplot2::facet_wrap(
     dplyr::vars(.data$pkg),
     scales = "free_x",
-    ncol = 2) +
+    ncol = 2
+  ) +
   ggplot2::theme_bw() +
   ggplot2::theme(
     legend.position = "none",
-    axis.text.x = (ggplot2::element_text(angle = 45, hjust = 1, vjust = 1)))
+    axis.text.x = (ggplot2::element_text(angle = 45, hjust = 1, vjust = 1))
+  )
 ```
 
 ## Further reading

From 0f274434ea86f490b1634e9b13487f047dd72a58 Mon Sep 17 00:00:00 2001
From: mvankessel-EMC <m.vankessel@mi-erasmusmc.nl>
Date: Wed, 4 Feb 2026 13:54:08 +0100
Subject: [PATCH 8/8] updated news

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 1bb4788..9f02ffb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,6 @@
 PaRe 0.1.16
 ==========
-1. Use `dplyr::reframe()` instead of `dplyr::summarise()`
+1. Use `dplyr::reframe()` instead of `dplyr::summarise()` for dplyr >= 1.2.0 compatability
 
 PaRe 0.1.15
 ==========