From feeb9410b55df019ff71a25458bc6641f8138d06 Mon Sep 17 00:00:00 2001
From: Ming Liu <mingl@uchicago.edu>
Date: Mon, 27 Mar 2023 10:29:10 -0400
Subject: [PATCH 01/11] Added new example_dataset and used it in the example
 for the euclideanDist function

---
 .Rbuildignore           |  4 ++++
 .gitignore              |  4 ++++
 DESCRIPTION             |  2 +-
 NAMESPACE               |  1 +
 R/data.R                | 11 +++++++++++
 data-raw/example_data.R |  6 ++++++
 6 files changed, 27 insertions(+), 1 deletion(-)
 create mode 100644 R/data.R
 create mode 100644 data-raw/example_data.R

diff --git a/.Rbuildignore b/.Rbuildignore
index 88b0533..f03f591 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
@@ -6,3 +8,5 @@
 ^docs$
 ^pkgdown$
 ^\.lintr$
+renv*
+^data-raw$
diff --git a/.gitignore b/.gitignore
index 0dddc4b..44bf24f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,10 @@
 .Rhistory
 .Rapp.history
 
+# R things
+.Rprofile
+renv/
+
 # Session Data files
 .RData
 
diff --git a/DESCRIPTION b/DESCRIPTION
index e2161da..44e2b55 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Encoding: UTF-8
 biocViews: Clustering
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Suggests: 
     knitr,
     rmarkdown,
diff --git a/NAMESPACE b/NAMESPACE
index 01843dc..6bd620a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(euclideanDist)
 export(hello)
diff --git a/R/data.R b/R/data.R
new file mode 100644
index 0000000..15bcc79
--- /dev/null
+++ b/R/data.R
@@ -0,0 +1,11 @@
+#' Example dataset
+#'
+#' A dataset containing a matrix with two columns that were generated
+#' with a random normal distribution with a mean of 0 and stdev of 1. 
+#'
+#' @format A matrix with 100 rows and 2 columns
+#' @keywords datasets
+#' @usage data("example_data")
+#' @examples
+#' data("example_data")
+"example_data"
diff --git a/data-raw/example_data.R b/data-raw/example_data.R
new file mode 100644
index 0000000..9adb098
--- /dev/null
+++ b/data-raw/example_data.R
@@ -0,0 +1,6 @@
+## code to prepare `example_data` dataset goes here
+set.seed(123)
+a <- rnorm(100)
+b <- rnorm(100)
+example_data <- cbind(a, b)
+usethis::use_data(example_data, overwrite = TRUE)
\ No newline at end of file

From 191ecefed4643edfc03f7ee2faa6fb63f6cd14f5 Mon Sep 17 00:00:00 2001
From: Ming Liu <mingl@uchicago.edu>
Date: Mon, 27 Mar 2023 10:30:58 -0400
Subject: [PATCH 02/11] added new example dataset and used it in the example
 for the euclidianDist function

---
 R/distance.R         |  31 ++
 man/euclideanDist.Rd |  25 ++
 renv.lock            | 854 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 910 insertions(+)
 create mode 100644 R/distance.R
 create mode 100644 man/euclideanDist.Rd
 create mode 100644 renv.lock

diff --git a/R/distance.R b/R/distance.R
new file mode 100644
index 0000000..b55d3e4
--- /dev/null
+++ b/R/distance.R
@@ -0,0 +1,31 @@
+#' @title Euclidean distance
+#' @description Calculates Euclidean distance between two vectors. An error will be 
+#' given if NAs are present in either vector.
+#'
+#' @param a The first vector to use in the distance calculation.
+#' @param b The second vector to use in the distance calculation.
+#' @param verbose Boolean. If \code{TRUE}, a message will be printed. Default \code{TRUE}.
+#' @return A numeric value of a distance#' 
+#' @examples
+#' data(example_data)
+#' euclideanDist(example_data[,1], example_data[,2], verbose = FALSE)
+#' @export
+euclideanDist <- function(a, b, verbose = FALSE) {
+  if (isTRUE(verbose)) {
+    message("Calculating distance ...")
+  }
+  
+  # Check validity of data
+  .check_data(a)
+  .check_data(b)
+  
+  # Perform calculation
+  res <- sqrt(sum((a-b)^2))
+  return(res)
+}
+
+.check_data <- function(input) {
+  if (any(is.na(input))) {
+    stop("'input' must not contain NAs")
+  }
+}
\ No newline at end of file
diff --git a/man/euclideanDist.Rd b/man/euclideanDist.Rd
new file mode 100644
index 0000000..f5e51f4
--- /dev/null
+++ b/man/euclideanDist.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/distance.R
+\name{euclideanDist}
+\alias{euclideanDist}
+\title{Euclidean distance}
+\usage{
+euclideanDist(a, b, verbose = FALSE)
+}
+\arguments{
+\item{a}{The first vector to use in the distance calculation.}
+
+\item{b}{The second vector to use in the distance calculation.}
+
+\item{verbose}{Boolean. If \code{TRUE}, a message will be printed. Default \code{TRUE}.}
+}
+\value{
+A numeric value of a distance
+}
+\description{
+Calculates Euclidean distance between two vectors. An error will be
+given if NAs are present in either vector.
+}
+\examples{
+euclideanDist(c(1, 2), c(2, 3), verbose = FALSE)
+}
diff --git a/renv.lock b/renv.lock
new file mode 100644
index 0000000..75b8717
--- /dev/null
+++ b/renv.lock
@@ -0,0 +1,854 @@
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+      "Package": "rmarkdown",
+      "Version": "2.21",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bslib",
+        "evaluate",
+        "fontawesome",
+        "htmltools",
+        "jquerylib",
+        "jsonlite",
+        "knitr",
+        "methods",
+        "stringr",
+        "tinytex",
+        "tools",
+        "utils",
+        "xfun",
+        "yaml"
+      ],
+      "Hash": "493df4ae51e2e984952ea4d5c75786a3"
+    },
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+        "R6",
+        "fs",
+        "htmltools",
+        "rappdirs",
+        "rlang"
+      ],
+      "Hash": "2bb4371a4c80115518261866eab6ab11"
+    },
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+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "stats",
+        "tools",
+        "utils"
+      ],
+      "Hash": "ca8bd84263c77310739d2cf64d84d7c9"
+    },
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+      "Package": "stringr",
+      "Version": "1.5.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "magrittr",
+        "rlang",
+        "stringi",
+        "vctrs"
+      ],
+      "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8"
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+        "digest",
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+        "evaluate",
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+        "processx",
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+        "withr"
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+        "pkgconfig",
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+        "utils",
+        "vctrs"
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+      "Repository": "CRAN",
+      "Requirements": [
+        "xfun"
+      ],
+      "Hash": "c0f007e2eeed7722ce13d42b84a22e07"
+    },
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+      "Package": "utf8",
+      "Version": "1.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "1fe17157424bb09c48a8b3b550c753bc"
+    },
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+      "Package": "vctrs",
+      "Version": "0.6.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "glue",
+        "lifecycle",
+        "rlang"
+      ],
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+    },
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+      "Requirements": [
+        "cli",
+        "diffobj",
+        "fansi",
+        "glue",
+        "methods",
+        "rematch2",
+        "rlang",
+        "tibble"
+      ],
+      "Hash": "035fba89d0c86e2113120f93301b98ad"
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+    },
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+      "Package": "withr",
+      "Version": "2.5.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "graphics",
+        "stats"
+      ],
+      "Hash": "c0e49a9760983e81e55cdd9be92e7182"
+    },
+    "xfun": {
+      "Package": "xfun",
+      "Version": "0.38",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "stats",
+        "tools"
+      ],
+      "Hash": "1ed71215d45e85562d3b1b29a068ccec"
+    },
+    "xml2": {
+      "Package": "xml2",
+      "Version": "1.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "methods"
+      ],
+      "Hash": "40682ed6a969ea5abfd351eb67833adc"
+    },
+    "yaml": {
+      "Package": "yaml",
+      "Version": "2.3.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+    }
+  }
+}

From 0ecc7ec077a1eb1d3084e9355251430703da2d07 Mon Sep 17 00:00:00 2001
From: Ming Liu <mingl@uchicago.edu>
Date: Mon, 27 Mar 2023 12:32:58 -0400
Subject: [PATCH 03/11] finished tutorial

---
 DESCRIPTION                    |   4 +-
 NEWS.md                        |   3 +
 R/data.R                       |   2 +-
 R/distance.R                   |   6 +-
 _pkgdown.yml                   |   4 +
 data-raw/example_data.R        |   1 +
 data/example_data.rda          | Bin 0 -> 2016 bytes
 man/euclideanDist.Rd           |   3 +-
 man/example_data.Rd            |  20 +++++
 renv.lock                      | 136 +++++++++++++++++++++++++++++++++
 tests/testthat.R               |   8 ++
 tests/testthat/test-distance.R |  14 ++++
 vignettes/DevelExample.Rmd     |  12 +++
 13 files changed, 207 insertions(+), 6 deletions(-)
 create mode 100644 data/example_data.rda
 create mode 100644 man/example_data.Rd
 create mode 100644 tests/testthat/test-distance.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 44e2b55..5884c4a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DevelExample
 Title: A Basic R Package to Demonstrate a Cycle of Code Development
-Version: 0.0.1
+Version: 0.1.0
 Authors@R: 
     person(given = "Joshua",
            family = "Campbell",
@@ -22,3 +22,5 @@ Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 VignetteBuilder: knitr
+Depends: 
+    R (>= 2.10)
diff --git a/NEWS.md b/NEWS.md
index 4cd8ae2..86504fb 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,6 @@
+# Changes in Version 0.1.0 (2022-05-20)
+* Added function to calculate euclidean distance
+
 # Changes in Version 0.0.1 (2022-05-08)
 * Created package
 * Added Hello World function
diff --git a/R/data.R b/R/data.R
index 15bcc79..be00067 100644
--- a/R/data.R
+++ b/R/data.R
@@ -8,4 +8,4 @@
 #' @usage data("example_data")
 #' @examples
 #' data("example_data")
-"example_data"
+"example_data"
\ No newline at end of file
diff --git a/R/distance.R b/R/distance.R
index b55d3e4..e7f644f 100644
--- a/R/distance.R
+++ b/R/distance.R
@@ -1,11 +1,11 @@
 #' @title Euclidean distance
-#' @description Calculates Euclidean distance between two vectors. An error will be 
+#' @description Calculates Euclidean distance between two vectors. An error will be
 #' given if NAs are present in either vector.
 #'
 #' @param a The first vector to use in the distance calculation.
 #' @param b The second vector to use in the distance calculation.
 #' @param verbose Boolean. If \code{TRUE}, a message will be printed. Default \code{TRUE}.
-#' @return A numeric value of a distance#' 
+#' @return A numeric value of a distance
 #' @examples
 #' data(example_data)
 #' euclideanDist(example_data[,1], example_data[,2], verbose = FALSE)
@@ -20,7 +20,7 @@ euclideanDist <- function(a, b, verbose = FALSE) {
   .check_data(b)
   
   # Perform calculation
-  res <- sqrt(sum((a-b)^2))
+  res <- sqrt(sum((a - b) ^ 2))
   return(res)
 }
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index e69de29..d71acfb 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+
diff --git a/data-raw/example_data.R b/data-raw/example_data.R
index 9adb098..beb2a6e 100644
--- a/data-raw/example_data.R
+++ b/data-raw/example_data.R
@@ -1,4 +1,5 @@
 ## code to prepare `example_data` dataset goes here
+
 set.seed(123)
 a <- rnorm(100)
 b <- rnorm(100)
diff --git a/data/example_data.rda b/data/example_data.rda
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diff --git a/man/euclideanDist.Rd b/man/euclideanDist.Rd
index f5e51f4..ed10e85 100644
--- a/man/euclideanDist.Rd
+++ b/man/euclideanDist.Rd
@@ -21,5 +21,6 @@ Calculates Euclidean distance between two vectors. An error will be
 given if NAs are present in either vector.
 }
 \examples{
-euclideanDist(c(1, 2), c(2, 3), verbose = FALSE)
+data(example_data)
+euclideanDist(example_data[,1], example_data[,2], verbose = FALSE)
 }
diff --git a/man/example_data.Rd b/man/example_data.Rd
new file mode 100644
index 0000000..e724347
--- /dev/null
+++ b/man/example_data.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{example_data}
+\alias{example_data}
+\title{Example dataset}
+\format{
+A matrix with 100 rows and 2 columns
+}
+\usage{
+data("example_data")
+}
+\description{
+A dataset containing a matrix with two columns that were generated
+with a random normal distribution with a mean of 0 and stdev of 1.
+}
+\examples{
+data("example_data")
+}
+\keyword{datasets}
diff --git a/renv.lock b/renv.lock
index 75b8717..14a3242 100644
--- a/renv.lock
+++ b/renv.lock
@@ -121,6 +121,16 @@
       ],
       "Hash": "89e6d8219950eac806ae0c489052048a"
     },
+    "clipr": {
+      "Package": "clipr",
+      "Version": "0.8.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "utils"
+      ],
+      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
+    },
     "cpp11": {
       "Package": "cpp11",
       "Version": "0.4.3",
@@ -140,6 +150,20 @@
       ],
       "Hash": "e8a1e41acf02548751f45c718d55aa6a"
     },
+    "credentials": {
+      "Package": "credentials",
+      "Version": "1.3.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "askpass",
+        "curl",
+        "jsonlite",
+        "openssl",
+        "sys"
+      ],
+      "Hash": "93762d0a34d78e6a025efdbfb5c6bb41"
+    },
     "curl": {
       "Package": "curl",
       "Version": "5.0.0",
@@ -274,6 +298,47 @@
       ],
       "Hash": "f4dcd23b67e33d851d2079f703e8b985"
     },
+    "gert": {
+      "Package": "gert",
+      "Version": "1.9.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "askpass",
+        "credentials",
+        "openssl",
+        "rstudioapi",
+        "sys",
+        "zip"
+      ],
+      "Hash": "9122b3958e749badb5c939f498038b57"
+    },
+    "gh": {
+      "Package": "gh",
+      "Version": "1.4.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "gitcreds",
+        "httr2",
+        "ini",
+        "jsonlite",
+        "rlang"
+      ],
+      "Hash": "03533b1c875028233598f848fda44c4c"
+    },
+    "gitcreds": {
+      "Package": "gitcreds",
+      "Version": "0.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe"
+    },
     "glue": {
       "Package": "glue",
       "Version": "1.6.2",
@@ -328,6 +393,32 @@
       ],
       "Hash": "f6844033201269bec3ca0097bc6c97b3"
     },
+    "httr2": {
+      "Package": "httr2",
+      "Version": "0.2.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "R6",
+        "cli",
+        "curl",
+        "glue",
+        "magrittr",
+        "openssl",
+        "rappdirs",
+        "rlang",
+        "withr"
+      ],
+      "Hash": "5c09fe33064978ede54de42309c8b532"
+    },
+    "ini": {
+      "Package": "ini",
+      "Version": "0.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "6154ec2223172bce8162d4153cda21f7"
+    },
     "jquerylib": {
       "Package": "jquerylib",
       "Version": "0.1.4",
@@ -627,6 +718,13 @@
       ],
       "Hash": "1de7ab598047a87bba48434ba35d497d"
     },
+    "rstudioapi": {
+      "Package": "rstudioapi",
+      "Version": "0.14",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "690bd2acc42a9166ce34845884459320"
+    },
     "sass": {
       "Package": "sass",
       "Version": "0.4.5",
@@ -760,6 +858,37 @@
       ],
       "Hash": "c0f007e2eeed7722ce13d42b84a22e07"
     },
+    "usethis": {
+      "Package": "usethis",
+      "Version": "2.1.6",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cli",
+        "clipr",
+        "crayon",
+        "curl",
+        "desc",
+        "fs",
+        "gert",
+        "gh",
+        "glue",
+        "jsonlite",
+        "lifecycle",
+        "purrr",
+        "rappdirs",
+        "rlang",
+        "rprojroot",
+        "rstudioapi",
+        "stats",
+        "utils",
+        "whisker",
+        "withr",
+        "yaml"
+      ],
+      "Hash": "a67a22c201832b12c036cc059f1d137d"
+    },
     "utf8": {
       "Package": "utf8",
       "Version": "1.2.3",
@@ -849,6 +978,13 @@
       "Source": "Repository",
       "Repository": "CRAN",
       "Hash": "0d0056cc5383fbc240ccd0cb584bf436"
+    },
+    "zip": {
+      "Package": "zip",
+      "Version": "2.2.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "c42bfcec3fa6a0cce17ce1f8bc684f88"
     }
   }
 }
diff --git a/tests/testthat.R b/tests/testthat.R
index 35ab969..94ef759 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,3 +1,11 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
 library(testthat)
 library(DevelExample)
 
diff --git a/tests/testthat/test-distance.R b/tests/testthat/test-distance.R
new file mode 100644
index 0000000..36f50a2
--- /dev/null
+++ b/tests/testthat/test-distance.R
@@ -0,0 +1,14 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})
+
+
+library("DevelExample")
+data(example_data)
+
+test_that("Testing euclideanDist function", {
+  res <- dist(rbind(example_data[,1], example_data[,2]))[1]
+  expect_equal(euclideanDist(example_data[,1], example_data[,2]), res)
+  
+  expect_error(euclideanDist(c(1, 2), c(NA, 2)), regexp = "contain NAs")
+})
\ No newline at end of file
diff --git a/vignettes/DevelExample.Rmd b/vignettes/DevelExample.Rmd
index 170fadb..86007ac 100644
--- a/vignettes/DevelExample.Rmd
+++ b/vignettes/DevelExample.Rmd
@@ -40,3 +40,15 @@ It is usually a good idea to show the session information to help with reproduci
 sessionInfo()
 ```
 
+
+To calculate the euclidean distance between two vectors, we can use the `euclideanDist` function. In this example we will generate two random vectors from normal distributions with two different means and calculate the distance between them:
+
+```{r dist}
+set.seed(12345)
+v1 <- rnorm(10000, mean = 1)
+v2 <- rnorm(10000, mean = 2)
+res <- euclideanDist(v1, v2, verbose = FALSE)
+res
+```
+
+The `set.seed` function is used for the random number generator and ensures the same vectors will be produced each time for reproducibility.
\ No newline at end of file

From c3b88ca41ed26e28e11ebd1eab0404c888f30e0e Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Mon, 27 Mar 2023 13:37:12 -0400
Subject: [PATCH 04/11] Update R-CMD-check.yaml

updated to v2
---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d9de82f..836d04e 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -45,7 +45,7 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}

From 114acdd2fe6ad873b3239034d0ad0c558b01d307 Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Mon, 27 Mar 2023 13:38:15 -0400
Subject: [PATCH 05/11] Update lint.yaml

updated to rv2
---
 .github/workflows/lint.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 6388f75..9d66461 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -16,11 +16,11 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: lintr
 

From 6cbbee4ebf26cb0b5a959fecd2a8be8d1e2285fc Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 08:48:33 -0400
Subject: [PATCH 06/11] Update R-CMD-check.yaml

---
 .github/workflows/R-CMD-check.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 836d04e..be5b617 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -51,11 +51,11 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: rcmdcheck, knitr
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
 
       - name: Show testthat output
         if: always()

From b170dea20e2edfd50442f179edd91439281ff6eb Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 09:12:54 -0400
Subject: [PATCH 07/11] Update R-CMD-check.yaml

---
 .github/workflows/R-CMD-check.yaml | 12 +++++-------
 1 file changed, 5 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index be5b617..4a4036a 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -29,12 +29,10 @@ jobs:
           - {os: windows-latest, r: '3.6'}
 
           # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-18.04,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-18.04,   r: 'release'}
-          - {os: ubuntu-18.04,   r: 'oldrel-1'}
-          - {os: ubuntu-18.04,   r: 'oldrel-2'}
-          - {os: ubuntu-18.04,   r: 'oldrel-3'}
-          - {os: ubuntu-18.04,   r: 'oldrel-4'}
+          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04,   r: 'release'}
+          - {os: ubuntu-20.04,   r: 'oldrel-1'}
+          - {os: ubuntu-20.04,   r: 'oldrel-2'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -43,7 +41,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:

From 7a1aac286a91660ce09e66f0b18b793a3843e827 Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 09:27:32 -0400
Subject: [PATCH 08/11] Update BioC-check.yaml

updated depreciated versions
---
 .github/workflows/BioC-check.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/BioC-check.yaml b/.github/workflows/BioC-check.yaml
index cd13eff..659030e 100644
--- a/.github/workflows/BioC-check.yaml
+++ b/.github/workflows/BioC-check.yaml
@@ -25,17 +25,17 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: rcmdcheck, BiocManager
 

From 515dffc10242f41bad2c11ada51bf15d662ecd73 Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 09:28:52 -0400
Subject: [PATCH 09/11] Update lint.yaml

---
 .github/workflows/lint.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 9d66461..efad6b6 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -25,5 +25,5 @@ jobs:
           extra-packages: lintr
 
       - name: Lint
-        run: lintr::lint_package()
+        run: lintr::lint_package(path = ".")
         shell: Rscript {0}

From 624b533ef026f5eb0e0bb9bcefac5157b4ab28f9 Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 09:33:52 -0400
Subject: [PATCH 10/11] Update R-CMD-check.yaml

updated to checkout v3
---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 4a4036a..ea8af59 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -39,7 +39,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

From ef92a125c3602cd30f4fb6584fb85bba403aa6ea Mon Sep 17 00:00:00 2001
From: mingl1997 <129070787+mingl1997@users.noreply.github.com>
Date: Tue, 28 Mar 2023 09:50:58 -0400
Subject: [PATCH 11/11] Update lint.yaml

---
 .github/workflows/lint.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index efad6b6..530929c 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -25,5 +25,5 @@ jobs:
           extra-packages: lintr
 
       - name: Lint
-        run: lintr::lint_package(path = ".")
+        run: lintr::lint_package(linters = lintr::linters_with_defaults(object_name_linter = lintr::object_name_linter("camelCase")))
         shell: Rscript {0}