From 470bf1c1f0cdfb301f52364dc3c9848b49dcfcd0 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Fri, 29 Sep 2023 21:36:19 +0200
Subject: [PATCH 01/17] Add parsing issues to attributes dfs as problems

---
 R/read_camtrap_dp.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/read_camtrap_dp.R b/R/read_camtrap_dp.R
index aea7e58b..8a8e3f03 100644
--- a/R/read_camtrap_dp.R
+++ b/R/read_camtrap_dp.R
@@ -168,7 +168,11 @@ read_camtrap_dp <- function(file = NULL,
   check_package(package, media = media)
   
   # Inherit parsing issues from reading
+  attr(package$data$deployments, which = "problems") <- issues_deployments
   attr(package$data$observations, which = "problems") <- issues_observations
+  if (media) {
+    attr(package$data$media, which = "problems") <- issues_media
+  }
 
   return(package)
 }

From d653451b6cb4f01c50f04c2333df436211445ae7 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Fri, 29 Sep 2023 21:36:39 +0200
Subject: [PATCH 02/17] Bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 41bdb40b..c386a999 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: camtraptor
 Title: Read, Explore and Visualize Camera Trap Data Packages
-Version: 0.20.1
+Version: 0.20.2
 Authors@R: c(
     person("Damiano", "Oldoni", email = "damiano.oldoni@inbo.be",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),

From 3a0414d4e2dbccfceb557f3144c2e036c9a3d431 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Fri, 29 Sep 2023 21:58:00 +0200
Subject: [PATCH 03/17] Add tests for the dataframes with problems

---
 tests/testthat/test-read_camtrap_dp.R | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 48cd60c8..1bd0eb3c 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -48,7 +48,6 @@ test_that("test warnings while reading files with parsing issues", {
     package = "camtraptor"
   )
   w <- capture_warnings(
-    camtraptor::read_camtrap_dp(file = camtrap_dp_file_with_issues)
   )
   # warning on deployments
   expect_equal(
@@ -59,6 +58,12 @@ test_that("test warnings while reading files with parsing issues", {
       "`readr::problems()`."
     )
   )
+  problems_deploys <- readr::problems(dp_issues$data$deployments)
+  expect_equal(nrow(problems_deploys), 2)
+  expect_equal(problems_deploys$row, c(1,2))
+  expect_equal(problems_deploys$col, c(7,7))
+  expect_equal(problems_deploys$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
+  
   # warning on observations
   expect_equal(
     w[4], # w[3] is returned by readr via frictionless
@@ -68,6 +73,12 @@ test_that("test warnings while reading files with parsing issues", {
       "`readr::problems()`."
     )
   )
+  problems_obs <- readr::problems(dp_issues$data$observations)
+  expect_equal(nrow(problems_obs), 2)
+  expect_equal(problems_obs$row, c(1,2))
+  expect_equal(problems_obs$col, c(5,5))
+  expect_equal(problems_obs$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
+  
   # warning on media
   expect_equal(
     w[6], # w[5] is returned by readr via frictionless
@@ -77,6 +88,11 @@ test_that("test warnings while reading files with parsing issues", {
       "`readr::problems()`."
     )
   )
+  problems_media <- readr::problems(dp_issues$data$media)
+  expect_equal(nrow(problems_media), 1)
+  expect_equal(problems_media$row, 2)
+  expect_equal(problems_media$col, 5)
+  expect_equal(problems_media$expected, "date like %Y-%m-%dT%H:%M:%S%z")
 })
 
 test_that("media is checked properly", {

From d79224fd87f9e722425b4e6feb9d40a3c3b6df4a Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Fri, 29 Sep 2023 21:58:32 +0200
Subject: [PATCH 04/17] Assign to variable for checking problems

---
 tests/testthat/test-read_camtrap_dp.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 1bd0eb3c..021274be 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -48,6 +48,7 @@ test_that("test warnings while reading files with parsing issues", {
     package = "camtraptor"
   )
   w <- capture_warnings(
+    dp_issues <- camtraptor::read_camtrap_dp(file = camtrap_dp_file_with_issues)
   )
   # warning on deployments
   expect_equal(

From 0e2cb313611bf269a09cea09546ce532ca4ada08 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:24:00 +0200
Subject: [PATCH 05/17] Tests should be able to run in any order

init object if you are going to use it, or alternatively create it outside of a test in the beginning of this file.
---
 tests/testthat/test-read_camtrap_dp.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 021274be..5fa3727f 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -114,6 +114,12 @@ test_that("output is a list", {
     file = dp_path,
     media = FALSE
   ))
+  dp_v1_rc1_with_media <- suppressMessages(
+    read_camtrap_dp(path_to_json_v1rc1)
+  )
+  dp_v1_rc1_without_media <- suppressMessages(
+    read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
+  )
   expect_true(is.list(dp_without_media))
   expect_equal(class(dp_without_media), "list")
   expect_true(is.list(dp_v1_rc1_with_media))

From a4626db0b5e999689b69372f18938649c5e2b125 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:24:47 +0200
Subject: [PATCH 06/17] `expect_type` is easier to read than
 `expect_equal(class())`

---
 tests/testthat/test-read_camtrap_dp.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 5fa3727f..f0884ee8 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -121,11 +121,11 @@ test_that("output is a list", {
     read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
   )
   expect_true(is.list(dp_without_media))
-  expect_equal(class(dp_without_media), "list")
+  expect_type(dp_without_media, "list")
   expect_true(is.list(dp_v1_rc1_with_media))
-  expect_equal(class(dp_v1_rc1_with_media), "list")
+  expect_type(dp_v1_rc1_with_media, "list")
   expect_true(is.list(dp_v1_rc1_without_media))
-  expect_equal(class(dp_v1_rc1_without_media), "list")
+  expect_type(dp_v1_rc1_without_media, "list")
 })
 
 test_that("output data slot is a list of length 3", {

From fc8f00bfefccb1f91a7194bdda23d94f030ff0c5 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:31:17 +0200
Subject: [PATCH 07/17] init object in test so tests can run in any order

---
 tests/testthat/test-read_camtrap_dp.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index f0884ee8..4e9d7770 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -136,6 +136,9 @@ test_that("output data slot is a list of length 3", {
     file = dp_path,
     media = FALSE
   ))
+  dp_v1_rc1_without_media <- suppressMessages(
+    read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
+  )
   expect_true("data" %in% names(dp_without_media))
   expect_equal(length(dp_without_media$data), 3)
   expect_true("data" %in% names(dp_v1_rc1_with_media))

From 464c08e525b014eecaf74392fe6dffc524ede3d0 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:32:12 +0200
Subject: [PATCH 08/17] `expect_length()` is easier to read than
 `expect_equal(length())`

---
 tests/testthat/test-read_camtrap_dp.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 4e9d7770..e7e0d688 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -140,11 +140,11 @@ test_that("output data slot is a list of length 3", {
     read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
   )
   expect_true("data" %in% names(dp_without_media))
-  expect_equal(length(dp_without_media$data), 3)
+  expect_length(dp_without_media$data, 3)
   expect_true("data" %in% names(dp_v1_rc1_with_media))
-  expect_equal(length(dp_v1_rc1_with_media$data), 3)
+  expect_length(dp_v1_rc1_with_media$data, 3)
   expect_true("data" %in% names(dp_v1_rc1_without_media))
-  expect_equal(length(dp_v1_rc1_without_media$data), 3)
+  expect_length(dp_v1_rc1_without_media$data, 3)
 })
 
 test_that("media arg influences only slot media", {

From f5ac2fc189e834a13598a3c4454a1c126dd21401 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:35:12 +0200
Subject: [PATCH 09/17] init object if used, so tests can run in any order

---
 tests/testthat/test-read_camtrap_dp.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index e7e0d688..8378f64f 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -405,6 +405,9 @@ test_that(
       file = dp_path,
       media = FALSE
     ))
+    dp_v1_rc1_without_media <- suppressMessages(
+      read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
+    )
     cols_deployments_dp_v1_rc1 <- dp_v1_rc1_without_media$data$deployments %>%
       names()
     cols_deployments_dp_v0_1_6 <- dp_without_media$data$deployments %>%

From fbc890b40854f6ab7f75bd29fd988f11c5ed3fb8 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:35:27 +0200
Subject: [PATCH 10/17] increase test strictness, remove tolerance

---
 tests/testthat/test-read_camtrap_dp.R | 36 +++++++++++++--------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 8378f64f..fe1307b9 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -51,7 +51,7 @@ test_that("test warnings while reading files with parsing issues", {
     dp_issues <- camtraptor::read_camtrap_dp(file = camtrap_dp_file_with_issues)
   )
   # warning on deployments
-  expect_equal(
+  expect_identical(
     w[2], # w[1] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `deployments`. ",
@@ -60,13 +60,13 @@ test_that("test warnings while reading files with parsing issues", {
     )
   )
   problems_deploys <- readr::problems(dp_issues$data$deployments)
-  expect_equal(nrow(problems_deploys), 2)
-  expect_equal(problems_deploys$row, c(1,2))
-  expect_equal(problems_deploys$col, c(7,7))
-  expect_equal(problems_deploys$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
+  expect_identical(nrow(problems_deploys), 2L)
+  expect_identical(problems_deploys$row, c(1L,2L))
+  expect_identical(problems_deploys$col, c(7L,7L))
+  expect_identical(problems_deploys$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
   
   # warning on observations
-  expect_equal(
+  expect_identical(
     w[4], # w[3] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `observations`. ",
@@ -75,13 +75,13 @@ test_that("test warnings while reading files with parsing issues", {
     )
   )
   problems_obs <- readr::problems(dp_issues$data$observations)
-  expect_equal(nrow(problems_obs), 2)
-  expect_equal(problems_obs$row, c(1,2))
-  expect_equal(problems_obs$col, c(5,5))
-  expect_equal(problems_obs$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
+  expect_identical(nrow(problems_obs), 2L)
+  expect_identical(problems_obs$row, c(1L,2L))
+  expect_identical(problems_obs$col, c(5L,5L))
+  expect_identical(problems_obs$expected, rep("date like %Y-%m-%dT%H:%M:%S%z", 2))
   
   # warning on media
-  expect_equal(
+  expect_identical(
     w[6], # w[5] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `media`. ",
@@ -90,10 +90,10 @@ test_that("test warnings while reading files with parsing issues", {
     )
   )
   problems_media <- readr::problems(dp_issues$data$media)
-  expect_equal(nrow(problems_media), 1)
-  expect_equal(problems_media$row, 2)
-  expect_equal(problems_media$col, 5)
-  expect_equal(problems_media$expected, "date like %Y-%m-%dT%H:%M:%S%z")
+  expect_identical(nrow(problems_media), 1L)
+  expect_identical(problems_media$row, 2L)
+  expect_identical(problems_media$col, 5L)
+  expect_identical(problems_media$expected, "date like %Y-%m-%dT%H:%M:%S%z")
 })
 
 test_that("media is checked properly", {
@@ -360,7 +360,7 @@ test_that(
   "read deployments v1.0-rc1: baitUse is a factor, not a boolean", {
     expect_s3_class(dp_v1_rc1_with_media$data$deployments$baitUse, "factor")
     baitUse_levels <- c("none", "scent", "food", "visual", "acoustic", "other")
-    expect_equal(
+    expect_identical(
       levels(dp_v1_rc1_with_media$data$deployments$baitUse), baitUse_levels
     )
     # boolean NA becomes a factor NA
@@ -412,7 +412,7 @@ test_that(
       names()
     cols_deployments_dp_v0_1_6 <- dp_without_media$data$deployments %>%
       names()
-    expect_equal(cols_deployments_dp_v0_1_6, cols_deployments_dp_v1_rc1)
+    expect_identical(cols_deployments_dp_v0_1_6, cols_deployments_dp_v1_rc1)
   }
 )
 
@@ -602,6 +602,6 @@ test_that(
       names()
     cols_media_dp_v0_1_6 <- dp_with_media$data$media %>%
       names()
-    expect_equal(cols_media_dp_v1_rc1, cols_media_dp_v0_1_6)
+    expect_identical(cols_media_dp_v1_rc1, cols_media_dp_v0_1_6)
   }
 )

From 57146c33d252bc94b66a7922b957f8e74d55685f Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:39:41 +0200
Subject: [PATCH 11/17] move object creation needed for tests to start of file,
 remove inits from individual tests

---
 tests/testthat/test-read_camtrap_dp.R | 33 ++++++++++-----------------
 1 file changed, 12 insertions(+), 21 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index fe1307b9..c6160f07 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -1,3 +1,12 @@
+## read camera trap data package from v1.0-rc1
+path_to_json_v1rc1 <- "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0-rc.1/example/datapackage.json"
+dp_v1_rc1_with_media <- suppressMessages(
+  read_camtrap_dp(path_to_json_v1rc1)
+)
+dp_v1_rc1_without_media <- suppressMessages(
+  read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
+)
+
 test_that("file argument is checked properly", {
   expect_error(read_camtrap_dp("aaa"))
   expect_error(read_camtrap_dp(1))
@@ -31,15 +40,6 @@ test_that("only DP versions 1.0-rc.1 and dp 0.1.6 are supported", {
   )
 })
 
-## read camera trap data package from v1.0-rc1
-path_to_json_v1rc1 <- "https://raw.githubusercontent.com/tdwg/camtrap-dp/1.0-rc.1/example/datapackage.json"
-dp_v1_rc1_with_media <- suppressMessages(
-  read_camtrap_dp(path_to_json_v1rc1)
-)
-dp_v1_rc1_without_media <- suppressMessages(
-  read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
-)
-
 test_that("test warnings while reading files with parsing issues", {
   local_edition(2)
   camtrap_dp_file_with_issues <- system.file(
@@ -114,12 +114,7 @@ test_that("output is a list", {
     file = dp_path,
     media = FALSE
   ))
-  dp_v1_rc1_with_media <- suppressMessages(
-    read_camtrap_dp(path_to_json_v1rc1)
-  )
-  dp_v1_rc1_without_media <- suppressMessages(
-    read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
-  )
+  
   expect_true(is.list(dp_without_media))
   expect_type(dp_without_media, "list")
   expect_true(is.list(dp_v1_rc1_with_media))
@@ -136,9 +131,7 @@ test_that("output data slot is a list of length 3", {
     file = dp_path,
     media = FALSE
   ))
-  dp_v1_rc1_without_media <- suppressMessages(
-    read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
-  )
+
   expect_true("data" %in% names(dp_without_media))
   expect_length(dp_without_media$data, 3)
   expect_true("data" %in% names(dp_v1_rc1_with_media))
@@ -405,9 +398,7 @@ test_that(
       file = dp_path,
       media = FALSE
     ))
-    dp_v1_rc1_without_media <- suppressMessages(
-      read_camtrap_dp(path_to_json_v1rc1, media = FALSE)
-    )
+
     cols_deployments_dp_v1_rc1 <- dp_v1_rc1_without_media$data$deployments %>%
       names()
     cols_deployments_dp_v0_1_6 <- dp_without_media$data$deployments %>%

From 1b749cd1ba692b9860640ddb611f4124a32f9fc2 Mon Sep 17 00:00:00 2001
From: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
Date: Mon, 2 Oct 2023 11:50:37 +0200
Subject: [PATCH 12/17] use glue::glue to collapse instead of writeLines, so we
 can suppress this message in tests

---
 R/zzz.R | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/R/zzz.R b/R/zzz.R
index cb886e00..fa012d91 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -462,12 +462,11 @@ convert_to_0.1.6 <- function(package, from = "1.0-rc.1", media = TRUE){
   
   # notify about conversion
   message(
-    writeLines(
-      c(
+    glue::glue(
         "The dataset uses Camtrap DP version 1.0-rc.1, it has been converted to 0.1.6.",
-        "See https://inbo.github.io/camtraptor/#camtrap-dp for details."
+        "See https://inbo.github.io/camtraptor/#camtrap-dp for details.",
+        .seq = "\n"
       )
-    )
   )
   # convert metadata
   package <- convert_metadata_to_0.1.6(package, from)  

From 49272246acd506bc259f038174c60b819d8237fb Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 8 Nov 2023 15:26:55 +0100
Subject: [PATCH 13/17] Remove windows-latest with R3.6.3

---
 .github/workflows/R-CMD-check.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 38221a8e..ff1dc0c6 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -29,7 +29,6 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: '3.6.3'}
-          - {os: windows-latest, r: '3.6.0'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

From 161339c6e4c7b718c3ab7f351f0d15d05f465090 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 16:32:04 +0100
Subject: [PATCH 14/17] Add camtraptor:: in what arg in lifecycle

This should avoid returning an error while running covr as found by @PietrH.

Co-Authored-By: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
---
 R/read_camtrap_dp.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/read_camtrap_dp.R b/R/read_camtrap_dp.R
index 4d6b2384..2337fa45 100644
--- a/R/read_camtrap_dp.R
+++ b/R/read_camtrap_dp.R
@@ -58,7 +58,7 @@ read_camtrap_dp <- function(file = NULL,
   if (lifecycle::is_present(path) | (!is.null(file) && dir.exists(file))) {
     lifecycle::deprecate_warn(
       when = "0.6.0",
-      what = "read_camtrap_dp(path)",
+      what = "camtraptor::read_camtrap_dp(path)",
       details = warning_detail
     )
   }

From 6860d5e43b1cc91b7e4b454f475847d9ba96ae64 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 16:35:34 +0100
Subject: [PATCH 15/17] Use captured_warnings instead of w

Co-Authored-By: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
---
 tests/testthat/test-read_camtrap_dp.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index de2ed3e3..aee3e39f 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -49,12 +49,12 @@ test_that("test warnings while reading files with parsing issues", {
     "datapackage_for_parsing_issues.json", 
     package = "camtraptor"
   )
-  w <- capture_warnings(
+  captured_warnings <- capture_warnings(
     dp_issues <- camtraptor::read_camtrap_dp(file = camtrap_dp_file_with_issues)
   )
   # warning on deployments
   expect_identical(
-    w[2], # w[1] is returned by readr via frictionless
+    captured_warnings[2], # captured_warnings[1] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `deployments`. ",
       "Check `?read_camtrap_dp()` for examples on how to use ",

From e9e94e7193623c6ec7aad106aeecc4ac14eab34d Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 16:46:39 +0100
Subject: [PATCH 16/17] Replace w with captured_warnings where forgotten

Co-Authored-By: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
---
 tests/testthat/test-read_camtrap_dp.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index aee3e39f..1816392d 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -70,7 +70,7 @@ test_that("test warnings while reading files with parsing issues", {
   
   # warning on observations
   expect_identical(
-    w[4], # w[3] is returned by readr via frictionless
+    captured_warnings[4], # captured_warnings[3] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `observations`. ",
       "Check `?read_camtrap_dp()` for examples on how to use ",
@@ -85,7 +85,7 @@ test_that("test warnings while reading files with parsing issues", {
   
   # warning on media
   expect_identical(
-    w[6], # w[5] is returned by readr via frictionless
+    captured_warnings[6], # captured_warnings[5] is returned by readr via frictionless
     paste0(
       "One or more parsing issues occurred while reading `media`. ",
       "Check `?read_camtrap_dp()` for examples on how to use ",

From 36960137729a1b1f9e6f14a973abe9583a887818 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Thu, 9 Nov 2023 16:46:54 +0100
Subject: [PATCH 17/17] Add check about number of warnings

Co-Authored-By: Pieter Huybrechts <48065851+PietrH@users.noreply.github.com>
---
 tests/testthat/test-read_camtrap_dp.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/testthat/test-read_camtrap_dp.R b/tests/testthat/test-read_camtrap_dp.R
index 1816392d..7b6d9da9 100644
--- a/tests/testthat/test-read_camtrap_dp.R
+++ b/tests/testthat/test-read_camtrap_dp.R
@@ -52,6 +52,10 @@ test_that("test warnings while reading files with parsing issues", {
   captured_warnings <- capture_warnings(
     dp_issues <- camtraptor::read_camtrap_dp(file = camtrap_dp_file_with_issues)
   )
+  
+  # check number of warnings
+  expect_length(captured_warnings, 6)
+  
   # warning on deployments
   expect_identical(
     captured_warnings[2], # captured_warnings[1] is returned by readr via frictionless