From cc6a9f5c9545bbf3e81f586388cfd261f69b63af Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 12:16:03 +0200
Subject: [PATCH 01/14] replaces qc files with dv.templates ones

---
 .github/workflows/test.yml | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 10e227a..7cb3125 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -33,6 +33,33 @@ jobs:
             inst/validation
           path: templates
 
+      - name: Overwrite quality control scripts with dv.templates ones 🧹
+        run: |
+          # Paths to the directories
+          TEMPLATE_DIR="templates/inst/validation"
+          REPO_DIR="inst/validation"
+          
+          # Run the diff command and capture the output
+          DIFF_OUTPUT=$(diff -qr "$TEMPLATE_DIR" "$REPO_DIR")
+
+          echo "# Quality control files" | tee -a $GITHUB_STEP_SUMMARY
+          
+          # Check if the diff command found any differences
+          if [ -n "$DIFF_OUTPUT" ]; then
+            echo "Warning: The contents of the directories are different!" | tee -a $GITHUB_STEP_SUMMARY
+            echo "Modified files:" | tee -a $GITHUB_STEP_SUMMARY
+            echo "$DIFF_OUTPUT" | tee -a $GITHUB_STEP_SUMMARY
+          else
+            echo "The directories are identical." | tee -a $GITHUB_STEP_SUMMARY
+          fi
+
+          # Always overwrite
+
+          rm -rf "$REPO_DIR"/*
+
+          # Move contents of REPO_DIR to TEMPLATE_DIR
+          mv "$TEMPLATE_DIR"/* "$REPO_DIR"
+
       - name: Install package dependencies 📄
         uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main     
 

From dda6d414f618064a109867805ebb0e750f8f8799 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 12:36:48 +0200
Subject: [PATCH 02/14] add pkgdown examples to qc documentation

---
 .../pkgdown_examples/vignettes/_pkgdown.yml   | 18 +++++++++++
 .../pkgdown_examples/vignettes/qc.Rmd         | 32 +++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100644 inst/validation/pkgdown_examples/vignettes/_pkgdown.yml
 create mode 100644 inst/validation/pkgdown_examples/vignettes/qc.Rmd

diff --git a/inst/validation/pkgdown_examples/vignettes/_pkgdown.yml b/inst/validation/pkgdown_examples/vignettes/_pkgdown.yml
new file mode 100644
index 0000000..bb1ae5e
--- /dev/null
+++ b/inst/validation/pkgdown_examples/vignettes/_pkgdown.yml
@@ -0,0 +1,18 @@
+template:
+  bootstrap: 5
+  
+navbar:
+  type: inverted
+  structure:
+    left: [intro, reference, articles, tutorials, news, qc]
+  components:
+    qc:
+      text: Quality Control
+      href: articles/qc.html  
+
+articles:
+
+- title: Quality Control
+  desc: Quality Control
+  contents:
+  - qc
diff --git a/inst/validation/pkgdown_examples/vignettes/qc.Rmd b/inst/validation/pkgdown_examples/vignettes/qc.Rmd
new file mode 100644
index 0000000..87bb735
--- /dev/null
+++ b/inst/validation/pkgdown_examples/vignettes/qc.Rmd
@@ -0,0 +1,32 @@
+---
+title: "Quality Control"
+output:
+  rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Quality Control}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  echo = FALSE
+)
+```
+
+```{r, params, echo = FALSE, include = FALSE}
+val_param_rds <- "../inst/validation/results/val_param.rds"
+val_param_rds_exists <- file.exists(val_param_rds)
+if (file.exists(val_param_rds)) params <- readRDS(val_param_rds)
+```
+
+```{r, results = "asis", echo = FALSE}
+if (val_param_rds_exists) {
+  res <- knitr::knit_child("../inst/validation/val_report_child.Rmd", quiet = TRUE, envir = environment())
+  cat(res, sep = "\n")
+} else {
+  "No quality control results found"
+}
+```

From dd2f97976fef4659d893ae7c8f27143d9797d8e1 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 13:52:41 +0200
Subject: [PATCH 03/14] add example setup.R

---
 inst/validation/pkgdown_examples/setup.R | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 inst/validation/pkgdown_examples/setup.R

diff --git a/inst/validation/pkgdown_examples/setup.R b/inst/validation/pkgdown_examples/setup.R
new file mode 100644
index 0000000..da85709
--- /dev/null
+++ b/inst/validation/pkgdown_examples/setup.R
@@ -0,0 +1,8 @@
+package_name <- %%REPLACE_WITH_YOUR_PACKAGE_NAME%%
+# validation (S)
+vdoc <- source(
+  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
+  local = TRUE
+)[["value"]]
+specs <- vdoc[["specs"]]
+#  validation (F)

From d5f5cdeb0e89c7b31f730b49150feac781b5fdeb Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 18:08:11 +0200
Subject: [PATCH 04/14] avoids error when diffing. Checks for qc skipping

By default bash is run with -e in GH Actions.
---
 .github/workflows/test.yml | 42 +++++++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7cb3125..ccda0f9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -34,31 +34,41 @@ jobs:
           path: templates
 
       - name: Overwrite quality control scripts with dv.templates ones 🧹
+        shell: bash
         run: |
-          # Paths to the directories
           TEMPLATE_DIR="templates/inst/validation"
           REPO_DIR="inst/validation"
+
+          if test ! -d "${REPO_DIR}"; then
+            echo "### Quality Control documentation is not present"
+            echo "### Include quality control documentation or skip it by creating following file 'inst/validation/skip_qc'"
+            exit 1
+          fi
+
+          if test -f "${REPO_DIR}/skip_qc"; then
+            echo "skip_qc file found skipping qc documentation"
+            exit 0
+          fi
           
-          # Run the diff command and capture the output
-          DIFF_OUTPUT=$(diff -qr "$TEMPLATE_DIR" "$REPO_DIR")
+          # Conserve specs.R file
+          cp "${REPO_DIR}/specs.R" "${TEMPLATE_DIR}/specs.R"
 
-          echo "# Quality control files" | tee -a $GITHUB_STEP_SUMMARY
+          set +e  # Disable immediate exit in conflicting parts on error for diff command
+          DIFF_OUTPUT=$(diff -qr "${TEMPLATE_DIR}" "${REPO_DIR}")
+          set -e  # Enable immediate exit on error after diff command
+
+          echo "# Quality control files" | tee -a "${GITHUB_STEP_SUMMARY}"
           
-          # Check if the diff command found any differences
-          if [ -n "$DIFF_OUTPUT" ]; then
-            echo "Warning: The contents of the directories are different!" | tee -a $GITHUB_STEP_SUMMARY
-            echo "Modified files:" | tee -a $GITHUB_STEP_SUMMARY
-            echo "$DIFF_OUTPUT" | tee -a $GITHUB_STEP_SUMMARY
+          if [ -n "${DIFF_OUTPUT}" ]; then
+            echo "Warning: The contents of the directories are different!" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "Modified files:" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "$DIFF_OUTPUT" | tee -a "${GITHUB_STEP_SUMMARY}"
           else
-            echo "The directories are identical." | tee -a $GITHUB_STEP_SUMMARY
+            echo "The directories are identical." | tee -a "${GITHUB_STEP_SUMMARY}"
           fi
 
-          # Always overwrite
-
-          rm -rf "$REPO_DIR"/*
-
-          # Move contents of REPO_DIR to TEMPLATE_DIR
-          mv "$TEMPLATE_DIR"/* "$REPO_DIR"
+          rm -rf "${REPO_DIR}"
+          mv "${TEMPLATE_DIR}" "${REPO_DIR}"
 
       - name: Install package dependencies 📄
         uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main     

From 804cea85e08d06deefc57075d8208b4564e41277 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 18:08:49 +0200
Subject: [PATCH 05/14] automatically finds package name. Reorders templates

---
 inst/validation/pkgdown_examples/setup.R        |  8 --------
 inst/validation/run_validation.R                |  4 ++++
 inst/validation/val_report_child.Rmd            | 11 +++++++++--
 .../_pkgdown.yml                                |  0
 .../validation_templates/tests/testthat/setup.R | 17 +++++++++++++++++
 .../vignettes/qc.Rmd                            |  0
 6 files changed, 30 insertions(+), 10 deletions(-)
 delete mode 100644 inst/validation/pkgdown_examples/setup.R
 rename inst/{validation/pkgdown_examples/vignettes => validation_templates}/_pkgdown.yml (100%)
 create mode 100644 inst/validation_templates/tests/testthat/setup.R
 rename inst/{validation/pkgdown_examples => validation_templates}/vignettes/qc.Rmd (100%)

diff --git a/inst/validation/pkgdown_examples/setup.R b/inst/validation/pkgdown_examples/setup.R
deleted file mode 100644
index da85709..0000000
--- a/inst/validation/pkgdown_examples/setup.R
+++ /dev/null
@@ -1,8 +0,0 @@
-package_name <- %%REPLACE_WITH_YOUR_PACKAGE_NAME%%
-# validation (S)
-vdoc <- source(
-  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-  local = TRUE
-)[["value"]]
-specs <- vdoc[["specs"]]
-#  validation (F)
diff --git a/inst/validation/run_validation.R b/inst/validation/run_validation.R
index e66e4c0..465c65c 100644
--- a/inst/validation/run_validation.R
+++ b/inst/validation/run_validation.R
@@ -1,3 +1,7 @@
+pkg_name <- read.dcf("DESCRIPTION")[, "Package"]
+pkg_version <- read.dcf("DESCRIPTION")[, "Version"]
+test_results <- tibble::as_tibble(devtools::test())
+
 local({
   # This is evaluated inside a local because, otherwise, all the variables created in the chunks of the rendered
   # document leak into the environment
diff --git a/inst/validation/val_report_child.Rmd b/inst/validation/val_report_child.Rmd
index 38e631f..e743960 100644
--- a/inst/validation/val_report_child.Rmd
+++ b/inst/validation/val_report_child.Rmd
@@ -14,11 +14,18 @@
 
 ```{r setup, message = FALSE}
 # Import vdoc functions ----
-vdoc <- source(
-  system.file("validation", "utils-validation.R", package = params[["package"]], mustWork = TRUE),
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########  
+  package_name <- params[["package"]]
+  source(
+  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
   local = TRUE
 )[["value"]]
 
+})
+
 # Set required packages ----
 suppressPackageStartupMessages(stopifnot(requireNamespace("DT")))
 suppressPackageStartupMessages(stopifnot(requireNamespace("devtools")))
diff --git a/inst/validation/pkgdown_examples/vignettes/_pkgdown.yml b/inst/validation_templates/_pkgdown.yml
similarity index 100%
rename from inst/validation/pkgdown_examples/vignettes/_pkgdown.yml
rename to inst/validation_templates/_pkgdown.yml
diff --git a/inst/validation_templates/tests/testthat/setup.R b/inst/validation_templates/tests/testthat/setup.R
new file mode 100644
index 0000000..9340b83
--- /dev/null
+++ b/inst/validation_templates/tests/testthat/setup.R
@@ -0,0 +1,17 @@
+
+
+# validation (S)
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########  
+  package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
+
+  source(
+  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
+  local = TRUE
+)[["value"]]
+
+})
+specs <- vdoc[["specs"]]
+#  validation (F)
diff --git a/inst/validation/pkgdown_examples/vignettes/qc.Rmd b/inst/validation_templates/vignettes/qc.Rmd
similarity index 100%
rename from inst/validation/pkgdown_examples/vignettes/qc.Rmd
rename to inst/validation_templates/vignettes/qc.Rmd

From 8e312877a4233f329f8f37251f68f7044d14ade3 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 18:19:16 +0200
Subject: [PATCH 06/14] fix setup.R

---
 tests/testthat/setup.R | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 92d0bdb..4e1c4b4 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1,8 +1,16 @@
-package_name <- "dv.templates"
 # validation (S)
-vdoc <- source(
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########  
+  package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
+
+  source(
   system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
   local = TRUE
 )[["value"]]
+
+})
 specs <- vdoc[["specs"]]
 #  validation (F)
+

From c790faa5be2d197e251ec67a9bd29f0be1aabc4e Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 18:37:26 +0200
Subject: [PATCH 07/14] fixes utils package name finding

---
 inst/validation/utils-validation.R               |  2 +-
 inst/validation/val_report_child.Rmd             |  7 ++-----
 inst/validation_templates/tests/testthat/setup.R | 12 +++---------
 tests/testthat/setup.R                           | 11 +++--------
 4 files changed, 9 insertions(+), 23 deletions(-)

diff --git a/inst/validation/utils-validation.R b/inst/validation/utils-validation.R
index 5dc7360..eaf8e06 100644
--- a/inst/validation/utils-validation.R
+++ b/inst/validation/utils-validation.R
@@ -4,7 +4,7 @@
 #' 2. Copy that variable and the contents of if block to tests/testthat/setup.R
 #' (If you are using the template this may already be in place for you)
 
-package_name <- "dv.templates"
+if(!exists("package_name")) stop("package name must be in the environment when this script is sourced")
 
 if (FALSE) {
   # validation (S)
diff --git a/inst/validation/val_report_child.Rmd b/inst/validation/val_report_child.Rmd
index e743960..01c703d 100644
--- a/inst/validation/val_report_child.Rmd
+++ b/inst/validation/val_report_child.Rmd
@@ -19,11 +19,8 @@ vdoc <- local({
   # package_name is used # INSIDE # the sourced file below
   #                      ##########  
   package_name <- params[["package"]]
-  source(
-  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-  local = TRUE
-)[["value"]]
-
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
 })
 
 # Set required packages ----
diff --git a/inst/validation_templates/tests/testthat/setup.R b/inst/validation_templates/tests/testthat/setup.R
index 9340b83..2c6e9ab 100644
--- a/inst/validation_templates/tests/testthat/setup.R
+++ b/inst/validation_templates/tests/testthat/setup.R
@@ -1,17 +1,11 @@
-
-
 # validation (S)
 vdoc <- local({
   #                      ##########
   # package_name is used # INSIDE # the sourced file below
   #                      ##########  
   package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
-
-  source(
-  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-  local = TRUE
-)[["value"]]
-
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
 })
 specs <- vdoc[["specs"]]
-#  validation (F)
+#  validation (F)
\ No newline at end of file
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 4e1c4b4..2c6e9ab 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -4,13 +4,8 @@ vdoc <- local({
   # package_name is used # INSIDE # the sourced file below
   #                      ##########  
   package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
-
-  source(
-  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-  local = TRUE
-)[["value"]]
-
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
 })
 specs <- vdoc[["specs"]]
-#  validation (F)
-
+#  validation (F)
\ No newline at end of file

From aee652f9e50a37ab4b4edb8258a4ad12ad20a677 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 21:55:54 +0200
Subject: [PATCH 08/14] fix summary symbols

---
 scripts/test_qc_pkg.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/test_qc_pkg.R b/scripts/test_qc_pkg.R
index 517785c..e49ad25 100644
--- a/scripts/test_qc_pkg.R
+++ b/scripts/test_qc_pkg.R
@@ -127,9 +127,9 @@ summary <- c(
   summary,
   purrr::imap_chr(success, ~{
     symbol <- "\U02753"
-    symbol <- if (isTRUE(.x)) "\U02705"
-    symbol <- if (isFALSE(.x)) "\U0274C"
-    symbol <- if (is.na(.x)) "\U02757"
+    if (isTRUE(.x)) symbol <- "\U02705"
+    if (isFALSE(.x)) symbol <- "\U0274C"
+    if (is.na(.x)) symbol <- "\U02757"
     paste(" - ", symbol, .y)
   })
 )

From c95b3d863ba0bbf846c2ae29b33fc2fa98a0ad36 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 21:59:51 +0200
Subject: [PATCH 09/14] lint & style

---
 inst/validation/utils-validation.R               | 2 +-
 inst/validation_templates/tests/testthat/setup.R | 2 +-
 tests/testthat/setup.R                           | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/inst/validation/utils-validation.R b/inst/validation/utils-validation.R
index eaf8e06..185c8dc 100644
--- a/inst/validation/utils-validation.R
+++ b/inst/validation/utils-validation.R
@@ -4,7 +4,7 @@
 #' 2. Copy that variable and the contents of if block to tests/testthat/setup.R
 #' (If you are using the template this may already be in place for you)
 
-if(!exists("package_name")) stop("package name must be in the environment when this script is sourced")
+if (!exists("package_name")) stop("package name must be in the environment when this script is sourced")
 
 if (FALSE) {
   # validation (S)
diff --git a/inst/validation_templates/tests/testthat/setup.R b/inst/validation_templates/tests/testthat/setup.R
index 2c6e9ab..01b056d 100644
--- a/inst/validation_templates/tests/testthat/setup.R
+++ b/inst/validation_templates/tests/testthat/setup.R
@@ -8,4 +8,4 @@ vdoc <- local({
   source(utils_file_path, local = TRUE)[["value"]]
 })
 specs <- vdoc[["specs"]]
-#  validation (F)
\ No newline at end of file
+#  validation (F)
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 2c6e9ab..fb131cf 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -2,10 +2,10 @@
 vdoc <- local({
   #                      ##########
   # package_name is used # INSIDE # the sourced file below
-  #                      ##########  
+  #                      ##########
   package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
   utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
   source(utils_file_path, local = TRUE)[["value"]]
 })
 specs <- vdoc[["specs"]]
-#  validation (F)
\ No newline at end of file
+#  validation (F)

From 5ec4e06c0a548375e0238f3136989436ff34b75a Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 22:13:55 +0200
Subject: [PATCH 10/14] update news

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

diff --git a/NEWS.md b/NEWS.md
index 855de90..28cf50c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,4 @@
 # dv.templates 0.1.0
 
 - add release checks
+- qc check is done with centralized scripts from dv.templates

From 91fb2395e441996bcf218f4063358906ca1b1727 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 22:25:23 +0200
Subject: [PATCH 11/14] include an empty file in results when qc is skipped

otherwise it would upload an empty artifact and the ci will fail in the pkgdown step
---
 scripts/test_qc_pkg.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/test_qc_pkg.R b/scripts/test_qc_pkg.R
index e49ad25..d6b5f41 100644
--- a/scripts/test_qc_pkg.R
+++ b/scripts/test_qc_pkg.R
@@ -71,6 +71,7 @@ if (!dir.exists(validation_root)) {
 }
 
 if (file.exists(validation_skip)) {
+  writeLines("", file.path(validation_results, "skipped_qc"))
   success[["valdoc"]] <- NA
 } else {
 

From c7530272b786dca4821d5daafd6b19c7f3eb00cb Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Wed, 5 Jun 2024 22:27:37 +0200
Subject: [PATCH 12/14] allows passing with no qc documentation

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

diff --git a/scripts/test_qc_pkg.R b/scripts/test_qc_pkg.R
index d6b5f41..b4b582d 100644
--- a/scripts/test_qc_pkg.R
+++ b/scripts/test_qc_pkg.R
@@ -139,7 +139,7 @@ CON <- file(github_summary_file, "a")
 on.exit(close(CON))
 writeLines(summary, CON)
 
-stopifnot(isTRUE(all(success)))
+stopifnot(all(success | is.na(sucess)))
 
 message("##############################")
 message("###### BUILD RESULT (F) ######")

From d2d7df380137d24eff1abd8b91fdf109337fc3a7 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Thu, 6 Jun 2024 11:34:00 +0200
Subject: [PATCH 13/14] clarify utils doc

---
 inst/validation/utils-validation.R | 26 ++++++++------------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/inst/validation/utils-validation.R b/inst/validation/utils-validation.R
index 185c8dc..72a1808 100644
--- a/inst/validation/utils-validation.R
+++ b/inst/validation/utils-validation.R
@@ -1,32 +1,18 @@
 #' Setting up the validation
-#'
-#' 1. Add package_name
-#' 2. Copy that variable and the contents of if block to tests/testthat/setup.R
-#' (If you are using the template this may already be in place for you)
 
 if (!exists("package_name")) stop("package name must be in the environment when this script is sourced")
 
-if (FALSE) {
-  # validation (S)
-  vdoc <- source(
-    system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-    local = TRUE
-  )[["value"]]
-  specs <- vdoc[["specs"]]
-  # validation (F)
-}
-
-#' 2. For those tests that cover an specific spec
+#' How to link tests and specs
 
 if (FALSE) {
   test_that(
-    vdoc[["add_spec"]]("my test description", specs[["a_spec"]]),
+    vdoc[["add_spec"]]("my test description", specs$a_spec),
     {
       expect_true(TRUE)
     }
   )
 }
-#' The specs variable on the call references the one declared in point 1
+#' The specs variable on the call references the one declared in specs.R
 
 #' 3. For those tests covering more than one spec.
 #' NOTE: It must be c() and not list()
@@ -47,7 +33,11 @@ if (FALSE) {
 
 if (FALSE) {
   my_spec <- specs$my$hier$spec
-  test_that(vdoc$parse_spec(my_spec, "my test_description"), {
+  test_that(vdoc[["add_spec"]]("my test_description", my_spec), {
+    ...
+  })
+  
+  test_that(vdoc[["add_spec"]]("my test_description", specs[["my"]][["hier"]][["spec"]]), {
     ...
   })
 }

From 85d359bb9afc52df43e8ada9b2c1e8861191ac59 Mon Sep 17 00:00:00 2001
From: Luis Moris Fernandez <luis.moris.fernandez@gmail.com>
Date: Thu, 6 Jun 2024 11:34:10 +0200
Subject: [PATCH 14/14] include date in qc report

---
 inst/validation/val_report_child.Rmd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/inst/validation/val_report_child.Rmd b/inst/validation/val_report_child.Rmd
index 01c703d..95cb47c 100644
--- a/inst/validation/val_report_child.Rmd
+++ b/inst/validation/val_report_child.Rmd
@@ -86,6 +86,7 @@ title <- paste(result_symbol, params[["package"]], params[["version"]])
 ```
 
 ## `r title`
+Date: `r format(Sys.time(), "%Y-%b-%d %H:%M:%S")`
 
 The following document generates a report for R packages, to satisfy the criteria of a "Released" status under the **Non-GxP** project. The QC report contains the following information: