From 77c1974051675ff65af91c1c82dbfdc337b7be01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Tue, 7 Jan 2025 17:10:57 +0100
Subject: [PATCH 1/6] Add two more sections

---
 inst/report/pkg_template.qmd | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index 8fddf8a..c4a3546 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -136,3 +136,19 @@ Overall the package has these dependencies:
 d_riskmetric$dependencies
 ```
 
+## Dependencies
+
+Overall the package has these dependencies:
+
+```{r dependencies}
+d_riskmetric$dependencies
+```
+
+## Namespace
+
+Overall the package has `r length(d_riskmetric$exported_namespace)` namespace directives.
+
+```{r namespace}
+d_riskmetric$exported_namespace
+```
+

From 773da6e1d5bfb4afc571c5442ae6a73815e5db57 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 8 Jan 2025 17:01:50 +0100
Subject: [PATCH 2/6] Add gfm format

---
 inst/report/pkg_template.qmd | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index c4a3546..e74608c 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -10,6 +10,8 @@ format:
   html: 
     toc: true  
     embed-resources: true
+  gfm:
+    html-math-method: webtex    
   # typst:
   #   toc: true
   #   section-numbering: 1.1.1

From 56f841a212d3221e48f76d197436bc888f3a89a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Wed, 8 Jan 2025 17:05:57 +0100
Subject: [PATCH 3/6] Add reverse dependencies

---
 inst/report/pkg_template.qmd | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index e74608c..a94f47c 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -138,12 +138,12 @@ Overall the package has these dependencies:
 d_riskmetric$dependencies
 ```
 
-## Dependencies
+## Reverse dependencies
 
-Overall the package has these dependencies:
+Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse dependencies:
 
 ```{r dependencies}
-d_riskmetric$dependencies
+d_riskmetric$reverse_dependencies
 ```
 
 ## Namespace

From 3937a9ee5f32404e31cf2e2a05ca7850e4120d60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 9 Jan 2025 13:09:18 +0100
Subject: [PATCH 4/6] Add NEWS, License, examples

---
 inst/report/pkg_template.qmd | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index 1ff50a1..55b4e5a 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -191,9 +191,21 @@ d_riskmetric$reverse_dependencies
 
 ## Namespace
 
-Overall the package has `r length(d_riskmetric$exported_namespace)` namespace directives.
+Overall the package has `r length(d_riskmetric$exported_namespace)` exported objects.
+`r sum(d_riskmetric$export_help)` are documented:
 
 ```{r namespace}
-d_riskmetric$exported_namespace
+d_riskmetric$export_help[sort(d_riskmetric$exported_namespace)]
 ```
 
+### Examples
+
+There are `r sum(d_riskmetric$has_examples)` help pages with examples from `r length(d_riskmetric$has_examples)`, (`r sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100) ` %)
+
+### NEWS
+
+The package has `r d_riskmetric$has_news` and they are `r if(!d_riskmetric$news_current) "not"` current.
+
+### License
+
+The package uses `r d_riskmetric$license`.

From 85137b93277f779ef603cfac031387cb849046db Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 16 Jan 2025 15:22:01 +0100
Subject: [PATCH 5/6] Reorganize content to the top

---
 R/reporter.R                 |   2 +-
 inst/report/pkg_template.qmd | 148 ++++++++++++++++++-----------------
 2 files changed, 79 insertions(+), 71 deletions(-)

diff --git a/R/reporter.R b/R/reporter.R
index fff77ce..5be7e6d 100644
--- a/R/reporter.R
+++ b/R/reporter.R
@@ -54,7 +54,7 @@ package_report <- function(
 
     params$package <- normalizePath(params$package, mustWork = FALSE)
     if (!is.null(params$assessment_path)) {
-      params$assessment_path <- normalizePath(params$assessment_path)
+      params$assessment_path <- normalizePath(params$assessment_path, mustWork = TRUE)
     }
     # Bug on https://github.com/quarto-dev/quarto-cli/issues/5765
     suppressMessages({suppressWarnings({
diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index bbd2f65..086a04f 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -1,5 +1,5 @@
 ---
-title: "Validation Report - `r params$package_name` v `r params$package_version`"
+title: "Validation Report - `r paste0(params$package_name, '@', params$package_version)`"
 date: "`r Sys.time()`"
 date-format: "ddd MMM DD hh:mm:ss A YYYY"
 params:
@@ -37,6 +37,15 @@ library("tools")
 # Context
 
 
+```{r loading}
+pkg <- params$package
+pkg_name <- params$package_name
+pkg_version <- params$package_version
+risk_path <- params$assessment_path
+image <- params$image
+```
+
+
 ```{r image}
 image <- Sys.getenv("DOCKER_IMAGE", unset = NA)
 is_empty <- function(x) {
@@ -56,23 +65,83 @@ Documents the installation of this package on an open source R environment, focu
 It is limited to assess whether unit tests and documentation are present and can execute without error. 
 An assessment would be required that the tests and documentation are meaningful. 
 
-# Installation environment
 
-```{r loading}
-pkg <- params$package
-pkg_name <- params$package_name
-pkg_version <- params$package_version
-risk_path <- params$assessment_path
+# Package `r basename(pkg)`
+
+## Metric based risk assessment
+
+The following metrics are derived from the `riskmetric` R package.
+
+```{r read-riskmetric, warning=FALSE}
+d_riskmetric <- readRDS(risk_path)
+```
+
+
+```{r general-riskmetric, warning=FALSE}
+#| tab.cap: "**Package general assessment:** Coverage, check results, size, 
+#|  download the last year, reverse dependencies and number of dependencies."
+
+# Assesment produces a data.frame with one row
+r_riskmetric <- riskreports::assessment(d_riskmetric)
+is_na <- sapply(r_riskmetric, is.na)
+knitr::kable(r_riskmetric[, !is_na]) # Use this to have some summary text and report it.
+# d_riskmetric
 ```
 
 
+## Dependencies
+
+Overall the package has these dependencies:
+
+```{r dependencies-riskmetric}
+#| tab.cap: "**Package dependencies**"
+deps <- d_riskmetric$dependencies
+deps$package <- gsub("\\n", " ", deps$package)
+knitr::kable(deps)
+```
+
+## Reverse dependencies
+
+Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse dependencies:
+
+```{r dependencies}
+d_riskmetric$reverse_dependencies
+```
+
+## Namespace
+
+Overall the package has `r length(d_riskmetric$exported_namespace)` exported objects.
+`r sum(d_riskmetric$export_help)` are documented:
+
+```{r namespace}
+d_riskmetric$export_help[sort(d_riskmetric$exported_namespace)]
+```
+
+### Examples
+
+There are `r sum(d_riskmetric$has_examples)` help pages with examples, from `r length(d_riskmetric$has_examples)` (`r sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100) ` %).
+
+### NEWS
+
+The package has `r d_riskmetric$has_news` NEWS file and it is `r if(!d_riskmetric$news_current) "not"` current.
+
+### License
+
+The package uses `r d_riskmetric$license`.
+
+
+
+# Installation environment
+
+
 ## System Info
 
 ```{r execution_info}
-#| tab.cap: "table"
+#| tab.cap: "**System information**. Table about the system used to check the package."
 tt_sys_info_df <- data.frame(
-  Field = c("OS", "Platform", "System", "Execution Time"),
+  Field = c("Image", "OS", "Platform", "System", "Execution Time"),
   Value = c(
+    image,
     sessionInfo()$running,
     R.version$platform,
     R.version$system,
@@ -148,64 +217,3 @@ These are the options set to generate the report:
 riskreports::options_report(exclude = c("usethis.full_name", "usethis.description", "usethis.destdir"))
 ```
 
-
-# Package `r pkg`
-
-## Metric based risk assessment
-
-The following metrics are derived from the `riskmetric` R package.
-
-```{r read-riskmetric, warning=FALSE}
-d_riskmetric <- readRDS(risk_path)
-```
-
-
-```{r general-riskmetric, warning=FALSE}
-#| tab.cap: "**Package general assessment.** Coverage, check results, size, 
-#|  download the last year, reverse dependencies and number of dependencies."
-
-# Assesment produces a data.frame with one row
-r_riskmetric <- riskreports::assessment(d_riskmetric)
-knitr::kable(r_riskmetric) # Use this to have some summary text and report it.
-# d_riskmetric
-```
-
-
-## Dependencies
-
-Overall the package has these dependencies:
-
-```{r dependencies-riskmetric}
-#| tab.cap: "**Package dependencies**"
-
-knitr::kable(gsub("\\n", " ", d_riskmetric$dependencies))
-```
-
-## Reverse dependencies
-
-Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse dependencies:
-
-```{r dependencies}
-d_riskmetric$reverse_dependencies
-```
-
-## Namespace
-
-Overall the package has `r length(d_riskmetric$exported_namespace)` exported objects.
-`r sum(d_riskmetric$export_help)` are documented:
-
-```{r namespace}
-d_riskmetric$export_help[sort(d_riskmetric$exported_namespace)]
-```
-
-### Examples
-
-There are `r sum(d_riskmetric$has_examples)` help pages with examples from `r length(d_riskmetric$has_examples)`, (`r sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100) ` %)
-
-### NEWS
-
-The package has `r d_riskmetric$has_news` and they are `r if(!d_riskmetric$news_current) "not"` current.
-
-### License
-
-The package uses `r d_riskmetric$license`.

From 9ae68dafecfd1ec03771f54403106603eed59826 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= <lluis.revilla_sancho@roche.com>
Date: Thu, 16 Jan 2025 15:38:46 +0100
Subject: [PATCH 6/6] Simplify dependency table and reverse_dependencies list

---
 inst/report/pkg_template.qmd | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/inst/report/pkg_template.qmd b/inst/report/pkg_template.qmd
index 086a04f..d7d0cc1 100644
--- a/inst/report/pkg_template.qmd
+++ b/inst/report/pkg_template.qmd
@@ -97,15 +97,16 @@ Overall the package has these dependencies:
 #| tab.cap: "**Package dependencies**"
 deps <- d_riskmetric$dependencies
 deps$package <- gsub("\\n", " ", deps$package)
-knitr::kable(deps)
+row.names(deps) <- NULL
+knitr::kable(deps, row.names = TRUE)
 ```
 
 ## Reverse dependencies
 
 Overall the package has `r length(d_riskmetric$reverse_dependencies)` reverse dependencies:
 
-```{r dependencies}
-d_riskmetric$reverse_dependencies
+```{r dependencies, results='asis'}
+cat(paste(d_riskmetric$reverse_dependencies, collapse = ", "))
 ```
 
 ## Namespace