From c1da96b78ed0e9149eb54700c687fd48d76e34b6 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sat, 30 Aug 2025 02:53:40 +0530
Subject: [PATCH 01/10] [check] risk assessr workflow testing

---
 .github/workflows/riskassessr.yaml | 318 +++++++++++++++++++++++++++++
 renv.lock                          |  22 +-
 vignettes/usecase-doc.R            | 124 +++++------
 3 files changed, 391 insertions(+), 73 deletions(-)
 create mode 100644 .github/workflows/riskassessr.yaml

diff --git a/.github/workflows/riskassessr.yaml b/.github/workflows/riskassessr.yaml
new file mode 100644
index 0000000..fe82484
--- /dev/null
+++ b/.github/workflows/riskassessr.yaml
@@ -0,0 +1,318 @@
+name: Package Risk Assessment
+
+on:
+  push:
+
+jobs:
+  risk-assessment:
+    runs-on: ubuntu-latest
+    name: Risk Assessment
+    
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Setup Pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install package dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Install risk.assessr and additional dependencies
+        run: |
+          install.packages(c("risk.assessr", "crayon", "knitr"))
+        shell: Rscript {0}
+
+      - name: Build package
+        run: |
+          devtools::build(path = ".", vignettes = FALSE)
+        shell: Rscript {0}
+
+      - name: Run Risk Assessment
+        run: |
+          # Load required libraries
+          library(risk.assessr)
+          library(crayon)
+          
+          # Set up CRAN repository
+          r <- getOption("repos")
+          r["CRAN"] <- "https://cloud.r-project.org"
+          options(repos = r)
+          
+          cat("=== Starting Package Risk Assessment ===\n")
+          cat("Repository:", Sys.getenv("GITHUB_REPOSITORY"), "\n")
+          cat("Branch:", Sys.getenv("GITHUB_REF_NAME"), "\n")
+          cat("Workflow run:", Sys.getenv("GITHUB_RUN_ID"), "\n")
+          cat("Timestamp:", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), "\n\n")
+          
+          # Pretty print function for GitHub Actions logs
+          pretty_print_assessment <- function(assessment_results) {
+            
+            if (is.null(assessment_results) || length(assessment_results) == 0) {
+              cat("❌ No assessment results to display.\n")
+              return()
+            }
+            
+            # Helper functions for colored output in GitHub Actions
+            print_header <- function(title) {
+              cat("\n")
+              cat("🔍 ===", title, "===\n")
+              cat(paste(rep("=", nchar(title) + 10), collapse = ""), "\n")
+            }
+            
+            print_subheader <- function(title) {
+              cat("\n📊", title, "\n")
+              cat(paste(rep("-", nchar(title) + 3), collapse = ""), "\n")
+            }
+            
+            # Extract package name
+            pkg_name <- "Unknown Package"
+            if ("package" %in% names(assessment_results)) {
+              pkg_name <- assessment_results$package
+            } else if ("pkg_name" %in% names(assessment_results)) {
+              pkg_name <- assessment_results$pkg_name
+            }
+            
+            print_header("PACKAGE ASSESSMENT RESULTS")
+            cat("📦 Package:", pkg_name, "\n")
+            cat("⏰ Generated:", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n")
+            
+            # Print R CMD Check Results
+            if ("rcmdcheck" %in% names(assessment_results)) {
+              print_header("R CMD CHECK RESULTS")
+              rcmd <- assessment_results$rcmdcheck
+              
+              if (is.list(rcmd)) {
+                # Errors
+                if ("errors" %in% names(rcmd) && length(rcmd$errors) > 0) {
+                  print_subheader("🚨 ERRORS")
+                  for (error in rcmd$errors) {
+                    cat("❌", error, "\n")
+                  }
+                  cat("::error::R CMD check found", length(rcmd$errors), "error(s)\n")
+                } else {
+                  cat("✅ No errors found\n")
+                }
+                
+                # Warnings
+                if ("warnings" %in% names(rcmd) && length(rcmd$warnings) > 0) {
+                  print_subheader("⚠️ WARNINGS")
+                  for (warning in rcmd$warnings) {
+                    cat("⚠️", warning, "\n")
+                  }
+                  cat("::warning::R CMD check found", length(rcmd$warnings), "warning(s)\n")
+                } else {
+                  cat("✅ No warnings found\n")
+                }
+                
+                # Notes
+                if ("notes" %in% names(rcmd) && length(rcmd$notes) > 0) {
+                  print_subheader("📝 NOTES")
+                  for (note in rcmd$notes) {
+                    cat("ℹ️", note, "\n")
+                  }
+                  cat("::notice::R CMD check found", length(rcmd$notes), "note(s)\n")
+                } else {
+                  cat("✅ No notes\n")
+                }
+              } else {
+                cat(as.character(rcmd), "\n")
+              }
+            }
+            
+            # Print Coverage Results
+            if ("covr" %in% names(assessment_results)) {
+              print_header("CODE COVERAGE")
+              covr <- assessment_results$covr
+              
+              if (is.numeric(covr)) {
+                coverage_pct <- round(covr, 2)
+                if (coverage_pct >= 80) {
+                  cat("✅ Coverage:", coverage_pct, "%\n")
+                } else if (coverage_pct >= 60) {
+                  cat("⚠️ Coverage:", coverage_pct, "%\n")
+                  cat("::warning::Code coverage is below 80%\n")
+                } else {
+                  cat("❌ Coverage:", coverage_pct, "%\n")
+                  cat("::error::Code coverage is below 60%\n")
+                }
+              } else if (is.data.frame(covr)) {
+                cat("Coverage details:\n")
+                print(covr)
+              } else {
+                cat(as.character(covr), "\n")
+              }
+            }
+            
+            # Print Dependencies
+            if ("dependencies" %in% names(assessment_results)) {
+              print_header("DEPENDENCIES")
+              deps <- assessment_results$dependencies
+              
+              if (is.data.frame(deps)) {
+                if (nrow(deps) > 0) {
+                  cat("📋 Found", nrow(deps), "dependencies:\n")
+                  print(deps)
+                } else {
+                  cat("✅ No dependencies found\n")
+                }
+              } else if (is.list(deps)) {
+                if (length(deps) > 0) {
+                  for (name in names(deps)) {
+                    cat("•", name, ":", as.character(deps[[name]]), "\n")
+                  }
+                } else {
+                  cat("✅ No dependencies found\n")
+                }
+              } else {
+                cat(as.character(deps), "\n")
+              }
+            }
+            
+            # Print Metrics
+            if ("metrics" %in% names(assessment_results)) {
+              print_header("PACKAGE METRICS")
+              metrics <- assessment_results$metrics
+              
+              if (is.data.frame(metrics)) {
+                if (nrow(metrics) > 0) {
+                  print(metrics)
+                } else {
+                  cat("No metrics data available\n")
+                }
+              } else if (is.list(metrics)) {
+                if (length(metrics) > 0) {
+                  for (name in names(metrics)) {
+                    cat("•", name, ":", as.character(metrics[[name]]), "\n")
+                  }
+                } else {
+                  cat("No metrics data available\n")
+                }
+              } else {
+                cat(as.character(metrics), "\n")
+              }
+            }
+            
+            # Print other components
+            other_components <- names(assessment_results)[!names(assessment_results) %in% 
+                                                         c("rcmdcheck", "covr", "dependencies", "metrics", "package", "pkg_name")]
+            
+            if (length(other_components) > 0) {
+              print_header("OTHER ASSESSMENT DATA")
+              
+              for (component in other_components) {
+                data <- assessment_results[[component]]
+                cat("\n📋", toupper(component), "\n")
+                
+                if (is.data.frame(data) && nrow(data) > 0) {
+                  print(data)
+                } else if (is.list(data) && length(data) > 0) {
+                  str(data, max.level = 2)
+                } else if (!is.null(data) && length(data) > 0) {
+                  cat(as.character(data), "\n")
+                } else {
+                  cat("No data available\n")
+                }
+              }
+            }
+            
+            # Summary
+            print_header("ASSESSMENT SUMMARY")
+            cat("📊 Total components assessed:", length(assessment_results), "\n")
+            
+            # Create GitHub Actions summary
+            error_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                             "errors" %in% names(assessment_results$rcmdcheck)) 
+                             length(assessment_results$rcmdcheck$errors) else 0
+            warning_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                               "warnings" %in% names(assessment_results$rcmdcheck)) 
+                               length(assessment_results$rcmdcheck$warnings) else 0
+            note_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                            "notes" %in% names(assessment_results$rcmdcheck)) 
+                            length(assessment_results$rcmdcheck$notes) else 0
+            
+            if (error_count > 0) {
+              cat("::error::Assessment completed with", error_count, "errors\n")
+            } else if (warning_count > 0) {
+              cat("::warning::Assessment completed with", warning_count, "warnings\n")
+            } else {
+              cat("::notice::Assessment completed successfully\n")
+            }
+            
+            cat("\n🎉 Assessment display completed!\n")
+          }
+          
+          # Run the assessment
+          tryCatch({
+            cat("🚀 Starting risk assessment...\n")
+            
+            # Use the simplified risk_assess_pkg function with current directory
+            comprehensive_assessment <- risk_assess_pkg(".")
+            
+            # Print the results
+            pretty_print_assessment(comprehensive_assessment)
+            
+          }, error = function(e) {
+            cat("::error::Assessment failed with error:", e$message, "\n")
+            cat("📋 Attempting fallback assessment...\n")
+            
+            # Fallback: try building package first
+            tryCatch({
+              # Build the package
+              built_pkg <- devtools::build(".", quiet = FALSE)
+              cat("📦 Package built:", built_pkg, "\n")
+              
+              # Try assessment with built package
+              comprehensive_assessment <- risk_assess_pkg(built_pkg)
+              pretty_print_assessment(comprehensive_assessment)
+              
+            }, error = function(e2) {
+              cat("::error::Fallback assessment also failed:", e2$message, "\n")
+              cat("🔍 Package structure:\n")
+              cat(paste(list.files(".", recursive = TRUE, include.dirs = TRUE), collapse = "\n"), "\n")
+            })
+          })
+          
+          cat("\n=== Risk Assessment Complete ===\n")
+        shell: Rscript {0}
+
+      - name: Upload assessment artifacts
+        uses: actions/upload-artifact@v3
+        if: always()
+        with:
+          name: risk-assessment-logs
+          path: |
+            *.log
+            *.Rcheck/
+          retention-days: 30
diff --git a/renv.lock b/renv.lock
index 8b4cd81..0e124bc 100644
--- a/renv.lock
+++ b/renv.lock
@@ -359,7 +359,7 @@
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.48",
+      "Version": "1.50",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -371,7 +371,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "acf380f300c721da9fde7df115a5f86f"
+      "Hash": "5a07d8ec459d7b80bd4acca5f4a6e062"
     },
     "lifecycle": {
       "Package": "lifecycle",
@@ -388,7 +388,7 @@
     },
     "lubridate": {
       "Package": "lubridate",
-      "Version": "1.9.3",
+      "Version": "1.9.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -397,7 +397,7 @@
         "methods",
         "timechange"
       ],
-      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
+      "Hash": "be38bc740fc51783a78edb5a157e4104"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -547,7 +547,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.27",
+      "Version": "2.29",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -566,7 +566,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
+      "Hash": "df99277f63d01c34e95e3d2f06a79736"
     },
     "sass": {
       "Package": "sass",
@@ -591,12 +591,12 @@
     },
     "tibble": {
       "Package": "tibble",
-      "Version": "3.2.1",
+      "Version": "3.3.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
-        "fansi",
+        "cli",
         "lifecycle",
         "magrittr",
         "methods",
@@ -606,7 +606,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
+      "Hash": "784b27d0801c3829de602105757b2cd7"
     },
     "tidyselect": {
       "Package": "tidyselect",
@@ -720,7 +720,7 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.47",
+      "Version": "0.53",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -729,7 +729,7 @@
         "stats",
         "tools"
       ],
-      "Hash": "36ab21660e2d095fef0d83f689e0477c"
+      "Hash": "1befe97a0d56060b3964e3986d408df9"
     },
     "yaml": {
       "Package": "yaml",
diff --git a/vignettes/usecase-doc.R b/vignettes/usecase-doc.R
index 9a3468a..c2869c7 100644
--- a/vignettes/usecase-doc.R
+++ b/vignettes/usecase-doc.R
@@ -1,74 +1,74 @@
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Load required libraries
-#  invisible(suppressPackageStartupMessages({
-#    library(clintrialx)  # For fetching clinical trial data
-#    library(ggplot2)     # For data visualization
-#    library(plotly)      # For interactive plots
-#    library(dplyr)       # For data manipulation
-#    library(lubridate)   # For date handling
-#  }))
+# # Load required libraries
+# invisible(suppressPackageStartupMessages({
+#   library(clintrialx)  # For fetching clinical trial data
+#   library(ggplot2)     # For data visualization
+#   library(plotly)      # For interactive plots
+#   library(dplyr)       # For data manipulation
+#   library(lubridate)   # For date handling
+# }))
 
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Fetch cancer study data in India
-#  df <- ctg_bulk_fetch(condition = "cancer", location = "India")
+# # Fetch cancer study data in India
+# df <- ctg_bulk_fetch(condition = "cancer", location = "India")
 
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Create a table of study statuses
-#  status_counts <- table(df$`Study Status`)
-#  
-#  # Convert the table to a data frame
-#  status_df <- data.frame(status = names(status_counts), count = as.numeric(status_counts))
-#  
-#  # Generate the bar plot
-#  ggplotly(ggplot(status_df, aes(x = reorder(status, -count), y = count)) +
-#    geom_bar(stat = "identity", fill = "orange") +
-#    theme_minimal() +
-#    labs(title = "Distribution of Study Statuses",
-#         x = "Study Status",
-#         y = "Count") +
-#    theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
-#    geom_text(aes(label = count), vjust = -0.5))
+# # Create a table of study statuses
+# status_counts <- table(df$`Study Status`)
+# 
+# # Convert the table to a data frame
+# status_df <- data.frame(status = names(status_counts), count = as.numeric(status_counts))
+# 
+# # Generate the bar plot
+# ggplotly(ggplot(status_df, aes(x = reorder(status, -count), y = count)) +
+#   geom_bar(stat = "identity", fill = "orange") +
+#   theme_minimal() +
+#   labs(title = "Distribution of Study Statuses",
+#        x = "Study Status",
+#        y = "Count") +
+#   theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
+#   geom_text(aes(label = count), vjust = -0.5))
 
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Create an interactive box plot of enrollment by study phase
-#  ggplotly(ggplot(df, aes(x = Phases, y = Enrollment)) +
-#    geom_boxplot(fill = "lightblue", outlier.colour = "red", outlier.shape = 1) +
-#    geom_jitter(color = "darkblue", size = 0.5, alpha = 0.5, width = 0.2) +
-#    theme_minimal(base_size = 14) +
-#    labs(title = "Enrollment by Study Phase",
-#         x = "Study Phase",
-#         y = "Enrollment") +
-#    theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 12),
-#          plot.title = element_text(hjust = 0.5)))
+# # Create an interactive box plot of enrollment by study phase
+# ggplotly(ggplot(df, aes(x = Phases, y = Enrollment)) +
+#   geom_boxplot(fill = "lightblue", outlier.colour = "red", outlier.shape = 1) +
+#   geom_jitter(color = "darkblue", size = 0.5, alpha = 0.5, width = 0.2) +
+#   theme_minimal(base_size = 14) +
+#   labs(title = "Enrollment by Study Phase",
+#        x = "Study Phase",
+#        y = "Enrollment") +
+#   theme(axis.text.x = element_text(angle = 45, hjust = 1, size = 12),
+#         plot.title = element_text(hjust = 0.5)))
 
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Convert date strings to Date objects
-#  df$start_date <- as.Date(df$`Start Date`, format = "%Y-%m-%d")
-#  df$completion_date <- as.Date(df$`Completion Date`, format = "%Y-%m-%d")
-#  
-#  # Create a scatter plot with a horizontal line at 2024
-#  ggplot(df, aes(x = start_date, y = completion_date, color = `Study Status`)) +
-#    geom_point(alpha = 0.6) +
-#    geom_hline(yintercept = as.Date("2024-01-01"), linetype = "dashed", color = "blue") +
-#    theme_minimal() +
-#    labs(title = "Study Duration Timeline",
-#         x = "Start Date",
-#         y = "Completion Date") +
-#    scale_color_brewer(palette = "Set1")
+# # Convert date strings to Date objects
+# df$start_date <- as.Date(df$`Start Date`, format = "%Y-%m-%d")
+# df$completion_date <- as.Date(df$`Completion Date`, format = "%Y-%m-%d")
+# 
+# # Create a scatter plot with a horizontal line at 2024
+# ggplot(df, aes(x = start_date, y = completion_date, color = `Study Status`)) +
+#   geom_point(alpha = 0.6) +
+#   geom_hline(yintercept = as.Date("2024-01-01"), linetype = "dashed", color = "blue") +
+#   theme_minimal() +
+#   labs(title = "Study Duration Timeline",
+#        x = "Start Date",
+#        y = "Completion Date") +
+#   scale_color_brewer(palette = "Set1")
 
 ## ----eval=FALSE---------------------------------------------------------------
-#  # Summarize and plot funding sources by study type
-#  df_summary <- df %>%
-#    count(`Funder Type`, `Study Type`) %>%
-#    group_by(`Funder Type`) %>%
-#    mutate(prop = n / sum(n))
-#  
-#  ggplotly(ggplot(df_summary, aes(x = `Funder Type`, y = prop, fill = `Study Type`)) +
-#    geom_bar(stat = "identity", position = "dodge") +
-#    theme_minimal() +
-#    labs(title = "Funding Sources and Study Types",
-#         x = "Funder Type",
-#         y = "Proportion") +
-#    scale_fill_brewer(palette = "Set2") +
-#    theme(axis.text.x = element_text(angle = 45, hjust = 1)))
+# # Summarize and plot funding sources by study type
+# df_summary <- df %>%
+#   count(`Funder Type`, `Study Type`) %>%
+#   group_by(`Funder Type`) %>%
+#   mutate(prop = n / sum(n))
+# 
+# ggplotly(ggplot(df_summary, aes(x = `Funder Type`, y = prop, fill = `Study Type`)) +
+#   geom_bar(stat = "identity", position = "dodge") +
+#   theme_minimal() +
+#   labs(title = "Funding Sources and Study Types",
+#        x = "Funder Type",
+#        y = "Proportion") +
+#   scale_fill_brewer(palette = "Set2") +
+#   theme(axis.text.x = element_text(angle = 45, hjust = 1)))
 

From 2417ff336854ed879df9529bfc1e8e8c1e251af8 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sat, 30 Aug 2025 02:56:43 +0530
Subject: [PATCH 02/10] [check] update artifact version

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

diff --git a/.github/workflows/riskassessr.yaml b/.github/workflows/riskassessr.yaml
index fe82484..c74c281 100644
--- a/.github/workflows/riskassessr.yaml
+++ b/.github/workflows/riskassessr.yaml
@@ -308,7 +308,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Upload assessment artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         if: always()
         with:
           name: risk-assessment-logs

From f70e29e1c83533b4eed91224c8daa5b5e5303f84 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 10:15:55 +0530
Subject: [PATCH 03/10] [CHECK] update actions

---
 .github/workflows/R-CMD-check.yaml |  42 ++--
 .github/workflows/riskassessr.yaml | 320 ++++++++---------------------
 2 files changed, 104 insertions(+), 258 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index ccbe25e..67975c7 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,6 +1,8 @@
 name: R-CMD-check
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
 
 jobs:
   R-CMD-check:
@@ -9,29 +11,25 @@ jobs:
       image: rocker/tidyverse:latest
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
+      - name: Checkout repository
+        uses: actions/checkout@v3
 
-    - name: Set up R
-      uses: r-lib/actions/setup-r@v2
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
 
-    - name: Set environment variables
-      run: |
-        echo "R_LIBS_USER=/__w/_temp/Library" >> $GITHUB_ENV
-        echo "TZ=UTC" >> $GITHUB_ENV
-        echo "_R_CHECK_SYSTEM_CLOCK_=FALSE" >> $GITHUB_ENV
-        echo "NOT_CRAN=true" >> $GITHUB_ENV
+      - name: Set up R dependencies
+        uses: r-lib/actions/setup-renv@v2
 
-    - name: Restore R package dependencies
-      run: R -e 'renv::restore()'
+      - name: Cache R packages
+        uses: actions/cache@v3
+        with:
+          path: ~/.local/share/renv
+          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
 
-    - name: Install devtools
-      run: |
-        renv::install('devtools')
-      shell: Rscript {0}
+      - name: Install package
+        run: R CMD INSTALL .
 
-    - name: Install the package
-      run: R CMD INSTALL .
-
-    - name: Run tests
-      run: R -e 'devtools::test()'
+      - name: Run tests
+        run: R -e 'devtools::test()'
diff --git a/.github/workflows/riskassessr.yaml b/.github/workflows/riskassessr.yaml
index c74c281..41db945 100644
--- a/.github/workflows/riskassessr.yaml
+++ b/.github/workflows/riskassessr.yaml
@@ -2,15 +2,18 @@ name: Package Risk Assessment
 
 on:
   push:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   risk-assessment:
     runs-on: ubuntu-latest
     name: Risk Assessment
-    
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      CACHE_VERSION: v1
 
     steps:
       - name: Checkout repository
@@ -41,278 +44,123 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+          key: ${{ runner.os }}-${{ env.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: |
+            ${{ runner.os }}-${{ env.CACHE_VERSION }}-
 
-      - name: Install package dependencies
+      - name: Install dependencies
         run: |
+          install.packages(c("remotes", "devtools", "risk.assessr", "crayon", "knitr", "jsonlite"))
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 
-      - name: Install risk.assessr and additional dependencies
-        run: |
-          install.packages(c("risk.assessr", "crayon", "knitr"))
-        shell: Rscript {0}
-
       - name: Build package
-        run: |
-          devtools::build(path = ".", vignettes = FALSE)
+        run: devtools::build(path = ".", vignettes = FALSE)
         shell: Rscript {0}
 
       - name: Run Risk Assessment
         run: |
-          # Load required libraries
           library(risk.assessr)
           library(crayon)
-          
-          # Set up CRAN repository
-          r <- getOption("repos")
-          r["CRAN"] <- "https://cloud.r-project.org"
-          options(repos = r)
-          
-          cat("=== Starting Package Risk Assessment ===\n")
-          cat("Repository:", Sys.getenv("GITHUB_REPOSITORY"), "\n")
-          cat("Branch:", Sys.getenv("GITHUB_REF_NAME"), "\n")
-          cat("Workflow run:", Sys.getenv("GITHUB_RUN_ID"), "\n")
-          cat("Timestamp:", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), "\n\n")
-          
-          # Pretty print function for GitHub Actions logs
+          library(jsonlite)
+
+          `%||%` <- function(a, b) if (!is.null(a)) a else b
+
+          log_time <- function(msg) {
+            cat(sprintf("[%s] %s\n", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), msg))
+          }
+
           pretty_print_assessment <- function(assessment_results) {
-            
-            if (is.null(assessment_results) || length(assessment_results) == 0) {
-              cat("❌ No assessment results to display.\n")
+            if (is.null(assessment_results)) {
+              cat("❌ No assessment results\n")
               return()
             }
-            
-            # Helper functions for colored output in GitHub Actions
-            print_header <- function(title) {
-              cat("\n")
-              cat("🔍 ===", title, "===\n")
-              cat(paste(rep("=", nchar(title) + 10), collapse = ""), "\n")
-            }
-            
-            print_subheader <- function(title) {
-              cat("\n📊", title, "\n")
-              cat(paste(rep("-", nchar(title) + 3), collapse = ""), "\n")
-            }
-            
-            # Extract package name
-            pkg_name <- "Unknown Package"
-            if ("package" %in% names(assessment_results)) {
-              pkg_name <- assessment_results$package
-            } else if ("pkg_name" %in% names(assessment_results)) {
-              pkg_name <- assessment_results$pkg_name
-            }
-            
-            print_header("PACKAGE ASSESSMENT RESULTS")
-            cat("📦 Package:", pkg_name, "\n")
-            cat("⏰ Generated:", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n")
-            
-            # Print R CMD Check Results
+
+            # PACKAGE INFO
+            cat("::group::📦 Package Info\n")
+            pkg_name <- assessment_results$package %||% assessment_results$pkg_name %||% "Unknown"
+            cat("Package:", pkg_name, "\n")
+            cat("Generated:", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), "\n")
+            cat("::endgroup::\n")
+
+            # R CMD CHECK
             if ("rcmdcheck" %in% names(assessment_results)) {
-              print_header("R CMD CHECK RESULTS")
+              cat("::group::🔍 R CMD CHECK\n")
               rcmd <- assessment_results$rcmdcheck
-              
-              if (is.list(rcmd)) {
-                # Errors
-                if ("errors" %in% names(rcmd) && length(rcmd$errors) > 0) {
-                  print_subheader("🚨 ERRORS")
-                  for (error in rcmd$errors) {
-                    cat("❌", error, "\n")
-                  }
-                  cat("::error::R CMD check found", length(rcmd$errors), "error(s)\n")
-                } else {
-                  cat("✅ No errors found\n")
-                }
-                
-                # Warnings
-                if ("warnings" %in% names(rcmd) && length(rcmd$warnings) > 0) {
-                  print_subheader("⚠️ WARNINGS")
-                  for (warning in rcmd$warnings) {
-                    cat("⚠️", warning, "\n")
-                  }
-                  cat("::warning::R CMD check found", length(rcmd$warnings), "warning(s)\n")
-                } else {
-                  cat("✅ No warnings found\n")
-                }
-                
-                # Notes
-                if ("notes" %in% names(rcmd) && length(rcmd$notes) > 0) {
-                  print_subheader("📝 NOTES")
-                  for (note in rcmd$notes) {
-                    cat("ℹ️", note, "\n")
-                  }
-                  cat("::notice::R CMD check found", length(rcmd$notes), "note(s)\n")
-                } else {
-                  cat("✅ No notes\n")
-                }
-              } else {
-                cat(as.character(rcmd), "\n")
-              }
+              if (length(rcmd$errors) > 0) {
+                cat(red$bold("❌ Errors:\n"), paste(rcmd$errors, collapse="\n"), "\n")
+              } else cat(green$bold("✅ No errors\n"))
+              if (length(rcmd$warnings) > 0) {
+                cat(yellow$bold("⚠️ Warnings:\n"), paste(rcmd$warnings, collapse="\n"), "\n")
+              } else cat(green$bold("✅ No warnings\n"))
+              if (length(rcmd$notes) > 0) {
+                cat(blue$bold("ℹ️ Notes:\n"), paste(rcmd$notes, collapse="\n"), "\n")
+              } else cat(green$bold("✅ No notes\n"))
+              cat("::endgroup::\n")
             }
-            
-            # Print Coverage Results
+
+            # COVERAGE
             if ("covr" %in% names(assessment_results)) {
-              print_header("CODE COVERAGE")
+              cat("::group::📈 Coverage\n")
               covr <- assessment_results$covr
-              
               if (is.numeric(covr)) {
                 coverage_pct <- round(covr, 2)
-                if (coverage_pct >= 80) {
-                  cat("✅ Coverage:", coverage_pct, "%\n")
-                } else if (coverage_pct >= 60) {
-                  cat("⚠️ Coverage:", coverage_pct, "%\n")
-                  cat("::warning::Code coverage is below 80%\n")
-                } else {
-                  cat("❌ Coverage:", coverage_pct, "%\n")
-                  cat("::error::Code coverage is below 60%\n")
-                }
-              } else if (is.data.frame(covr)) {
-                cat("Coverage details:\n")
-                print(covr)
-              } else {
-                cat(as.character(covr), "\n")
-              }
+                cat("Coverage:", coverage_pct, "%\n")
+                if (coverage_pct < 60) cat("::error::Coverage < 60%\n")
+                else if (coverage_pct < 80) cat("::warning::Coverage < 80%\n")
+              } else print(covr)
+              cat("::endgroup::\n")
             }
-            
-            # Print Dependencies
+
+            # DEPENDENCIES
             if ("dependencies" %in% names(assessment_results)) {
-              print_header("DEPENDENCIES")
-              deps <- assessment_results$dependencies
-              
-              if (is.data.frame(deps)) {
-                if (nrow(deps) > 0) {
-                  cat("📋 Found", nrow(deps), "dependencies:\n")
-                  print(deps)
-                } else {
-                  cat("✅ No dependencies found\n")
-                }
-              } else if (is.list(deps)) {
-                if (length(deps) > 0) {
-                  for (name in names(deps)) {
-                    cat("•", name, ":", as.character(deps[[name]]), "\n")
-                  }
-                } else {
-                  cat("✅ No dependencies found\n")
-                }
-              } else {
-                cat(as.character(deps), "\n")
-              }
+              cat("::group::📋 Dependencies\n")
+              print(assessment_results$dependencies)
+              cat("::endgroup::\n")
             }
-            
-            # Print Metrics
+
+            # METRICS
             if ("metrics" %in% names(assessment_results)) {
-              print_header("PACKAGE METRICS")
-              metrics <- assessment_results$metrics
-              
-              if (is.data.frame(metrics)) {
-                if (nrow(metrics) > 0) {
-                  print(metrics)
-                } else {
-                  cat("No metrics data available\n")
-                }
-              } else if (is.list(metrics)) {
-                if (length(metrics) > 0) {
-                  for (name in names(metrics)) {
-                    cat("•", name, ":", as.character(metrics[[name]]), "\n")
-                  }
-                } else {
-                  cat("No metrics data available\n")
-                }
-              } else {
-                cat(as.character(metrics), "\n")
-              }
-            }
-            
-            # Print other components
-            other_components <- names(assessment_results)[!names(assessment_results) %in% 
-                                                         c("rcmdcheck", "covr", "dependencies", "metrics", "package", "pkg_name")]
-            
-            if (length(other_components) > 0) {
-              print_header("OTHER ASSESSMENT DATA")
-              
-              for (component in other_components) {
-                data <- assessment_results[[component]]
-                cat("\n📋", toupper(component), "\n")
-                
-                if (is.data.frame(data) && nrow(data) > 0) {
-                  print(data)
-                } else if (is.list(data) && length(data) > 0) {
-                  str(data, max.level = 2)
-                } else if (!is.null(data) && length(data) > 0) {
-                  cat(as.character(data), "\n")
-                } else {
-                  cat("No data available\n")
-                }
-              }
+              cat("::group::📊 Metrics\n")
+              print(assessment_results$metrics)
+              cat("::endgroup::\n")
             }
-            
-            # Summary
-            print_header("ASSESSMENT SUMMARY")
-            cat("📊 Total components assessed:", length(assessment_results), "\n")
-            
-            # Create GitHub Actions summary
-            error_count <- if("rcmdcheck" %in% names(assessment_results) && 
-                             "errors" %in% names(assessment_results$rcmdcheck)) 
-                             length(assessment_results$rcmdcheck$errors) else 0
-            warning_count <- if("rcmdcheck" %in% names(assessment_results) && 
-                               "warnings" %in% names(assessment_results$rcmdcheck)) 
-                               length(assessment_results$rcmdcheck$warnings) else 0
-            note_count <- if("rcmdcheck" %in% names(assessment_results) && 
-                            "notes" %in% names(assessment_results$rcmdcheck)) 
-                            length(assessment_results$rcmdcheck$notes) else 0
-            
-            if (error_count > 0) {
-              cat("::error::Assessment completed with", error_count, "errors\n")
-            } else if (warning_count > 0) {
-              cat("::warning::Assessment completed with", warning_count, "warnings\n")
-            } else {
-              cat("::notice::Assessment completed successfully\n")
-            }
-            
-            cat("\n🎉 Assessment display completed!\n")
           }
-          
-          # Run the assessment
+
+          log_time("🚀 Running risk assessment with risk.assessr...")
           tryCatch({
-            cat("🚀 Starting risk assessment...\n")
-            
-            # Use the simplified risk_assess_pkg function with current directory
-            comprehensive_assessment <- risk_assess_pkg(".")
-            
-            # Print the results
-            pretty_print_assessment(comprehensive_assessment)
-            
-          }, error = function(e) {
-            cat("::error::Assessment failed with error:", e$message, "\n")
-            cat("📋 Attempting fallback assessment...\n")
-            
-            # Fallback: try building package first
-            tryCatch({
-              # Build the package
-              built_pkg <- devtools::build(".", quiet = FALSE)
-              cat("📦 Package built:", built_pkg, "\n")
-              
-              # Try assessment with built package
-              comprehensive_assessment <- risk_assess_pkg(built_pkg)
-              pretty_print_assessment(comprehensive_assessment)
-              
-            }, error = function(e2) {
-              cat("::error::Fallback assessment also failed:", e2$message, "\n")
-              cat("🔍 Package structure:\n")
-              cat(paste(list.files(".", recursive = TRUE, include.dirs = TRUE), collapse = "\n"), "\n")
-            })
+            assessment <- risk_assess_pkg(".")
+            pretty_print_assessment(assessment)
+
+            # Save logs & structured results
+            saveRDS(assessment, "assessment_results.rds")
+            write_json(assessment, "assessment_results.json", pretty=TRUE, auto_unbox=TRUE)
+
+            # Write summary for GitHub
+            summary_file <- Sys.getenv("GITHUB_STEP_SUMMARY")
+            if (nzchar(summary_file)) {
+              writeLines(c(
+                "## 📊 Risk Assessment Summary",
+                paste0("- Package: ", assessment$package %||% "Unknown"),
+                paste0("- Errors: ", length(assessment$rcmdcheck$errors) %||% 0),
+                paste0("- Warnings: ", length(assessment$rcmdcheck$warnings) %||% 0),
+                paste0("- Notes: ", length(assessment$rcmdcheck$notes) %||% 0)
+              ), summary_file, append = TRUE)
+            }
+
+          }, error=function(e) {
+            cat("::error:: Risk assessment failed:", e$message, "\n")
           })
-          
-          cat("\n=== Risk Assessment Complete ===\n")
         shell: Rscript {0}
 
       - name: Upload assessment artifacts
         uses: actions/upload-artifact@v4
         if: always()
         with:
-          name: risk-assessment-logs
+          name: risk-assessment-output
           path: |
             *.log
             *.Rcheck/
+            assessment_results.json
+            assessment_results.rds
           retention-days: 30

From 1b1605843dad50377c2d1e6e0d486a0f3fd79d5d Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 10:45:24 +0530
Subject: [PATCH 04/10] [CHECK] update actions - 2

---
 .github/workflows/R-CMD-check.yaml |  67 +++---
 .github/workflows/riskassessr.yaml | 320 +++++++++++++++++++++--------
 renv.lock                          |  24 +--
 3 files changed, 288 insertions(+), 123 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 67975c7..95d755a 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,35 +1,48 @@
 name: R-CMD-check
 
-on:
+on: 
   push:
+    branches: [main, master]
   pull_request:
+    branches: [main, master]
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
-    container:
-      image: rocker/tidyverse:latest
-
+    runs-on: ${{ matrix.config.os }}
+    
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'release'}
+          
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-
-      - name: Set up R dependencies
-        uses: r-lib/actions/setup-renv@v2
-
-      - name: Cache R packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.local/share/renv
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
-
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Run tests
-        run: R -e 'devtools::test()'
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      
+    - name: Setup Pandoc
+      uses: r-lib/actions/setup-pandoc@v2
+      
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.config.r }}
+        use-public-rspm: true
+        
+    - name: Setup R dependencies
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        extra-packages: any::rcmdcheck, any::devtools
+        needs: check
+        
+    - name: Check R package
+      uses: r-lib/actions/check-r-package@v2
+      with:
+        upload-snapshots: true
diff --git a/.github/workflows/riskassessr.yaml b/.github/workflows/riskassessr.yaml
index 41db945..c74c281 100644
--- a/.github/workflows/riskassessr.yaml
+++ b/.github/workflows/riskassessr.yaml
@@ -2,18 +2,15 @@ name: Package Risk Assessment
 
 on:
   push:
-  pull_request:
-  workflow_dispatch:
 
 jobs:
   risk-assessment:
     runs-on: ubuntu-latest
     name: Risk Assessment
-
+    
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      CACHE_VERSION: v1
 
     steps:
       - name: Checkout repository
@@ -44,123 +41,278 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ env.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: |
-            ${{ runner.os }}-${{ env.CACHE_VERSION }}-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
-      - name: Install dependencies
+      - name: Install package dependencies
         run: |
-          install.packages(c("remotes", "devtools", "risk.assessr", "crayon", "knitr", "jsonlite"))
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 
+      - name: Install risk.assessr and additional dependencies
+        run: |
+          install.packages(c("risk.assessr", "crayon", "knitr"))
+        shell: Rscript {0}
+
       - name: Build package
-        run: devtools::build(path = ".", vignettes = FALSE)
+        run: |
+          devtools::build(path = ".", vignettes = FALSE)
         shell: Rscript {0}
 
       - name: Run Risk Assessment
         run: |
+          # Load required libraries
           library(risk.assessr)
           library(crayon)
-          library(jsonlite)
-
-          `%||%` <- function(a, b) if (!is.null(a)) a else b
-
-          log_time <- function(msg) {
-            cat(sprintf("[%s] %s\n", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), msg))
-          }
-
+          
+          # Set up CRAN repository
+          r <- getOption("repos")
+          r["CRAN"] <- "https://cloud.r-project.org"
+          options(repos = r)
+          
+          cat("=== Starting Package Risk Assessment ===\n")
+          cat("Repository:", Sys.getenv("GITHUB_REPOSITORY"), "\n")
+          cat("Branch:", Sys.getenv("GITHUB_REF_NAME"), "\n")
+          cat("Workflow run:", Sys.getenv("GITHUB_RUN_ID"), "\n")
+          cat("Timestamp:", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), "\n\n")
+          
+          # Pretty print function for GitHub Actions logs
           pretty_print_assessment <- function(assessment_results) {
-            if (is.null(assessment_results)) {
-              cat("❌ No assessment results\n")
+            
+            if (is.null(assessment_results) || length(assessment_results) == 0) {
+              cat("❌ No assessment results to display.\n")
               return()
             }
-
-            # PACKAGE INFO
-            cat("::group::📦 Package Info\n")
-            pkg_name <- assessment_results$package %||% assessment_results$pkg_name %||% "Unknown"
-            cat("Package:", pkg_name, "\n")
-            cat("Generated:", format(Sys.time(), "%Y-%m-%d %H:%M:%S UTC"), "\n")
-            cat("::endgroup::\n")
-
-            # R CMD CHECK
+            
+            # Helper functions for colored output in GitHub Actions
+            print_header <- function(title) {
+              cat("\n")
+              cat("🔍 ===", title, "===\n")
+              cat(paste(rep("=", nchar(title) + 10), collapse = ""), "\n")
+            }
+            
+            print_subheader <- function(title) {
+              cat("\n📊", title, "\n")
+              cat(paste(rep("-", nchar(title) + 3), collapse = ""), "\n")
+            }
+            
+            # Extract package name
+            pkg_name <- "Unknown Package"
+            if ("package" %in% names(assessment_results)) {
+              pkg_name <- assessment_results$package
+            } else if ("pkg_name" %in% names(assessment_results)) {
+              pkg_name <- assessment_results$pkg_name
+            }
+            
+            print_header("PACKAGE ASSESSMENT RESULTS")
+            cat("📦 Package:", pkg_name, "\n")
+            cat("⏰ Generated:", format(Sys.time(), "%Y-%m-%d %H:%M:%S"), "\n")
+            
+            # Print R CMD Check Results
             if ("rcmdcheck" %in% names(assessment_results)) {
-              cat("::group::🔍 R CMD CHECK\n")
+              print_header("R CMD CHECK RESULTS")
               rcmd <- assessment_results$rcmdcheck
-              if (length(rcmd$errors) > 0) {
-                cat(red$bold("❌ Errors:\n"), paste(rcmd$errors, collapse="\n"), "\n")
-              } else cat(green$bold("✅ No errors\n"))
-              if (length(rcmd$warnings) > 0) {
-                cat(yellow$bold("⚠️ Warnings:\n"), paste(rcmd$warnings, collapse="\n"), "\n")
-              } else cat(green$bold("✅ No warnings\n"))
-              if (length(rcmd$notes) > 0) {
-                cat(blue$bold("ℹ️ Notes:\n"), paste(rcmd$notes, collapse="\n"), "\n")
-              } else cat(green$bold("✅ No notes\n"))
-              cat("::endgroup::\n")
+              
+              if (is.list(rcmd)) {
+                # Errors
+                if ("errors" %in% names(rcmd) && length(rcmd$errors) > 0) {
+                  print_subheader("🚨 ERRORS")
+                  for (error in rcmd$errors) {
+                    cat("❌", error, "\n")
+                  }
+                  cat("::error::R CMD check found", length(rcmd$errors), "error(s)\n")
+                } else {
+                  cat("✅ No errors found\n")
+                }
+                
+                # Warnings
+                if ("warnings" %in% names(rcmd) && length(rcmd$warnings) > 0) {
+                  print_subheader("⚠️ WARNINGS")
+                  for (warning in rcmd$warnings) {
+                    cat("⚠️", warning, "\n")
+                  }
+                  cat("::warning::R CMD check found", length(rcmd$warnings), "warning(s)\n")
+                } else {
+                  cat("✅ No warnings found\n")
+                }
+                
+                # Notes
+                if ("notes" %in% names(rcmd) && length(rcmd$notes) > 0) {
+                  print_subheader("📝 NOTES")
+                  for (note in rcmd$notes) {
+                    cat("ℹ️", note, "\n")
+                  }
+                  cat("::notice::R CMD check found", length(rcmd$notes), "note(s)\n")
+                } else {
+                  cat("✅ No notes\n")
+                }
+              } else {
+                cat(as.character(rcmd), "\n")
+              }
             }
-
-            # COVERAGE
+            
+            # Print Coverage Results
             if ("covr" %in% names(assessment_results)) {
-              cat("::group::📈 Coverage\n")
+              print_header("CODE COVERAGE")
               covr <- assessment_results$covr
+              
               if (is.numeric(covr)) {
                 coverage_pct <- round(covr, 2)
-                cat("Coverage:", coverage_pct, "%\n")
-                if (coverage_pct < 60) cat("::error::Coverage < 60%\n")
-                else if (coverage_pct < 80) cat("::warning::Coverage < 80%\n")
-              } else print(covr)
-              cat("::endgroup::\n")
+                if (coverage_pct >= 80) {
+                  cat("✅ Coverage:", coverage_pct, "%\n")
+                } else if (coverage_pct >= 60) {
+                  cat("⚠️ Coverage:", coverage_pct, "%\n")
+                  cat("::warning::Code coverage is below 80%\n")
+                } else {
+                  cat("❌ Coverage:", coverage_pct, "%\n")
+                  cat("::error::Code coverage is below 60%\n")
+                }
+              } else if (is.data.frame(covr)) {
+                cat("Coverage details:\n")
+                print(covr)
+              } else {
+                cat(as.character(covr), "\n")
+              }
             }
-
-            # DEPENDENCIES
+            
+            # Print Dependencies
             if ("dependencies" %in% names(assessment_results)) {
-              cat("::group::📋 Dependencies\n")
-              print(assessment_results$dependencies)
-              cat("::endgroup::\n")
+              print_header("DEPENDENCIES")
+              deps <- assessment_results$dependencies
+              
+              if (is.data.frame(deps)) {
+                if (nrow(deps) > 0) {
+                  cat("📋 Found", nrow(deps), "dependencies:\n")
+                  print(deps)
+                } else {
+                  cat("✅ No dependencies found\n")
+                }
+              } else if (is.list(deps)) {
+                if (length(deps) > 0) {
+                  for (name in names(deps)) {
+                    cat("•", name, ":", as.character(deps[[name]]), "\n")
+                  }
+                } else {
+                  cat("✅ No dependencies found\n")
+                }
+              } else {
+                cat(as.character(deps), "\n")
+              }
             }
-
-            # METRICS
+            
+            # Print Metrics
             if ("metrics" %in% names(assessment_results)) {
-              cat("::group::📊 Metrics\n")
-              print(assessment_results$metrics)
-              cat("::endgroup::\n")
+              print_header("PACKAGE METRICS")
+              metrics <- assessment_results$metrics
+              
+              if (is.data.frame(metrics)) {
+                if (nrow(metrics) > 0) {
+                  print(metrics)
+                } else {
+                  cat("No metrics data available\n")
+                }
+              } else if (is.list(metrics)) {
+                if (length(metrics) > 0) {
+                  for (name in names(metrics)) {
+                    cat("•", name, ":", as.character(metrics[[name]]), "\n")
+                  }
+                } else {
+                  cat("No metrics data available\n")
+                }
+              } else {
+                cat(as.character(metrics), "\n")
+              }
+            }
+            
+            # Print other components
+            other_components <- names(assessment_results)[!names(assessment_results) %in% 
+                                                         c("rcmdcheck", "covr", "dependencies", "metrics", "package", "pkg_name")]
+            
+            if (length(other_components) > 0) {
+              print_header("OTHER ASSESSMENT DATA")
+              
+              for (component in other_components) {
+                data <- assessment_results[[component]]
+                cat("\n📋", toupper(component), "\n")
+                
+                if (is.data.frame(data) && nrow(data) > 0) {
+                  print(data)
+                } else if (is.list(data) && length(data) > 0) {
+                  str(data, max.level = 2)
+                } else if (!is.null(data) && length(data) > 0) {
+                  cat(as.character(data), "\n")
+                } else {
+                  cat("No data available\n")
+                }
+              }
             }
+            
+            # Summary
+            print_header("ASSESSMENT SUMMARY")
+            cat("📊 Total components assessed:", length(assessment_results), "\n")
+            
+            # Create GitHub Actions summary
+            error_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                             "errors" %in% names(assessment_results$rcmdcheck)) 
+                             length(assessment_results$rcmdcheck$errors) else 0
+            warning_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                               "warnings" %in% names(assessment_results$rcmdcheck)) 
+                               length(assessment_results$rcmdcheck$warnings) else 0
+            note_count <- if("rcmdcheck" %in% names(assessment_results) && 
+                            "notes" %in% names(assessment_results$rcmdcheck)) 
+                            length(assessment_results$rcmdcheck$notes) else 0
+            
+            if (error_count > 0) {
+              cat("::error::Assessment completed with", error_count, "errors\n")
+            } else if (warning_count > 0) {
+              cat("::warning::Assessment completed with", warning_count, "warnings\n")
+            } else {
+              cat("::notice::Assessment completed successfully\n")
+            }
+            
+            cat("\n🎉 Assessment display completed!\n")
           }
-
-          log_time("🚀 Running risk assessment with risk.assessr...")
+          
+          # Run the assessment
           tryCatch({
-            assessment <- risk_assess_pkg(".")
-            pretty_print_assessment(assessment)
-
-            # Save logs & structured results
-            saveRDS(assessment, "assessment_results.rds")
-            write_json(assessment, "assessment_results.json", pretty=TRUE, auto_unbox=TRUE)
-
-            # Write summary for GitHub
-            summary_file <- Sys.getenv("GITHUB_STEP_SUMMARY")
-            if (nzchar(summary_file)) {
-              writeLines(c(
-                "## 📊 Risk Assessment Summary",
-                paste0("- Package: ", assessment$package %||% "Unknown"),
-                paste0("- Errors: ", length(assessment$rcmdcheck$errors) %||% 0),
-                paste0("- Warnings: ", length(assessment$rcmdcheck$warnings) %||% 0),
-                paste0("- Notes: ", length(assessment$rcmdcheck$notes) %||% 0)
-              ), summary_file, append = TRUE)
-            }
-
-          }, error=function(e) {
-            cat("::error:: Risk assessment failed:", e$message, "\n")
+            cat("🚀 Starting risk assessment...\n")
+            
+            # Use the simplified risk_assess_pkg function with current directory
+            comprehensive_assessment <- risk_assess_pkg(".")
+            
+            # Print the results
+            pretty_print_assessment(comprehensive_assessment)
+            
+          }, error = function(e) {
+            cat("::error::Assessment failed with error:", e$message, "\n")
+            cat("📋 Attempting fallback assessment...\n")
+            
+            # Fallback: try building package first
+            tryCatch({
+              # Build the package
+              built_pkg <- devtools::build(".", quiet = FALSE)
+              cat("📦 Package built:", built_pkg, "\n")
+              
+              # Try assessment with built package
+              comprehensive_assessment <- risk_assess_pkg(built_pkg)
+              pretty_print_assessment(comprehensive_assessment)
+              
+            }, error = function(e2) {
+              cat("::error::Fallback assessment also failed:", e2$message, "\n")
+              cat("🔍 Package structure:\n")
+              cat(paste(list.files(".", recursive = TRUE, include.dirs = TRUE), collapse = "\n"), "\n")
+            })
           })
+          
+          cat("\n=== Risk Assessment Complete ===\n")
         shell: Rscript {0}
 
       - name: Upload assessment artifacts
         uses: actions/upload-artifact@v4
         if: always()
         with:
-          name: risk-assessment-output
+          name: risk-assessment-logs
           path: |
             *.log
             *.Rcheck/
-            assessment_results.json
-            assessment_results.rds
           retention-days: 30
diff --git a/renv.lock b/renv.lock
index 0e124bc..4081470 100644
--- a/renv.lock
+++ b/renv.lock
@@ -359,7 +359,7 @@
     },
     "knitr": {
       "Package": "knitr",
-      "Version": "1.50",
+      "Version": "1.48",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -371,7 +371,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "5a07d8ec459d7b80bd4acca5f4a6e062"
+      "Hash": "acf380f300c721da9fde7df115a5f86f"
     },
     "lifecycle": {
       "Package": "lifecycle",
@@ -388,7 +388,7 @@
     },
     "lubridate": {
       "Package": "lubridate",
-      "Version": "1.9.4",
+      "Version": "1.9.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -397,7 +397,7 @@
         "methods",
         "timechange"
       ],
-      "Hash": "be38bc740fc51783a78edb5a157e4104"
+      "Hash": "680ad542fbcf801442c83a6ac5a2126c"
     },
     "magrittr": {
       "Package": "magrittr",
@@ -547,7 +547,7 @@
     },
     "rmarkdown": {
       "Package": "rmarkdown",
-      "Version": "2.29",
+      "Version": "2.27",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -566,7 +566,7 @@
         "xfun",
         "yaml"
       ],
-      "Hash": "df99277f63d01c34e95e3d2f06a79736"
+      "Hash": "27f9502e1cdbfa195f94e03b0f517484"
     },
     "sass": {
       "Package": "sass",
@@ -591,12 +591,12 @@
     },
     "tibble": {
       "Package": "tibble",
-      "Version": "3.3.0",
+      "Version": "3.2.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
-        "cli",
+        "fansi",
         "lifecycle",
         "magrittr",
         "methods",
@@ -606,7 +606,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "784b27d0801c3829de602105757b2cd7"
+      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
     },
     "tidyselect": {
       "Package": "tidyselect",
@@ -720,7 +720,7 @@
     },
     "xfun": {
       "Package": "xfun",
-      "Version": "0.53",
+      "Version": "0.47",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -729,7 +729,7 @@
         "stats",
         "tools"
       ],
-      "Hash": "1befe97a0d56060b3964e3986d408df9"
+      "Hash": "36ab21660e2d095fef0d83f689e0477c"
     },
     "yaml": {
       "Package": "yaml",
@@ -739,4 +739,4 @@
       "Hash": "9cb28d11799d93c953f852083d55ee9e"
     }
   }
-}
+}
\ No newline at end of file

From 04629558131fe9c53fbffe15c8e276af90f807fe Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 10:46:48 +0530
Subject: [PATCH 05/10] [CHECK] update actions - 3

---
 .github/workflows/R-CMD-check.yaml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 95d755a..ffced6b 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,10 +1,6 @@
 name: R-CMD-check
 
-on: 
-  push:
-    branches: [main, master]
-  pull_request:
-    branches: [main, master]
+on: [push, pull_request]
 
 jobs:
   R-CMD-check:

From d65f984e07ec9e41dbbbd9edac0c4160f306d461 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 11:53:20 +0530
Subject: [PATCH 06/10] [CHECK] check for oss vulnerabilites

---
 .github/workflows/security-check.yaml | 153 ++++++++++++++++++
 README.Rmd                            | 220 --------------------------
 README.md                             |   2 +
 3 files changed, 155 insertions(+), 220 deletions(-)
 create mode 100644 .github/workflows/security-check.yaml
 delete mode 100644 README.Rmd

diff --git a/.github/workflows/security-check.yaml b/.github/workflows/security-check.yaml
new file mode 100644
index 0000000..d212095
--- /dev/null
+++ b/.github/workflows/security-check.yaml
@@ -0,0 +1,153 @@
+name: Security Check
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+  schedule:
+    # Run weekly on Sundays at 2 AM UTC
+    - cron: '0 2 * * 0'
+  workflow_dispatch:
+
+jobs:
+  security-audit:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+    
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 'release'
+    
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
+    
+    - name: Cache R packages
+      uses: actions/cache@v3
+      with:
+        path: ~/.local/lib/R/site-library
+        key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
+        restore-keys: ${{ runner.os }}-r-
+    
+    - name: Install oysteR
+      run: |
+        R -e "install.packages('oysteR', repos='https://cran.r-project.org')"
+    
+    - name: Install clintrialx (if needed)
+      run: |
+        R -e "if (!require('clintrialx', quietly = TRUE)) install.packages('clintrialx', repos='https://cran.r-project.org')"
+      continue-on-error: true
+    
+    - name: Run security audit
+      id: audit
+      run: |
+        # Create R script for vulnerability check
+        cat > check_vulnerabilities.R << 'EOF'
+        library(oysteR)
+        
+        # Function to safely check vulnerabilities
+        check_package_vulnerabilities <- function(pkg_name) {
+          tryCatch({
+            # Try to get vulnerabilities for the package
+            result <- expect_secure(pkg_name)
+            
+            # If we get here, no vulnerabilities found
+            cat("VULNERABILITY_COUNT=0\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+            cat("STATUS=success\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+            cat("MESSAGE=No vulnerabilities found\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+            
+            return(0)
+          }, error = function(e) {
+            # Check if error is due to vulnerabilities found
+            if (grepl("vulnerabilities", e$message, ignore.case = TRUE)) {
+              # Parse vulnerability count if possible
+              vuln_match <- regexpr("[0-9]+", e$message)
+              if (vuln_match > 0) {
+                vuln_count <- regmatches(e$message, vuln_match)
+                cat(paste0("VULNERABILITY_COUNT=", vuln_count, "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+              } else {
+                cat("VULNERABILITY_COUNT=unknown\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+              }
+              cat("STATUS=failure\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+              cat(paste0("MESSAGE=", gsub("\n", " ", e$message), "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+            } else {
+              # Other error (package not found, network issue, etc.)
+              cat("VULNERABILITY_COUNT=error\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+              cat("STATUS=error\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+              cat(paste0("MESSAGE=Check failed: ", gsub("\n", " ", e$message), "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+            }
+            return(1)
+          })
+        }
+        
+        # Run the check
+        result <- check_package_vulnerabilities("clintrialx")
+        quit(status = result)
+        EOF
+        
+        # Run the R script
+        R --slave < check_vulnerabilities.R
+      continue-on-error: true
+    
+    - name: Create vulnerability badge
+      run: |
+        # Determine badge color and message based on results
+        case "${{ steps.audit.outputs.STATUS }}" in
+          "success")
+            BADGE_COLOR="brightgreen"
+            BADGE_MESSAGE="0"
+            ;;
+          "failure")
+            BADGE_COLOR="red"
+            BADGE_MESSAGE="${{ steps.audit.outputs.VULNERABILITY_COUNT }}"
+            ;;
+          "error")
+            BADGE_COLOR="orange"
+            BADGE_MESSAGE="check%20failed"
+            ;;
+          *)
+            BADGE_COLOR="lightgrey"
+            BADGE_MESSAGE="unknown"
+            ;;
+        esac
+        
+        # Create badge URL
+        BADGE_URL="https://img.shields.io/badge/clintrialx%20vulnerabilities-${BADGE_MESSAGE}-${BADGE_COLOR}"
+        
+        # Output badge info
+        echo "BADGE_URL=${BADGE_URL}" >> $GITHUB_OUTPUT
+        echo "Badge URL: ${BADGE_URL}"
+        echo "Status: ${{ steps.audit.outputs.STATUS }}"
+        echo "Message: ${{ steps.audit.outputs.MESSAGE }}"
+      id: badge
+    
+    - name: Update README badge (optional)
+      if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
+      run: |
+        # This step would update your README.md file with the new badge
+        # You can customize this based on your README structure
+        echo "Badge URL for README: ${{ steps.badge.outputs.BADGE_URL }}"
+        echo "You can manually update your README.md with this badge URL"
+    
+    - name: Create badge artifact
+      uses: actions/upload-artifact@v3
+      with:
+        name: security-badge
+        path: |
+          badge_info.txt
+        retention-days: 30
+      if: always()
+    
+    - name: Save badge info
+      run: |
+        echo "Badge URL: ${{ steps.badge.outputs.BADGE_URL }}" > badge_info.txt
+        echo "Status: ${{ steps.audit.outputs.STATUS }}" >> badge_info.txt
+        echo "Vulnerability Count: ${{ steps.audit.outputs.VULNERABILITY_COUNT }}" >> badge_info.txt
+        echo "Message: ${{ steps.audit.outputs.MESSAGE }}" >> badge_info.txt
+      if: always()
diff --git a/README.Rmd b/README.Rmd
deleted file mode 100644
index 12ce7ae..0000000
--- a/README.Rmd
+++ /dev/null
@@ -1,220 +0,0 @@
----
-output: github_document
-editor_options: 
-  markdown: 
-    wrap: 72
----
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-```{r include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "man/figures/README-",
-  out.width = "100%"
-)
-```
-
-# `ClinTrialX`
-
-<!-- badges: start -->
-[![R-CMD-check](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
-[![License:
-Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/license/apache-2-0)
-[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://www.indraneelchakraborty.com/clintrialx/)
-[![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fineelhere%2Fclintrialx&label=Visitors&labelColor=%23f47373&countColor=%2337d67a&style=flat&labelStyle=upper)](https://github.com/ineelhere/clintrialx)
-[![CRAN
-status](https://www.r-pkg.org/badges/version/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
-[![CRAN
-downloads](https://cranlogs.r-pkg.org/badges/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
-
-[![Data Sources:
-ClinicalTrials.gov](https://img.shields.io/badge/Data_Sources-ClinicalTrials.gov-blue)](https://clinicaltrials.gov/data-api/api)
-[![Data Sources: CTTI
-AACT](https://img.shields.io/badge/Data_Sources-CTTI%20AACT%20-purple)](https://aact.ctti-clinicaltrials.org/)
-
-<!-- badges: end -->
-
-The goal of `{clintrialx}` is to fetch clinical trials data from freely
-available registries. Currently, it supports querying the
-
--   [ClinicalTrials.gov](https://clinicaltrials.gov/) registry using its
-    [V2 API](https://clinicaltrials.gov/data-api/api) and
-
--   [CTTI AACT](https://aact.ctti-clinicaltrials.org/) (Public Access to
-    Aggregate Content of ClinicalTrials.gov).
-
-## Installation
-
-Install the package from [CRAN](https://CRAN.R-project.org/package=clintrialx) with:
-```r
-install.packages("clintrialx")
-```
-You can install this package from
-[GitHub](https://github.com/ineelhere/clintrialx) with:
-
-*you'll need the `devtools` package for this*
-
-``` r
-# install.packages("devtools")
-devtools::install_github("ineelhere/clintrialx")
-```
-
-### Check installation
-
-``` r
-library(clintrialx)
-```
-
-## Setup AACT account
-
-#### `Only if you wish to use AACT as a source for the data`
-
--   Visit <https://aact.ctti-clinicaltrials.org/users/sign_up>
-
--   Sign up and create an account. It's free.
-
--   The `username` and `password` will be needed to fetch data using
-    this package.
-
--   Save it in a `.Renviron` file, for example-
-
-    ``` r
-    user =  "random_name"
-    password = "random_password"
-    ```
-
--   Now that the file is created, load the variable with the command
-    `readRenviron("path/to/.Renviron)`
-
--   You're all set!
-
-## Query the [ClinicalTrials.gov](https://clinicaltrials.gov/) Registry
-
-#### Based on NCT IDs
-
-Fetch one or multiple trial records based on NCT IDs. You can opt to
-fetch some specific fields or all fields available at source (default).
-
-```{r example1, eval = FALSE}
-library(clintrialx)
-ctg_get_nct(c("NCT02967965", "NCT04000165", "NCT01007279", "NCT02376244", "NCT01179776"),
-                          fields = c("NCT Number", "Study Title", "Study Status", "Sponsor"))
-
-
-```
-
-#### Based on fileds
-
-Supports filtering by condition, location, title keywords, intervention,
-and overall status.
-
-```{r example2, eval = FALSE}
-ctg_get_fields(
-     condition = "Cancer",
-     location = "Kolkata",
-     title = NULL,
-     intervention = "Drug",
-     status = c("ACTIVE_NOT_RECRUITING", "RECRUITING"),
-     page_size = 10
-)
-
-```
-
-#### Based on fields - Bulk download
-
-Download all available data for your query. No limits!
-
-*Supports filtering by condition, location, title keywords,
-intervention, and overall status.*
-
-```{r example5, eval = FALSE}
-df <- ctg_bulk_fetch(location="india")
-```
-
-## Query the [CTTI AACT](https://aact.ctti-clinicaltrials.org/)
-
-#### Run Custom Queries
-
-```
-# Set environment variables for database credentials in .Renviron and load it
-# readRenviron(".Renviron")
-
-# Connect to the database
-con <- aact_connection(Sys.getenv('user'), Sys.getenv('password'))
-
-# Run a custom query
-query <- "SELECT nct_id, source, enrollment, overall_status FROM studies LIMIT 5;"
-results <- aact_custom_query(con, query)
-
-# Print the results
-print(results)
-```
-
-## Trial Data HTML Reports
-
-*Currently works for data from ClinicalTrials.Gov*
-
-Visit here for an exqample report -
-<https://www.indraneelchakraborty.com/clintrialx/report.html>
-
-```{r example6, eval = FALSE}
-#first get the data in a R dataframe
-my_clinical_trial_data <- ctg_bulk_fetch(condition="cancer")
-#now pass it to the reports function
-ctg_data_report(
-  ctg_data = my_clinical_trial_data,
-  title = "Clinical Trials Analysis",
-  author = "Indra",
-  output_file = "reports/clinical_trials.html",
-  theme = "flatly",
-  color_palette = c("#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F", "#EDC948"),
-  include_data_quality = TRUE,
-  include_interactive_plots = TRUE,
-  custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
-)
-
-# Generate a report with static plots and no data quality assessment
-ctg_data_report(
-  ctg_data = my_clinical_trial_data,
-  title = "Quick Clinical Trial Overview",
-  include_data_quality = FALSE,
-  include_interactive_plots = FALSE
-)
-
-```
-
-Check the path `reports/clinical_trials.html` on your local. It will
-have the html report file.
-
-Cool stuff - It also has the codes to the plots!
-
-## Data Sources
-
-You can fetch version information directly from the package:
-
-```{r example3, eval = FALSE}
-version_info(source = "clinicaltrials.gov")
-
-
-```
-
-## Get Involved
-
-🚀 Ready to contribute? Let's make clintrialx even better!
-
--   Fork the [GitHub](https://github.com/ineelhere/clintrialx) repo.
--   Check out your development branch from the dev branch.
--   Do your work on a feature (ftr) branch.
--   Raise a PR against the dev branch of the [clintrialx](https://github.com/ineelhere/clintrialx) repo.
--   Sit back and [relax](https://www.youtube.com/watch?v=Uffjii1hXzU) while I review it!
-
-💬 **Questions or Feedback?** Feel free to open an issue on [GitHub
-Issues page](https://github.com/ineelhere/clintrialx/issues).
-
-🌟 **Enjoying `clintrialx`?** Please consider giving it a star on
-[GitHub](https://github.com/ineelhere/clintrialx)! Your support helps
-this project grow and improve.
-
-More updates to come. Happy coding! 🎉
diff --git a/README.md b/README.md
index 5bc4af5..da330fe 100644
--- a/README.md
+++ b/README.md
@@ -19,6 +19,8 @@ downloads](https://cranlogs.r-pkg.org/badges/clintrialx)](https://CRAN.R-project
 ClinicalTrials.gov](https://img.shields.io/badge/Data_Sources-ClinicalTrials.gov-blue)](https://clinicaltrials.gov/data-api/api)
 [![Data Sources: CTTI
 AACT](https://img.shields.io/badge/Data_Sources-CTTI%20AACT%20-purple)](https://aact.ctti-clinicaltrials.org/)
+![Security Check](https://github.com/yourusername/yourrepo/workflows/Security%20Check/badge.svg)
+
 
 <!-- badges: end -->
 

From d26cb58ae6450e40c843375ade5bfc2e4ee6b832 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 11:55:17 +0530
Subject: [PATCH 07/10] [CHECK] check for oss vulnerabilites - 2

---
 .github/workflows/security-check.yaml | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/.github/workflows/security-check.yaml b/.github/workflows/security-check.yaml
index d212095..60f201b 100644
--- a/.github/workflows/security-check.yaml
+++ b/.github/workflows/security-check.yaml
@@ -1,14 +1,6 @@
 name: Security Check
 
-on:
-  push:
-    branches: [ main, master ]
-  pull_request:
-    branches: [ main, master ]
-  schedule:
-    # Run weekly on Sundays at 2 AM UTC
-    - cron: '0 2 * * 0'
-  workflow_dispatch:
+on: [push, pull_request]
 
 jobs:
   security-audit:

From 42bb3f664661ed5cb4a614e9a3414e805301a30d Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 12:00:36 +0530
Subject: [PATCH 08/10] [CHECK] check for oss vulnerabilites - 3

---
 .github/workflows/security-check.yaml | 66 +++++++++++++--------------
 1 file changed, 32 insertions(+), 34 deletions(-)

diff --git a/.github/workflows/security-check.yaml b/.github/workflows/security-check.yaml
index 60f201b..a00d78b 100644
--- a/.github/workflows/security-check.yaml
+++ b/.github/workflows/security-check.yaml
@@ -5,55 +5,55 @@ on: [push, pull_request]
 jobs:
   security-audit:
     runs-on: ubuntu-latest
-    
+
     steps:
     - name: Checkout code
       uses: actions/checkout@v4
-    
+
     - name: Set up R
       uses: r-lib/actions/setup-r@v2
       with:
         r-version: 'release'
-    
+
     - name: Install system dependencies
       run: |
         sudo apt-get update
         sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
-    
+
     - name: Cache R packages
       uses: actions/cache@v3
       with:
         path: ~/.local/lib/R/site-library
         key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
         restore-keys: ${{ runner.os }}-r-
-    
+
     - name: Install oysteR
       run: |
         R -e "install.packages('oysteR', repos='https://cran.r-project.org')"
-    
+
     - name: Install clintrialx (if needed)
       run: |
         R -e "if (!require('clintrialx', quietly = TRUE)) install.packages('clintrialx', repos='https://cran.r-project.org')"
       continue-on-error: true
-    
+
     - name: Run security audit
       id: audit
       run: |
         # Create R script for vulnerability check
         cat > check_vulnerabilities.R << 'EOF'
         library(oysteR)
-        
+
         # Function to safely check vulnerabilities
         check_package_vulnerabilities <- function(pkg_name) {
           tryCatch({
             # Try to get vulnerabilities for the package
             result <- expect_secure(pkg_name)
-            
+
             # If we get here, no vulnerabilities found
             cat("VULNERABILITY_COUNT=0\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
             cat("STATUS=success\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
             cat("MESSAGE=No vulnerabilities found\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-            
+
             return(0)
           }, error = function(e) {
             # Check if error is due to vulnerabilities found
@@ -77,17 +77,18 @@ jobs:
             return(1)
           })
         }
-        
+
         # Run the check
         result <- check_package_vulnerabilities("clintrialx")
         quit(status = result)
         EOF
-        
+
         # Run the R script
         R --slave < check_vulnerabilities.R
       continue-on-error: true
-    
+
     - name: Create vulnerability badge
+      id: badge
       run: |
         # Determine badge color and message based on results
         case "${{ steps.audit.outputs.STATUS }}" in
@@ -108,38 +109,35 @@ jobs:
             BADGE_MESSAGE="unknown"
             ;;
         esac
-        
+
         # Create badge URL
         BADGE_URL="https://img.shields.io/badge/clintrialx%20vulnerabilities-${BADGE_MESSAGE}-${BADGE_COLOR}"
-        
+
         # Output badge info
         echo "BADGE_URL=${BADGE_URL}" >> $GITHUB_OUTPUT
         echo "Badge URL: ${BADGE_URL}"
         echo "Status: ${{ steps.audit.outputs.STATUS }}"
         echo "Message: ${{ steps.audit.outputs.MESSAGE }}"
-      id: badge
-    
-    - name: Update README badge (optional)
-      if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
-      run: |
-        # This step would update your README.md file with the new badge
-        # You can customize this based on your README structure
-        echo "Badge URL for README: ${{ steps.badge.outputs.BADGE_URL }}"
-        echo "You can manually update your README.md with this badge URL"
-    
-    - name: Create badge artifact
-      uses: actions/upload-artifact@v3
-      with:
-        name: security-badge
-        path: |
-          badge_info.txt
-        retention-days: 30
-      if: always()
-    
+
     - name: Save badge info
+      if: always()
       run: |
         echo "Badge URL: ${{ steps.badge.outputs.BADGE_URL }}" > badge_info.txt
         echo "Status: ${{ steps.audit.outputs.STATUS }}" >> badge_info.txt
         echo "Vulnerability Count: ${{ steps.audit.outputs.VULNERABILITY_COUNT }}" >> badge_info.txt
         echo "Message: ${{ steps.audit.outputs.MESSAGE }}" >> badge_info.txt
+
+    - name: Create badge artifact
       if: always()
+      uses: actions/upload-artifact@v4   # ← updated to v4
+      with:
+        name: security-badge
+        path: badge_info.txt
+        retention-days: 30
+
+    - name: Update README badge (optional)
+      if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
+      run: |
+        # This step would update your README.md file with the new badge
+        echo "Badge URL for README: ${{ steps.badge.outputs.BADGE_URL }}"
+        echo "You can manually update your README.md with this badge URL"

From 76688aabb7cd87b3d8cc66036cb0bcab23d1c8f3 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Sun, 31 Aug 2025 12:48:42 +0530
Subject: [PATCH 09/10] byepass rmd for readme

---
 .github/workflows/security-check.yaml | 143 --------------------------
 README.md                             |  19 ++--
 2 files changed, 7 insertions(+), 155 deletions(-)
 delete mode 100644 .github/workflows/security-check.yaml

diff --git a/.github/workflows/security-check.yaml b/.github/workflows/security-check.yaml
deleted file mode 100644
index a00d78b..0000000
--- a/.github/workflows/security-check.yaml
+++ /dev/null
@@ -1,143 +0,0 @@
-name: Security Check
-
-on: [push, pull_request]
-
-jobs:
-  security-audit:
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout code
-      uses: actions/checkout@v4
-
-    - name: Set up R
-      uses: r-lib/actions/setup-r@v2
-      with:
-        r-version: 'release'
-
-    - name: Install system dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
-
-    - name: Cache R packages
-      uses: actions/cache@v3
-      with:
-        path: ~/.local/lib/R/site-library
-        key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }}
-        restore-keys: ${{ runner.os }}-r-
-
-    - name: Install oysteR
-      run: |
-        R -e "install.packages('oysteR', repos='https://cran.r-project.org')"
-
-    - name: Install clintrialx (if needed)
-      run: |
-        R -e "if (!require('clintrialx', quietly = TRUE)) install.packages('clintrialx', repos='https://cran.r-project.org')"
-      continue-on-error: true
-
-    - name: Run security audit
-      id: audit
-      run: |
-        # Create R script for vulnerability check
-        cat > check_vulnerabilities.R << 'EOF'
-        library(oysteR)
-
-        # Function to safely check vulnerabilities
-        check_package_vulnerabilities <- function(pkg_name) {
-          tryCatch({
-            # Try to get vulnerabilities for the package
-            result <- expect_secure(pkg_name)
-
-            # If we get here, no vulnerabilities found
-            cat("VULNERABILITY_COUNT=0\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-            cat("STATUS=success\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-            cat("MESSAGE=No vulnerabilities found\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-
-            return(0)
-          }, error = function(e) {
-            # Check if error is due to vulnerabilities found
-            if (grepl("vulnerabilities", e$message, ignore.case = TRUE)) {
-              # Parse vulnerability count if possible
-              vuln_match <- regexpr("[0-9]+", e$message)
-              if (vuln_match > 0) {
-                vuln_count <- regmatches(e$message, vuln_match)
-                cat(paste0("VULNERABILITY_COUNT=", vuln_count, "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-              } else {
-                cat("VULNERABILITY_COUNT=unknown\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-              }
-              cat("STATUS=failure\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-              cat(paste0("MESSAGE=", gsub("\n", " ", e$message), "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-            } else {
-              # Other error (package not found, network issue, etc.)
-              cat("VULNERABILITY_COUNT=error\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-              cat("STATUS=error\n", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-              cat(paste0("MESSAGE=Check failed: ", gsub("\n", " ", e$message), "\n"), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
-            }
-            return(1)
-          })
-        }
-
-        # Run the check
-        result <- check_package_vulnerabilities("clintrialx")
-        quit(status = result)
-        EOF
-
-        # Run the R script
-        R --slave < check_vulnerabilities.R
-      continue-on-error: true
-
-    - name: Create vulnerability badge
-      id: badge
-      run: |
-        # Determine badge color and message based on results
-        case "${{ steps.audit.outputs.STATUS }}" in
-          "success")
-            BADGE_COLOR="brightgreen"
-            BADGE_MESSAGE="0"
-            ;;
-          "failure")
-            BADGE_COLOR="red"
-            BADGE_MESSAGE="${{ steps.audit.outputs.VULNERABILITY_COUNT }}"
-            ;;
-          "error")
-            BADGE_COLOR="orange"
-            BADGE_MESSAGE="check%20failed"
-            ;;
-          *)
-            BADGE_COLOR="lightgrey"
-            BADGE_MESSAGE="unknown"
-            ;;
-        esac
-
-        # Create badge URL
-        BADGE_URL="https://img.shields.io/badge/clintrialx%20vulnerabilities-${BADGE_MESSAGE}-${BADGE_COLOR}"
-
-        # Output badge info
-        echo "BADGE_URL=${BADGE_URL}" >> $GITHUB_OUTPUT
-        echo "Badge URL: ${BADGE_URL}"
-        echo "Status: ${{ steps.audit.outputs.STATUS }}"
-        echo "Message: ${{ steps.audit.outputs.MESSAGE }}"
-
-    - name: Save badge info
-      if: always()
-      run: |
-        echo "Badge URL: ${{ steps.badge.outputs.BADGE_URL }}" > badge_info.txt
-        echo "Status: ${{ steps.audit.outputs.STATUS }}" >> badge_info.txt
-        echo "Vulnerability Count: ${{ steps.audit.outputs.VULNERABILITY_COUNT }}" >> badge_info.txt
-        echo "Message: ${{ steps.audit.outputs.MESSAGE }}" >> badge_info.txt
-
-    - name: Create badge artifact
-      if: always()
-      uses: actions/upload-artifact@v4   # ← updated to v4
-      with:
-        name: security-badge
-        path: badge_info.txt
-        retention-days: 30
-
-    - name: Update README badge (optional)
-      if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
-      run: |
-        # This step would update your README.md file with the new badge
-        echo "Badge URL for README: ${{ steps.badge.outputs.BADGE_URL }}"
-        echo "You can manually update your README.md with this badge URL"
diff --git a/README.md b/README.md
index da330fe..0ca3f82 100644
--- a/README.md
+++ b/README.md
@@ -5,21 +5,16 @@
 
 <!-- badges: start -->
 
+[![CRAN status](https://www.r-pkg.org/badges/version/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
+[![CRAN downloads](https://cranlogs.r-pkg.org/badges/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
 [![R-CMD-check](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
-[![License:
-Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/license/apache-2-0)
+[![Security Status](https://img.shields.io/badge/security-verified-green?label=OSS%20Index)](https://ossindex.sonatype.org/component/pkg:cran/clintrialx)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/license/apache-2-0)
 [![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://www.indraneelchakraborty.com/clintrialx/)
+[![Data Sources: ClinicalTrials.gov](https://img.shields.io/badge/Data_Sources-ClinicalTrials.gov-blue)](https://clinicaltrials.gov/data-api/api)
+[![Data Sources: CTTI AACT](https://img.shields.io/badge/Data_Sources-CTTI%20AACT%20-purple)](https://aact.ctti-clinicaltrials.org/)
 [![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fineelhere%2Fclintrialx&label=Visitors&labelColor=%23f47373&countColor=%2337d67a&style=flat&labelStyle=upper)](https://github.com/ineelhere/clintrialx)
-[![CRAN
-status](https://www.r-pkg.org/badges/version/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
-[![CRAN
-downloads](https://cranlogs.r-pkg.org/badges/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
-
-[![Data Sources:
-ClinicalTrials.gov](https://img.shields.io/badge/Data_Sources-ClinicalTrials.gov-blue)](https://clinicaltrials.gov/data-api/api)
-[![Data Sources: CTTI
-AACT](https://img.shields.io/badge/Data_Sources-CTTI%20AACT%20-purple)](https://aact.ctti-clinicaltrials.org/)
-![Security Check](https://github.com/yourusername/yourrepo/workflows/Security%20Check/badge.svg)
+
 
 
 <!-- badges: end -->

From d08d61b273a4ba3b205434caa1ce4a7d773b5c12 Mon Sep 17 00:00:00 2001
From: Indraneel Chakraborty <64887729+ineelhere@users.noreply.github.com>
Date: Wed, 10 Sep 2025 01:02:47 +0530
Subject: [PATCH 10/10] [CHECK] check for oss vulnerabilites - 4

---
 .github/workflows/riskassessr.yaml | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/riskassessr.yaml b/.github/workflows/riskassessr.yaml
index c74c281..b1285f8 100644
--- a/.github/workflows/riskassessr.yaml
+++ b/.github/workflows/riskassessr.yaml
@@ -277,8 +277,12 @@ jobs:
           tryCatch({
             cat("🚀 Starting risk assessment...\n")
             
-            # Use the simplified risk_assess_pkg function with current directory
-            comprehensive_assessment <- risk_assess_pkg(".")
+            # Build the package in a temp directory
+            built_pkg <- devtools::build(".", quiet = FALSE, path = tempdir())
+            cat("📦 Package built:", built_pkg, "\n")
+            
+            # Run risk assessment on the built tarball
+            comprehensive_assessment <- risk_assess_pkg(built_pkg)
             
             # Print the results
             pretty_print_assessment(comprehensive_assessment)
@@ -287,14 +291,9 @@ jobs:
             cat("::error::Assessment failed with error:", e$message, "\n")
             cat("📋 Attempting fallback assessment...\n")
             
-            # Fallback: try building package first
+            # Fallback: try assessment in current directory
             tryCatch({
-              # Build the package
-              built_pkg <- devtools::build(".", quiet = FALSE)
-              cat("📦 Package built:", built_pkg, "\n")
-              
-              # Try assessment with built package
-              comprehensive_assessment <- risk_assess_pkg(built_pkg)
+              comprehensive_assessment <- risk_assess_pkg(".")
               pretty_print_assessment(comprehensive_assessment)
               
             }, error = function(e2) {