12 function to get r packages list

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^adrgOS\.Rproj$
 ^\.Rproj\.user$
 ^README\.Rmd$
@@ -8,3 +10,6 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^adrgOS\.Rcheck$
+^adrgOS.*\.tar\.gz$
+^adrgOS.*\.tgz$

.Rhistory

@@ -0,0 +1,271 @@
+# libraries
+# adams
+library(haven)
+library_lines <- c(
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(stringr)",
+"library(dplyr)",
+"library(tidyr)",
+"library(admiral)",
+"library(metacore)",
+"library(metatools)",
+"library(stringr)",
+"library(xportr)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(lubridate)",
+"library(stringr)",
+"library(xportr)",
+"library(metacore)",
+"library(metatools)",
+"library(haven)",
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(janitor)",
+"library(tidyr)",
+"library(dplyr)",
+"library(Tplyr)",
+"library(pharmaRTF)",
+"library(haven)",
+"library(dplyr)",
+"library(ggplot2)",
+"library(cowplot)",
+"library(visR)",
+"library(dplyr)",
+"library(haven)",
+"library(r2rtf)",
+"library(emmeans)",
+"library(haven)",
+"library(dplyr)",
+"library(rtables)"
+)
+# Extract package names from the library() calls
+package_names <- gsub("library\\((.*?)\\)", "\\1", library_lines)
+# Find the unique package names
+unique_package_names <- unique(package_names)
+# Print the unique package names
+print(unique_package_names)
+# install these packages
+install.packages(unique_package_names)
+#Optional: Load all the packages
+for(package_name in unique_package_names){
+library(package_name, character.only = TRUE)
+}
+install.packages("visR")
+library_lines <- c(
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(stringr)",
+"library(dplyr)",
+"library(tidyr)",
+"library(admiral)",
+"library(metacore)",
+"library(metatools)",
+"library(stringr)",
+"library(xportr)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(lubridate)",
+"library(stringr)",
+"library(xportr)",
+"library(metacore)",
+"library(metatools)",
+"library(haven)",
+"library(haven)",
+"library(admiral)",
+"library(dplyr)",
+"library(tidyr)",
+"library(metacore)",
+"library(metatools)",
+"library(xportr)",
+"library(janitor)",
+"library(tidyr)",
+"library(dplyr)",
+"library(Tplyr)",
+"library(pharmaRTF)",
+"library(haven)",
+"library(dplyr)",
+"library(ggplot2)",
+"library(cowplot)",
+"library(visR)",
+"library(dplyr)",
+"library(haven)",
+"library(r2rtf)",
+"library(emmeans)",
+"library(haven)",
+"library(dplyr)",
+"library(rtables)"
+)
+# Extract package names from the library() calls
+package_names <- gsub("library\\((.*?)\\)", "\\1", library_lines)
+# Find the unique package names
+unique_package_names <- unique(package_names)
+# Print the unique package names
+print(unique_package_names)
+# install these packages
+install.packages(unique_package_names)
+#Optional: Load all the packages
+for(package_name in unique_package_names){
+library(package_name, character.only = TRUE)
+}
+install.packages("visR")
+install.packages("renv")
+# Get the list of loaded packages
+loaded_packages <- names(sessionInfo()$otherPkgs)
+# Create an empty data frame to store the results
+package_info <- data.frame(
+Package = character(),
+Version = character(),
+Title = character(),
+stringsAsFactors = FALSE
+)
+# Loop through each loaded package and extract the required information
+for (pkg in loaded_packages) {
+pkg_desc <- packageDescription(pkg)
+# Extract the package name, version, and title
+pkg_name <- pkg_desc$Package
+pkg_version <- pkg_desc$Version
+pkg_title <- pkg_desc$Title
+# Append the information to the data frame
+package_info <- rbind(package_info, data.frame(
+Package = pkg_name,
+Version = pkg_version,
+Title = pkg_title,
+stringsAsFactors = FALSE
+))
+}
+# Print the resulting data frame
+print(package_info)
+#If you want to include base packages as well.
+base_packages <- names(sessionInfo()$basePkgs)
+base_package_info <- data.frame(
+Package = character(),
+Version = character(),
+Title = character(),
+stringsAsFactors = FALSE
+)
+for (pkg in base_packages) {
+pkg_desc <- packageDescription(pkg)
+pkg_name <- pkg_desc$Package
+pkg_version <- pkg_desc$Version
+pkg_title <- pkg_desc$Title
+base_package_info <- rbind(base_package_info, data.frame(
+Package = pkg_name,
+Version = pkg_version,
+Title = pkg_title,
+stringsAsFactors = FALSE
+))
+}
+print("Base Packages:")
+print(base_package_info)
+all_packages_info <- rbind(package_info, base_package_info)
+print("All Packages (Base and Loaded):")
+print(all_packages_info)
+# Print the resulting data frame
+print(package_info)
+sessionInfo()
+sinfo <- sessionInfo()
+View(sinfo)
+#If you want to include base packages as well.
+base_packages <- names(sessionInfo()$basePkgs)
+sinfo$basePkgs
+sessionInfo()$basePkgs
+names(sessionInfo()$basePkgs)
+# Get the list of loaded packages
+loaded_packages <- names(sessionInfo()$otherPkgs)
+renv::lockfile_read()
+# Get the list of loaded packages
+loaded_packages <- names(sessionInfo()$loadedOnly)
+# Get the list of loaded packages
+loaded_packages <- names(sessionInfo()$loadedOnly)
+# Create an empty data frame to store the results
+package_info <- data.frame(
+Package = character(),
+Version = character(),
+Title = character(),
+stringsAsFactors = FALSE
+)
+# Loop through each loaded package and extract the required information
+for (pkg in loaded_packages) {
+pkg_desc <- packageDescription(pkg)
+# Extract the package name, version, and title
+pkg_name <- pkg_desc$Package
+pkg_version <- pkg_desc$Version
+pkg_title <- pkg_desc$Title
+# Append the information to the data frame
+package_info <- rbind(package_info, data.frame(
+Package = pkg_name,
+Version = pkg_version,
+Title = pkg_title,
+stringsAsFactors = FALSE
+))
+}
+# Print the resulting data frame
+print(package_info)
+#If you want to include base packages as well.
+base_packages <- sessionInfo()$basePkgs
+base_package_info <- data.frame(
+Package = character(),
+Version = character(),
+Title = character(),
+stringsAsFactors = FALSE
+)
+for (pkg in base_packages) {
+pkg_desc <- packageDescription(pkg)
+pkg_name <- pkg_desc$Package
+pkg_version <- pkg_desc$Version
+pkg_title <- pkg_desc$Title
+base_package_info <- rbind(base_package_info, data.frame(
+Package = pkg_name,
+Version = pkg_version,
+Title = pkg_title,
+stringsAsFactors = FALSE
+))
+}
+print("Base Packages:")
+print(base_package_info)
+all_packages_info <- rbind(package_info, base_package_info)
+print("All Packages (Base and Loaded):")
+print(all_packages_info)
+source("/cloud/project/R/list_r_packages.r")
+list_r_packages(use_renv = TRUE, lockfile_loc = "~/dev/renv.lock")
+renv::activate()
+renv::init()
+renv::status()
+source("/cloud/project/R/list_r_packages.r")
+list_r_packages(use_renv = TRUE, lockfile_loc = "~/renv.lock")
+list_r_packages(use_renv = TRUE, lockfile_loc = ".")
+revn::restore(packages = "renv")
+renv::restore(packages = "renv")

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.gitignore

@@ -1,2 +1,5 @@
 .Rproj.user
 docs
+adrgOS.Rcheck/
+adrgOS*.tar.gz
+adrgOS*.tgz

R/list_r_packages.r

@@ -0,0 +1,85 @@
+list_r_packages <- function(use_renv = FALSE, lockfile_loc = NULL) {
+
+  if (use_renv == TRUE) {
+
+    # renv code
+    lockfile_path <- lockfile_loc
+
+    if (file.exists(lockfile_path)) {
+      lockfile <- renv::lockfile_read(lockfile_path)
+      packages <- lockfile$Packages
+
+      if (!is.null(packages) && length(packages) > 0) {
+        package_list <- data.frame(
+          Package = names(packages),
+          Version = sapply(packages, function(x) x$Version),
+          Title = sapply(packages, function(x) x$Title),
+          stringsAsFactors = FALSE
+        )
+        print(package_list)
+      } else {
+        print("No packages found in the lockfile.")
+      }
+    } else {
+      print("renv lockfile not found. Make sure renv has been initialized.")
+    }
+  }
+  else if (use_renv == FALSE) {
+    # Non-renv code
+    loaded_packages <- names(sessionInfo()$loadedOnly)
+
+    package_info <- data.frame(
+      Package = character(),
+      Version = character(),
+      Title = character(),
+      stringsAsFactors = FALSE
+    )
+
+    for (pkg in loaded_packages) {
+      pkg_desc <- packageDescription(pkg)
+      pkg_name <- pkg_desc$Package
+      pkg_version <- pkg_desc$Version
+      pkg_title <- pkg_desc$Title
+
+      package_info <- rbind(package_info, data.frame(
+        Package = pkg_name,
+        Version = pkg_version,
+        Title = pkg_title,
+        stringsAsFactors = FALSE
+      ))
+    }
+
+    print(package_info)
+
+    base_packages <- sessionInfo()$basePkgs
+
+    base_package_info <- data.frame(
+      Package = character(),
+      Version = character(),
+      Title = character(),
+      stringsAsFactors = FALSE
+    )
+
+    for (pkg in base_packages) {
+      pkg_desc <- packageDescription(pkg)
+      pkg_name <- pkg_desc$Package
+      pkg_version <- pkg_desc$Version
+      pkg_title <- pkg_desc$Title
+
+      base_package_info <- rbind(base_package_info, data.frame(
+        Package = pkg_name,
+        Version = pkg_version,
+        Title = pkg_title,
+        stringsAsFactors = FALSE
+      ))
+    }
+
+    print("Base Packages:")
+    print(base_package_info)
+
+    all_packages_info <- rbind(package_info, base_package_info)
+
+    print("All Packages (Base and Loaded):")
+    print(all_packages_info)
+  }
+}

adrgOS.Rproj

@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix