Add support for binary dependencies (#9)

README.md

@@ -34,7 +34,7 @@ Real-life example with multiple input packages and repositories.
 Please see below for [an example](#configuration-file) how to set package and repository lists more easily in a configuration file.
 
 ```bash
-locksmith --inputPackageList https://raw.githubusercontent.com/insightsengineering/formatters/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rtables/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda.2022/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/nestcolor/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/tern/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rlistings/main/DESCRIPTION --inputRepositoryList BioC=https://bioconductor.org/packages/release/bioc,CRAN=https://cran.rstudio.com/
+locksmith --inputPackageList https://raw.githubusercontent.com/insightsengineering/formatters/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rtables/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda.2022/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/nestcolor/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/tern/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rlistings/main/DESCRIPTION --inputRepositoryList BioC=https://bioconductor.org/packages/release/bioc,CRAN=https://cran.rstudio.com
 ```
 
 In order to download the packages from GitHub or GitLab repositories, please set the environment variables containing the Personal Access Tokens.
@@ -63,15 +63,56 @@ inputPackages:
   - https://raw.githubusercontent.com/insightsengineering/scda/main/DESCRIPTION
   - https://raw.githubusercontent.com/insightsengineering/scda.2022/main/DESCRIPTION
 inputRepositories:
-  - Bioconductor.BioCsoft=https://bioconductor.org/packages/release/bioc/
-  - CRAN=https://cran.rstudio.com/
+  - Bioconductor.BioCsoft=https://bioconductor.org/packages/release/bioc
+  - CRAN=https://cran.rstudio.com
 ```
 
 The example above shows an alternative way of providing input packages, and input repositories,
 as opposed to `inputPackageList` and `inputRepositoryList` CLI flags/YAML keys.
 
 Additionally, `inputPackageList`/`inputRepositoryList` CLI flags take precendence over `inputPackages`/`inputRepositories` YAML keys.
 
+## Binary dependencies
+
+For `locksmith` in order to generate an `renv.lock` with binary R packages, it is necessary to provide URLs to binary repositories in `inputRepositories`/`inputRepositoryList`.
+
+Examples illustrating the expected format of URLs to repositories with binary packages:
+
+* Linux:
+  * `https://packagemanager.posit.co/cran/__linux__/<distribution-name>/latest`
+* Windows:
+  * `https://cloud.r-project.org/bin/windows/contrib/<r-version>`
+  * `https://www.bioconductor.org/packages/release/bioc/bin/windows/contrib/<r-version>`
+  * `https://packagemanager.posit.co/cran/latest/bin/windows/contrib/<r-version>`
+* macOS:
+  * `https://cloud.r-project.org/bin/macosx/contrib/<r-version>`
+  * `https://www.bioconductor.org/packages/release/bioc/bin/macosx/big-sur-arm64/contrib/<r-version>`
+  * `https://www.bioconductor.org/packages/release/bioc/bin/macosx/big-sur-x86_64/contrib/<r-version>`
+  * `https://packagemanager.posit.co/cran/latest/bin/macosx/big-sur-x86_64/contrib/<r-version>`
+  * `https://packagemanager.posit.co/cran/latest/bin/macosx/big-sur-arm64/contrib/<r-version>`
+
+where `<r-version>` is e.g. `4.2`, `4.3` etc.
+
+In all cases the URL points to a directory where the `PACKAGES` file is located.
+
+As a result, the configuration file could look like this:
+
+* for macOS:
+
+    ```yaml
+    inputRepositories:
+      - CRAN-macOS=https://cloud.r-project.org/bin/macosx/contrib/4.2
+      - Bioc-macOS=https://www.bioconductor.org/packages/release/bioc/bin/macosx/big-sur-x86_64/contrib/4.3
+    ```
+
+* for Windows:
+
+    ```yaml
+    inputRepositories:
+      - CRAN-Windows=https://cloud.r-project.org/bin/windows/contrib/4.2
+      - Bioc-Windows=https://www.bioconductor.org/packages/release/bioc/bin/windows/contrib/4.3
+    ```
+
 ## Environment variables
 
 `locksmith` reads environment variables with `LOCKSMITH_` prefix and tries to match them with CLI flags.

cmd/download.go

@@ -237,11 +237,20 @@ func DownloadPackagesFiles(repositoryList []string,
 	downloadFileFunction func(string, map[string]string) (int, int64, string)) map[string]string {
 	inputPackagesFiles := make(map[string]string)
 	for _, repository := range repositoryList {
-		statusCode, _, packagesFileContent := downloadFileFunction(repository+"/src/contrib/PACKAGES", map[string]string{})
+		var packagesFileURL string
+		if strings.Contains(repository, "/bin/windows/") || strings.Contains(repository, "/bin/macosx") {
+			// If we're dealing with a repository with binary Windows or macOS packages,
+			// we're expecting it to be in a specific format documented in the README.
+			packagesFileURL = repository + "/PACKAGES"
+		} else {
+			packagesFileURL = repository + "/src/contrib/PACKAGES"
+		}
+		log.Debug("Downloading ", packagesFileURL)
+		statusCode, _, packagesFileContent := downloadFileFunction(packagesFileURL, map[string]string{})
 		if statusCode == 200 {
 			inputPackagesFiles[repository] = packagesFileContent
 		} else {
-			log.Warn("An error occurred while downloading ", repository+"/src/contrib/PACKAGES")
+			log.Warn("An error occurred while downloading ", packagesFileURL)
 		}
 	}
 	return inputPackagesFiles

cmd/parse.go

@@ -36,6 +36,7 @@ func ParseDescriptionFileList(inputDescriptionFiles []DescriptionFile) []Package
 func ParsePackagesFiles(repositoryPackageFiles map[string]string) map[string]PackagesFile {
 	packagesFilesMap := make(map[string]PackagesFile)
 	for repository, packagesFile := range repositoryPackageFiles {
+		log.Debug("Parsing PACKAGES file for ", repository)
 		packagesFilesMap[repository] = ProcessPackagesFile(packagesFile)
 	}
 	return packagesFilesMap
@@ -45,7 +46,7 @@ func ParsePackagesFiles(repositoryPackageFiles map[string]string) map[string]Pac
 // with those fields/properties that are required for further processing.
 func ProcessPackagesFile(content string) PackagesFile {
 	var allPackages PackagesFile
-	for _, lineGroup := range strings.Split(content, "\n\n") {
+	for _, lineGroup := range strings.Split(strings.ReplaceAll(content, "\r\n", "\n"), "\n\n") {
 		if lineGroup == "" {
 			continue
 		}