#772: Check installation of R packages

ext/scripts/install_scripts/install_via_r_remotes.pl

@@ -7,14 +7,15 @@ =head1 SYNOPSIS
 
   install_via_r_versions.pl [OPTIONS]
   Options:
-    --help                Brief help message
-    --dry-run             Doesn't execute the command, only prints it to STDOUT
-    --file                Input file with each line represents a input. 
-                          A line can have multiple elements separated by --element-separator. 
-                          Lines everything after a # is interpreted as comment
-    --with-versions       Uses versions specified in the input file in the second element of each line
-    --allow-no-versions   If --with-versions is active, allow packages to have no version specified
-    --rscript-binary      Rscript binary to use for installation
+    --help                      Brief help message
+    --dry-run                   Doesn't execute the command, only prints it to STDOUT
+    --file                      Input file with each line represents a input.
+                                A line can have multiple elements separated by --element-separator.
+                                Lines everything after a # is interpreted as comment
+    --with-versions             Uses versions specified in the input file in the second element of each line
+    --allow-no-versions         If --with-versions is active, allow packages to have no version specified
+    --no-version-validation     If --with-versions is active, this flag controls if the version validation should be executed.
+    --rscript-binary            Rscript binary to use for installation
 
 =cut
 
@@ -33,13 +34,15 @@ =head1 SYNOPSIS
 my $rscript_binary = '';
 my $with_versions = 0;
 my $allow_no_version = 0;
+my $no_version_validation = 0;
 
 GetOptions (
             "help" => \$help,
             "dry-run" => \$dry_run,
             "file=s" => \$file,
             "with-versions" => \$with_versions,
             "allow-no-version" => \$allow_no_version,
+            "no-version-validation" => \$no_version_validation,
             "rscript-binary=s" => \$rscript_binary,
           ) or package_mgmt_utils::print_usage_and_abort(__FILE__,"Error in command line arguments",2);
 package_mgmt_utils::print_usage_and_abort(__FILE__,"",0) if $help;
@@ -54,11 +57,65 @@ =head1 SYNOPSIS
 }
 
 
-my $combining_template = "library(remotes)\n<<<<0>>>>";
+my $combining_template_install = '
+library(remotes)
+install_or_fail <- function(package_name, version){
+
+   tryCatch({install_version(package_name, version, repos="https://cloud.r-project.org", Ncpus=4, upgrade="never")
+         library(package_name, character.only = TRUE)},
+         error = function(e){
+             print(e)
+             stop(paste("installation failed for:",package_name ))},
+         warning = function(w){
+           catch <-
+             grepl("download of package .* failed", w$message) ||
+             grepl("(dependenc|package).*(is|are) not available", w$message) ||
+             grepl("installation of package.*had non-zero exit status", w$message) ||
+             grepl("installation of one or more packages failed", w$message)
+           if(catch){ print(w$message)
+             stop(paste("installation failed for:",package_name ))}}
+         )
+
+ }
+
+<<<<0>>>>
+';
+
+my $combining_template_validation = '
+
+installed_packages <- installed.packages()
+installed_package_names <- installed_packages[, "Package"]
+
+validate_or_fail <- function(package_name, version){
+    # Check if the package is in the list of available packages
+    is_installed <- package_name %in% installed_package_names
+
+    # Check the result
+    if (!is_installed) {
+        stop(paste("Package nor installed:", package_name))
+    }
+
+    if (!is.null(version)) {
+       desc <- packageDescription(package_name)
+       if (version != desc$Version) {
+        stop(paste("Version of  installed installed package does not match:", package_name))
+       }
+    }
+}
+
+<<<<0>>>>
+';
+
+
 my @separators = ("\n");
-my @templates = ('install_version("<<<<0>>>>",NULL,repos="https://cloud.r-project.org", Ncpus=4)');
+my @install_templates = ('install_or_fail("<<<<0>>>>",NULL)');
 if($with_versions){  
-    @templates = ('install_version("<<<<0>>>>","<<<<1>>>>",repos="https://cloud.r-project.org", Ncpus=4)');
+    @install_templates = ('install_or_fail("<<<<0>>>>","<<<<1>>>>")');
+}
+
+my @validation_templates = ('validate_or_fail("<<<<0>>>>", NULL)');
+if($with_versions && !$no_version_validation){
+    @validation_templates = ('validate_or_fail("<<<<0>>>>","<<<<1>>>>")');
 }
 
 sub identity {
@@ -74,13 +131,19 @@ sub replace_missing_version{
 }
 
 my @rendered_line_transformation_functions = (\&identity);
+my @rendered_line_transformation_functions_validation = (\&identity);
 if($with_versions and $allow_no_version){
     @rendered_line_transformation_functions = (\&replace_missing_version);
+    @rendered_line_transformation_functions_validation = (\&replace_missing_version);
 }
 
 my $script = 
     package_mgmt_utils::generate_joined_and_transformed_string_from_file(
-        $file,$element_separator,$combining_template,\@templates,\@separators,\@rendered_line_transformation_functions);
+        $file,$element_separator,$combining_template_install,\@install_templates,\@separators,\@rendered_line_transformation_functions) .
+    package_mgmt_utils::generate_joined_and_transformed_string_from_file(
+        $file,$element_separator,$combining_template_validation,\@validation_templates,\@separators,\@rendered_line_transformation_functions_validation);
+
+
 
 if($with_versions and not $allow_no_version){
     if (index($script, "<<<<1>>>>") != -1) {

ext/scripts/tests/install_scripts/run_tests.sh

@@ -17,8 +17,5 @@ bash run_apt_tests.sh "$@"
 echo Run Pip Tests
 bash run_pip_tests.sh "$@"
 
-# echo Run R versions Tests
-# bash run_r_versions_tests.sh "$@"
-
 echo Run R remotes Tests
 bash run_r_remotes_tests.sh "$@"

test_container/tests/test/standard-flavor/all/import_r_modules.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+from typing import List, Tuple
+
+from exasol_python_test_framework import udf
+from exasol_python_test_framework.udf.udf_debug import UdfDebugger
+
+class ImportAllModulesTest(udf.TestCase):
+
+    def setUp(self):
+        self.query('create schema import_all_r_modules', ignore_errors=True)
+
+    def get_all_root_modules(self) -> List[Tuple[str, str]]:
+        self.query(udf.fixindent('''
+            CREATE OR REPLACE r SCALAR SCRIPT import_all_r_modules.get_all_root_modules() 
+            EMITS (module_name VARCHAR(200000), version VARCHAR(200)) AS
+                run <- function(ctx) {
+                    library(data.table)
+                    file_pattern <- "cran_packages"
+                    directory <- "/build_info/packages"
+                    files <- list.files(path = directory, pattern = file_pattern, full.names = TRUE, recursive = TRUE)
+                    for (file in files) {
+                        package_list <- fread(file, sep="|", header = FALSE, col.names = c("Package", "Version"))
+                        package_names <- package_list[[1]]
+                        versions <- package_list[[2]]
+                        ctx$emit(package_names, versions)
+                    }
+                }
+            /
+            '''))
+        rows = self.query('''SELECT import_all_r_modules.get_all_root_modules() FROM dual''')
+        print("Number of modules:",len(rows))
+        root_modules = [(row[0], row[1]) for row in rows]
+        print(f"Found {len(root_modules)} root modules.")
+        return root_modules
+
+    def create_check_installed_package_udf(self):
+        self.query(udf.fixindent('''
+            CREATE OR REPLACE r SCALAR SCRIPT
+                import_all_r_modules.check_installed_package(package_name VARCHAR(200000), version VARCHAR(200))
+            RETURNS DECIMAL(11,0) AS
+            run <- function(ctx) {
+             library(ctx$package_name, character.only = TRUE)
+             desc <- packageDescription(ctx$package_name)
+             if (ctx$version != desc$Version) {
+                stop(paste("Version of  installed installed package does not match:", ctx$package_name))
+                return(1)
+             }
+             0
+            }
+            /
+            '''))
+
+    def test_import_all_modules(self):
+        root_modules = self.get_all_root_modules()
+        assert len(root_modules) > 0
+        self.create_check_installed_package_udf()
+        for root_module in root_modules:
+            # with UdfDebugger(test_case=self):
+            rows = self.query(f'''SELECT import_all_r_modules.check_installed_package('{root_module[0]}', '{root_module[1]}') FROM dual''')
+
+    def tearDown(self):
+        self.query("drop schema import_all_r_modules cascade", ignore_errors=True)
+
+
+if __name__ == '__main__':
+    udf.main()