[SPARK-20815][SPARKR] NullPointerException in RPackageUtils#checkManifestForR

## What changes were proposed in this pull request?

- Add a null check to RPackageUtils#checkManifestForR so that jars w/o manifests don't NPE.

## How was this patch tested?

- Unit tests and manual tests.

Author: James Shuster <jshuster@palantir.com>

Closes #18040 from jrshust/feature/r-package-utils.

core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala

@@ -92,6 +92,9 @@ private[deploy] object RPackageUtils extends Logging {
    * Exposed for testing.
    */
   private[deploy] def checkManifestForR(jar: JarFile): Boolean = {
+    if (jar.getManifest == null) {
+      return false
+    }
     val manifest = jar.getManifest.getMainAttributes
     manifest.getValue(hasRPackage) != null && manifest.getValue(hasRPackage).trim == "true"
   }

core/src/test/scala/org/apache/spark/deploy/IvyTestUtils.scala

@@ -243,16 +243,22 @@ private[deploy] object IvyTestUtils {
       withManifest: Option[Manifest] = None): File = {
     val jarFile = new File(dir, artifactName(artifact, useIvyLayout))
     val jarFileStream = new FileOutputStream(jarFile)
-    val manifest = withManifest.getOrElse {
-      val mani = new Manifest()
+    val manifest: Manifest = withManifest.getOrElse {
       if (withR) {
+        val mani = new Manifest()
         val attr = mani.getMainAttributes
         attr.put(Name.MANIFEST_VERSION, "1.0")
         attr.put(new Name("Spark-HasRPackage"), "true")
+        mani
+      } else {
+        null
       }
-      mani
     }
-    val jarStream = new JarOutputStream(jarFileStream, manifest)
+    val jarStream = if (manifest != null) {
+      new JarOutputStream(jarFileStream, manifest)
+    } else {
+      new JarOutputStream(jarFileStream)
+    }
 
     for (file <- files) {
       val jarEntry = new JarEntry(file._1)

core/src/test/scala/org/apache/spark/deploy/RPackageUtilsSuite.scala

@@ -133,6 +133,16 @@ class RPackageUtilsSuite
     }
   }
 
+  test("jars without manifest return false") {
+    IvyTestUtils.withRepository(main, None, None) { repo =>
+      val jar = IvyTestUtils.packJar(new File(new URI(repo)), dep1, Nil,
+        useIvyLayout = false, withR = false, None)
+      val jarFile = new JarFile(jar)
+      assert(jarFile.getManifest == null, "jar file should have null manifest")
+      assert(!RPackageUtils.checkManifestForR(jarFile), "null manifest should return false")
+    }
+  }
+
   test("SparkR zipping works properly") {
     val tempDir = Files.createTempDir()
     Utils.tryWithSafeFinally {