diff --git a/source/dub/dependency.d b/source/dub/dependency.d
index d7a8681..2cb70b5 100644
--- a/source/dub/dependency.d
+++ b/source/dub/dependency.d
@@ -576,7 +576,7 @@
 	private void forAllDependencies(void delegate (const PkgType* avail, string pkgId, Dependency d, const Package issuer) dg) const {
 		foreach(string issuerPackag, issuer; m_packages) {
 			foreach(string depPkg, dependency; issuer.dependencies) {
-				auto availPkg = depPkg in m_packages;
+				auto availPkg = depPkg.getBasePackage() in m_packages;
 				dg(availPkg, depPkg, dependency, issuer);
 			}
 		}
@@ -689,7 +689,9 @@
 		Package r_master = new Package(R_json);
 		auto graph = new DependencyGraph(r_master);
 
+		// See #100, a dependency on a subpackage should only refer the base
+		// project.
 		auto missing = graph.missing();
-		//assert(missing.length == 0);
+		assert(missing.length == 0);
 	}
 }
\ No newline at end of file
diff --git a/source/dub/package_.d b/source/dub/package_.d
index 5cce361..963b0d7 100644
--- a/source/dub/package_.d
+++ b/source/dub/package_.d
@@ -719,8 +719,15 @@
 	}
 }
 
-
+// @deprecated (move to private?)
 string[] getSubPackagePath(string package_name)
 {
 	return package_name.split(":");
-}
\ No newline at end of file
+}
+
+// Returns the name of the base package in the case of some sub package or the
+// package itself, if it is already a full package.
+string getBasePackage(string package_name)
+{
+	return package_name.getSubPackagePath()[0];
+}
diff --git a/source/dub/project.d b/source/dub/project.d
index c33abcb..586890f 100644
--- a/source/dub/project.d
+++ b/source/dub/project.d
@@ -413,7 +413,7 @@
 		}
 
 		auto graph = new DependencyGraph(m_main);
-		if(!gatherMissingDependencies(packageSuppliers, graph)  || graph.missing().length > 0) {
+		if(!gatherMissingDependencies(packageSuppliers, graph) || graph.missing().length > 0) {
 			// Check the conflicts first.
 			auto conflicts = graph.conflicted();
 			if(conflicts.length > 0) {
@@ -421,6 +421,7 @@
 				Action[] actions;
 				foreach( string pkg, dbp; graph.conflicted())
 					actions ~= Action.conflict(pkg, dbp.dependency, dbp.packages);
+				
 				// Missing dependencies could have some bogus results, therefore
 				// return only the conflicts.
 				return actions;
@@ -452,8 +453,9 @@
 
 		// Check against installed and add install actions
 		Action[] actions;
+		int[string] upgradePackages;
 		foreach( string pkg, d; graph.needed() ) {
-			auto basepkg = pkg.getSubPackagePath()[0];
+			auto basepkg = pkg.getBasePackage();
 			auto p = basepkg in installed;
 			// TODO: auto update to latest head revision
 			if(!p || (!d.dependency.matches(p.vers) && !d.dependency.matches(Version.MASTER))) {
@@ -462,8 +464,13 @@
 				actions ~= Action.install(basepkg, InstallLocation.userWide, d.dependency, d.packages);
 			} else {
 				logDiagnostic("Required package '"~basepkg~"' found with version '"~p.vers~"'");
-				if( option & UpdateOptions.Upgrade )
-					actions ~= Action.install(basepkg, InstallLocation.userWide, d.dependency, d.packages);
+				if( option & UpdateOptions.Upgrade ) {
+					// Only add one upgrade action for each package.
+					if(basepkg !in upgradePackages) {
+						upgradePackages[basepkg] = 1;
+						actions ~= Action.install(basepkg, InstallLocation.userWide, d.dependency, d.packages);
+					}
+				}
 			}
 		}