diff --git a/source/dub/dub.d b/source/dub/dub.d
index 181e592..000f8f8 100644
--- a/source/dub/dub.d
+++ b/source/dub/dub.d
@@ -215,7 +215,7 @@
 			fetchOpts |= (options & UpgradeOptions.preRelease) != 0 ? FetchOptions.usePrerelease : FetchOptions.none;
 			fetchOpts |= (options & UpgradeOptions.forceRemove) != 0 ? FetchOptions.forceRemove : FetchOptions.none;
 			if (!pack) fetch(p, ver, PlacementLocation.userWide, fetchOpts);
-			if ((options & UpgradeOptions.select) && ver.path.empty)
+			if ((options & UpgradeOptions.select) && ver.path.empty && p != m_project.rootPackage.name)
 				m_project.selections.selectVersion(p, ver.version_);
 		}
 
diff --git a/source/dub/project.d b/source/dub/project.d
index fe919c6..d9e50bd 100644
--- a/source/dub/project.d
+++ b/source/dub/project.d
@@ -787,12 +787,14 @@
 	this(Json data)
 	{
 		deserialize(data);
+		m_dirty = false;
 	}
 
 	this(Path path)
 	{
 		auto json = jsonFromFile(path);
 		deserialize(json);
+		m_dirty = false;
 	}
 
 	@property string[] selectedPackages() const { return m_selections.keys; }