diff --git a/src/incremental/makefileUtil.ml b/src/incremental/makefileUtil.ml
index 5752691405..d8e9bcb693 100644
--- a/src/incremental/makefileUtil.ml
+++ b/src/incremental/makefileUtil.ml
@@ -61,7 +61,8 @@ let run_cilly (path: string) ~all_cppflags =
     remove_comb_files path;
     (* Combine source files with make using cilly as compiler *)
     let gcc_path = GobConfig.get_string "exp.gcc_path" in
-    let (exit_code, output) = exec_command ~path ("make CC=\"cilly --gcc=" ^ gcc_path ^ " --merge --keepmerged\" CFLAGS+=" ^ String.join " " (List.map Filename.quote all_cppflags) ^ " " ^
+    let cflags = if all_cppflags = [] then "" else " CFLAGS+=" ^ Filename.quote (String.join " " all_cppflags) in
+    let (exit_code, output) = exec_command ~path ("make CC=\"cilly --gcc=" ^ gcc_path ^ " --merge --keepmerged\"" ^cflags ^ " " ^
                                                   "LD=\"cilly --gcc=" ^ gcc_path ^ " --merge --keepmerged\"") in
     print_string output;
     (* fail if make failed *)
@@ -80,9 +81,9 @@ let generate_and_combine makefile ~all_cppflags =
     let generate_makefile_with (name, command, file) = if Sys.file_exists file then (
         print_endline ("Trying to run " ^ name ^ " to generate Makefile");
         let exit_code, output = exec_command ~path command in
-        print_endline (command ^ GobUnix.string_of_process_status exit_code ^ ". Output: " ^ output);
+        print_endline (command ^ " " ^ GobUnix.string_of_process_status exit_code ^ ". Output: " ^ output);
         if not (Sys.file_exists makefile) then raise MakefileNotGenerated
-      ); raise MakefileNotGenerated in
+      ) else raise MakefileNotGenerated in
     try generate_makefile_with configure
     with MakefileNotGenerated ->
     try generate_makefile_with autogen
diff --git a/src/util/compilationDatabase.ml b/src/util/compilationDatabase.ml
index d93fb0bf4e..1d845e08ef 100644
--- a/src/util/compilationDatabase.ml
+++ b/src/util/compilationDatabase.ml
@@ -60,25 +60,31 @@ let load_and_preprocess ~all_cppflags filename =
           (* TODO: extract o_file *)
           let command = reroot command in
           let preprocess_command = Str.replace_first command_program_regexp ("\\1 " ^ String.join " " (List.map Filename.quote all_cppflags) ^ " -E") command in
-          let preprocess_command = Str.replace_first command_o_regexp ("-o " ^ preprocessed_file) preprocess_command in
           if preprocess_command = command then (* easier way to check if match was found (and replaced) *)
-            failwith "CompilationDatabase.preprocess: no -o argument found for " ^ file
+            failwith ("CompilationDatabase.preprocess: no program found for " ^ file)
           else
-            preprocess_command
+            let preprocess_command_o = Str.replace_first command_o_regexp ("-o " ^ preprocessed_file) preprocess_command in
+            if preprocess_command_o = preprocess_command then (* easier way to check if match was found (and replaced) *)
+              preprocess_command ^ " -o " ^ preprocessed_file
+            else
+              preprocess_command_o
         | None, Some arguments ->
-          let arguments = List.map reroot arguments in
-          begin match List.findi (fun i e -> e = "-o") arguments with
+          let arguments_program, arguments =
+            match List.map reroot arguments with
+            | arguments_program :: arguments -> arguments_program, arguments
+            | _ -> failwith ("CompilationDatabase.preprocess: no program found for " ^ file)
+          in
+          let preprocess_arguments =
+            match List.findi (fun i e -> e = "-o") arguments with
             | (o_i, _) ->
               begin match List.split_at o_i arguments with
-                | (arguments_program :: arguments_init, _ :: o_file :: arguments_tl) ->
-                  let preprocess_arguments = all_cppflags @ "-E" :: arguments_init @ "-o" :: preprocessed_file :: arguments_tl in
-                  Filename.quote_command arguments_program preprocess_arguments
-                | _ ->
-                  failwith "CompilationDatabase.preprocess: no -o argument value found for " ^ file
+                | (arguments_init, _ :: o_file :: arguments_tl) -> arguments_init @ "-o" :: preprocessed_file :: arguments_tl
+                | _ -> failwith ("CompilationDatabase.preprocess: no argument found for -o option for " ^ file)
               end
-            | exception Not_found ->
-              failwith "CompilationDatabase.preprocess: no -o argument found for " ^ file
-          end
+            | exception Not_found -> arguments @ "-o" :: [preprocessed_file]
+          in
+          let preprocess_arguments = all_cppflags @ "-E" :: preprocess_arguments in
+          Filename.quote_command arguments_program preprocess_arguments
         | Some _, Some _ ->
           failwith "CompilationDatabase.preprocess: both command and arguments specified for " ^ file
         | None, None ->
@@ -89,6 +95,6 @@ let load_and_preprocess ~all_cppflags filename =
         Printf.printf "Preprocessing %s\n  to %s\n  using %s\n  in %s\n" file preprocessed_file preprocess_command cwd;
       system ~cwd preprocess_command; (* command/arguments might have paths relative to directory *)
       Some preprocessed_file
-    in
+  in
   parse_file filename
   |> BatList.filter_map preprocess