diff --git a/utils/CPPLINT.cfg b/utils/CPPLINT.cfg
index 94339b9bf..91cf906d5 100644
--- a/utils/CPPLINT.cfg
+++ b/utils/CPPLINT.cfg
@@ -1,3 +1,3 @@
 set noparent
 linelength=100
-filter=+build,-legal,+readability,+runtime,+whitespace,-runtime/references,-runtime/printf
+filter=+build,-legal,+readability,+runtime,+whitespace,-runtime/references,-runtime/printf,-build/include_subdir
diff --git a/utils/ioda_example/gdas_meanioda.cc b/utils/ioda_example/gdas_meanioda.cc
index 3844b92b4..6e18ff5fa 100644
--- a/utils/ioda_example/gdas_meanioda.cc
+++ b/utils/ioda_example/gdas_meanioda.cc
@@ -1,4 +1,4 @@
-#include "ioda_example/gdas_meanioda.h"
+#include "gdas_meanioda.h"
 #include "oops/runs/Run.h"
 
 // this is an example application that
diff --git a/utils/soca/gdas_incr_handler.cc b/utils/soca/gdas_incr_handler.cc
index ebba07282..65ce9ac43 100644
--- a/utils/soca/gdas_incr_handler.cc
+++ b/utils/soca/gdas_incr_handler.cc
@@ -1,4 +1,4 @@
-#include "soca/gdas_incr_handler.h"
+#include "gdas_incr_handler.h"
 #include "oops/runs/Run.h"
 
 int main(int argc,  char ** argv) {
diff --git a/utils/soca/gdas_incr_handler.h b/utils/soca/gdas_incr_handler.h
index f8e1ddc4c..de0db5a05 100644
--- a/utils/soca/gdas_incr_handler.h
+++ b/utils/soca/gdas_incr_handler.h
@@ -23,7 +23,7 @@
 #include "soca/LinearVariableChange/LinearVariableChange.h"
 #include "soca/State/State.h"
 
-#include "soca/gdas_postprocincr.h"
+#include "gdas_postprocincr.h"
 
 namespace gdasapp {
 
diff --git a/utils/soca/gdas_socahybridweights.cc b/utils/soca/gdas_socahybridweights.cc
index a01612bc6..1a6ae38e1 100644
--- a/utils/soca/gdas_socahybridweights.cc
+++ b/utils/soca/gdas_socahybridweights.cc
@@ -1,4 +1,4 @@
-#include "soca/gdas_socahybridweights.h"
+#include "gdas_socahybridweights.h"
 #include "oops/runs/Run.h"
 
 int main(int argc,  char ** argv) {