diff --git a/bin/Makefile.am b/bin/Makefile.am
index bb60ff3dd..0b2b9a77e 100644
--- a/bin/Makefile.am
+++ b/bin/Makefile.am
@@ -13,7 +13,8 @@ if HAVE_LIBSQUASHFUSE
 ch_run_SOURCES += ch_fuse.h ch_fuse.c
 endif
 
-ch_run_CFLAGS = $(CFLAGS) $(PTHREAD_CFLAGS)
+# additional build flags for ch-run
+ch_run_CFLAGS = $(PTHREAD_CFLAGS)
 ch_run_LDADD = $(CH_RUN_LIBS)
 
 
diff --git a/configure.ac b/configure.ac
index 3ca364e80..b3668680e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -941,7 +941,7 @@ Building Charliecloud
     test suite ... ${enable_test}
 
   required:
-    C99 compiler ... ${CC} ${CC_VERSION}
+    C99 compiler ... ${CC} ${CFLAGS}
 
   optional:
     extended glob patterns in --unset-env ... ${have_fnm_extmatch}