The wrong variable is saved before the test and CFLAGS gets overwritten with an empty one afterwards. --- a/configure.in 2020-05-11 15:34:13.000000000 +0200 +++ b/configure.in 2020-05-21 08:45:20.113154658 +0200 @@ -604,7 +604,7 @@ fi fi -SAVE_CPPFLAGS="$CPPFLAGS" +save_CFLAGS="$CFLAGS" CFLAGS=`python-config --includes` if [ $? -eq 0 ] then