To remove the pid file, its directory must be writable by suricata user.

Index: configure.ac
--- configure.ac.orig
+++ configure.ac
@@ -2599,7 +2599,7 @@ if test "$WINDOWS_PATH" = "yes"; then
     fi
 else
     EXPAND_VARIABLE(localstatedir, e_logdir, "/log/suricata/")
-    EXPAND_VARIABLE(localstatedir, e_rundir, "/run/")
+    EXPAND_VARIABLE(localstatedir, e_rundir, "/run/suricata/")
     EXPAND_VARIABLE(localstatedir, e_logfilesdir, "/log/suricata/files")
     EXPAND_VARIABLE(localstatedir, e_logcertsdir, "/log/suricata/certs")
     EXPAND_VARIABLE(sysconfdir, e_sysconfdir, "/suricata/")
