Fix graphviz generation #12564

Job	Run time
ruby-bench (--warmup=1 --bench=1 --excludes=lobsters)	16m 50s
make (check, i686)	12m 7s
make (test-bundler-parallel, 50)	24m 2s
make (check, --disable-yjit)	7m 26s
make (check, --enable-shared --enable-load-relative)	8m 42s
make (check, cppflags=-DVM_CHECK_MODE)	9m 21s
make (check, ubuntu-24.04, capi)	11m 7s
make (test-bundled-gems)	21m 14s
make-ibm	-1s
Ubuntu result	3s
	1h 50m 51s

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