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Unless I'm mistaken (based on a read of js_of_ocaml --help) there is no specific flag that allows to disable these error messages:
[jsont.test_brr js_of_ocaml][0]: (b0 log --id 4813)
There are some missing primitives
Dummy implementations (raising 'Failure' exception) will be used if they are not available at runtime.
You can prevent the generation of dummy implementations with the commandline option '--disable genprim'
Missing primitives:
caml_unix_access
caml_unix_chdir
caml_unix_dup
caml_unix_environment
caml_unix_getcwd
caml_unix_spawn
caml_unix_waitpid