Mode `(byte shared_object)` cannot find stubs in Dune >= 2.1

Hi all,

I'm trying to build https://github.com/janestreet/pythonlib/tree/master/examples , however, there seems to be a regression from dune 2.0 to dune 2.1.3 ; with dune 2.0.1 things build fine, however with >= 2.1.3. I get:

 ocamlc examples/ocaml.bc.so (exit 2)
(cd _build/default && /home/egallego/.opam/coq-dune/bin/ocamlc.opt -w @1..3@5..28@30..39@43@46..47@49..57@61..62-40 -strict-sequence -strict-formats -short-paths -keep-locs -linkall -g -o examples/ocaml.bc.so -output-complete-obj -runtime-variant _pic /home/egallego/.opam/coq-dune/lib/base/base_internalhash_types/base_internalhash_types.cma /home/egallego/.opam/coq-dune/lib/base/caml/caml.cma /home/egallego/.opam/coq-dune/lib/sexplib0/sexplib0.cma /home/egallego/.opam/coq-dune/lib/base/shadow_stdlib/shadow_stdlib.cma /home/egallego/.opam/coq-dune/lib/base/base.cma /home/egallego/.opam/coq-dune/lib/ocaml/compiler-libs/ocamlcommon.cma /home/egallego/.opam/coq-dune/lib/ocaml/compiler-libs/ocamlbytecomp.cma /home/egallego/.opam/coq-dune/lib/ocaml/compiler-libs/ocamltoplevel.cma /home/egallego/.opam/coq-dune/lib/ocaml/unix.cma /home/egallego/.opam/coq-dune/lib/stdcompat/stdcompat.cma /home/egallego/.opam/coq-dune/lib/pyml/pyml.cma /home/egallego/.opam/coq-dune/lib/pyml/numpy.cma /home/egallego/.opam/coq-dune/lib/stdio/stdio.cma /home/egallego/.opam/coq-dune/lib/typerep/typerep_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_sexp_conv/runtime-lib/ppx_sexp_conv_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_compare/runtime-lib/ppx_compare_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_enumerate/runtime-lib/ppx_enumerate_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_hash/runtime-lib/ppx_hash_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_python/runtime/ppx_python_runtime.cma /home/egallego/.opam/coq-dune/lib/ppx_inline_test/config/inline_test_config.cma /home/egallego/.opam/coq-dune/lib/jane-street-headers/jane_street_headers.cma /home/egallego/.opam/coq-dune/lib/time_now/time_now.cma /home/egallego/.opam/coq-dune/lib/ppx_inline_test/runtime-lib/ppx_inline_test_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_here/runtime-lib/ppx_here_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_expect/common/expect_test_common.cma /home/egallego/.opam/coq-dune/lib/ppx_expect/config_types/expect_test_config_types.cma /home/egallego/.opam/coq-dune/lib/ppx_expect/collector/expect_test_collector.cma /home/egallego/.opam/coq-dune/lib/ppx_expect/config/expect_test_config.cma src/python_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_assert/runtime-lib/ppx_assert_lib.cma /home/egallego/.opam/coq-dune/lib/ppx_bench/runtime-lib/ppx_bench_lib.cma /home/egallego/.opam/coq-dune/lib/base/md5/md5_lib.cma /home/egallego/.opam/coq-dune/lib/ocaml/bigarray.cma /home/egallego/.opam/coq-dune/lib/fieldslib/fieldslib.cma /home/egallego/.opam/coq-dune/lib/variantslib/variantslib.cma /home/egallego/.opam/coq-dune/lib/bin_prot/shape/bin_shape_lib.cma /home/egallego/.opam/coq-dune/lib/bin_prot/bin_prot.cma /home/egallego/.opam/coq-dune/lib/ppx_module_timer/runtime/ppx_module_timer_runtime.cma /home/egallego/.opam/coq-dune/lib/splittable_random/splittable_random.cma /home/egallego/.opam/coq-dune/lib/base_quickcheck/base_quickcheck.cma examples/init/python_ocaml_init.cma -I examples/init examples/.ocaml.eobjs/byte/dune__exe.cmo examples/.ocaml.eobjs/byte/dune__exe__Toploop_bindings.cmo examples/.ocaml.eobjs/byte/dune__exe__Ocaml.cmo)
/usr/bin/ld: cannot find -lbin_prot_stubs
/usr/bin/ld: cannot find -lexpect_test_collector_stubs
/usr/bin/ld: cannot find -ltime_now_stubs
/usr/bin/ld: cannot find -lnumpy_stubs
/usr/bin/ld: cannot find -lpyml_stubs
/usr/bin/ld: cannot find -lstdcompat__stubs
/usr/bin/ld: cannot find -lbase_stubs
/usr/bin/ld: cannot find -lbase_internalhash_types_stubs
collect2: error: ld returned 1 exit status
File "_none_", line 1:
Error: Error while building custom runtime system

Any idea on what is going on? I could research more, but I'm not very familiar with the code so maybe anyone here has an idea on what is going on.

This is likely related to #2994 ; other users are facing the same problem, see https://github.com/janestreet/pythonlib/issues/1

Reproduce the failure by building the pythonlib examples with Dune 2.0.1 and 2.1.3 or later. Start with the examples directory, the custom runtime link command, and related issue #2994; done means the byte shared_object build locates the listed native stubs and completes successfully.