Build:
- 0
2026-06-16 12:08.11: New job: build hlarp.0.0.3 (7929ac6600ce)
2026-06-16 12:08.11: Waiting for resource in pool day11-builds
2026-06-16 12:47.57: Got resource from pool day11-builds
2026-06-16 12:47.57: [profile full] build hlarp.0.0.3
2026-06-16 12:47.57: build hlarp.0.0.3 (7929ac6600ce)
=== DEPENDENCIES (13 transitive) ===
base-threads.base b7164ff76afe
base-unix.base 839dc585f12d
cmdliner.1.3.0 dad70bc4de20
dune.3.23.1 5402470d931c
nonstd.0.0.1 198c0f245521
ocaml.4.14.4 cb826ea44eb2
ocaml-base-compiler.4.14.4 d2f775f983d7
ocaml-config.2 669e0fcf9e4d
ocamlbuild.0.16.1 8f6c52e6fce8
ocamlfind.1.9.8 6025f4a8e98e
oml.0.0.7 2433dbe502ff
re.1.14.0 8d7c1999492d
topkg.1.1.1 ab549298f3fc
=== STDOUT ===
Processing: [default: loading data]
[hlarp.0.0.3: dl]
[hlarp.0.0.3: extract]
[hlarp.0.0.3/hlarp.install: dl]
-> retrieved hlarp.0.0.3 (https://opam.ocaml.org/cache)
[hlarp: make]
+ /usr/bin/make (CWD=/home/opam/.opam/default/.opam-switch/build/hlarp.0.0.3)
- ocamlbuild -use-ocamlfind -package nonstd -package re -package cmdliner -package oml -package re.posix -package re.glob \
- -I src/app -I src/lib hlarp.cma hlarp.cmxs hlarp.cmxa hlarp_cli.native
- + ocamlfind ocamlc -config
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/std.ml > src/lib/std.ml.depends
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/seq2HLA.ml > src/lib/seq2HLA.ml.depends
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/std.cmo src/lib/std.ml
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/optiType.ml > src/lib/optiType.ml.depends
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/athlates.ml > src/lib/athlates.ml.depends
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/prohlatype.ml > src/lib/prohlatype.ml.depends
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/compare.ml > src/lib/compare.ml.depends
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/athlates.cmo src/lib/athlates.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/athlates.cmo src/lib/athlates.ml
- File "src/lib/athlates.ml", line 6, characters 21-41:
- 6 | let filename_regex = Re_posix.compile_pat ("([^/]+)/[^/]+" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/optiType.cmo src/lib/optiType.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/optiType.cmo src/lib/optiType.ml
- File "src/lib/optiType.ml", line 11, characters 21-41:
- 11 | let filename_regex = Re_posix.compile_pat ("([^/]+)/([^/]+)/[^/]+" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/optiType.ml", line 43, characters 29-41:
- 43 | let glob_regex = Re.compile (Re_glob.glob ("*" ^ suffix))
- ^^^^^^^^^^^^
- Alert deprecated: module Re_glob
- Use Re.Glob
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/prohlatype.cmo src/lib/prohlatype.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/prohlatype.cmo src/lib/prohlatype.ml
- File "src/lib/prohlatype.ml", line 9, characters 2-22:
- 9 | Re_posix.compile_pat ("([^/]+)/([^/]+)_[^/]+(_(nuc|gen))?" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/seq2HLA.cmo src/lib/seq2HLA.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/seq2HLA.cmo src/lib/seq2HLA.ml
- File "src/lib/seq2HLA.ml", line 5, characters 21-41:
- 5 | let filename_regex = Re_posix.compile_pat ("(.+)-Class(I{1,2})" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/seq2HLA.ml", line 59, characters 29-41:
- 59 | let glob_regex = Re.compile (Re_glob.glob ("*" ^ suffix))
- ^^^^^^^^^^^^
- Alert deprecated: module Re_glob
- Use Re.Glob
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/lib/output.ml > src/lib/output.ml.depends
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/compare.cmo src/lib/compare.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/compare.cmo src/lib/compare.ml
- File "src/lib/compare.ml", line 141, characters 18-38:
- 141 | let colon_regex = Re_posix.compile_pat ":"
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/compare.ml", line 164, characters 12-32:
- 164 | Re.execp (Re_posix.compile_pat ("^" ^ p)) ai.Info.allele
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/compare.ml", line 189, characters 33-40:
- 189 | let specific_grouped_view ?loci ?classes ~typer1 ~ilist1 ~typer2 ~ilist2 =
- ^^^^^^^
- Warning 16 [unerasable-optional-argument]: this optional argument cannot be erased.
- File "src/lib/compare.ml", line 189, characters 27-31:
- 189 | let specific_grouped_view ?loci ?classes ~typer1 ~ilist1 ~typer2 ~ilist2 =
- ^^^^
- Warning 16 [unerasable-optional-argument]: this optional argument cannot be erased.
- File "src/lib/compare.ml", line 250, characters 7-21:
- 250 | if List.mem_assoc k acc then begin
- ^^^^^^^^^^^^^^
- Warning 6 [labels-omitted]: label map was omitted in the application of this function.
- File "src/lib/compare.ml", line 301, characters 26-40:
- 301 | if not (List.mem_assoc k q) then Some k else None)
- ^^^^^^^^^^^^^^
- Warning 6 [labels-omitted]: label map was omitted in the application of this function.
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/output.cmo src/lib/output.ml
- + ocamlfind ocamlc -pack -annot -bin-annot src/lib/std.cmo src/lib/seq2HLA.cmo src/lib/optiType.cmo src/lib/athlates.cmo src/lib/prohlatype.cmo src/lib/compare.cmo src/lib/output.cmo -o src/lib/hlarp.cmo
- + ocamlfind ocamlc -a -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib src/lib/hlarp.cmo -o src/lib/hlarp.cma
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/std.cmx src/lib/std.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/athlates.cmx src/lib/athlates.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/athlates.cmx src/lib/athlates.ml
- File "src/lib/athlates.ml", line 6, characters 21-41:
- 6 | let filename_regex = Re_posix.compile_pat ("([^/]+)/[^/]+" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/optiType.cmx src/lib/optiType.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/optiType.cmx src/lib/optiType.ml
- File "src/lib/optiType.ml", line 11, characters 21-41:
- 11 | let filename_regex = Re_posix.compile_pat ("([^/]+)/([^/]+)/[^/]+" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/optiType.ml", line 43, characters 29-41:
- 43 | let glob_regex = Re.compile (Re_glob.glob ("*" ^ suffix))
- ^^^^^^^^^^^^
- Alert deprecated: module Re_glob
- Use Re.Glob
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/prohlatype.cmx src/lib/prohlatype.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/prohlatype.cmx src/lib/prohlatype.ml
- File "src/lib/prohlatype.ml", line 9, characters 2-22:
- 9 | Re_posix.compile_pat ("([^/]+)/([^/]+)_[^/]+(_(nuc|gen))?" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/seq2HLA.cmx src/lib/seq2HLA.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/seq2HLA.cmx src/lib/seq2HLA.ml
- File "src/lib/seq2HLA.ml", line 5, characters 21-41:
- 5 | let filename_regex = Re_posix.compile_pat ("(.+)-Class(I{1,2})" ^ suffix)
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/seq2HLA.ml", line 59, characters 29-41:
- 59 | let glob_regex = Re.compile (Re_glob.glob ("*" ^ suffix))
- ^^^^^^^^^^^^
- Alert deprecated: module Re_glob
- Use Re.Glob
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/compare.cmx src/lib/compare.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/compare.cmx src/lib/compare.ml
- File "src/lib/compare.ml", line 141, characters 18-38:
- 141 | let colon_regex = Re_posix.compile_pat ":"
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/compare.ml", line 164, characters 12-32:
- 164 | Re.execp (Re_posix.compile_pat ("^" ^ p)) ai.Info.allele
- ^^^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Re_posix
- Use Re.Posix
- File "src/lib/compare.ml", line 189, characters 33-40:
- 189 | let specific_grouped_view ?loci ?classes ~typer1 ~ilist1 ~typer2 ~ilist2 =
- ^^^^^^^
- Warning 16 [unerasable-optional-argument]: this optional argument cannot be erased.
- File "src/lib/compare.ml", line 189, characters 27-31:
- 189 | let specific_grouped_view ?loci ?classes ~typer1 ~ilist1 ~typer2 ~ilist2 =
- ^^^^
- Warning 16 [unerasable-optional-argument]: this optional argument cannot be erased.
- File "src/lib/compare.ml", line 250, characters 7-21:
- 250 | if List.mem_assoc k acc then begin
- ^^^^^^^^^^^^^^
- Warning 6 [labels-omitted]: label map was omitted in the application of this function.
- File "src/lib/compare.ml", line 301, characters 26-40:
- 301 | if not (List.mem_assoc k q) then Some k else None)
- ^^^^^^^^^^^^^^
- Warning 6 [labels-omitted]: label map was omitted in the application of this function.
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -for-pack Hlarp -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app -o src/lib/output.cmx src/lib/output.ml
- + touch src/lib/hlarp.mli ; if ocamlfind ocamlopt -pack -annot -bin-annot -I src/lib src/lib/std.cmx src/lib/seq2HLA.cmx src/lib/optiType.cmx src/lib/athlates.cmx src/lib/prohlatype.cmx src/lib/compare.cmx src/lib/output.cmx -o src/lib/hlarp.cmx ; then rm -f src/lib/hlarp.mli ; else rm -f src/lib/hlarp.mli ; exit 1; fi
- + ocamlfind ocamlopt -a -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib src/lib/hlarp.cmx -o src/lib/hlarp.cmxa
- + ocamlfind ocamlopt -shared -linkall -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib src/lib/hlarp.cmxa -o src/lib/hlarp.cmxs
- + ocamlfind ocamldep -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -modules src/app/hlarp_cli.ml > src/app/hlarp_cli.ml.depends
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/app -I src/lib -o src/app/hlarp_cli.cmo src/app/hlarp_cli.ml
- + ocamlfind ocamlc -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/app -I src/lib -o src/app/hlarp_cli.cmo src/app/hlarp_cli.ml
- File "src/app/hlarp_cli.ml", line 54, characters 15-19:
- 54 | Term.(ret (pure (`Help (`Plain, None)))
- ^^^^
- Alert deprecated: Cmdliner.Term.pure
- Use Term.const instead.
- File "src/app/hlarp_cli.ml", line 55, characters 10-14:
- 55 | , info project_name ~version ~doc ~man)
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 72, characters 10-14:
- 72 | , info tool ~doc:"Parse seq2HLA output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 78, characters 10-14:
- 78 | , info tool ~doc:"Parse OptiType output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 102, characters 10-14:
- 102 | , info tool ~doc:"Parse ATHLATES output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 108, characters 10-14:
- 108 | , info tool ~doc:"Parse Prohlatype output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 125, characters 10-14:
- 125 | , info "multiple"
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 195, characters 10-14:
- 195 | , info "compare"
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 199, characters 8-24:
- 199 | match Term.eval_choice help_cmd cmds with
- ^^^^^^^^^^^^^^^^
- Alert deprecated: Cmdliner.Term.eval_choice
- Use Cmd.group and one of Cmd.eval* instead.
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/app -I src/lib -o src/app/hlarp_cli.cmx src/app/hlarp_cli.ml
- + ocamlfind ocamlopt -c -annot -bin-annot -principal -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/app -I src/lib -o src/app/hlarp_cli.cmx src/app/hlarp_cli.ml
- File "src/app/hlarp_cli.ml", line 54, characters 15-19:
- 54 | Term.(ret (pure (`Help (`Plain, None)))
- ^^^^
- Alert deprecated: Cmdliner.Term.pure
- Use Term.const instead.
- File "src/app/hlarp_cli.ml", line 55, characters 10-14:
- 55 | , info project_name ~version ~doc ~man)
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 72, characters 10-14:
- 72 | , info tool ~doc:"Parse seq2HLA output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 78, characters 10-14:
- 78 | , info tool ~doc:"Parse OptiType output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 102, characters 10-14:
- 102 | , info tool ~doc:"Parse ATHLATES output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 108, characters 10-14:
- 108 | , info tool ~doc:"Parse Prohlatype output")
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 125, characters 10-14:
- 125 | , info "multiple"
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 195, characters 10-14:
- 195 | , info "compare"
- ^^^^
- Alert deprecated: Cmdliner.Term.info
- Use Cmd.info instead.
- File "src/app/hlarp_cli.ml", line 199, characters 8-24:
- 199 | match Term.eval_choice help_cmd cmds with
- ^^^^^^^^^^^^^^^^
- Alert deprecated: Cmdliner.Term.eval_choice
- Use Cmd.group and one of Cmd.eval* instead.
- + ocamlfind ocamlopt -linkpkg -package re.glob -package re.posix -package oml -package cmdliner -package re -package nonstd -I src/lib -I src/app src/lib/hlarp.cmx src/app/hlarp_cli.cmx -o src/app/hlarp_cli.native
- cp hlarp_cli.native hlarp
-> compiled hlarp.0.0.3
[hlarp: make install]
+ /usr/bin/make "install" (CWD=/home/opam/.opam/default/.opam-switch/build/hlarp.0.0.3)
- ocamlfind install hlarp META \
- _build/src/lib/hlarp.a \
- _build/src/lib/hlarp.o \
- _build/src/lib/hlarp.cma \
- _build/src/lib/hlarp.cmi \
- _build/src/lib/hlarp.cmo \
- _build/src/lib/hlarp.cmx \
- _build/src/lib/hlarp.cmxa \
- _build/src/lib/hlarp.cmxs
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cmxs
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cmxa
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cmx
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cmo
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cmi
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.cma
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.o
- Installed /home/opam/.opam/default/lib/hlarp/hlarp.a
- Installed /home/opam/.opam/default/lib/hlarp/META
-> installed hlarp.0.0.3
=== STDERR ===
2026-06-16 12:48.05: OK: build hlarp.0.0.3 (runc: 4.1s, disk: 25KB)
2026-06-16 12:48.05: Job succeeded