(not at the head of any monitored branch or PR)
2022-07-26 15:58.09: New job: test bistro-bio.0.6.0 with ounit2.2.2.0, using opam dev
                              from https://github.com/ocaml/opam-repository.git#refs/pull/21354/head (10b49fadb0efcff442ed8cae85f7cc119fe28629)
                              on debian-11-ocaml-4.14/amd64

To reproduce locally:

git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/21354/head" && git reset --hard 10b49fad
git fetch origin master
git merge 42e749bdca1e36a9f7bbef60b3507d34c6c57fa3
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-11-ocaml-4.14@sha256:1461d919411f5999f6d7ffd573b9b5385cda91accf83d3866b26097e791220be
USER 1000:1000
WORKDIR /home/opam
RUN for pkg in $(opam pin list --short); do opam pin remove "$pkg"; done
RUN opam repository remove -a multicore || true
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMSOLVERTIMEOUT="500"
ENV OPAMPRECISETRACKING="1"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam pin add -k version -yn ounit2.2.2.0 2.2.0
RUN opam update --depexts
RUN opam remove ounit2.2.2.0 && opam install --deps-only ounit2.2.2.0 && opam install -v ounit2.2.2.0; \
    res=$?; \
    test "$res" != 31 && exit "$res"; \
    export OPAMCLI=2.0; \
    build_dir=$(opam var prefix)/.opam-switch/build; \
    failed=$(ls "$build_dir"); \
    for pkg in $failed; do \
    if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-11\""; then \
    echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
    fi; \
    done; \
    exit 1
RUN opam update --depexts
RUN opam remove bistro-bio.0.6.0 && opam install --deps-only bistro-bio.0.6.0 && opam install -v bistro-bio.0.6.0; \
    res=$?; \
    test "$res" != 31 && exit "$res"; \
    export OPAMCLI=2.0; \
    build_dir=$(opam var prefix)/.opam-switch/build; \
    failed=$(ls "$build_dir"); \
    for pkg in $failed; do \
    if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-11\""; then \
    echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
    fi; \
    done; \
    exit 1
RUN opam update --depexts
RUN opam remove bistro-bio.0.6.0 && opam install --deps-only --with-test bistro-bio.0.6.0 && opam install -v --with-test bistro-bio.0.6.0; \
    res=$?; \
    test "$res" != 31 && exit "$res"; \
    export OPAMCLI=2.0; \
    build_dir=$(opam var prefix)/.opam-switch/build; \
    failed=$(ls "$build_dir"); \
    for pkg in $failed; do \
    if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-11\""; then \
    echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
    fi; \
    done; \
    exit 1

END-OF-DOCKERFILE
docker build -f ../Dockerfile .

2022-07-26 15:58.09: Using cache hint "ocaml/opam:debian-11-ocaml-4.14@sha256:1461d919411f5999f6d7ffd573b9b5385cda91accf83d3866b26097e791220be-ounit2.2.2.0-bistro-bio.0.6.0-10b49fadb0efcff442ed8cae85f7cc119fe28629"
2022-07-26 15:58.09: Using OBuilder spec:
((from ocaml/opam:debian-11-ocaml-4.14@sha256:1461d919411f5999f6d7ffd573b9b5385cda91accf83d3866b26097e791220be)
 (user (uid 1000) (gid 1000))
 (workdir /home/opam)
 (run (shell "for pkg in $(opam pin list --short); do opam pin remove \"$pkg\"; done"))
 (run (shell "opam repository remove -a multicore || true"))
 (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
 (run (shell "opam init --reinit --config .opamrc-sandbox -ni"))
 (env OPAMDOWNLOADJOBS 1)
 (env OPAMERRLOGLEN 0)
 (env OPAMSOLVERTIMEOUT 500)
 (env OPAMPRECISETRACKING 1)
 (run (shell "rm -rf opam-repository/"))
 (copy (src .) (dst opam-repository/))
 (run (shell "opam repository set-url --strict default opam-repository/"))
 (run (shell "opam pin add -k version -yn ounit2.2.2.0 2.2.0"))
 (run (network host)
      (shell "opam update --depexts"))
 (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
      (network host)
      (shell  "opam remove ounit2.2.2.0 && opam install --deps-only ounit2.2.2.0 && opam install -v ounit2.2.2.0;\
             \n        res=$?;\
             \n        test \"$res\" != 31 && exit \"$res\";\
             \n        export OPAMCLI=2.0;\
             \n        build_dir=$(opam var prefix)/.opam-switch/build;\
             \n        failed=$(ls \"$build_dir\");\
             \n        for pkg in $failed; do\
             \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
             \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
             \n          fi;\
             \n        done;\
             \n        exit 1"))
 (run (network host)
      (shell "opam update --depexts"))
 (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
      (network host)
      (shell  "opam remove bistro-bio.0.6.0 && opam install --deps-only bistro-bio.0.6.0 && opam install -v bistro-bio.0.6.0;\
             \n        res=$?;\
             \n        test \"$res\" != 31 && exit \"$res\";\
             \n        export OPAMCLI=2.0;\
             \n        build_dir=$(opam var prefix)/.opam-switch/build;\
             \n        failed=$(ls \"$build_dir\");\
             \n        for pkg in $failed; do\
             \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
             \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
             \n          fi;\
             \n        done;\
             \n        exit 1"))
 (run (network host)
      (shell "opam update --depexts"))
 (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
      (network host)
      (shell  "opam remove bistro-bio.0.6.0 && opam install --deps-only --with-test bistro-bio.0.6.0 && opam install -v --with-test bistro-bio.0.6.0;\
             \n        res=$?;\
             \n        test \"$res\" != 31 && exit \"$res\";\
             \n        export OPAMCLI=2.0;\
             \n        build_dir=$(opam var prefix)/.opam-switch/build;\
             \n        failed=$(ls \"$build_dir\");\
             \n        for pkg in $failed; do\
             \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
             \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
             \n          fi;\
             \n        done;\
             \n        exit 1"))
)

2022-07-26 15:58.09: Waiting for resource in pool OCluster
2022-07-27 05:22.37: Waiting for worker...
2022-07-27 05:24.30: Got resource from pool OCluster
Building on asteria.ocamllabs.io
All commits already cached
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HEAD is now at 42e749bdca Merge pull request #21885 from kit-ty-kate/fix-123
Merge made by the 'ort' strategy.
 packages/ounit2/ounit2.2.2.0/opam | 3 +++
 packages/ounit2/ounit2.2.2.1/opam | 3 +++
 packages/ounit2/ounit2.2.2.2/opam | 3 +++
 packages/ounit2/ounit2.2.2.3/opam | 3 +++
 packages/ounit2/ounit2.2.2.4/opam | 3 +++
 packages/ounit2/ounit2.2.2.5/opam | 3 +++
 packages/ounit2/ounit2.2.2.6/opam | 3 +++
 7 files changed, 21 insertions(+)

(from ocaml/opam:debian-11-ocaml-4.14@sha256:1461d919411f5999f6d7ffd573b9b5385cda91accf83d3866b26097e791220be)
2022-07-27 05:39.12 ---> using "d837bbe1b6e58c32e942b55a1eb695ef30d2cac63c8a5d708beb3548d17192b4" from cache

/: (user (uid 1000) (gid 1000))

/: (workdir /home/opam)

/home/opam: (run (shell "for pkg in $(opam pin list --short); do opam pin remove \"$pkg\"; done"))
Ok, ocaml-base-compiler is no longer pinned to https://github.com/ocaml/ocaml/archive/4.14.0.tar.gz (version 4.14.0)
No package build needed.
Nothing to do.
# Run eval $(opam env) to update the current shell environment
2022-07-27 05:39.12 ---> using "543d29c04ee698e03faf7cfdc4bb3cf9e04a80ab924d981f1055393f1479d117" from cache

/home/opam: (run (shell "opam repository remove -a multicore || true"))
[WARNING] No configured repositories by these names found: multicore
2022-07-27 05:39.12 ---> using "e8a5c58b05459f7be98d7b03e29623d3a05b15b34833b50ebffb60eff7871cde" from cache

/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2022-07-27 05:39.12 ---> using "4687a20afa7557b4b2498b537430ed75c7b51cd6cad60d9c4757ff852befb1a7" from cache

/home/opam: (run (shell "opam init --reinit --config .opamrc-sandbox -ni"))
Configuring from /home/opam/.opamrc-sandbox, then /home/opam/.opamrc, and finally from built-in defaults.
Checking for available remotes: rsync and local, git.
  - you won't be able to use mercurial repositories unless you install the hg command on your system.
  - you won't be able to use darcs repositories unless you install the darcs command on your system.

Continue? [y/n] y
This development version of opam requires an update to the layout of /home/opam/.opam from version 2.0 to version 2.1, which can't be reverted.
You may want to back it up before going further.

Format upgrade done.

<><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
[default] synchronised from file:///home/opam/opam-repository
2022-07-27 05:39.12 ---> using "87c4051d859f505ce794fbdc2ed87105744babed536dd4b09731a9b1e22fd3d4" from cache

/home/opam: (env OPAMDOWNLOADJOBS 1)

/home/opam: (env OPAMERRLOGLEN 0)

/home/opam: (env OPAMSOLVERTIMEOUT 500)

/home/opam: (env OPAMPRECISETRACKING 1)

/home/opam: (run (shell "rm -rf opam-repository/"))
2022-07-27 05:39.12 ---> using "96a067e6b08152c0f77ff1628817c13e12ac3db1ba1ac882a90278edcbb3d011" from cache

/home/opam: (copy (src .) (dst opam-repository/))
2022-07-27 05:39.13 ---> using "5ce106567f73501cd746c3358ba50b49e5b3ad28d47e7894c1f65b44fcda87e7" from cache

/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2022-07-27 05:39.13 ---> using "0981e55d831537155c9e161d0ab37d0aeee18cf4c3d1dbad8143304b4c508a5d" from cache

/home/opam: (run (shell "opam pin add -k version -yn ounit2.2.2.0 2.2.0"))
ounit2 is now pinned to version 2.2.0
2022-07-27 05:39.13 ---> using "a5b811fe2c6ab2fd90efb98285ea9db0346a5de8dadc9481e3cd36fb68f11371" from cache

/home/opam: (run (network host)
                 (shell "opam update --depexts"))
+ /usr/bin/sudo "apt-get" "update"
- Hit:1 http://deb.debian.org/debian bullseye InRelease
- Get:2 http://deb.debian.org/debian-security bullseye-security InRelease [48.4 kB]
- Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB]
- Get:4 http://deb.debian.org/debian-security bullseye-security/main amd64 Packages [168 kB]
- Fetched 261 kB in 0s (773 kB/s)
- Reading package lists...
2022-07-27 05:39.13 ---> using "db2d7bb6f3a492dbe20e0d4ddb4733d768da5e64ce8f97c3cbc89325acd13b48" from cache

/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
                 (network host)
                 (shell  "opam remove ounit2.2.2.0 && opam install --deps-only ounit2.2.2.0 && opam install -v ounit2.2.2.0;\
                        \n        res=$?;\
                        \n        test \"$res\" != 31 && exit \"$res\";\
                        \n        export OPAMCLI=2.0;\
                        \n        build_dir=$(opam var prefix)/.opam-switch/build;\
                        \n        failed=$(ls \"$build_dir\");\
                        \n        for pkg in $failed; do\
                        \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
                        \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
                        \n          fi;\
                        \n        done;\
                        \n        exit 1"))
[NOTE] ounit2.2.2.0 is not installed.

Nothing to do.
The following actions will be performed:
=== install 4 packages
  - install base-bytes   base  [required by ounit2]
  - install dune         3.4.1 [required by ounit2]
  - install ocamlfind    1.9.5 [required by base-bytes]
  - install stdlib-shims 0.3.0 [required by ounit2]

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.4.1  (cached)
-> retrieved ocamlfind.1.9.5  (cached)
-> retrieved stdlib-shims.0.3.0  (cached)
-> installed ocamlfind.1.9.5
-> installed base-bytes.base
-> installed dune.3.4.1
-> installed stdlib-shims.0.3.0
Done.
# Run eval $(opam env) to update the current shell environment
The following actions will be performed:
=== install 1 package
  - install ounit2 2.2.0 (pinned)

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing  1/3:
-> retrieved ounit2.2.2.0  (cached)
Processing  2/3: [ounit2: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "ounit2" "-j" "31" (CWD=/home/opam/.opam/4.14/.opam-switch/build/ounit2.2.2.0)
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -I /home/opam/.opam/4.14/lib/stdlib-shims -no-alias-deps -o src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte/oUnitAssert.cmo -c -impl src/lib/ounit2/advanced/oUnitAssert.ml)
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 130, characters 13-27:
- 130 |     ?(sinput=Stream.of_list [])
-                    ^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 270, characters 13-24:
- 270 |              Stream.iter
-                    ^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 315, characters 26-43:
- 315 |                  foutput (Stream.of_channel chn)
-                                 ^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlopt.opt -w -40 -g -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/native -I /home/opam/.opam/4.14/lib/stdlib-shims -intf-suffix .ml -no-alias-deps -o src/lib/ounit2/advanced/.oUnitAdvanced.objs/native/oUnitAssert.cmx -c -impl src/lib/ounit2/advanced/oUnitAssert.ml)
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 130, characters 13-27:
- 130 |     ?(sinput=Stream.of_list [])
-                    ^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 270, characters 13-24:
- 270 |              Stream.iter
-                    ^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/advanced/oUnitAssert.ml", line 315, characters 26-43:
- 315 |                  foutput (Stream.of_channel chn)
-                                 ^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/lib/ounit2/.oUnit.objs/byte -I /home/opam/.opam/4.14/lib/stdlib-shims -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -no-alias-deps -o src/lib/ounit2/.oUnit.objs/byte/oUnit2.cmi -c -intf src/lib/ounit2/oUnit2.mli)
- File "src/lib/ounit2/oUnit2.mli", line 88, characters 17-25:
- 88 |     ?sinput:char Stream.t ->
-                       ^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/oUnit2.mli", line 89, characters 19-27:
- 89 |     ?foutput:(char Stream.t -> unit) ->
-                         ^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/lib/ounit2/.oUnit.objs/byte -I /home/opam/.opam/4.14/lib/stdlib-shims -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -no-alias-deps -o src/lib/ounit2/.oUnit.objs/byte/oUnit.cmi -c -intf src/lib/ounit2/oUnit.mli)
- File "src/lib/ounit2/oUnit.mli", line 80, characters 17-25:
- 80 |     ?sinput:char Stream.t ->
-                       ^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- File "src/lib/ounit2/oUnit.mli", line 81, characters 19-27:
- 81 |     ?foutput:(char Stream.t -> unit) ->
-                         ^^^^^^^^
- Alert deprecated: module Stdlib.Stream
- Use the camlp-streams library instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/lib/ounit2/threads/.oUnitThreads.objs/byte -I src/lib/ounit2/threads/.oUnitThreads.objs/public_cmi -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/stdlib-shims -I src/lib/ounit2/.oUnit.objs/byte -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -no-alias-deps -open OUnitThreads__ -o src/lib/ounit2/threads/.oUnitThreads.objs/byte/oUnitThreads__OUnitRunnerThreads.cmo -c -impl src/lib/ounit2/threads/oUnitRunnerThreads.ml)
- File "src/lib/ounit2/threads/oUnitRunnerThreads.ml", line 147, characters 8-19:
- 147 |         Thread.kill thread;
-               ^^^^^^^^^^^
- Alert deprecated: Thread.kill
- Not implemented, do not use
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlopt.opt -w -40 -g -I src/lib/ounit2/threads/.oUnitThreads.objs/byte -I src/lib/ounit2/threads/.oUnitThreads.objs/native -I src/lib/ounit2/threads/.oUnitThreads.objs/public_cmi -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/stdlib-shims -I src/lib/ounit2/.oUnit.objs/byte -I src/lib/ounit2/.oUnit.objs/native -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/byte -I src/lib/ounit2/advanced/.oUnitAdvanced.objs/native -intf-suffix .ml -no-alias-deps -open OUnitThreads__ -o src/lib/ounit2/threads/.oUnitThreads.objs/native/oUnitThreads__OUnitRunnerThreads.cmx -c -impl src/lib/ounit2/threads/oUnitRunnerThreads.ml)
- File "src/lib/ounit2/threads/oUnitRunnerThreads.ml", line 147, characters 8-19:
- 147 |         Thread.kill thread;
-               ^^^^^^^^^^^
- Alert deprecated: Thread.kill
- Not implemented, do not use
-> compiled  ounit2.2.2.0
-> installed ounit2.2.2.0
Done.
# Run eval $(opam env) to update the current shell environment
2022-07-27 05:39.13 ---> using "549816a256be73d9a20d8aac9e10b779e4fdffd8e09de149b8d5e327ac84c14f" from cache

/home/opam: (run (network host)
                 (shell "opam update --depexts"))
+ /usr/bin/sudo "apt-get" "update"
- Hit:1 http://deb.debian.org/debian bullseye InRelease
- Hit:2 http://deb.debian.org/debian-security bullseye-security InRelease
- Hit:3 http://deb.debian.org/debian bullseye-updates InRelease
- Reading package lists...
- 
2022-07-27 05:39.13 ---> using "ed77e423a302c60a5809ee2b791a97889b346ae238a3ae55d40f898cb095304c" from cache

/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
                 (network host)
                 (shell  "opam remove bistro-bio.0.6.0 && opam install --deps-only bistro-bio.0.6.0 && opam install -v bistro-bio.0.6.0;\
                        \n        res=$?;\
                        \n        test \"$res\" != 31 && exit \"$res\";\
                        \n        export OPAMCLI=2.0;\
                        \n        build_dir=$(opam var prefix)/.opam-switch/build;\
                        \n        failed=$(ls \"$build_dir\");\
                        \n        for pkg in $failed; do\
                        \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
                        \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
                        \n          fi;\
                        \n        done;\
                        \n        exit 1"))
[NOTE] bistro-bio.0.6.0 is not installed.

Nothing to do.
The following actions will be performed:
=== install 108 packages
  - install angstrom             0.15.0   [required by biotk]
  - install angstrom-unix        0.15.0   [required by biotk]
  - install astring              0.8.5    [required by bos]
  - install base                 v0.14.3  [required by ppx_csv_conv]
  - install base64               3.5.0    [required by biocaml, bistro]
  - install base_bigstring       v0.14.0  [required by core_kernel]
  - install base_quickcheck      v0.14.1  [required by core_kernel]
  - install bigstringaf          0.9.0    [required by angstrom]
  - install bin_prot             v0.14.1  [required by core_kernel]
  - install biocaml              0.11.1   [required by bistro-bio]
  - install biotk                0.1.0    [required by bistro-bio]
  - install bistro               0.6.0    [required by bistro-bio]
  - install bos                  0.2.1    [required by bistro]
  - install camlzip              1.11     [required by biocaml]
  - install cfstream             1.3.1    [required by biocaml]
  - install cmdliner             1.1.1    [required by crunch, fmt]
  - install conf-m4              1        [required by cfstream]
  - install conf-pkg-config      2        [required by conf-zlib]
  - install conf-zlib            1        [required by camlzip]
  - install core                 v0.14.1  [required by biotk, biocaml, bistro]
  - install core_kernel          v0.14.2  [required by biocaml]
  - install cppo                 1.6.9    [required by ppx_deriving, lwt, lwt_react]
  - install crunch               3.3.0    [required by biotk]
  - install csexp                1.5.1    [required by dune-configurator]
  - install csvfields            v0.14.0  [required by ppx_csv_conv]
  - install dune-configurator    3.4.1    [required by lwt]
  - install fieldslib            v0.14.0  [required by core_kernel]
  - install fmt                  0.9.0    [required by biotk]
  - install fpath                0.7.3    [required by bos]
  - install gg                   1.0.0    [required by vg]
  - install jane-street-headers  v0.14.0  [required by core_kernel]
  - install js_of_ocaml          4.0.0    [required by vg]
  - install js_of_ocaml-compiler 4.0.0    [required by vg]
  - install js_of_ocaml-ppx      4.0.0    [required by vg]
  - install jst-config           v0.14.1  [required by core]
  - install logs                 0.7.0    [required by bos]
  - install lwt                  5.6.1    [required by biocaml, bistro]
  - install lwt_react            1.2.0    [required by bistro]
  - install menhir               20220210 [required by js_of_ocaml-compiler]
  - install menhirLib            20220210 [required by js_of_ocaml-compiler]
  - install menhirSdk            20220210 [required by js_of_ocaml-compiler]
  - install num                  1.4      [required by csvfields]
  - install ocaml-compiler-libs  v0.12.4  [required by ppxlib]
  - install ocaml-syntax-shims   1.0.0    [required by angstrom]
  - install ocamlbuild           0.14.1   [required by vg, ocamlnet, xmlm, etc.]
  - install ocamlgraph           2.0.0    [required by bistro]
  - install ocamlnet             4.1.9-2  [required by biotk]
  - install ocplib-endian        1.2      [required by lwt]
  - install octavius             1.2.2    [required by ppx_js_style]
  - install otfm                 0.4.0    [required by biotk]
  - install parsexp              v0.14.2  [required by sexplib]
  - install ppx_assert           v0.14.0  [required by core_kernel]
  - install ppx_base             v0.14.0  [required by core_kernel]
  - install ppx_bench            v0.14.1  [required by ppx_jane]
  - install ppx_bin_prot         v0.14.0  [required by ppx_jane]
  - install ppx_cold             v0.14.0  [required by ppx_base]
  - install ppx_compare          v0.14.0  [required by biocaml]
  - install ppx_conv_func        v0.14.0  [required by ppx_csv_conv]
  - install ppx_csv_conv         v0.14.0  [required by biotk]
  - install ppx_custom_printf    v0.14.1  [required by ppx_jane]
  - install ppx_derivers         1.2.1    [required by ppx_deriving]
  - install ppx_deriving         5.2.1    [required by biotk]
  - install ppx_enumerate        v0.14.0  [required by ppx_base]
  - install ppx_expect           v0.14.2  [required by ppx_jane]
  - install ppx_fields_conv      v0.14.2  [required by ppx_csv_conv]
  - install ppx_fixed_literal    v0.14.0  [required by ppx_jane]
  - install ppx_hash             v0.14.0  [required by core_kernel]
  - install ppx_here             v0.14.0  [required by ppx_jane]
  - install ppx_inline_test      v0.14.1  [required by core_kernel]
  - install ppx_jane             v0.14.0  [required by core]
  - install ppx_js_style         v0.14.1  [required by ppx_base]
  - install ppx_let              v0.14.0  [required by ppx_jane]
  - install ppx_module_timer     v0.14.0  [required by ppx_jane]
  - install ppx_optcomp          v0.14.3  [required by core_kernel]
  - install ppx_optional         v0.14.0  [required by ppx_jane]
  - install ppx_pipebang         v0.14.0  [required by ppx_jane]
  - install ppx_sexp_conv        v0.14.3  [required by biocaml, bistro]
  - install ppx_sexp_message     v0.14.1  [required by core_kernel]
  - install ppx_sexp_value       v0.14.0  [required by ppx_jane]
  - install ppx_stable           v0.14.1  [required by ppx_jane]
  - install ppx_string           v0.14.1  [required by ppx_jane]
  - install ppx_typerep_conv     v0.14.2  [required by ppx_jane]
  - install ppx_variants_conv    v0.14.2  [required by ppx_jane]
  - install ppxlib               0.25.1   [required by bistro]
  - install ptime                1.0.0    [required by crunch]
  - install re                   1.10.4   [required by biocaml]
  - install react                1.2.2    [required by lwt_react]
  - install result               1.5      [required by biotk]
  - install rresult              0.7.0    [required by biotk, biocaml, bistro]
  - install seq                  base     [required by tyxml]
  - install sexplib              v0.14.0  [required by biocaml, bistro]
  - install sexplib0             v0.14.0  [required by base, sexplib]
  - install spawn                v0.15.1  [required by core]
  - install splittable_random    v0.14.0  [required by core_kernel]
  - install stdio                v0.14.0  [required by core_kernel]
  - install stringext            1.6.0    [required by uri]
  - install time_now             v0.14.0  [required by core_kernel]
  - install timezone             v0.14.0  [required by core]
  - install topkg                1.0.5    [required by vg, fmt, rresult, etc.]
  - install typerep              v0.14.0  [required by core_kernel]
  - install tyxml                4.5.0    [required by bistro-bio]
  - install uchar                0.0.2    [required by js_of_ocaml]
  - install uri                  4.2.0    [required by biocaml]
  - install uutf                 1.0.3    [required by tyxml, otfm, vg]
  - install variantslib          v0.14.0  [required by core_kernel]
  - install vg                   0.9.4    [required by biotk]
  - install xmlm                 1.4.0    [required by biocaml]
  - install yojson               2.0.1    [required by js_of_ocaml-compiler]

The following system packages will first need to be installed:
    m4 pkg-config zlib1g-dev

<><> Handling external dependencies <><><><><><><><><><><><><><><><><><><><><><>

opam believes some required external dependencies are missing. opam can:
> 1. Run apt-get to install them (may need root/sudo access)
  2. Display the recommended apt-get command and wait while you run it manually (e.g. in another terminal)
  3. Attempt installation anyway, and permanently register that this external dependency is present, but not detectable
  4. Abort the installation

[1/2/3/4] 1
+ /usr/bin/sudo "apt-get" "install" "-qq" "-yy" "m4" "pkg-config" "zlib1g-dev"
- debconf: delaying package configuration, since apt-utils is not installed
- Selecting previously unselected package libglib2.0-0:amd64.
- (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 18331 files and directories currently installed.)
- Preparing to unpack .../0-libglib2.0-0_2.66.8-1_amd64.deb ...
- Unpacking libglib2.0-0:amd64 (2.66.8-1) ...
- Selecting previously unselected package libglib2.0-data.
- Preparing to unpack .../1-libglib2.0-data_2.66.8-1_all.deb ...
- Unpacking libglib2.0-data (2.66.8-1) ...
- Selecting previously unselected package libicu67:amd64.
- Preparing to unpack .../2-libicu67_67.1-7_amd64.deb ...
- Unpacking libicu67:amd64 (67.1-7) ...
- Selecting previously unselected package libsigsegv2:amd64.
- Preparing to unpack .../3-libsigsegv2_2.13-1_amd64.deb ...
- Unpacking libsigsegv2:amd64 (2.13-1) ...
- Selecting previously unselected package libxml2:amd64.
- Preparing to unpack .../4-libxml2_2.9.10+dfsg-6.7+deb11u2_amd64.deb ...
- Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u2) ...
- Selecting previously unselected package m4.
- Preparing to unpack .../5-m4_1.4.18-5_amd64.deb ...
- Unpacking m4 (1.4.18-5) ...
- Selecting previously unselected package pkg-config.
- Preparing to unpack .../6-pkg-config_0.29.2-1_amd64.deb ...
- Unpacking pkg-config (0.29.2-1) ...
- Selecting previously unselected package shared-mime-info.
- Preparing to unpack .../7-shared-mime-info_2.0-1_amd64.deb ...
- Unpacking shared-mime-info (2.0-1) ...
- Selecting previously unselected package xdg-user-dirs.
- Preparing to unpack .../8-xdg-user-dirs_0.17-2_amd64.deb ...
- Unpacking xdg-user-dirs (0.17-2) ...
- Selecting previously unselected package zlib1g-dev:amd64.
- Preparing to unpack .../9-zlib1g-dev_1%3a1.2.11.dfsg-2+deb11u1_amd64.deb ...
- Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u1) ...
- Setting up libicu67:amd64 (67.1-7) ...
- Setting up xdg-user-dirs (0.17-2) ...
- Setting up libglib2.0-0:amd64 (2.66.8-1) ...
- No schema files found: doing nothing.
- Setting up libglib2.0-data (2.66.8-1) ...
- Setting up libsigsegv2:amd64 (2.13-1) ...
- Setting up pkg-config (0.29.2-1) ...
- Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u1) ...
- Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u2) ...
- Setting up m4 (1.4.18-5) ...
- Setting up shared-mime-info (2.0-1) ...
- Processing triggers for libc-bin (2.31-13+deb11u3) ...

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.15.0, angstrom-unix.0.15.0  (cached)
-> retrieved astring.0.8.5  (cached)
-> retrieved base.v0.14.3  (cached)
-> retrieved base64.3.5.0  (cached)
-> retrieved base_bigstring.v0.14.0  (cached)
-> retrieved base_quickcheck.v0.14.1  (cached)
-> retrieved bigstringaf.0.9.0  (cached)
-> retrieved bin_prot.v0.14.1  (cached)
-> retrieved biocaml.0.11.1  (cached)
-> retrieved biotk.0.1.0  (cached)
-> retrieved bistro.0.6.0  (cached)
-> retrieved bos.0.2.1  (cached)
-> retrieved camlzip.1.11  (cached)
-> retrieved cfstream.1.3.1  (cached)
-> retrieved cmdliner.1.1.1  (cached)
-> retrieved core.v0.14.1  (cached)
-> installed conf-m4.1
-> retrieved core_kernel.v0.14.2  (cached)
-> retrieved cppo.1.6.9  (cached)
-> retrieved crunch.3.3.0  (cached)
-> retrieved csexp.1.5.1  (cached)
-> retrieved csvfields.v0.14.0  (cached)
-> installed conf-pkg-config.2
-> installed base64.3.5.0
-> retrieved dune-configurator.3.4.1  (cached)
-> retrieved fieldslib.v0.14.0  (cached)
-> retrieved fmt.0.9.0  (cached)
-> retrieved fpath.0.7.3  (cached)
-> retrieved gg.1.0.0  (cached)
-> retrieved jane-street-headers.v0.14.0  (cached)
-> installed cmdliner.1.1.1
-> installed bigstringaf.0.9.0
-> installed conf-zlib.1
-> installed csexp.1.5.1
-> retrieved js_of_ocaml.4.0.0, js_of_ocaml-compiler.4.0.0, js_of_ocaml-ppx.4.0.0  (cached)
-> retrieved jst-config.v0.14.1  (cached)
-> retrieved logs.0.7.0  (cached)
-> retrieved lwt.5.6.1  (cached)
-> retrieved lwt_react.1.2.0  (cached)
-> retrieved menhir.20220210, menhirLib.20220210, menhirSdk.20220210  (cached)
-> retrieved num.1.4  (cached)
-> retrieved ocaml-compiler-libs.v0.12.4  (cached)
-> retrieved ocaml-syntax-shims.1.0.0  (cached)
-> retrieved ocamlbuild.0.14.1  (cached)
-> retrieved ocamlgraph.2.0.0  (cached)
-> installed camlzip.1.11
-> installed cppo.1.6.9
-> installed jane-street-headers.v0.14.0
-> installed menhirSdk.20220210
-> retrieved ocamlnet.4.1.9-2  (cached)
-> installed menhirLib.20220210
-> retrieved ocplib-endian.1.2  (cached)
-> retrieved octavius.1.2.2  (cached)
-> retrieved otfm.0.4.0  (cached)
-> retrieved parsexp.v0.14.2  (cached)
-> retrieved ppx_assert.v0.14.0  (cached)
-> installed ocaml-syntax-shims.1.0.0
-> retrieved ppx_base.v0.14.0  (cached)
-> installed ocaml-compiler-libs.v0.12.4
-> retrieved ppx_bench.v0.14.1  (cached)
-> retrieved ppx_bin_prot.v0.14.0  (cached)
-> retrieved ppx_cold.v0.14.0  (cached)
-> retrieved ppx_compare.v0.14.0  (cached)
-> retrieved ppx_conv_func.v0.14.0  (cached)
-> installed num.1.4
-> installed ocplib-endian.1.2
-> installed dune-configurator.3.4.1
-> retrieved ppx_csv_conv.v0.14.0  (https://ocaml.janestreet.com/ocaml-core/v0.14/files/ppx_csv_conv-v0.14.0.tar.gz)
-> retrieved ppx_custom_printf.v0.14.1  (cached)
-> retrieved ppx_derivers.1.2.1  (cached)
-> retrieved ppx_deriving.5.2.1  (cached)
-> retrieved ppx_enumerate.v0.14.0  (cached)
-> retrieved ppx_expect.v0.14.2  (cached)
-> retrieved ppx_fields_conv.v0.14.2  (cached)
-> retrieved ppx_fixed_literal.v0.14.0  (cached)
-> retrieved ppx_hash.v0.14.0  (cached)
-> retrieved ppx_here.v0.14.0  (cached)
-> retrieved ppx_inline_test.v0.14.1  (cached)
-> retrieved ppx_jane.v0.14.0  (cached)
-> retrieved ppx_js_style.v0.14.1  (cached)
-> retrieved ppx_let.v0.14.0  (cached)
-> retrieved ppx_module_timer.v0.14.0  (cached)
-> retrieved ppx_optcomp.v0.14.3  (cached)
-> retrieved ppx_optional.v0.14.0  (cached)
-> retrieved ppx_pipebang.v0.14.0  (cached)
-> retrieved ppx_sexp_conv.v0.14.3  (cached)
-> installed ppx_derivers.1.2.1
-> retrieved ppx_sexp_message.v0.14.1  (cached)
-> retrieved ppx_sexp_value.v0.14.0  (cached)
-> retrieved ppx_stable.v0.14.1  (cached)
-> retrieved ppx_string.v0.14.1  (cached)
-> retrieved ppx_typerep_conv.v0.14.2  (cached)
-> retrieved ppx_variants_conv.v0.14.2  (cached)
-> retrieved ppxlib.0.25.1  (cached)
-> retrieved ptime.1.0.0  (cached)
-> retrieved re.1.10.4  (cached)
-> retrieved react.1.2.2  (cached)
-> retrieved result.1.5  (cached)
-> retrieved rresult.0.7.0  (cached)
-> installed seq.base
-> retrieved sexplib.v0.14.0  (cached)
-> retrieved sexplib0.v0.14.0  (cached)
-> retrieved spawn.v0.15.1  (cached)
-> retrieved splittable_random.v0.14.0  (cached)
-> retrieved stdio.v0.14.0  (cached)
-> retrieved stringext.1.6.0  (cached)
-> retrieved time_now.v0.14.0  (cached)
-> retrieved timezone.v0.14.0  (cached)
-> installed octavius.1.2.2
-> retrieved topkg.1.0.5  (cached)
-> retrieved typerep.v0.14.0  (cached)
-> installed ocamlgraph.2.0.0
-> installed result.1.5
-> installed spawn.v0.15.1
-> installed stringext.1.6.0
-> retrieved tyxml.4.5.0  (cached)
-> retrieved uchar.0.0.2  (cached)
-> retrieved uri.4.2.0  (cached)
-> retrieved uutf.1.0.3  (cached)
-> retrieved variantslib.v0.14.0  (cached)
-> retrieved vg.0.9.4  (cached)
-> retrieved xmlm.1.4.0  (cached)
-> retrieved yojson.2.0.1  (cached)
-> installed sexplib0.v0.14.0
-> installed re.1.10.4
-> installed angstrom.0.15.0
-> installed angstrom-unix.0.15.0
-> installed yojson.2.0.1
-> installed lwt.5.6.1
-> installed uri.4.2.0
-> installed ocamlbuild.0.14.1
-> installed uchar.0.0.2
-> installed base.v0.14.3
-> installed fieldslib.v0.14.0
-> installed variantslib.v0.14.0
-> installed stdio.v0.14.0
-> installed topkg.1.0.5
-> installed typerep.v0.14.0
-> installed parsexp.v0.14.2
-> installed rresult.0.7.0
-> installed uutf.1.0.3
-> installed react.1.2.2
-> installed astring.0.8.5
-> installed fmt.0.9.0
-> installed xmlm.1.4.0
-> installed ptime.1.0.0
-> installed sexplib.v0.14.0
-> installed gg.1.0.0
-> installed lwt_react.1.2.0
-> installed fpath.0.7.3
-> installed crunch.3.3.0
-> installed menhir.20220210
-> installed otfm.0.4.0
-> installed ppxlib.0.25.1
-> installed tyxml.4.5.0
-> installed ppx_optcomp.v0.14.3
-> installed ppx_stable.v0.14.1
-> installed ppx_cold.v0.14.0
-> installed ppx_fields_conv.v0.14.2
-> installed ppx_compare.v0.14.0
-> installed ppx_here.v0.14.0
-> installed ppx_conv_func.v0.14.0
-> installed ppx_enumerate.v0.14.0
-> installed ppx_let.v0.14.0
-> installed ppx_typerep_conv.v0.14.2
-> installed ppx_variants_conv.v0.14.2
-> installed ppx_pipebang.v0.14.0
-> installed ppx_sexp_conv.v0.14.3
-> installed ppx_deriving.5.2.1
-> installed ppx_fixed_literal.v0.14.0
-> installed ppx_js_style.v0.14.1
-> installed ppx_optional.v0.14.0
-> installed ppx_hash.v0.14.0
-> installed ppx_sexp_value.v0.14.0
-> installed ppx_sexp_message.v0.14.1
-> installed ppx_assert.v0.14.0
-> installed ppx_custom_printf.v0.14.1
-> installed ppx_base.v0.14.0
-> installed js_of_ocaml-compiler.4.0.0
-> installed jst-config.v0.14.1
-> installed bin_prot.v0.14.1
-> installed ppx_string.v0.14.1
-> installed time_now.v0.14.0
-> installed ppx_bin_prot.v0.14.0
-> installed ppx_inline_test.v0.14.1
-> installed ppx_module_timer.v0.14.0
-> installed ppx_bench.v0.14.1
-> installed ppx_expect.v0.14.2
-> installed splittable_random.v0.14.0
-> installed base_quickcheck.v0.14.1
-> installed js_of_ocaml.4.0.0
-> installed ppx_jane.v0.14.0
-> installed logs.0.7.0
-> installed base_bigstring.v0.14.0
-> installed bos.0.2.1
-> installed js_of_ocaml-ppx.4.0.0
-> installed vg.0.9.4
-> installed core_kernel.v0.14.2
-> installed cfstream.1.3.1
-> installed timezone.v0.14.0
-> installed ocamlnet.4.1.9-2
-> installed core.v0.14.1
-> installed csvfields.v0.14.0
-> installed ppx_csv_conv.v0.14.0
-> installed biocaml.0.11.1
-> installed bistro.0.6.0
-> installed biotk.0.1.0
Done.
# Run eval $(opam env) to update the current shell environment
The following actions will be performed:
=== install 1 package
  - install bistro-bio 0.6.0

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing  1/3:
-> retrieved bistro-bio.0.6.0  (cached)
Processing  2/3: [bistro-bio: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "bistro-bio" "-j" "31" "@install" (CWD=/home/opam/.opam/4.14/.opam-switch/build/bistro-bio.0.6.0)
-> compiled  bistro-bio.0.6.0
-> installed bistro-bio.0.6.0
Done.
# Run eval $(opam env) to update the current shell environment
2022-07-27 05:43.09 ---> saved as "12e6c87e4dba3537b85b381eb746a7491e69a66691fb6e52b33eab42b97cfb41"

/home/opam: (run (network host)
                 (shell "opam update --depexts"))
+ /usr/bin/sudo "apt-get" "update"
- Hit:1 http://deb.debian.org/debian bullseye InRelease
- Hit:2 http://deb.debian.org/debian-security bullseye-security InRelease
- Hit:3 http://deb.debian.org/debian bullseye-updates InRelease
- Reading package lists...
- 
2022-07-27 05:43.19 ---> saved as "97945b83bc627832ba7c41ecbb3adebfc8194b708c6b0fc8c1012bdd9ec8ef1f"

/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
                 (network host)
                 (shell  "opam remove bistro-bio.0.6.0 && opam install --deps-only --with-test bistro-bio.0.6.0 && opam install -v --with-test bistro-bio.0.6.0;\
                        \n        res=$?;\
                        \n        test \"$res\" != 31 && exit \"$res\";\
                        \n        export OPAMCLI=2.0;\
                        \n        build_dir=$(opam var prefix)/.opam-switch/build;\
                        \n        failed=$(ls \"$build_dir\");\
                        \n        for pkg in $failed; do\
                        \n          if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-11\\\"\"; then\
                        \n            echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
                        \n          fi;\
                        \n        done;\
                        \n        exit 1"))
The following actions will be performed:
=== remove 1 package
  - remove bistro-bio 0.6.0

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> removed   bistro-bio.0.6.0
Done.
# Run eval $(opam env) to update the current shell environment
Nothing to do.
# Run eval $(opam env) to update the current shell environment
The following actions will be performed:
=== install 1 package
  - install bistro-bio 0.6.0

<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing  1/3:
-> retrieved bistro-bio.0.6.0  (cached)
Processing  2/3: [bistro-bio: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "bistro-bio" "-j" "31" "@install" "@runtest" (CWD=/home/opam/.opam/4.14/.opam-switch/build/bistro-bio.0.6.0)
-> compiled  bistro-bio.0.6.0
-> installed bistro-bio.0.6.0
Done.
# Run eval $(opam env) to update the current shell environment
2022-07-27 05:45.45 ---> saved as "02f4c25f6de1d8b8fee77b7f1667f04f11c2c726de1d8e457db38072a4fa1375"
Job succeeded
2022-07-27 05:46.36: Job succeeded