Build:
- 0
2026-03-02 19:24.07: New job: test bistro-bio.0.6.0 with dune.3.22.0~alpha0, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29497/head (118a690db616b1df5c53d5fa00eb70791a80ae2c)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29497/head" && git reset --hard 118a690d
git fetch origin master
git merge --no-edit a7b8d1036328cf727af175b657f3d2b732b4d868
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn dune.3.22.0~alpha0 3.22.0~alpha0
RUN opam reinstall dune.3.22.0~alpha0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'dune.3.22.0~alpha0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall bistro-bio.0.6.0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'bistro-bio.0.6.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test bistro-bio.0.6.0) || true
RUN opam reinstall --with-test --verbose bistro-bio.0.6.0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'bistro-bio.0.6.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-03-02 19:24.07: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a-dune.3.22.0~alpha0-bistro-bio.0.6.0-118a690db616b1df5c53d5fa00eb70791a80ae2c"
2026-03-02 19:24.07: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn dune.3.22.0~alpha0 3.22.0~alpha0"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.22.0~alpha0;\
\n res=$?;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'dune.3.22.0~alpha0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall bistro-bio.0.6.0;\
\n res=$?;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'bistro-bio.0.6.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test bistro-bio.0.6.0) || true"))
(run (shell "opam reinstall --with-test --verbose bistro-bio.0.6.0;\
\n res=$?;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'bistro-bio.0.6.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2026-03-02 19:24.07: Waiting for resource in pool OCluster
2026-03-03 06:17.20: Waiting for worker…
2026-03-03 06:20.38: Got resource from pool OCluster
Building on doris.caelum.ci.dev
All commits already cached
HEAD is now at a7b8d10363 Merge pull request #29489 from anuragsoni/opam-publish-kqueue.0.7.0
Updating a7b8d10363..118a690db6
Fast-forward
.../chrome-trace/chrome-trace.3.22.0~alpha0/opam | 39 +++++++++++
.../dune-action-plugin.3.22.0~alpha0/opam | 52 +++++++++++++++
.../dune-action-trace.3.22.0~alpha0/opam | 40 ++++++++++++
.../dune-build-info.3.22.0~alpha0/opam | 45 +++++++++++++
.../dune-configurator.3.22.0~alpha0/opam | 49 ++++++++++++++
packages/dune-glob/dune-glob.3.22.0~alpha0/opam | 42 ++++++++++++
.../dune-private-libs.3.22.0~alpha0/opam | 50 +++++++++++++++
.../dune-rpc-lwt/dune-rpc-lwt.3.22.0~alpha0/opam | 41 ++++++++++++
packages/dune-rpc/dune-rpc.3.22.0~alpha0/opam | 44 +++++++++++++
packages/dune-site/dune-site.3.22.0~alpha0/opam | 37 +++++++++++
packages/dune/dune.3.22.0~alpha0/opam | 75 ++++++++++++++++++++++
packages/dyn/dyn.3.22.0~alpha0/opam | 40 ++++++++++++
packages/fs-io/fs-io.3.22.0~alpha0/opam | 39 +++++++++++
packages/ocamlc-loc/ocamlc-loc.3.22.0~alpha0/opam | 43 +++++++++++++
packages/ordering/ordering.3.22.0~alpha0/opam | 38 +++++++++++
packages/stdune/stdune.3.22.0~alpha0/opam | 46 +++++++++++++
.../top-closure/top-closure.3.22.0~alpha0/opam | 38 +++++++++++
packages/xdg/xdg.3.22.0~alpha0/opam | 39 +++++++++++
18 files changed, 797 insertions(+)
create mode 100644 packages/chrome-trace/chrome-trace.3.22.0~alpha0/opam
create mode 100644 packages/dune-action-plugin/dune-action-plugin.3.22.0~alpha0/opam
create mode 100644 packages/dune-action-trace/dune-action-trace.3.22.0~alpha0/opam
create mode 100644 packages/dune-build-info/dune-build-info.3.22.0~alpha0/opam
create mode 100644 packages/dune-configurator/dune-configurator.3.22.0~alpha0/opam
create mode 100644 packages/dune-glob/dune-glob.3.22.0~alpha0/opam
create mode 100644 packages/dune-private-libs/dune-private-libs.3.22.0~alpha0/opam
create mode 100644 packages/dune-rpc-lwt/dune-rpc-lwt.3.22.0~alpha0/opam
create mode 100644 packages/dune-rpc/dune-rpc.3.22.0~alpha0/opam
create mode 100644 packages/dune-site/dune-site.3.22.0~alpha0/opam
create mode 100644 packages/dune/dune.3.22.0~alpha0/opam
create mode 100644 packages/dyn/dyn.3.22.0~alpha0/opam
create mode 100644 packages/fs-io/fs-io.3.22.0~alpha0/opam
create mode 100644 packages/ocamlc-loc/ocamlc-loc.3.22.0~alpha0/opam
create mode 100644 packages/ordering/ordering.3.22.0~alpha0/opam
create mode 100644 packages/stdune/stdune.3.22.0~alpha0/opam
create mode 100644 packages/top-closure/top-closure.3.22.0~alpha0/opam
create mode 100644 packages/xdg/xdg.3.22.0~alpha0/opam
(from ocaml/opam:debian-13-ocaml-4.14@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a)
Unable to find image 'ocaml/opam:debian-13-ocaml-4.14@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a' locally
docker.io/ocaml/opam@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a: Pulling from ocaml/opam
866771c43bf5: Already exists
4a5c2c0f49fb: Already exists
14afc2e314e3: Already exists
b428db3c7f23: Already exists
714e2830ade6: Already exists
a32341fba7c4: Already exists
14c4d29b0669: Already exists
8098743a84e0: Already exists
b649ef0e5c7c: Already exists
fdf90895ece2: Already exists
2a1862103e3b: Already exists
a5b8900899a7: Already exists
3afd77c1671d: Already exists
4109c0e61944: Already exists
72c2140c0b8a: Already exists
a569aea0e6d2: Already exists
bda663408b80: Already exists
c85973dbeea6: Already exists
d0f7673c2c0f: Already exists
5ba6b3c63b75: Already exists
0fe1cfdd36e8: Already exists
c9392670ba0b: Already exists
4f4fb700ef54: Already exists
15c31e04da2e: Already exists
e891433acb08: Already exists
7bf28702178d: Already exists
4b2b9fb8d21c: Already exists
9741c41ba88b: Already exists
f7c5927b37c0: Already exists
10106e0ac766: Already exists
4b02e669a449: Already exists
968217c73ddd: Already exists
af2f12562aab: Already exists
19a04a291720: Already exists
ceb537a14cf6: Already exists
338d3c82b545: Already exists
95eb1e8c1267: Already exists
ad354d8e0d09: Already exists
b036852fb10e: Already exists
12e59cb649ae: Already exists
8ca6b163450a: Already exists
cb5689abf9e7: Pulling fs layer
510fc5682812: Pulling fs layer
c15873485d9f: Pulling fs layer
11a3c22082ed: Pulling fs layer
11a3c22082ed: Waiting
c15873485d9f: Download complete
510fc5682812: Verifying Checksum
510fc5682812: Download complete
11a3c22082ed: Verifying Checksum
11a3c22082ed: Download complete
cb5689abf9e7: Download complete
cb5689abf9e7: Pull complete
510fc5682812: Pull complete
c15873485d9f: Pull complete
11a3c22082ed: Pull complete
Digest: sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a
Status: Downloaded newer image for ocaml/opam@sha256:ae45d5e5a934874dc44b0d004f6b8a813fba3f355216f78a39ed4f25a53e478a
2026-03-03 06:20.43 ---> using "40de8e47c13dd397f7466181b47c70cd31f6d05f624f7f51643a7089a29a5322" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-03-03 06:20.43 ---> using "11e955cadb21ab08a7e8407d7e49d7e8b8232723aa9e80323bab6a7d993e9a38" from cache
/home/opam: (run (network host)
(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.
This version of opam requires an update to the layout of /home/opam/.opam from version 2.0 to version 2.2, which can't be reverted.
You may want to back it up before going further.
Continue? [Y/n] y
[NOTE] The 'jobs' option was reset, its value was 71 and its new value will vary according to the current number of cores on your machine. You can restore the fixed value using:
opam option jobs=71 --global
Format upgrade done.
<><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
[default] Initialised
2026-03-03 06:20.43 ---> using "b84411f14b612833c97eea3b0fb49d7afb0294cf8c4774caaff1f8b0f1bd5849" from cache
/home/opam: (run (shell "opam option solver=builtin-0install && opam config report"))
Set to 'builtin-0install' the field solver in global configuration
# opam config report
# opam-version 2.5.0
# self-upgrade no
# system arch=x86_64 os=linux os-distribution=debian os-version=13
# solver builtin-0install
# install-criteria -changed,-count[avoid-version,solution]
# upgrade-criteria -count[avoid-version,solution]
# jobs 255
# repositories 1 (version-controlled)
# pinned 1 (version)
# current-switch 4.14
# invariant ["ocaml-base-compiler" {= "4.14.2"}]
# compiler-packages ocaml-base-compiler.4.14.2, ocaml-options-vanilla.1
# ocaml:native true
# ocaml:native-tools true
# ocaml:native-dynlink true
# ocaml:stubsdir /home/opam/.opam/4.14/lib/ocaml/stublibs:/home/opam/.opam/4.14/lib/ocaml
# ocaml:preinstalled false
# ocaml:compiler 4.14.2
2026-03-03 06:20.43 ---> using "bc1392749f7c1b1568053e91f3061e53f54f3bf6892fcf3fa14761d0f2fabccc" from cache
/home/opam: (env OPAMDOWNLOADJOBS 1)
/home/opam: (env OPAMERRLOGLEN 0)
/home/opam: (env OPAMPRECISETRACKING 1)
/home/opam: (env CI true)
/home/opam: (env OPAM_REPO_CI true)
/home/opam: (run (shell "rm -rf opam-repository/"))
2026-03-03 06:20.43 ---> using "0f88aad717079fee185cb5f7b0853d5dede0158dafac18dc05292641ad1318aa" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-03-03 06:20.44 ---> using "cf2f29575da4e00ad2c0e3200eaf5375ace45ec778f515d81ffd2e5eb96c41f1" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-03-03 06:20.44 ---> using "c517023779902244dbe5c8fbf440d1dd4569daf367c1e2ee7dd7eb370c41d91c" from cache
/home/opam: (run (network host)
(shell "opam update --depexts || true"))
+ /usr/bin/sudo "apt-get" "update"
- Hit:1 http://deb.debian.org/debian trixie InRelease
- Get:2 http://deb.debian.org/debian trixie-updates InRelease [47.3 kB]
- Get:3 http://deb.debian.org/debian-security trixie-security InRelease [43.4 kB]
- Get:4 http://deb.debian.org/debian-security trixie-security/main amd64 Packages [113 kB]
- Fetched 203 kB in 0s (1291 kB/s)
- Reading package lists...
2026-03-03 06:20.44 ---> using "a2e6599fe15f34bfd0a71de19dbfccfacdc1f910f7a37fea793bb8ff67d4ba47" from cache
/home/opam: (run (shell "opam pin add -k version -yn dune.3.22.0~alpha0 3.22.0~alpha0"))
dune is now pinned to version 3.22.0~alpha0
2026-03-03 06:20.44 ---> using "9ecf7f496eb9b328aa3c8f7333a40a30e123b33b9d8b5606b7ac6bfc2b62fac7" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.22.0~alpha0;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'dune.3.22.0~alpha0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
dune.3.22.0~alpha0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 1 package
- install dune 3.22.0~alpha0 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.22.0~alpha0 (cached)
-> installed dune.3.22.0~alpha0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-03 06:20.44 ---> using "1d093925996c7908c33a8109d0c1a7be5172d79d6a00aabc511d552ee2499f33" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall bistro-bio.0.6.0;\
\n res=$?;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'bistro-bio.0.6.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
bistro-bio.0.6.0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 105 packages
- install angstrom 0.16.1 [required by biotk]
- install angstrom-unix 0.16.1 [required by biotk]
- install astring 0.8.5 [required by bos]
- install base v0.14.3 [required by ppx_csv_conv]
- install base-bytes base [required by ocamlnet]
- install base64 3.5.2 [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 0.10.0 [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 bistro-bio 0.6.0
- install bos 0.2.1 [required by bistro]
- install camlp-streams 5.0.1 [required by cfstream]
- install camlzip 1.14 [required by biocaml]
- install cfstream 1.3.2 [required by biocaml]
- install cmdliner 2.1.0 [required by crunch, fmt]
- install conf-m4 1 [required by cfstream]
- install conf-pkg-config 4 [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 1.8.0 [required by ppx_deriving, lwt, lwt_react]
- install crunch 4.0.0 [required by biotk]
- install csexp 1.5.2 [required by dune-configurator]
- install csvfields v0.14.0 [required by ppx_csv_conv]
- install dune-configurator 3.22.0~alpha0 [required by lwt]
- install fieldslib v0.14.0 [required by core_kernel]
- install fmt 0.11.0 [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 jst-config v0.14.1 [required by core]
- install logs 0.10.0 [required by bos]
- install lwt 6.1.1 [required by biocaml, bistro]
- install lwt_react 1.2.0 [required by bistro]
- install num 1.6 [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 0.16.1 [required by vg, ocamlnet, xmlm, etc.]
- install ocamlfind 1.9.8 [required by vg, otfm, fmt, etc.]
- install ocamlgraph 2.2.0 [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 1.2.0 [required by crunch]
- install re 1.14.0 [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 v0.17.0 [required by core]
- install splittable_random v0.14.0 [required by core_kernel]
- install stdio v0.14.0 [required by core_kernel]
- install stdlib-shims 0.3.0 [required by ppxlib]
- 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 1.1.1 [required by vg, fmt, rresult, etc.]
- install typerep v0.14.0 [required by core_kernel]
- install tyxml 4.6.0 [required by bistro-bio]
- install uri 4.4.0 [required by biocaml]
- install uutf 1.0.4 [required by otfm, tyxml]
- install variantslib v0.14.0 [required by core_kernel]
- install vg 0.9.5 [required by biotk]
- install xmlm 1.4.0 [required by biocaml]
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. Continue anyway, and, upon success, 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"
- Selecting previously unselected package libpkgconf3: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 ... 20623 files and directories currently installed.)
- Preparing to unpack .../0-libpkgconf3_1.8.1-4_amd64.deb ...
- Unpacking libpkgconf3:amd64 (1.8.1-4) ...
- Selecting previously unselected package m4.
- Preparing to unpack .../1-m4_1.4.19-8_amd64.deb ...
- Unpacking m4 (1.4.19-8) ...
- Selecting previously unselected package pkgconf-bin.
- Preparing to unpack .../2-pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../3-pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../4-pkg-config_1.8.1-4_amd64.deb ...
- Unpacking pkg-config:amd64 (1.8.1-4) ...
- Selecting previously unselected package zlib1g-dev:amd64.
- Preparing to unpack .../5-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ...
- Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up m4 (1.4.19-8) ...
- Setting up libpkgconf3:amd64 (1.8.1-4) ...
- Setting up pkgconf-bin (1.8.1-4) ...
- Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up pkgconf:amd64 (1.8.1-4) ...
- Setting up pkg-config:amd64 (1.8.1-4) ...
- Processing triggers for libc-bin (2.41-12+deb13u1) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
-> retrieved astring.0.8.5 (cached)
-> retrieved base.v0.14.3 (cached)
-> retrieved base64.3.5.2 (cached)
-> retrieved base_bigstring.v0.14.0 (cached)
-> retrieved base_quickcheck.v0.14.1 (cached)
-> retrieved bigstringaf.0.10.0 (cached)
-> retrieved bin_prot.v0.14.1 (cached)
-> retrieved biocaml.0.11.1 (cached)
-> installed base64.3.5.2
-> retrieved biotk.0.1.0 (cached)
-> retrieved bistro.0.6.0, bistro-bio.0.6.0 (cached)
-> retrieved bos.0.2.1 (cached)
-> retrieved camlp-streams.5.0.1 (cached)
-> retrieved camlzip.1.14 (cached)
-> retrieved cfstream.1.3.2 (cached)
-> retrieved cmdliner.2.1.0 (cached)
-> retrieved core.v0.14.1 (cached)
-> installed conf-m4.1
-> installed conf-pkg-config.4
-> retrieved core_kernel.v0.14.2 (cached)
-> installed camlp-streams.5.0.1
-> installed conf-zlib.1
-> retrieved cppo.1.8.0 (cached)
-> retrieved crunch.4.0.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved csvfields.v0.14.0 (cached)
-> installed csexp.1.5.2
-> retrieved dune-configurator.3.22.0~alpha0 (cached)
-> retrieved fieldslib.v0.14.0 (cached)
-> retrieved fmt.0.11.0 (cached)
-> retrieved fpath.0.7.3 (cached)
-> retrieved gg.1.0.0 (cached)
-> retrieved jane-street-headers.v0.14.0 (cached)
-> retrieved jst-config.v0.14.1 (cached)
-> retrieved logs.0.10.0 (cached)
-> retrieved lwt.6.1.1 (cached)
-> retrieved lwt_react.1.2.0 (cached)
-> retrieved num.1.6 (cached)
-> installed cmdliner.2.1.0
-> installed cppo.1.8.0
-> installed dune-configurator.3.22.0~alpha0
-> installed jane-street-headers.v0.14.0
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved ocamlgraph.2.2.0 (cached)
-> retrieved ocamlnet.4.1.9-2 (cached)
-> installed bigstringaf.0.10.0
-> installed ocaml-syntax-shims.1.0.0
-> installed ocaml-compiler-libs.v0.12.4
-> 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)
-> retrieved ppx_base.v0.14.0 (cached)
-> 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)
-> retrieved ppx_csv_conv.v0.14.0 (cached)
-> 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)
-> installed ppx_derivers.1.2.1
-> installed num.1.6
-> retrieved ppx_let.v0.14.0 (cached)
-> installed angstrom.0.16.1
-> 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)
-> 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)
-> installed angstrom-unix.0.16.1
-> retrieved ppxlib.0.25.1 (cached)
-> retrieved ptime.1.2.0 (cached)
-> retrieved re.1.14.0 (cached)
-> retrieved react.1.2.2 (cached)
-> retrieved result.1.5 (cached)
-> retrieved rresult.0.7.0 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexplib.v0.14.0 (cached)
-> retrieved sexplib0.v0.14.0 (cached)
-> retrieved spawn.v0.17.0 (cached)
-> retrieved splittable_random.v0.14.0 (cached)
-> retrieved stdio.v0.14.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved stringext.1.6.0 (cached)
-> retrieved time_now.v0.14.0 (cached)
-> retrieved timezone.v0.14.0 (cached)
-> retrieved topkg.1.1.1 (cached)
-> retrieved typerep.v0.14.0 (cached)
-> installed ocamlgraph.2.2.0
-> installed octavius.1.2.2
-> installed result.1.5
-> installed spawn.v0.17.0
-> installed stdlib-shims.0.3.0
-> installed stringext.1.6.0
-> retrieved tyxml.4.6.0 (cached)
-> installed sexplib0.v0.14.0
-> retrieved uri.4.4.0 (cached)
-> retrieved uutf.1.0.4 (cached)
-> retrieved variantslib.v0.14.0 (cached)
-> retrieved vg.0.9.5 (cached)
-> retrieved xmlm.1.4.0 (cached)
-> installed re.1.14.0
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed uri.4.4.0
-> installed ocplib-endian.1.2
-> installed camlzip.1.14
-> installed ocamlbuild.0.16.1
-> installed lwt.6.1.1
-> installed base.v0.14.3
-> installed fieldslib.v0.14.0
-> installed variantslib.v0.14.0
-> installed stdio.v0.14.0
-> installed typerep.v0.14.0
-> installed parsexp.v0.14.2
-> installed topkg.1.1.1
-> installed sexplib.v0.14.0
-> installed rresult.0.7.0
-> installed react.1.2.2
-> installed uutf.1.0.4
-> installed fmt.0.11.0
-> installed xmlm.1.4.0
-> installed ptime.1.2.0
-> installed astring.0.8.5
-> installed lwt_react.1.2.0
-> installed crunch.4.0.0
-> installed gg.1.0.0
-> installed fpath.0.7.3
-> installed otfm.0.4.0
-> installed ppxlib.0.25.1
-> installed logs.0.10.0
-> installed ppx_optcomp.v0.14.3
-> installed tyxml.4.6.0
-> installed vg.0.9.5
-> installed ppx_conv_func.v0.14.0
-> installed ppx_enumerate.v0.14.0
-> installed ppx_cold.v0.14.0
-> installed ppx_compare.v0.14.0
-> installed ppx_here.v0.14.0
-> installed ppx_let.v0.14.0
-> installed ppx_fields_conv.v0.14.2
-> installed ppx_variants_conv.v0.14.2
-> installed ppx_stable.v0.14.1
-> installed ppx_typerep_conv.v0.14.2
-> installed bos.0.2.1
-> installed ppx_pipebang.v0.14.0
-> installed ppx_fixed_literal.v0.14.0
-> installed ppx_optional.v0.14.0
-> installed ppx_js_style.v0.14.1
-> installed ppx_sexp_conv.v0.14.3
-> installed ppx_deriving.5.2.1
-> installed ppx_hash.v0.14.0
-> installed ppx_assert.v0.14.0
-> installed ppx_sexp_message.v0.14.1
-> installed ppx_sexp_value.v0.14.0
-> installed ppx_custom_printf.v0.14.1
-> installed ppx_base.v0.14.0
-> 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_module_timer.v0.14.0
-> installed ppx_inline_test.v0.14.1
-> 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 ppx_jane.v0.14.0
-> installed base_bigstring.v0.14.0
-> installed core_kernel.v0.14.2
-> installed cfstream.1.3.2
-> installed timezone.v0.14.0
-> 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 ocamlnet.4.1.9-2
-> installed biotk.0.1.0
-> installed bistro-bio.0.6.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-03 06:22.30 ---> saved as "9742ce5bec169ebfc07109a20fb63334bc0bf481ae71870d1e5a032e2a36e117"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test bistro-bio.0.6.0) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile bistro-bio 0.6.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved bistro-bio.0.6.0 (https://opam.ocaml.org/cache)
-> removed bistro-bio.0.6.0
-> installed bistro-bio.0.6.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-03 06:22.37 ---> saved as "27bd25aac8c0dafbc8c49ebb790516c09d722ce4f5766e8ff4ebe0a61fb079f1"
/home/opam: (run (shell "opam reinstall --with-test --verbose bistro-bio.0.6.0;\
\n res=$?;\
\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 partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'bistro-bio.0.6.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
The following actions will be performed:
=== recompile 1 package
- recompile bistro-bio 0.6.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [bistro-bio.0.6.0: extract]
-> retrieved bistro-bio.0.6.0 (cached)
Processing 2/4: [bistro-bio: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "bistro-bio" "-j" "255" "@install" "@runtest" (CWD=/home/opam/.opam/4.14/.opam-switch/build/bistro-bio.0.6.0)
-> compiled bistro-bio.0.6.0
-> removed bistro-bio.0.6.0
-> installed bistro-bio.0.6.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-03 06:22.44 ---> saved as "b0ead9220803346f19a22e6831c949c4c91d873e9a3be001da2f6b5013908967"
Job succeeded
2026-03-03 06:22.51: Job succeeded