- github
- ocaml
- opam-repository
- 3e0c39
- compilers,4.14,dune-configurator.3.22.2,revdeps,lbvs_consent.2.1.2
(not at the head of any monitored branch or PR)
2026-04-10 17:47.13: New job: test lbvs_consent.2.1.2 with dune-configurator.3.22.2, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29704/head (3e0c395e7b1393a792367f8edca3654dac71e6fd)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29704/head" && git reset --hard 3e0c395e
git fetch origin master
git merge --no-edit 9d8ceab8e9f49f5671cf459997c8a47cf0e675ca
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn dune-configurator.3.22.2 3.22.2
RUN opam reinstall dune-configurator.3.22.2; \
res=$?; \
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 "$pkg" != 'dune-configurator.3.22.2' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall lbvs_consent.2.1.2; \
res=$?; \
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 "$pkg" != 'lbvs_consent.2.1.2' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test lbvs_consent.2.1.2) || true
RUN opam reinstall --with-test --verbose lbvs_consent.2.1.2; \
res=$?; \
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 "$pkg" != 'lbvs_consent.2.1.2' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-04-10 17:47.13: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4-dune-configurator.3.22.2-lbvs_consent.2.1.2-3e0c395e7b1393a792367f8edca3654dac71e6fd"
2026-04-10 17:47.13: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn dune-configurator.3.22.2 3.22.2"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune-configurator.3.22.2;\
\n res=$?;\
\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 \"$pkg\" != 'dune-configurator.3.22.2' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.1.2;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.2' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.1.2) || true"))
(run (shell "opam reinstall --with-test --verbose lbvs_consent.2.1.2;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.2' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2026-04-10 17:47.13: Waiting for resource in pool OCluster
2026-04-10 20:43.07: Waiting for worker…
2026-04-10 20:44.57: Got resource from pool OCluster
Building on phoebe.caelum.ci.dev
All commits already cached
Updating files: 65% (12153/18686)
Updating files: 66% (12333/18686)
Updating files: 67% (12520/18686)
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Updating files: 100% (18686/18686)
Updating files: 100% (18686/18686), done.
HEAD is now at 9d8ceab8e9 Merge pull request #29697 from filipeom/opam-publish-smtml.0.25.0
Updating 9d8ceab8e9..3e0c395e7b
Fast-forward
packages/chrome-trace/chrome-trace.3.22.2/opam | 39 +++++++++++
.../dune-action-plugin.3.22.2/opam | 52 +++++++++++++++
.../dune-action-trace.3.22.2/opam | 39 +++++++++++
.../dune-build-info/dune-build-info.3.22.2/opam | 45 +++++++++++++
.../dune-configurator.3.22.2/opam | 49 ++++++++++++++
packages/dune-glob/dune-glob.3.22.2/opam | 42 ++++++++++++
.../dune-private-libs.3.22.2/opam | 50 +++++++++++++++
packages/dune-rpc-lwt/dune-rpc-lwt.3.22.2/opam | 41 ++++++++++++
packages/dune-rpc/dune-rpc.3.22.2/opam | 44 +++++++++++++
packages/dune-site/dune-site.3.22.2/opam | 37 +++++++++++
packages/dune/dune.3.22.2/opam | 75 ++++++++++++++++++++++
packages/dyn/dyn.3.22.2/opam | 40 ++++++++++++
packages/fs-io/fs-io.3.22.2/opam | 39 +++++++++++
packages/ocamlc-loc/ocamlc-loc.3.22.2/opam | 43 +++++++++++++
packages/ordering/ordering.3.22.2/opam | 38 +++++++++++
packages/stdune/stdune.3.22.2/opam | 46 +++++++++++++
packages/top-closure/top-closure.3.22.2/opam | 38 +++++++++++
packages/xdg/xdg.3.22.2/opam | 39 +++++++++++
18 files changed, 796 insertions(+)
create mode 100644 packages/chrome-trace/chrome-trace.3.22.2/opam
create mode 100644 packages/dune-action-plugin/dune-action-plugin.3.22.2/opam
create mode 100644 packages/dune-action-trace/dune-action-trace.3.22.2/opam
create mode 100644 packages/dune-build-info/dune-build-info.3.22.2/opam
create mode 100644 packages/dune-configurator/dune-configurator.3.22.2/opam
create mode 100644 packages/dune-glob/dune-glob.3.22.2/opam
create mode 100644 packages/dune-private-libs/dune-private-libs.3.22.2/opam
create mode 100644 packages/dune-rpc-lwt/dune-rpc-lwt.3.22.2/opam
create mode 100644 packages/dune-rpc/dune-rpc.3.22.2/opam
create mode 100644 packages/dune-site/dune-site.3.22.2/opam
create mode 100644 packages/dune/dune.3.22.2/opam
create mode 100644 packages/dyn/dyn.3.22.2/opam
create mode 100644 packages/fs-io/fs-io.3.22.2/opam
create mode 100644 packages/ocamlc-loc/ocamlc-loc.3.22.2/opam
create mode 100644 packages/ordering/ordering.3.22.2/opam
create mode 100644 packages/stdune/stdune.3.22.2/opam
create mode 100644 packages/top-closure/top-closure.3.22.2/opam
create mode 100644 packages/xdg/xdg.3.22.2/opam
(from ocaml/opam:debian-13-ocaml-4.14@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4)
Unable to find image 'ocaml/opam:debian-13-ocaml-4.14@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4' locally
docker.io/ocaml/opam@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4: Pulling from ocaml/opam
8f6ad858d0a4: Already exists
bcb8aca13f7d: Already exists
bee1401d6aa9: Already exists
70a4ec3f5a63: Already exists
946380c37df7: Already exists
40a16ba01935: Already exists
f4df01b7be08: Already exists
c7d14a9ac62c: Already exists
8ece799add44: Already exists
d3cb64c779a6: Already exists
d54da7bf4e54: Already exists
3111aa7c2023: Already exists
962186c6e1e2: Already exists
8745338b1e0b: Already exists
70494a8c0d08: Already exists
9fbe01dcf1e6: Already exists
742774a39128: Already exists
6780ddc6e8a5: Already exists
5049c6e21d97: Already exists
f8f7f2d621cc: Already exists
d221e77cf2b7: Already exists
ea40bd8c29fe: Already exists
4f4fb700ef54: Already exists
546c3ffe9fcf: Already exists
de88a7570f24: Already exists
614f1e6aac31: Already exists
4448849c2ba8: Already exists
ae7502e72140: Already exists
ff97726fb361: Already exists
20d3e00ca128: Already exists
734e3f9ef8d5: Already exists
a9623fbab448: Already exists
d9066aed5713: Already exists
df57d5f0aedf: Already exists
a963972287a7: Already exists
960128877639: Already exists
224d5050da5a: Already exists
f8105fbb3180: Already exists
670a1f9738fe: Already exists
10f42e6216ad: Already exists
1930c7997386: Already exists
3dfb608b80df: Pulling fs layer
35294222fbdf: Pulling fs layer
3dfb608b80df: Waiting
b427a5ce3ccf: Pulling fs layer
35294222fbdf: Waiting
159615597ae3: Pulling fs layer
159615597ae3: Waiting
b427a5ce3ccf: Waiting
3dfb608b80df: Verifying Checksum
3dfb608b80df: Download complete
35294222fbdf: Download complete
b427a5ce3ccf: Verifying Checksum
b427a5ce3ccf: Download complete
159615597ae3: Download complete
3dfb608b80df: Pull complete
35294222fbdf: Pull complete
b427a5ce3ccf: Pull complete
159615597ae3: Pull complete
Digest: sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4
Status: Downloaded newer image for ocaml/opam@sha256:4457c533769cd1c32fd9fb5fb13e5a0a285ba114860db7ac2f34c1c21e5690e4
2026-04-10 20:45.06 ---> using "e7349b5faa6e8ea47e3f73a0784842b9d8524e468ce596e92633dbea53bd1c16" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-04-10 20:45.06 ---> using "345d07c1ddcf0b692213607682954d9bdf190a7dc793f33951a109185e732dcb" 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
Format upgrade done.
<><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
[default] Initialised
2026-04-10 20:45.06 ---> using "6e021c655ca00bde9af60e23db55b09a0bcc3db0d3ca38d66f78ad53e254a31c" 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 71
# repositories 1 (version-controlled)
# pinned 1 (version)
# current-switch 4.14
# invariant ["ocaml-base-compiler" {= "4.14.3"}]
# compiler-packages ocaml-base-compiler.4.14.3, 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 4.14.3
2026-04-10 20:45.06 ---> using "7b2a5ae62cf702b99c177da358372ff585494a0b1c5dfffe5c4eda3046bc59fb" 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/"))
2026-04-10 20:45.06 ---> using "2d8e28a183d0990d4c5f7a587471f7c743cdf0d9f00bdf4de7761e94ec09202a" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-04-10 20:45.08 ---> using "43c49734bd8015921029b9a907dd77c0e05208c46b686916515831f5a9e9d500" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-04-10 20:45.08 ---> using "bb36992fd0066703535b2984ee1ead3db92bb1f04a8df092631924067dac4082" 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 [121 kB]
- Fetched 211 kB in 0s (2000 kB/s)
- Reading package lists...
2026-04-10 20:45.08 ---> using "e0d9ada0baddc41d2c835edef7d0cf7cceebd2dadac41fda17c9e860b5313a74" from cache
/home/opam: (run (shell "opam pin add -k version -yn dune-configurator.3.22.2 3.22.2"))
dune-configurator is now pinned to version 3.22.2
2026-04-10 20:45.08 ---> using "8fbece27eae7b8b1872db2d5ec5cbfc33cdb5add579ea9e48e614b0af190b025" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune-configurator.3.22.2;\
\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 \"$pkg\" != 'dune-configurator.3.22.2' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
dune-configurator.3.22.2 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 3 packages
- install csexp 1.5.2 [required by dune-configurator]
- install dune 3.22.2 [required by dune-configurator]
- install dune-configurator 3.22.2 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved csexp.1.5.2 (cached)
-> retrieved dune.3.22.2, dune-configurator.3.22.2 (cached)
-> installed dune.3.22.2
-> installed csexp.1.5.2
-> installed dune-configurator.3.22.2
Done.
# To update the current shell environment, run: eval $(opam env)
2026-04-10 20:45.08 ---> using "7277fb141e00e2b955fc61a1dc629ad545b3ac277f9cb3688ec3ccad1d94605e" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.1.2;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.2' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
lbvs_consent.2.1.2 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 41 packages
- install base-bytes base [required by dokeysto]
- install batteries 3.10.0 [required by lbvs_consent]
- install bitv 2.1 [required by lbvs_consent]
- install camlp-streams 5.0.1 [required by batteries]
- install camltc 0.9.8 [required by dokeysto_camltc]
- install camlzip 1.14 [required by lbvs_consent]
- install conf-bash 1 [required by camltc]
- install conf-boost 1 [required by lbvs_consent]
- install conf-openbabel 0.1 [required by lbvs_consent]
- install conf-pkg-config 4 [required by lbvs_consent]
- install conf-python-3 9.0.0 [required by lbvs_consent]
- install conf-rdkit 1 [required by lbvs_consent]
- install conf-zlib 1 [required by camlzip]
- install cpm 12.2.0 [required by lbvs_consent]
- install cppo 1.8.0 [required by lwt]
- install dokeysto 4.0.2 [required by dokeysto_camltc]
- install dokeysto_camltc 4.0.2 [required by lbvs_consent]
- install dolog 6.0.0 [required by lbvs_consent]
- install extunix 0.4.4 [required by dokeysto]
- install lbvs_consent 2.1.2
- install logs 0.10.0 [required by camltc]
- install lwt 6.1.1 [required by camltc]
- install minicli 5.0.2 [required by lbvs_consent]
- install minivpt 2.0.0 [required by lbvs_consent]
- install num 1.6 [required by batteries]
- install obuild 0.2.2 [required by minivpt]
- install ocaml-compiler-libs v0.12.4 [required by ppxlib]
- install ocamlbuild 0.16.1 [required by logs]
- install ocamlfind 1.9.8 [required by camlzip, batteries, minivpt]
- install ocplib-endian 1.2 [required by lwt]
- install ounit2 2.2.7 [required by qcheck-ounit]
- install parmap 1.2.5 [required by lbvs_consent]
- install ppx_derivers 1.2.1 [required by ppxlib]
- install ppxlib 0.38.0 [required by extunix]
- install qcheck 0.91 [required by lbvs_consent]
- install qcheck-core 0.91 [required by qcheck]
- install qcheck-ounit 0.91 [required by qcheck]
- install seq base [required by ounit2]
- install sexplib0 v0.17.0 [required by ppxlib]
- install stdlib-shims 0.3.0 [required by ounit2]
- install topkg 1.1.1 [required by logs]
The following system packages will first need to be installed:
libboost-dev libopenbabel-dev librdkit-dev pkg-config python3 python3-rdkit 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" "libboost-dev" "libopenbabel-dev" "librdkit-dev" "pkg-config" "python3" "python3-rdkit" "zlib1g-dev"
- Preconfiguring packages ...
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- Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
- Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
- Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
- Unpacking libreadline8t64:amd64 (8.2-6) ...
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- Unpacking libopenbabel-dev (3.1.1+dfsg-12) ...
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- Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up media-types (13.0.0) ...
- Setting up libboost-python1.83.0 (1.83.0-4.2) ...
- Setting up libpixman-1-0:amd64 (0.44.0-3) ...
- Setting up libboost1.83-dev:amd64 (1.83.0-4.2) ...
- Setting up libxrender1:amd64 (1:0.9.12-1) ...
- Setting up libxcb-render0:amd64 (1.17.0-2+b1) ...
- Setting up fonts-freefont-ttf (20211204+svn4273-2) ...
- Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ...
- Setting up rdkit-data (202503.1-4) ...
- Setting up libboost-serialization1.83.0:amd64 (1.83.0-4.2) ...
- Setting up libboost-numpy1.83.0 (1.83.0-4.2) ...
- Setting up libblas3:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
- Setting up libpkgconf3:amd64 (1.8.1-4) ...
- Setting up libboost-iostreams1.83.0:amd64 (1.83.0-4.2) ...
- Setting up fonts-dejavu-mono (2.37-8) ...
- Setting up libpng16-16t64:amd64 (1.6.48-1+deb13u4) ...
- Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ...
- Setting up fonts-dejavu-core (2.37-8) ...
- Setting up pkgconf-bin (1.8.1-4) ...
- Setting up libgfortran5:amd64 (14.2.0-19) ...
- Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up libboost-dev:amd64 (1.83.0.2+b2) ...
- Setting up libcoordgen3:amd64 (3.0.2-1+b2) ...
- Setting up libinchi1.07 (1.07.3+dfsg-1) ...
- Setting up readline-common (8.2-6) ...
- Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1+deb13u2) ...
- Setting up liblapack3:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
- Setting up fontconfig-config (2.15.0-2.3) ...
- Setting up pkgconf:amd64 (1.8.1-4) ...
- Setting up libmaeparser1:amd64 (1.3.1-1+b2) ...
- Setting up libfreetype6:amd64 (2.13.3+dfsg-1+deb13u1) ...
- Setting up pkg-config:amd64 (1.8.1-4) ...
- Setting up libreadline8t64:amd64 (8.2-6) ...
- Setting up libfontconfig1:amd64 (2.15.0-2.3) ...
- Setting up libpython3.13-stdlib:amd64 (3.13.5-2) ...
- Setting up libpython3-stdlib:amd64 (3.13.5-1) ...
- Setting up python3.13 (3.13.5-2) ...
- Setting up python3 (3.13.5-1) ...
- running python rtupdate hooks for python3.13...
- running python post-rtupdate hooks for python3.13...
- Setting up libcairo2:amd64 (1.18.4-1+b1) ...
- Setting up python3-numpy (1:2.2.4+ds-1) ...
- Setting up librdkit1t64 (202503.1-4) ...
- Setting up libopenbabel7 (3.1.1+dfsg-12) ...
- Setting up libopenbabel-dev (3.1.1+dfsg-12) ...
- Setting up python3-rdkit (202503.1-4) ...
- Setting up librdkit-dev (202503.1-4) ...
- Processing triggers for libc-bin (2.41-12+deb13u2) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved batteries.3.10.0 (cached)
-> retrieved bitv.2.1 (cached)
-> retrieved camlp-streams.5.0.1 (cached)
-> retrieved camltc.0.9.8 (cached)
-> retrieved camlzip.1.14 (cached)
-> retrieved conf-python-3.9.0.0 (cached)
-> retrieved conf-rdkit.1 (cached)
-> installed conf-boost.1
-> retrieved cpm.12.2.0 (cached)
-> retrieved cppo.1.8.0 (cached)
-> installed conf-bash.1
-> installed conf-pkg-config.4
-> retrieved dokeysto.4.0.2, dokeysto_camltc.4.0.2 (cached)
-> installed bitv.2.1
-> installed conf-python-3.9.0.0
-> installed conf-openbabel.0.1
-> installed conf-zlib.1
-> retrieved dolog.6.0.0 (cached)
-> installed conf-rdkit.1
-> retrieved extunix.0.4.4 (cached)
-> installed camlp-streams.5.0.1
-> retrieved lbvs_consent.2.1.2 (https://opam.ocaml.org/cache)
-> retrieved logs.0.10.0 (cached)
-> retrieved lwt.6.1.1 (cached)
-> retrieved minicli.5.0.2 (cached)
-> installed dolog.6.0.0
-> retrieved minivpt.2.0.0 (https://opam.ocaml.org/cache)
-> retrieved num.1.6 (cached)
-> retrieved obuild.0.2.2 (https://opam.ocaml.org/cache)
-> installed minicli.5.0.2
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved ocplib-endian.1.2 (cached)
-> retrieved ounit2.2.2.7 (cached)
-> retrieved parmap.1.2.5 (https://opam.ocaml.org/cache)
-> retrieved ppx_derivers.1.2.1 (cached)
-> installed cppo.1.8.0
-> installed ppx_derivers.1.2.1
-> retrieved ppxlib.0.38.0 (cached)
-> retrieved qcheck.0.91, qcheck-core.0.91, qcheck-ounit.0.91 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexplib0.v0.17.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved topkg.1.1.1 (cached)
-> installed stdlib-shims.0.3.0
-> installed parmap.1.2.5
-> installed ocaml-compiler-libs.v0.12.4
-> installed sexplib0.v0.17.0
-> installed num.1.6
-> installed ounit2.2.2.7
-> installed qcheck-core.0.91
-> installed qcheck-ounit.0.91
-> installed qcheck.0.91
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed ocplib-endian.1.2
-> installed camlzip.1.14
-> installed ocamlbuild.0.16.1
-> installed lwt.6.1.1
-> installed topkg.1.1.1
-> installed batteries.3.10.0
-> installed logs.0.10.0
-> installed obuild.0.2.2
-> installed cpm.12.2.0
-> installed minivpt.2.0.0
-> installed camltc.0.9.8
-> installed ppxlib.0.38.0
-> installed extunix.0.4.4
-> installed dokeysto.4.0.2
-> installed dokeysto_camltc.4.0.2
-> installed lbvs_consent.2.1.2
Done.
# To update the current shell environment, run: eval $(opam env)
2026-04-10 20:47.23 ---> saved as "2e5693dd2032d6c517d3b9873cb90cf56227c2d8fdc673e71211f9071767e9dd"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.1.2) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile lbvs_consent 2.1.2
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved lbvs_consent.2.1.2 (https://opam.ocaml.org/cache)
-> removed lbvs_consent.2.1.2
-> installed lbvs_consent.2.1.2
Done.
# To update the current shell environment, run: eval $(opam env)
2026-04-10 20:47.42 ---> saved as "9c759934b551a2e8e6770ba64321da8bf0215b93e6188127cff7b650f399add3"
/home/opam: (run (shell "opam reinstall --with-test --verbose lbvs_consent.2.1.2;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.2' && partial_fails=\"$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 lbvs_consent 2.1.2
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [lbvs_consent.2.1.2: extract]
-> retrieved lbvs_consent.2.1.2 (cached)
[lbvs_consent: patch] applying makefile.patch
Processing 2/4: [lbvs_consent: make obmaccs]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "make" "obmaccs" (CWD=/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2)
- cd src; make
- make[1]: Entering directory '/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2/src'
- c++ -W -Wall `pkg-config --silence-errors --cflags openbabel-2.0 || pkg-config --cflags openbabel-3` ob_maccs.cpp \
- -o lbvs_consent_ob_maccs `pkg-config --silence-errors --libs openbabel-2.0 || pkg-config --libs openbabel-3` -Wl,-R/usr/lib
- In file included from /usr/include/openbabel3/openbabel/fingerprint.h:28,
- from ob_maccs.cpp:1:
- /usr/include/openbabel3/openbabel/plugin.h:41:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
- 41 | struct OBERROR CharPtrLess : public std::binary_function<const char*,const char*, bool>
- | ^~~~~~~~~~~~~~~
- In file included from /usr/include/c++/14/bits/stl_tree.h:65,
- from /usr/include/c++/14/map:62,
- from /usr/include/openbabel3/openbabel/fingerprint.h:23:
- /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
- 131 | struct binary_function
- | ^~~~~~~~~~~~~~~
- In file included from /usr/include/openbabel3/openbabel/mol.h:48,
- from ob_maccs.cpp:2:
- /usr/include/openbabel3/openbabel/base.h: In member function 'virtual const char* OpenBabel::OBBase::GetTitle(bool) const':
- /usr/include/openbabel3/openbabel/base.h:286:49: warning: unused parameter 'replaceNewlines' [-Wunused-parameter]
- 286 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";}
- | ^
- /usr/include/openbabel3/openbabel/base.h:37:20: note: in definition of macro 'UNUSED'
- 37 | # define UNUSED(x) x
- | ^
- make[1]: Leaving directory '/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2/src'
Processing 2/4: [lbvs_consent: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "lbvs_consent" "-j" "71" (CWD=/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2)
-> compiled lbvs_consent.2.1.2
-> removed lbvs_consent.2.1.2
Processing 4/4: [lbvs_consent: cp]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "install" "cp" "bin/lbvs_consent_ecfp4.py" "/home/opam/.opam/4.14/bin/lbvs_consent_ecfp4.py" (CWD=/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2)
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "install" "cp" "src/lbvs_consent_ob_maccs" "/home/opam/.opam/4.14/bin/lbvs_consent_ob_maccs" (CWD=/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.2)
-> installed lbvs_consent.2.1.2
Done.
# To update the current shell environment, run: eval $(opam env)
2026-04-10 20:48.03 ---> saved as "18e52a5f4d273966c4c769d47af5cb0882b8dafaafc2a655cc8111b00fc4de07"
Job succeeded
2026-04-10 20:49.04: Job succeeded