Build:
- 0
2026-02-26 12:33.05: New job: test lbvs_consent.2.1.1 with conf-zlib.1, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29394/head (42b7d54d05b5bc7b2acd4b8e282016921f6064ca)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29394/head" && git reset --hard 42b7d54d
git fetch origin master
git merge --no-edit e5f44b75d9fef9e17658ad0da2eb5f9a3445c951
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:04864ce35c9a53a8f91e1b6ddfe19ff405f2881ec1201cdca698239b3b811633
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn conf-zlib.1 1
RUN opam reinstall conf-zlib.1; \
res=$?; \
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 "$pkg" != 'conf-zlib.1' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall lbvs_consent.2.1.1; \
res=$?; \
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 "$pkg" != 'lbvs_consent.2.1.1' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test lbvs_consent.2.1.1) || true
RUN opam reinstall --with-test --verbose lbvs_consent.2.1.1; \
res=$?; \
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 "$pkg" != 'lbvs_consent.2.1.1' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-02-26 12:33.05: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:04864ce35c9a53a8f91e1b6ddfe19ff405f2881ec1201cdca698239b3b811633-conf-zlib.1-lbvs_consent.2.1.1-42b7d54d05b5bc7b2acd4b8e282016921f6064ca"
2026-02-26 12:33.05: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:04864ce35c9a53a8f91e1b6ddfe19ff405f2881ec1201cdca698239b3b811633)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn conf-zlib.1 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall conf-zlib.1;\
\n res=$?;\
\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 \"$pkg\" != 'conf-zlib.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.1.1;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.1.1) || true"))
(run (shell "opam reinstall --with-test --verbose lbvs_consent.2.1.1;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2026-02-26 12:33.05: Waiting for resource in pool OCluster
2026-02-27 02:59.07: Waiting for worker…
2026-02-27 03:07.45: Got resource from pool OCluster
Building on toxis.caelum.ci.dev
All commits already cached
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Updating files: 100% (18322/18322), done.
HEAD is now at e5f44b75d9 Merge pull request #29458 from dinosaure/release-vif-v0.0.1_beta2
Merge made by the 'ort' strategy.
packages/conf-zlib/conf-zlib.1/opam | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
(from ocaml/opam:debian-13-ocaml-4.14@sha256:04864ce35c9a53a8f91e1b6ddfe19ff405f2881ec1201cdca698239b3b811633)
2026-02-27 03:07.55 ---> using "d6079ab6cce1b58b34ac9b5ed11aa86b7980ab728c75f5a6ba9271e98dc1ac1c" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-02-27 03:07.55 ---> using "3c00c47f9d923b8bd6ffb2b949e4b9efd562ec1af5385aec1656ef10f01c4450" 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
2026-02-27 03:07.55 ---> using "a92b73fe3956045426c13ac4a0686c952a1f3abe3c88ddfc7b2f3a6ed1e46736" 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" {= "4.14.2"}]
# 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
2026-02-27 03:07.55 ---> using "cae9d187aa902d60c82d0c2150bbd9c0de1870c923aa0b0063ad5a25247acae5" 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/"))
2026-02-27 03:07.55 ---> using "feb31a4f8ccbcfb9943e7338a457db5bc00688ce26b7db5634b111626cd4af24" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-02-27 03:07.56 ---> using "218dc454a30b7ab4404235db8c8fdb1f5422091dcaf54e0b4d4c2167f9e06097" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-02-27 03:07.56 ---> using "61576cb25f4b1f74a3a66394571bc64e478163c1e334ae43ae4cbd84e7d35da7" 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 (2085 kB/s)
- Reading package lists...
2026-02-27 03:07.56 ---> using "f9dbcae3c4d74eb0b927dae4c55293566c19eca2857d90411920e649cc5a13db" from cache
/home/opam: (run (shell "opam pin add -k version -yn conf-zlib.1 1"))
conf-zlib is now pinned to version 1
2026-02-27 03:07.56 ---> using "b3dc7723b35baee5e68f26c58db70bf95a6915aac55a46a8934396bddb440e1c" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall conf-zlib.1;\
\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 \"$pkg\" != 'conf-zlib.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
conf-zlib.1 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 2 packages
- install conf-pkg-config 4 [required by conf-zlib]
- install conf-zlib 1 (pinned)
The following system packages will first need to be installed:
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" "pkg-config" "zlib1g-dev"
- Selecting previously unselected package libpkgconf3:amd64.
- (Reading database ...
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- Preparing to unpack .../libpkgconf3_1.8.1-4_amd64.deb ...
- Unpacking libpkgconf3:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkgconf-bin.
- Preparing to unpack .../pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../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 .../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 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 <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> installed conf-pkg-config.4
-> installed conf-zlib.1
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-27 03:07.56 ---> using "065ee5357a4c3a6c6980a96c59bf7001822fe192a1af5dc7d4896c22789bc061" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.1.1;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
lbvs_consent.2.1.1 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 42 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-python-3 9.0.0 [required by lbvs_consent]
- install conf-rdkit 1 [required by lbvs_consent]
- install cpm 12.2.0 [required by lbvs_consent]
- install cppo 1.8.0 [required by lwt]
- install csexp 1.5.2 [required by dune-configurator]
- install dokeysto 4.0.2 [required by dokeysto_camltc]
- install dokeysto_camltc 4.0.2 [required by lbvs_consent]
- install dolog 4.0.0 [required by lbvs_consent]
- install dune 3.21.1 [required by lbvs_consent]
- install dune-configurator 3.21.1 [required by parmap]
- install extunix 0.4.4 [required by dokeysto]
- install lbvs_consent 2.1.1
- 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 0.1.11 [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 0.37.0 [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 python3 python3-rdkit
<><> 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" "python3" "python3-rdkit"
- Preconfiguring packages ...
- Selecting previously unselected package libpython3.13-minimal:amd64.
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- Preparing to unpack .../libpython3.13-minimal_3.13.5-2_amd64.deb ...
- Unpacking libpython3.13-minimal:amd64 (3.13.5-2) ...
- Selecting previously unselected package python3.13-minimal.
- Preparing to unpack .../python3.13-minimal_3.13.5-2_amd64.deb ...
- Unpacking python3.13-minimal (3.13.5-2) ...
- Setting up libpython3.13-minimal:amd64 (3.13.5-2) ...
- Setting up python3.13-minimal (3.13.5-2) ...
- Selecting previously unselected package python3-minimal.
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- 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) ...
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- Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ...
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- 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 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+deb13u3) ...
- Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1) ...
- Setting up fonts-dejavu-core (2.37-8) ...
- Setting up libgfortran5:amd64 (14.2.0-19) ...
- 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) ...
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- 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) ...
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- Processing triggers for libc-bin (2.41-12+deb13u1) ...
<><> 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)
-> retrieved csexp.1.5.2 (cached)
-> retrieved dokeysto.4.0.2, dokeysto_camltc.4.0.2 (cached)
-> installed conf-bash.1
-> installed conf-openbabel.0.1
-> retrieved dolog.4.0.0 (cached)
-> installed conf-python-3.9.0.0
-> installed conf-rdkit.1
-> retrieved dune.3.21.1, dune-configurator.3.21.1 (cached)
-> retrieved extunix.0.4.4 (cached)
-> retrieved lbvs_consent.2.1.1 (cached)
-> retrieved logs.0.10.0 (cached)
-> retrieved lwt.6.1.1 (cached)
-> retrieved minicli.5.0.2 (cached)
-> retrieved minivpt.2.0.0 (cached)
-> retrieved num.1.6 (cached)
-> retrieved obuild.0.1.11 (cached)
-> 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 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppxlib.0.37.0 (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 num.1.6
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed camlzip.1.14
-> installed ocamlbuild.0.16.1
-> installed obuild.0.1.11
-> installed minivpt.2.0.0
-> installed topkg.1.1.1
-> installed dune.3.21.1
-> installed ppx_derivers.1.2.1
-> installed camlp-streams.5.0.1
-> installed bitv.2.1
-> installed csexp.1.5.2
-> installed dolog.4.0.0
-> installed cppo.1.8.0
-> installed minicli.5.0.2
-> installed ocaml-compiler-libs.v0.12.4
-> installed sexplib0.v0.17.0
-> installed stdlib-shims.0.3.0
-> installed ocplib-endian.1.2
-> installed qcheck-core.0.91
-> installed ounit2.2.2.7
-> installed qcheck-ounit.0.91
-> installed dune-configurator.3.21.1
-> installed qcheck.0.91
-> installed parmap.1.2.5
-> installed batteries.3.10.0
-> installed lwt.6.1.1
-> installed cpm.12.2.0
-> installed logs.0.10.0
-> installed camltc.0.9.8
-> installed ppxlib.0.37.0
-> installed extunix.0.4.4
-> installed dokeysto.4.0.2
-> installed dokeysto_camltc.4.0.2
-> installed lbvs_consent.2.1.1
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-27 03:11.26 ---> saved as "bbf0dedfab42227d1cc4d4252384d7cb929d97fbe1908e8d691d378593662d9d"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.1.1) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile lbvs_consent 2.1.1
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved lbvs_consent.2.1.1 (https://opam.ocaml.org/cache)
-> removed lbvs_consent.2.1.1
-> installed lbvs_consent.2.1.1
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-27 03:11.43 ---> saved as "5aa4156f9e7a3c6f56a0104a2ba851129e918ed4eef69b6339615ed5d70e346e"
/home/opam: (run (shell "opam reinstall --with-test --verbose lbvs_consent.2.1.1;\
\n res=$?;\
\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 \"$pkg\" != 'lbvs_consent.2.1.1' && partial_fails=\"$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 2.1.1
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [lbvs_consent.2.1.1: extract]
-> retrieved lbvs_consent.2.1.1 (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.2.1.1)
- cd src; make
- make[1]: Entering directory '/home/opam/.opam/4.14/.opam-switch/build/lbvs_consent.2.1.1/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.2.1.1/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.2.1.1)
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.lbvs_consent.objs/byte -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/byte/lbvs_consent__MyList.cmo -c -impl src/myList.ml)
- File "src/myList.ml", line 51, characters 13-31:
- 51 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 64, characters 13-31:
- 64 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 193, characters 14-30:
- 193 | map of_str (BatString.nsplit s' ~by:";")
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.lbvs_consent.objs/byte -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/byte/lbvs_consent__MyIntSet.cmo -c -impl src/myIntSet.ml)
- File "src/myIntSet.ml", line 22, characters 20-36:
- 22 | let int_strings = BatString.nsplit ~by:";" chopped in
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlopt.opt -w -40 -g -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -intf-suffix .ml -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/native/lbvs_consent__MyList.cmx -c -impl src/myList.ml)
- File "src/myList.ml", line 51, characters 13-31:
- 51 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 64, characters 13-31:
- 64 | Array.sort Pervasives.compare xs;
- ^^^^^^^^^^^^^^^^^^
- Alert deprecated: module Stdlib.Pervasives
- Use Stdlib instead.
-
- If you need to stay compatible with OCaml < 4.07, you can use the
- stdlib-shims library: https://github.com/ocaml/stdlib-shims
- File "src/myList.ml", line 193, characters 14-30:
- 193 | map of_str (BatString.nsplit s' ~by:";")
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlopt.opt -w -40 -g -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -intf-suffix .ml -no-alias-deps -open Lbvs_consent -o src/.lbvs_consent.objs/native/lbvs_consent__MyIntSet.cmx -c -impl src/myIntSet.ml)
- File "src/myIntSet.ml", line 22, characters 20-36:
- 22 | let int_strings = BatString.nsplit ~by:";" chopped in
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlc.opt -w -40 -g -bin-annot -I src/.mol_get.eobjs/byte -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/bytes -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/camltc -I /home/opam/.opam/4.14/lib/camltc/tc -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dokeysto -I /home/opam/.opam/4.14/lib/dokeysto_camltc -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/extunix -I /home/opam/.opam/4.14/lib/logs -I /home/opam/.opam/4.14/lib/logs/lwt -I /home/opam/.opam/4.14/lib/lwt -I /home/opam/.opam/4.14/lib/lwt/unix -I /home/opam/.opam/4.14/lib/minicli -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/ocplib-endian -I /home/opam/.opam/4.14/lib/ocplib-endian/bigstring -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -I src/.lbvs_consent.objs/byte -no-alias-deps -o src/.mol_get.eobjs/byte/mol_get.cmo -c -impl src/mol_get.ml)
- File "src/mol_get.ml", line 77, characters 22-38:
- 77 | | On_cli names -> BatString.nsplit names ~by:","
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
- (cd _build/default && /home/opam/.opam/4.14/bin/ocamlopt.opt -w -40 -g -I src/.mol_get.eobjs/byte -I src/.mol_get.eobjs/native -I /home/opam/.opam/4.14/lib/batteries -I /home/opam/.opam/4.14/lib/batteries/unthreaded -I /home/opam/.opam/4.14/lib/bitv -I /home/opam/.opam/4.14/lib/bytes -I /home/opam/.opam/4.14/lib/camlp-streams -I /home/opam/.opam/4.14/lib/camltc -I /home/opam/.opam/4.14/lib/camltc/tc -I /home/opam/.opam/4.14/lib/cpm -I /home/opam/.opam/4.14/lib/dokeysto -I /home/opam/.opam/4.14/lib/dokeysto_camltc -I /home/opam/.opam/4.14/lib/dolog -I /home/opam/.opam/4.14/lib/extunix -I /home/opam/.opam/4.14/lib/logs -I /home/opam/.opam/4.14/lib/logs/lwt -I /home/opam/.opam/4.14/lib/lwt -I /home/opam/.opam/4.14/lib/lwt/unix -I /home/opam/.opam/4.14/lib/minicli -I /home/opam/.opam/4.14/lib/minivpt -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/ocplib-endian -I /home/opam/.opam/4.14/lib/ocplib-endian/bigstring -I /home/opam/.opam/4.14/lib/parmap -I /home/opam/.opam/4.14/lib/zip -I src/.lbvs_consent.objs/byte -I src/.lbvs_consent.objs/native -intf-suffix .ml -no-alias-deps -o src/.mol_get.eobjs/native/mol_get.cmx -c -impl src/mol_get.ml)
- File "src/mol_get.ml", line 77, characters 22-38:
- 77 | | On_cli names -> BatString.nsplit names ~by:","
- ^^^^^^^^^^^^^^^^
- Alert deprecated: BatString.nsplit
- Use split_on_string instead.
-> compiled lbvs_consent.2.1.1
-> removed lbvs_consent.2.1.1
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.2.1.1)
+ /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.2.1.1)
-> installed lbvs_consent.2.1.1
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-27 03:12.01 ---> saved as "69f4527724a28328e6814962f01df81d876d41595802657f3c4a4996c5d3bd5d"
Job succeeded
2026-02-27 03:12.32: Job succeeded