- github
- ocaml
- opam-repository
- c715a9
- compilers,5.3,qcheck-ounit.0.26,revdeps,lbvs_consent.2.2.0
(not at the head of any monitored branch or PR)
2025-07-08 20:22.37: New job: test lbvs_consent.2.2.0 with qcheck-ounit.0.26, using opam 2.3
from https://github.com/ocaml/opam-repository.git#refs/pull/28148/head (c715a95fe87d4397d1f0658b2ae5acd528de705e)
on debian-12-ocaml-5.3/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/28148/head" && git reset --hard c715a95f
git fetch origin master
git merge --no-edit 11a53009bd75423d805636ff9384bf7cce8b0a9a
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-12-ocaml-5.3@sha256:0c1d105ecd30926bc15c645f510475d0b65f37a8c9ca9e82c29259ac8876afc4
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-2.3 /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn qcheck-ounit.0.26 0.26
RUN opam reinstall qcheck-ounit.0.26; \
res=$?; \
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-12\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'qcheck-ounit.0.26' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall lbvs_consent.2.2.0; \
res=$?; \
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-12\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'lbvs_consent.2.2.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test lbvs_consent.2.2.0) || true
RUN opam reinstall --with-test --verbose lbvs_consent.2.2.0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-12\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'lbvs_consent.2.2.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2025-07-08 20:22.37: Using cache hint "ocaml/opam:debian-12-ocaml-5.3@sha256:0c1d105ecd30926bc15c645f510475d0b65f37a8c9ca9e82c29259ac8876afc4-qcheck-ounit.0.26-lbvs_consent.2.2.0-c715a95fe87d4397d1f0658b2ae5acd528de705e"
2025-07-08 20:22.37: Using OBuilder spec:
((from ocaml/opam:debian-12-ocaml-5.3@sha256:0c1d105ecd30926bc15c645f510475d0b65f37a8c9ca9e82c29259ac8876afc4)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-2.3 /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn qcheck-ounit.0.26 0.26"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall qcheck-ounit.0.26;\
\n res=$?;\
\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-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'qcheck-ounit.0.26' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'lbvs_consent.2.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.2.0) || true"))
(run (shell "opam reinstall --with-test --verbose lbvs_consent.2.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'lbvs_consent.2.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2025-07-08 20:22.37: Waiting for resource in pool OCluster
2025-07-08 20:23.10: Waiting for worker…
2025-07-08 20:24.33: Got resource from pool OCluster
Building on phoebe
All commits already cached
HEAD is now at 11a53009bd Merge pull request #27805 from fccm2/conf-gegl
Updating 11a53009bd..c715a95fe8
Fast-forward
packages/qcheck-alcotest/qcheck-alcotest.0.26/opam | 37 +++++++++++++++++++
packages/qcheck-core/qcheck-core.0.26/opam | 38 ++++++++++++++++++++
packages/qcheck-ounit/qcheck-ounit.0.26/opam | 37 +++++++++++++++++++
packages/qcheck/qcheck.0.26/opam | 42 ++++++++++++++++++++++
4 files changed, 154 insertions(+)
create mode 100644 packages/qcheck-alcotest/qcheck-alcotest.0.26/opam
create mode 100644 packages/qcheck-core/qcheck-core.0.26/opam
create mode 100644 packages/qcheck-ounit/qcheck-ounit.0.26/opam
create mode 100644 packages/qcheck/qcheck.0.26/opam
(from ocaml/opam:debian-12-ocaml-5.3@sha256:0c1d105ecd30926bc15c645f510475d0b65f37a8c9ca9e82c29259ac8876afc4)
2025-07-08 20:24.35 ---> using "794fb143e27aef19245a1292a46556b65f0250dc92342915a5954f6ff9b5080d" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-2.3 /usr/bin/opam"))
2025-07-08 20:24.35 ---> using "9dcba9e25cdddab1b93b09e925757989633d2b1988716efc0a66a6adf8d01ef2" 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.
Continue? [y/n] y
This development version of opam requires an update to the layout of /home/opam/.opam from version 2.0 to version 2.2, which can't be reverted.
You may want to back it up before going further.
Format upgrade done.
<><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
[default] Initialised
2025-07-08 20:24.35 ---> using "b9a54c51b8a3103677ef53a1c647aa827b0e2137f040935f0492bb8695c09705" 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 2.3.0 (35acd0c5abc5e66cdbd5be16ba77aa6c33a4c724)
# self-upgrade no
# system arch=x86_64 os=linux os-distribution=debian os-version=12
# 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 5.3
# invariant ["ocaml-base-compiler" {= "5.3.0"}]
# compiler-packages ocaml-base-compiler.5.3.0, ocaml-compiler.5.3.0, ocaml-options-vanilla.1
# ocaml:native true
# ocaml:native-tools true
# ocaml:native-dynlink true
# ocaml:stubsdir /home/opam/.opam/5.3/lib/ocaml/stublibs:/home/opam/.opam/5.3/lib/ocaml
# ocaml:preinstalled false
# ocaml:compiler 5.3.0
2025-07-08 20:24.35 ---> using "9ac8ae172e8007da6119d69891073b8166f73d4da54b130f44226a65ce3c5400" 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/"))
2025-07-08 20:24.35 ---> using "21f2ba21de2118dacb2334afecf22f096b7335ddcbd53132998d7fef14418c67" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2025-07-08 20:24.36 ---> using "0bb30839169b9737adc01516ac1a1bcf911fa5120d31dd5a4eb4f3caa89cce04" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2025-07-08 20:24.36 ---> using "3e9028d8e55b1b1b51ff51784bd34a26761b664d926cd3952dae0ba65ea4e31e" 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 bookworm InRelease
- Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]
- Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB]
- Get:4 http://deb.debian.org/debian-security bookworm-security/main amd64 Packages [272 kB]
- Fetched 375 kB in 0s (923 kB/s)
- Reading package lists...
-
2025-07-08 20:24.36 ---> using "d7b7e88a8ef704acb72777e7c7202d7572c357e1168cfe99e16d843adee7ea17" from cache
/home/opam: (run (shell "opam pin add -k version -yn qcheck-ounit.0.26 0.26"))
qcheck-ounit is now pinned to version 0.26
2025-07-08 20:24.37 ---> saved as "af7e003979fddf1cb970f15318fbe404a3578da0fc052fe0aec705abb2d3d77b"
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall qcheck-ounit.0.26;\
\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-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'qcheck-ounit.0.26' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
qcheck-ounit.0.26 is not installed. Install it? [y/n] y
The following actions will be performed:
=== install 6 packages
- install dune 3.19.1 [required by qcheck-ounit]
- install ounit2 2.2.7 [required by qcheck-ounit]
- install qcheck-core 0.26 [required by qcheck-ounit]
- install qcheck-ounit 0.26 (pinned)
- install seq base [required by ounit2]
- install stdlib-shims 0.3.0 [required by ounit2]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.19.1 (cached)
-> retrieved ounit2.2.2.7 (cached)
-> retrieved qcheck-core.0.26, qcheck-ounit.0.26 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved stdlib-shims.0.3.0 (cached)
-> installed dune.3.19.1
-> installed stdlib-shims.0.3.0
-> installed ounit2.2.2.7
-> installed qcheck-core.0.26
-> installed qcheck-ounit.0.26
Done.
# To update the current shell environment, run: eval $(opam env)
2025-07-08 20:25.23 ---> saved as "006d73fb7b6fb31bdfbf3667f7b6272b59bdfcd5d3ad6ba479a169b1bcf50bbc"
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall lbvs_consent.2.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'lbvs_consent.2.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
lbvs_consent.2.2.0 is not installed. Install it? [y/n] y
The following actions will be performed:
=== install 30 packages
- install base-bytes base [required by dokeysto]
- install batteries 3.9.0 [required by lbvs_consent]
- install bitv 2.0 [required by lbvs_consent]
- install camlp-streams 5.0.1 [required by batteries]
- install camlzip 1.13 [required by lbvs_consent]
- install conf-autoconf 0.2 [required by cpu]
- 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 cpu 2.0.0 [required by parany]
- install csexp 1.5.2 [required by dune-configurator]
- install dokeysto 4.0.1 [required by lbvs_consent]
- install dolog 6.0.0 [required by lbvs_consent]
- install dune-configurator 3.19.1 [required by extunix]
- install extunix 0.4.4 [required by dokeysto]
- install lbvs_consent 2.2.0
- install minicli 5.0.2 [required by lbvs_consent]
- install num 1.6 [required by batteries]
- install ocaml-compiler-libs v0.17.0 [required by ppxlib]
- install ocamlfind 1.9.8 [required by batteries, camlzip]
- install parany 14.0.1 [required by lbvs_consent]
- install ppx_derivers 1.2.1 [required by ppxlib]
- install ppxlib 0.36.0 [required by extunix]
- install qcheck 0.26 [required by lbvs_consent]
- install sexplib0 v0.17.0 [required by ppxlib]
- install vpt 5.0.0 [required by lbvs_consent]
The following system packages will first need to be installed:
autoconf 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" "autoconf" "libboost-dev" "libopenbabel-dev" "librdkit-dev" "pkg-config" "python3" "python3-rdkit" "zlib1g-dev"
- debconf: delaying package configuration, since apt-utils is not installed
- Selecting previously unselected package libpython3.11-minimal:amd64.
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- Preparing to unpack .../libpython3.11-minimal_3.11.2-6+deb12u6_amd64.deb ...
- Unpacking libpython3.11-minimal:amd64 (3.11.2-6+deb12u6) ...
- Selecting previously unselected package python3.11-minimal.
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- Selecting previously unselected package libboost1.74-dev:amd64.
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- Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-21) ...
- Selecting previously unselected package libboost-dev:amd64.
- Preparing to unpack .../08-libboost-dev_1.74.0.3_amd64.deb ...
- Unpacking libboost-dev:amd64 (1.74.0.3) ...
- Selecting previously unselected package libboost-iostreams1.74.0:amd64.
- Preparing to unpack .../09-libboost-iostreams1.74.0_1.74.0+ds1-21_amd64.deb ...
- Unpacking libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ...
- Selecting previously unselected package libboost-python1.74.0.
- Preparing to unpack .../10-libboost-python1.74.0_1.74.0+ds1-21_amd64.deb ...
- Unpacking libboost-python1.74.0 (1.74.0+ds1-21) ...
- Selecting previously unselected package libboost-serialization1.74.0:amd64.
- Preparing to unpack .../11-libboost-serialization1.74.0_1.74.0+ds1-21_amd64.deb ...
- Unpacking libboost-serialization1.74.0:amd64 (1.74.0+ds1-21) ...
- Selecting previously unselected package libpixman-1-0:amd64.
- Preparing to unpack .../12-libpixman-1-0_0.42.2-1_amd64.deb ...
- Unpacking libpixman-1-0:amd64 (0.42.2-1) ...
- Selecting previously unselected package libxcb-render0:amd64.
- Preparing to unpack .../13-libxcb-render0_1.15-1_amd64.deb ...
- Unpacking libxcb-render0:amd64 (1.15-1) ...
- Selecting previously unselected package libxcb-shm0:amd64.
- Preparing to unpack .../14-libxcb-shm0_1.15-1_amd64.deb ...
- Unpacking libxcb-shm0:amd64 (1.15-1) ...
- Selecting previously unselected package libxrender1:amd64.
- Preparing to unpack .../15-libxrender1_1%3a0.9.10-1.1_amd64.deb ...
- Unpacking libxrender1:amd64 (1:0.9.10-1.1) ...
- Selecting previously unselected package libcairo2:amd64.
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- Unpacking libcoordgen3:amd64 (3.0.1-1) ...
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- Unpacking libicu72:amd64 (72.1-3+deb12u1) ...
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- Unpacking libinchi1 (1.03+dfsg-4+b2) ...
- Selecting previously unselected package liblapack3:amd64.
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- Unpacking liblapack3:amd64 (3.11.0-2) ...
- Selecting previously unselected package libmaeparser1:amd64.
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- Unpacking libmaeparser1:amd64 (1.3.0-1) ...
- Selecting previously unselected package libxml2:amd64.
- Preparing to unpack .../23-libxml2_2.9.14+dfsg-1.3~deb12u2_amd64.deb ...
- Unpacking libxml2:amd64 (2.9.14+dfsg-1.3~deb12u2) ...
- Selecting previously unselected package libopenbabel7.
- Preparing to unpack .../24-libopenbabel7_3.1.1+dfsg-9+b3_amd64.deb ...
- Unpacking libopenbabel7 (3.1.1+dfsg-9+b3) ...
- Selecting previously unselected package libopenbabel-dev.
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- Unpacking libopenbabel-dev (3.1.1+dfsg-9+b3) ...
- Selecting previously unselected package libpkgconf3:amd64.
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- Unpacking libpkgconf3:amd64 (1.8.1-1) ...
- Selecting previously unselected package libpython3.11:amd64.
- Preparing to unpack .../27-libpython3.11_3.11.2-6+deb12u6_amd64.deb ...
- Unpacking libpython3.11:amd64 (3.11.2-6+deb12u6) ...
- Selecting previously unselected package librdkit1.
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- Unpacking librdkit1 (202209.3-1) ...
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- Selecting previously unselected package pkgconf-bin.
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- Selecting previously unselected package pkgconf:amd64.
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- Unpacking pkgconf:amd64 (1.8.1-1) ...
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- Unpacking pkg-config:amd64 (1.8.1-1) ...
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- Unpacking python3-pkg-resources (66.1.1-1+deb12u1) ...
- Selecting previously unselected package python3-numpy.
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- Unpacking python3-numpy (1:1.24.2-1+deb12u1) ...
- Selecting previously unselected package rdkit-data.
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- Unpacking rdkit-data (202209.3-1) ...
- Selecting previously unselected package python3-rdkit.
- Preparing to unpack .../36-python3-rdkit_202209.3-1_amd64.deb ...
- Unpacking python3-rdkit (202209.3-1) ...
- Selecting previously unselected package zlib1g-dev:amd64.
- Preparing to unpack .../37-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ...
- Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
- Setting up media-types (10.0.0) ...
- Setting up libpixman-1-0:amd64 (0.42.2-1) ...
- Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ...
- Setting up libicu72:amd64 (72.1-3+deb12u1) ...
- Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
- Setting up libxcb-render0:amd64 (1.15-1) ...
- Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ...
- Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u6) ...
- Setting up fonts-freefont-ttf (20120503-10) ...
- Setting up m4 (1.4.19-3) ...
- Setting up libxcb-shm0:amd64 (1.15-1) ...
- Setting up rdkit-data (202209.3-1) ...
- Setting up libcairo2:amd64 (1.16.0-7) ...
- Setting up libmaeparser1:amd64 (1.3.0-1) ...
- Setting up autotools-dev (20220109.1) ...
- Setting up libblas3:amd64 (3.11.0-2) ...
- 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 (1.8.1-1) ...
- Setting up pkgconf-bin (1.8.1-1) ...
- Setting up libgfortran5:amd64 (12.2.0-14+deb12u1) ...
- Setting up autoconf (2.71-3) ...
- Setting up libboost-serialization1.74.0:amd64 (1.74.0+ds1-21) ...
- Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ...
- Setting up libboost-dev:amd64 (1.74.0.3) ...
- Setting up libcoordgen3:amd64 (3.0.1-1) ...
- Setting up libboost-python1.74.0 (1.74.0+ds1-21) ...
- Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u2) ...
- Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ...
- Setting up libinchi1 (1.03+dfsg-4+b2) ...
- Setting up automake (1:1.16.5-1.3) ...
- update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
- Setting up python3.11 (3.11.2-6+deb12u6) ...
- Setting up liblapack3:amd64 (3.11.0-2) ...
- 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 libpython3.11:amd64 (3.11.2-6+deb12u6) ...
- Setting up librdkit1 (202209.3-1) ...
- Setting up libopenbabel7 (3.1.1+dfsg-9+b3) ...
- Setting up python3 (3.11.2-1+b1) ...
- running python rtupdate hooks for python3.11...
- running python post-rtupdate hooks for python3.11...
- Setting up pkgconf:amd64 (1.8.1-1) ...
- Setting up libopenbabel-dev (3.1.1+dfsg-9+b3) ...
- Setting up librdkit-dev (202209.3-1) ...
- Setting up pkg-config:amd64 (1.8.1-1) ...
- Setting up python3-pkg-resources (66.1.1-1+deb12u1) ...
- Setting up python3-numpy (1:1.24.2-1+deb12u1) ...
- Setting up python3-rdkit (202209.3-1) ...
- Processing triggers for libc-bin (2.36-9+deb12u10) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved batteries.3.9.0 (cached)
-> retrieved bitv.2.0 (cached)
-> retrieved camlp-streams.5.0.1 (cached)
-> retrieved camlzip.1.13 (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 cpu.2.0.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved dokeysto.4.0.1 (cached)
-> retrieved dolog.6.0.0 (cached)
-> installed conf-autoconf.0.2
-> installed conf-pkg-config.4
-> installed conf-python-3.9.0.0
-> installed conf-zlib.1
-> installed conf-openbabel.0.1
-> installed conf-rdkit.1
-> installed bitv.2.0
-> installed csexp.1.5.2
-> installed dolog.6.0.0
-> installed camlp-streams.5.0.1
-> retrieved dune-configurator.3.19.1 (cached)
-> retrieved extunix.0.4.4 (cached)
-> installed cpu.2.0.0
-> retrieved lbvs_consent.2.2.0 (https://opam.ocaml.org/cache)
-> retrieved minicli.5.0.2 (cached)
-> retrieved num.1.6 (cached)
-> retrieved ocaml-compiler-libs.v0.17.0 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved parany.14.0.1 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppxlib.0.36.0 (cached)
-> installed minicli.5.0.2
-> installed ppx_derivers.1.2.1
-> retrieved qcheck.0.26 (cached)
-> retrieved sexplib0.v0.17.0 (cached)
-> retrieved vpt.5.0.0 (cached)
-> installed parany.14.0.1
-> installed qcheck.0.26
-> installed vpt.5.0.0
-> installed dune-configurator.3.19.1
-> installed sexplib0.v0.17.0
-> installed ocaml-compiler-libs.v0.17.0
-> installed num.1.6
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed camlzip.1.13
-> installed batteries.3.9.0
-> installed cpm.12.2.0
-> installed ppxlib.0.36.0
-> installed extunix.0.4.4
-> installed dokeysto.4.0.1
-> installed lbvs_consent.2.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-07-08 20:26.28 ---> saved as "5db879117cb7a08000699532f9b0b7ecfce53adeb3384308b34b4c069ab3e0f0"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test lbvs_consent.2.2.0) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile lbvs_consent 2.2.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved lbvs_consent.2.2.0 (https://opam.ocaml.org/cache)
-> removed lbvs_consent.2.2.0
-> installed lbvs_consent.2.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-07-08 20:26.39 ---> saved as "a2a3855fd20ea51f446618dcef1316ca3f07a3491f506fab93d39e17d297a6aa"
/home/opam: (run (shell "opam reinstall --with-test --verbose lbvs_consent.2.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-12\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'lbvs_consent.2.2.0' && partial_fails=\"$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 lbvs_consent 2.2.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [lbvs_consent.2.2.0: extract]
-> retrieved lbvs_consent.2.2.0 (cached)
[lbvs_consent: patch] applying makefile.patch
Processing 2/4: [lbvs_consent: patch]
Processing 2/4: [lbvs_consent: make obmaccs]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "make" "obmaccs" (CWD=/home/opam/.opam/5.3/.opam-switch/build/lbvs_consent.2.2.0)
- cd src; make
- make[1]: Entering directory '/home/opam/.opam/5.3/.opam-switch/build/lbvs_consent.2.2.0/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++/12/bits/stl_tree.h:65,
- from /usr/include/c++/12/map:60,
- from /usr/include/openbabel3/openbabel/fingerprint.h:23:
- /usr/include/c++/12/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/5.3/.opam-switch/build/lbvs_consent.2.2.0/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/5.3/.opam-switch/build/lbvs_consent.2.2.0)
-> compiled lbvs_consent.2.2.0
-> removed lbvs_consent.2.2.0
Processing 4/4: [lbvs_consent: cp]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "install" "cp" "bin/lbvs_consent_ecfp4.py" "/home/opam/.opam/5.3/bin/lbvs_consent_ecfp4.py" (CWD=/home/opam/.opam/5.3/.opam-switch/build/lbvs_consent.2.2.0)
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "install" "cp" "src/lbvs_consent_ob_maccs" "/home/opam/.opam/5.3/bin/lbvs_consent_ob_maccs" (CWD=/home/opam/.opam/5.3/.opam-switch/build/lbvs_consent.2.2.0)
-> installed lbvs_consent.2.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-07-08 20:26.48 ---> saved as "a575a85fade61d9fed4b27f1a7477e66519a5fd896f23f5227dc764cc6a132ea"
Job succeeded
2025-07-08 20:26.53: Job succeeded