Build:
- 0
2026-01-23 16:25.23: New job: test biotk.0.3 with menhirCST.20260122, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29263/head (1b37faa806f25ffae47a4204ac0b15c79fa5a828)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29263/head" && git reset --hard 1b37faa8
git fetch origin master
git merge --no-edit 8e1b9a49e880d409b435a16017fd056e29befb09
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:423b7147c04b7e40a2168c2d5b3c2e77064aa5b144995d90eb305e6eb6874610
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn menhirCST.20260122 20260122
RUN opam reinstall menhirCST.20260122; \
res=$?; \
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 "$pkg" != 'menhirCST.20260122' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall biotk.0.3; \
res=$?; \
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 "$pkg" != 'biotk.0.3' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test biotk.0.3) || true
RUN opam reinstall --with-test --verbose biotk.0.3; \
res=$?; \
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 "$pkg" != 'biotk.0.3' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-01-23 16:25.23: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:423b7147c04b7e40a2168c2d5b3c2e77064aa5b144995d90eb305e6eb6874610-menhirCST.20260122-biotk.0.3-1b37faa806f25ffae47a4204ac0b15c79fa5a828"
2026-01-23 16:25.23: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:423b7147c04b7e40a2168c2d5b3c2e77064aa5b144995d90eb305e6eb6874610)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn menhirCST.20260122 20260122"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall menhirCST.20260122;\
\n res=$?;\
\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 \"$pkg\" != 'menhirCST.20260122' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall biotk.0.3;\
\n res=$?;\
\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 \"$pkg\" != 'biotk.0.3' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test biotk.0.3) || true"))
(run (shell "opam reinstall --with-test --verbose biotk.0.3;\
\n res=$?;\
\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 \"$pkg\" != 'biotk.0.3' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2026-01-23 16:25.23: Waiting for resource in pool OCluster
2026-01-24 11:01.39: Waiting for worker…
2026-01-24 11:08.20: Got resource from pool OCluster
Building on odawa.caelum.ci.dev
All commits already cached
HEAD is now at 8e1b9a49e8 Merge pull request #29269 from mseri/ocurl
Merge made by the 'ort' strategy.
packages/menhir/menhir.20260122/opam | 32 ++++++++++++++++++++++++++++++
packages/menhirCST/menhirCST.20260122/opam | 30 ++++++++++++++++++++++++++++
packages/menhirGLR/menhirGLR.20260122/opam | 30 ++++++++++++++++++++++++++++
packages/menhirLib/menhirLib.20260122/opam | 31 +++++++++++++++++++++++++++++
packages/menhirSdk/menhirSdk.20260122/opam | 31 +++++++++++++++++++++++++++++
5 files changed, 154 insertions(+)
create mode 100644 packages/menhir/menhir.20260122/opam
create mode 100644 packages/menhirCST/menhirCST.20260122/opam
create mode 100644 packages/menhirGLR/menhirGLR.20260122/opam
create mode 100644 packages/menhirLib/menhirLib.20260122/opam
create mode 100644 packages/menhirSdk/menhirSdk.20260122/opam
(from ocaml/opam:debian-13-ocaml-4.14@sha256:423b7147c04b7e40a2168c2d5b3c2e77064aa5b144995d90eb305e6eb6874610)
2026-01-24 11:17.51 ---> using "af1ebcbd2c0e8a2a9bd41972ff6b1f2b27bf9dd52d9b45e003eb0eaad274be03" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-01-24 11:17.51 ---> using "0b1605df1edd48befa60e43e28089d53de6288a60ab121fcfb5f9e2f9ffa99b9" from cache
/home/opam: (run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
Configuring from /home/opam/.opamrc-sandbox, then /home/opam/.opamrc, and finally from built-in defaults.
Checking for available remotes: rsync and local, git.
- you won't be able to use mercurial repositories unless you install the hg command on your system.
- you won't be able to use darcs repositories unless you install the darcs command on your system.
This version of opam requires an update to the layout of /home/opam/.opam from version 2.0 to version 2.2, which can't be reverted.
You may want to back it up before going further.
Continue? [Y/n] y
[NOTE] The 'jobs' option was reset, its value was 71 and its new value will vary according to the current number of cores on your machine. You can restore the fixed value using:
opam option jobs=71 --global
Format upgrade done.
<><> Updating repositories ><><><><><><><><><><><><><><><><><><><><><><><><><><>
[default] Initialised
2026-01-24 11:17.51 ---> using "0e536f61c2590e1a9131e4e3e33fd4f3ee72adbf5f314ed8459ef4692f4cb78a" from cache
/home/opam: (run (shell "opam option solver=builtin-0install && opam config report"))
Set to 'builtin-0install' the field solver in global configuration
# opam config report
# opam-version 2.5.0
# self-upgrade no
# system arch=x86_64 os=linux os-distribution=debian os-version=13
# solver builtin-0install
# install-criteria -changed,-count[avoid-version,solution]
# upgrade-criteria -count[avoid-version,solution]
# jobs 255
# repositories 1 (version-controlled)
# pinned 1 (version)
# current-switch 4.14
# invariant ["ocaml-base-compiler" {= "4.14.2"}]
# compiler-packages ocaml-base-compiler.4.14.2, ocaml-options-vanilla.1
# ocaml:native true
# ocaml:native-tools true
# ocaml:native-dynlink true
# ocaml:stubsdir /home/opam/.opam/4.14/lib/ocaml/stublibs:/home/opam/.opam/4.14/lib/ocaml
# ocaml:preinstalled false
# ocaml:compiler 4.14.2
2026-01-24 11:17.51 ---> using "7cc9884256c58e23e28c1fb52f1e0590db522ddca2def346a30d00cabed784f8" 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/"))
2026-01-24 11:17.51 ---> using "c6b197fb983b7c94be824da0b3230330cdb51a6a02ab45dc477f1716c05485d0" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-01-24 11:17.52 ---> using "de85270fc9919443df1ad0f37607458d0cc4b2ad1937c3250b49b6f24dbfe19f" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-01-24 11:17.52 ---> using "8793726468c55dd7a0801966d69b32171591c6d32174d5f305a408d7f7e0ef8a" from cache
/home/opam: (run (network host)
(shell "opam update --depexts || true"))
+ /usr/bin/sudo "apt-get" "update"
- Get:1 http://deb.debian.org/debian trixie InRelease [140 kB]
- 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 trixie/main amd64 Packages [9670 kB]
- Get:5 http://deb.debian.org/debian-security trixie-security/main amd64 Packages [97.9 kB]
- Fetched 9999 kB in 1s (11.1 MB/s)
- Reading package lists...
-
2026-01-24 11:17.52 ---> using "c87d17d9c10004cb7c14063ec8dde828d77cf7182f78248152f69e20f2068a70" from cache
/home/opam: (run (shell "opam pin add -k version -yn menhirCST.20260122 20260122"))
menhirCST is now pinned to version 20260122
2026-01-24 11:17.52 ---> using "6adb04c19be8a7addf5214b883a53bfd7504efb87f709deaf29d0f434d920f04" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall menhirCST.20260122;\
\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 \"$pkg\" != 'menhirCST.20260122' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
menhirCST.20260122 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 2 packages
- install dune 3.21.0 [required by menhirCST]
- install menhirCST 20260122 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.21.0 (cached)
-> retrieved menhirCST.20260122 (cached)
-> installed dune.3.21.0
-> installed menhirCST.20260122
Done.
# To update the current shell environment, run: eval $(opam env)
2026-01-24 11:17.52 ---> using "1e2b01cb8b51eff91643c34f2fd68775c9ea898dfca7d9892a6468afe26622b7" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall biotk.0.3;\
\n res=$?;\
\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 \"$pkg\" != 'biotk.0.3' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
biotk.0.3 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 99 packages
- install angstrom 0.16.1 [required by biotk]
- install angstrom-unix 0.16.1 [required by biotk]
- install base v0.16.4 [required by core, ppx_csv_conv]
- install base_bigstring v0.16.0 [required by core]
- install base_quickcheck v0.16.0 [required by core]
- install bigstringaf 0.10.0 [required by angstrom]
- install bin_prot v0.16.0 [required by core]
- install binning 0.0.0 [required by biotk]
- install biotk 0.3
- install camlzip 1.13 [required by biotk]
- install cmdliner 2.1.0 [required by crunch, fmt]
- install conf-gsl 2 [required by gsl]
- install conf-pkg-config 4 [required by gsl]
- install conf-zlib 1 [required by camlzip, zlib]
- install core v0.16.2 [required by biotk]
- install core_kernel v0.16.0 [required by core_unix]
- install core_unix v0.16.0 [required by biotk]
- install cppo 1.8.0 [required by ppx_deriving]
- install crunch 4.0.0 [required by biotk]
- install csexp 1.5.2 [required by dune-configurator]
- install csvfields v0.16.0 [required by ppx_csv_conv]
- install dune-configurator 3.21.0 [required by gsl]
- install expect_test_helpers_core v0.16.0 [required by core_unix]
- install fieldslib v0.16.0 [required by core]
- install fmt 0.11.0 [required by biotk]
- install gg 1.0.0 [required by vg]
- install gsl 1.25.1 [required by biotk]
- install int_repr v0.16.0 [required by base_bigstring, core_kernel]
- install jane-street-headers v0.16.0 [required by core, core_unix]
- install jst-config v0.16.0 [required by core, core_unix]
- install num 1.6 [required by csvfields]
- install ocaml-compiler-libs v0.12.4 [required by ppxlib]
- install ocaml-syntax-shims 1.0.0 [required by angstrom]
- install ocaml_intrinsics v0.16.2 [required by core_unix]
- install ocamlbuild 0.16.1 [required by rresult, fmt, otfm, vg]
- install ocamlfind 1.9.8 [required by rresult, otfm, camlzip, etc.]
- install otfm 0.4.0 [required by biotk]
- install parsexp v0.16.0 [required by sexplib]
- install ppx_assert v0.16.0 [required by core]
- install ppx_base v0.16.0 [required by core]
- install ppx_bench v0.16.0 [required by ppx_jane]
- install ppx_bin_prot v0.16.0 [required by ppx_jane]
- install ppx_cold v0.16.0 [required by ppx_base]
- install ppx_compare v0.16.0 [required by ppx_base, bin_prot]
- install ppx_conv_func v0.16.0 [required by ppx_csv_conv]
- install ppx_csv_conv v0.16.0 [required by biotk]
- install ppx_custom_printf v0.16.0 [required by ppx_jane]
- install ppx_derivers 1.2.1 [required by ppx_deriving]
- install ppx_deriving 6.0.3 [required by biotk]
- install ppx_disable_unused_warnings v0.16.0 [required by ppx_jane]
- install ppx_enumerate v0.16.0 [required by ppx_base]
- install ppx_expect v0.16.2 [required by ppx_jane]
- install ppx_fields_conv v0.16.0 [required by ppx_csv_conv]
- install ppx_fixed_literal v0.16.0 [required by ppx_jane]
- install ppx_globalize v0.16.0 [required by ppx_base]
- install ppx_hash v0.16.0 [required by core]
- install ppx_here v0.16.0 [required by ppx_jane]
- install ppx_ignore_instrumentation v0.16.0 [required by ppx_jane]
- install ppx_inline_test v0.16.1 [required by core]
- install ppx_jane v0.16.0 [required by core, core_unix]
- install ppx_let v0.16.0 [required by ppx_jane]
- install ppx_log v0.16.0 [required by ppx_jane]
- install ppx_module_timer v0.16.0 [required by ppx_jane]
- install ppx_optcomp v0.16.0 [required by core, core_unix]
- install ppx_optional v0.16.0 [required by ppx_jane]
- install ppx_pipebang v0.16.0 [required by ppx_jane]
- install ppx_sexp_conv v0.16.0 [required by core]
- install ppx_sexp_message v0.16.0 [required by core]
- install ppx_sexp_value v0.16.0 [required by ppx_jane]
- install ppx_stable v0.16.0 [required by ppx_jane]
- install ppx_stable_witness v0.16.0 [required by ppx_jane]
- install ppx_string v0.16.0 [required by ppx_jane]
- install ppx_tydi v0.16.0 [required by ppx_jane]
- install ppx_typerep_conv v0.16.0 [required by ppx_jane]
- install ppx_variants_conv v0.16.0 [required by ppx_jane]
- install ppxlib 0.35.0 [required by ppx_csv_conv, ppx_deriving]
- install ptime 1.2.0 [required by crunch]
- install re 1.14.0 [required by tyxml]
- install result 1.5 [required by biotk]
- install rresult 0.7.0 [required by biotk]
- install seq base [required by tyxml]
- install sexp_pretty v0.16.0 [required by expect_test_helpers_core]
- install sexplib v0.16.0 [required by core, core_unix]
- install sexplib0 v0.16.0 [required by base]
- install spawn v0.17.0 [required by core_unix]
- install splittable_random v0.16.0 [required by core]
- install stdio v0.16.0 [required by core]
- install stdlib-shims 0.3.0 [required by ppxlib]
- install stringext 1.6.0 [required by uri]
- install time_now v0.16.0 [required by core]
- install timezone v0.16.0 [required by core_unix]
- install topkg 1.1.1 [required by rresult, fmt, otfm, vg]
- install typerep v0.16.0 [required by core]
- install tyxml 4.6.0 [required by biotk]
- install uri 4.4.0 [required by biotk]
- install uutf 1.0.4 [required by otfm, tyxml]
- install variantslib v0.16.0 [required by core]
- install vg 0.9.5 [required by biotk]
- install zlib 0.8 [required by biotk]
The following system packages will first need to be installed:
libgsl-dev 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" "libgsl-dev" "pkg-config" "zlib1g-dev"
- Selecting previously unselected package libgslcblas0:amd64.
- (Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
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(Reading database ... 20622 files and directories currently installed.)
- Preparing to unpack .../0-libgslcblas0_2.8+dfsg-5_amd64.deb ...
- Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ...
- Selecting previously unselected package libgsl28:amd64.
- Preparing to unpack .../1-libgsl28_2.8+dfsg-5_amd64.deb ...
- Unpacking libgsl28:amd64 (2.8+dfsg-5) ...
- Selecting previously unselected package libgsl-dev.
- Preparing to unpack .../2-libgsl-dev_2.8+dfsg-5_amd64.deb ...
- Unpacking libgsl-dev (2.8+dfsg-5) ...
- Selecting previously unselected package libpkgconf3:amd64.
- Preparing to unpack .../3-libpkgconf3_1.8.1-4_amd64.deb ...
- Unpacking libpkgconf3:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkgconf-bin.
- Preparing to unpack .../4-pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../5-pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../6-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 .../7-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 libgslcblas0:amd64 (2.8+dfsg-5) ...
- 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 libgsl28:amd64 (2.8+dfsg-5) ...
- Setting up libgsl-dev (2.8+dfsg-5) ...
- 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) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
-> retrieved base.v0.16.4 (cached)
-> retrieved base_bigstring.v0.16.0 (cached)
-> retrieved base_quickcheck.v0.16.0 (cached)
-> retrieved bigstringaf.0.10.0 (cached)
-> retrieved bin_prot.v0.16.0 (cached)
-> retrieved binning.0.0.0 (cached)
-> retrieved biotk.0.3 (cached)
-> installed binning.0.0.0
-> retrieved camlzip.1.13 (cached)
-> retrieved cmdliner.2.1.0 (cached)
-> retrieved core.v0.16.2 (cached)
-> installed conf-pkg-config.4
-> retrieved core_kernel.v0.16.0 (cached)
-> installed conf-zlib.1
-> installed conf-gsl.2
-> retrieved core_unix.v0.16.0 (cached)
-> retrieved cppo.1.8.0 (cached)
-> retrieved crunch.4.0.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved csvfields.v0.16.0 (cached)
-> installed csexp.1.5.2
-> retrieved dune-configurator.3.21.0 (cached)
-> retrieved expect_test_helpers_core.v0.16.0 (cached)
-> retrieved fieldslib.v0.16.0 (cached)
-> retrieved fmt.0.11.0 (cached)
-> retrieved gg.1.0.0 (cached)
-> retrieved gsl.1.25.1 (cached)
-> retrieved int_repr.v0.16.0 (cached)
-> retrieved jane-street-headers.v0.16.0 (cached)
-> retrieved jst-config.v0.16.0 (cached)
-> retrieved num.1.6 (cached)
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocaml_intrinsics.v0.16.2 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> installed cmdliner.2.1.0
-> installed cppo.1.8.0
-> installed jane-street-headers.v0.16.0
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved otfm.0.4.0 (cached)
-> retrieved parsexp.v0.16.0 (cached)
-> retrieved ppx_assert.v0.16.0 (cached)
-> retrieved ppx_base.v0.16.0 (cached)
-> retrieved ppx_bench.v0.16.0 (cached)
-> retrieved ppx_bin_prot.v0.16.0 (cached)
-> retrieved ppx_cold.v0.16.0 (cached)
-> retrieved ppx_compare.v0.16.0 (cached)
-> retrieved ppx_conv_func.v0.16.0 (cached)
-> retrieved ppx_csv_conv.v0.16.0 (cached)
-> retrieved ppx_custom_printf.v0.16.0 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppx_deriving.6.0.3 (cached)
-> retrieved ppx_disable_unused_warnings.v0.16.0 (cached)
-> retrieved ppx_enumerate.v0.16.0 (cached)
-> retrieved ppx_expect.v0.16.2 (cached)
-> retrieved ppx_fields_conv.v0.16.0 (cached)
-> retrieved ppx_fixed_literal.v0.16.0 (cached)
-> retrieved ppx_globalize.v0.16.0 (cached)
-> retrieved ppx_hash.v0.16.0 (cached)
-> retrieved ppx_here.v0.16.0 (cached)
-> installed ppx_derivers.1.2.1
-> retrieved ppx_ignore_instrumentation.v0.16.0 (cached)
-> retrieved ppx_inline_test.v0.16.1 (cached)
-> retrieved ppx_jane.v0.16.0 (cached)
-> retrieved ppx_let.v0.16.0 (cached)
-> retrieved ppx_log.v0.16.0 (cached)
-> retrieved ppx_module_timer.v0.16.0 (cached)
-> retrieved ppx_optcomp.v0.16.0 (cached)
-> retrieved ppx_optional.v0.16.0 (cached)
-> retrieved ppx_pipebang.v0.16.0 (cached)
-> retrieved ppx_sexp_conv.v0.16.0 (cached)
-> retrieved ppx_sexp_message.v0.16.0 (cached)
-> retrieved ppx_sexp_value.v0.16.0 (cached)
-> retrieved ppx_stable.v0.16.0 (cached)
-> retrieved ppx_stable_witness.v0.16.0 (cached)
-> retrieved ppx_string.v0.16.0 (cached)
-> retrieved ppx_tydi.v0.16.0 (cached)
-> retrieved ppx_typerep_conv.v0.16.0 (cached)
-> retrieved ppx_variants_conv.v0.16.0 (cached)
-> retrieved ppxlib.0.35.0 (cached)
-> installed ocaml-syntax-shims.1.0.0
-> retrieved ptime.1.2.0 (cached)
-> retrieved re.1.14.0 (cached)
-> installed ocaml-compiler-libs.v0.12.4
-> retrieved result.1.5 (cached)
-> retrieved rresult.0.7.0 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexp_pretty.v0.16.0 (cached)
-> retrieved sexplib.v0.16.0 (cached)
-> retrieved sexplib0.v0.16.0 (cached)
-> retrieved spawn.v0.17.0 (cached)
-> retrieved splittable_random.v0.16.0 (cached)
-> retrieved stdio.v0.16.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved stringext.1.6.0 (cached)
-> retrieved time_now.v0.16.0 (cached)
-> retrieved timezone.v0.16.0 (cached)
-> installed dune-configurator.3.21.0
-> retrieved topkg.1.1.1 (cached)
-> installed result.1.5
-> retrieved typerep.v0.16.0 (cached)
-> retrieved tyxml.4.6.0 (cached)
-> installed num.1.6
-> installed stdlib-shims.0.3.0
-> installed stringext.1.6.0
-> retrieved uri.4.4.0 (cached)
-> retrieved uutf.1.0.4 (cached)
-> retrieved variantslib.v0.16.0 (cached)
-> installed spawn.v0.17.0
-> retrieved vg.0.9.5 (cached)
-> retrieved zlib.0.8 (cached)
-> installed sexplib0.v0.16.0
-> installed bigstringaf.0.10.0
-> installed zlib.0.8
-> installed re.1.14.0
-> installed angstrom.0.16.1
-> installed angstrom-unix.0.16.1
-> installed ocaml_intrinsics.v0.16.2
-> installed parsexp.v0.16.0
-> installed ocamlfind.1.9.8
-> installed gsl.1.25.1
-> installed uri.4.4.0
-> installed sexplib.v0.16.0
-> installed camlzip.1.13
-> installed ocamlbuild.0.16.1
-> installed base.v0.16.4
-> installed fieldslib.v0.16.0
-> installed variantslib.v0.16.0
-> installed stdio.v0.16.0
-> installed typerep.v0.16.0
-> installed topkg.1.1.1
-> installed rresult.0.7.0
-> installed uutf.1.0.4
-> installed fmt.0.11.0
-> installed ptime.1.2.0
-> installed crunch.4.0.0
-> installed gg.1.0.0
-> installed otfm.0.4.0
-> installed ppxlib.0.35.0
-> installed tyxml.4.6.0
-> installed vg.0.9.5
-> installed ppx_globalize.v0.16.0
-> installed ppx_optcomp.v0.16.0
-> installed ppx_conv_func.v0.16.0
-> installed ppx_enumerate.v0.16.0
-> installed ppx_cold.v0.16.0
-> installed ppx_disable_unused_warnings.v0.16.0
-> installed ppx_here.v0.16.0
-> installed ppx_compare.v0.16.0
-> installed ppx_tydi.v0.16.0
-> installed ppx_stable_witness.v0.16.0
-> installed ppx_typerep_conv.v0.16.0
-> installed ppx_variants_conv.v0.16.0
-> installed ppx_fields_conv.v0.16.0
-> installed ppx_stable.v0.16.0
-> installed ppx_pipebang.v0.16.0
-> installed ppx_ignore_instrumentation.v0.16.0
-> installed ppx_fixed_literal.v0.16.0
-> installed ppx_optional.v0.16.0
-> installed ppx_sexp_conv.v0.16.0
-> installed ppx_deriving.6.0.3
-> installed ppx_let.v0.16.0
-> installed ppx_hash.v0.16.0
-> installed ppx_assert.v0.16.0
-> installed ppx_sexp_value.v0.16.0
-> installed ppx_sexp_message.v0.16.0
-> installed ppx_custom_printf.v0.16.0
-> installed ppx_base.v0.16.0
-> installed jst-config.v0.16.0
-> installed ppx_log.v0.16.0
-> installed sexp_pretty.v0.16.0
-> installed ppx_string.v0.16.0
-> installed bin_prot.v0.16.0
-> installed time_now.v0.16.0
-> installed ppx_bin_prot.v0.16.0
-> installed ppx_module_timer.v0.16.0
-> installed ppx_inline_test.v0.16.1
-> installed ppx_bench.v0.16.0
-> installed ppx_expect.v0.16.2
-> installed splittable_random.v0.16.0
-> installed base_quickcheck.v0.16.0
-> installed ppx_jane.v0.16.0
-> installed int_repr.v0.16.0
-> installed base_bigstring.v0.16.0
-> installed core.v0.16.2
-> installed csvfields.v0.16.0
-> installed timezone.v0.16.0
-> installed expect_test_helpers_core.v0.16.0
-> installed ppx_csv_conv.v0.16.0
-> installed core_kernel.v0.16.0
-> installed core_unix.v0.16.0
-> installed biotk.0.3
Done.
# To update the current shell environment, run: eval $(opam env)
2026-01-24 11:19.11 ---> saved as "43f5fcc4b18f063f8b320b9534a930dd357de0819a95c2ccd121895f7018e75b"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test biotk.0.3) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile biotk 0.3
=== install 3 packages
- install core_bench v0.16.0 [required by biotk]
- install textutils v0.16.0 [required by core_bench]
- install textutils_kernel v0.16.0 [required by textutils]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved biotk.0.3 (https://opam.ocaml.org/cache)
-> retrieved core_bench.v0.16.0 (https://opam.ocaml.org/cache)
-> retrieved textutils.v0.16.0 (https://opam.ocaml.org/cache)
-> retrieved textutils_kernel.v0.16.0 (https://opam.ocaml.org/cache)
-> removed biotk.0.3
-> installed textutils_kernel.v0.16.0
-> installed textutils.v0.16.0
-> installed core_bench.v0.16.0
-> installed biotk.0.3
Done.
# To update the current shell environment, run: eval $(opam env)
2026-01-24 11:19.31 ---> saved as "ba926809fb175b933ecfd8bef3c0d7fc6a0eafb555f3588efa921f81acea2887"
/home/opam: (run (shell "opam reinstall --with-test --verbose biotk.0.3;\
\n res=$?;\
\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 \"$pkg\" != 'biotk.0.3' && partial_fails=\"$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 biotk 0.3
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [biotk.0.3: extract]
-> retrieved biotk.0.3 (cached)
Processing 2/4: [biotk: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "biotk" "-j" "255" "@install" "@runtest" (CWD=/home/opam/.opam/4.14/.opam-switch/build/biotk.0.3)
- (cd _build/default/lib/croquis && /home/opam/.opam/4.14/bin/ocaml-crunch --mode plain ../../fonts --output font_data.ml)
- Generating font_data.ml
- Skipping generation of .mli
- (cd _build/default/lib && /usr/bin/gcc -O2 -fno-strict-aliasing -fwrapv -pthread -fPIC -D_FILE_OFFSET_BITS=64 -Wall -fdiagnostics-color=always -O3 -g -I /home/opam/.opam/4.14/lib/ocaml -I /home/opam/.opam/4.14/lib/angstrom -I /home/opam/.opam/4.14/lib/angstrom-unix -I /home/opam/.opam/4.14/lib/base -I /home/opam/.opam/4.14/lib/base/base_internalhash_types -I /home/opam/.opam/4.14/lib/base/caml -I /home/opam/.opam/4.14/lib/base/md5 -I /home/opam/.opam/4.14/lib/base/shadow_stdlib -I /home/opam/.opam/4.14/lib/base_bigstring -I /home/opam/.opam/4.14/lib/base_quickcheck -I /home/opam/.opam/4.14/lib/base_quickcheck/ppx_quickcheck/runtime -I /home/opam/.opam/4.14/lib/bigstringaf -I /home/opam/.opam/4.14/lib/bin_prot -I /home/opam/.opam/4.14/lib/bin_prot/shape -I /home/opam/.opam/4.14/lib/binning -I /home/opam/.opam/4.14/lib/core -I /home/opam/.opam/4.14/lib/core/base_for_tests -I /home/opam/.opam/4.14/lib/core/command -I /home/opam/.opam/4.14/lib/core/filename_base -I /home/opam/.opam/4.14/lib/core/heap_block -I /home/opam/.opam/4.14/lib/core/univ_map -I /home/opam/.opam/4.14/lib/core/validate -I /home/opam/.opam/4.14/lib/core_kernel -I /home/opam/.opam/4.14/lib/core_kernel/binary_packing -I /home/opam/.opam/4.14/lib/core_kernel/caml_threads -I /home/opam/.opam/4.14/lib/core_kernel/caml_unix -I /home/opam/.opam/4.14/lib/core_kernel/flags -I /home/opam/.opam/4.14/lib/core_unix -I /home/opam/.opam/4.14/lib/core_unix/error_checking_mutex -I /home/opam/.opam/4.14/lib/core_unix/signal_unix -I /home/opam/.opam/4.14/lib/csvfields -I /home/opam/.opam/4.14/lib/csvfields/csvlib -I /home/opam/.opam/4.14/lib/csvfields/xml-light -I /home/opam/.opam/4.14/lib/fieldslib -I /home/opam/.opam/4.14/lib/fmt -I /home/opam/.opam/4.14/lib/gg -I /home/opam/.opam/4.14/lib/gsl -I /home/opam/.opam/4.14/lib/int_repr -I /home/opam/.opam/4.14/lib/jane-street-headers -I /home/opam/.opam/4.14/lib/num -I /home/opam/.opam/4.14/lib/ocaml/threads -I /home/opam/.opam/4.14/lib/otfm -I /home/opam/.opam/4.14/lib/parsexp -I /home/opam/.opam/4.14/lib/ppx_assert/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_bench/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_compare/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_deriving/runtime -I /home/opam/.opam/4.14/lib/ppx_enumerate/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_expect/collector -I /home/opam/.opam/4.14/lib/ppx_expect/common -I /home/opam/.opam/4.14/lib/ppx_expect/config -I /home/opam/.opam/4.14/lib/ppx_expect/config_types -I /home/opam/.opam/4.14/lib/ppx_hash/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_here/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_inline_test/config -I /home/opam/.opam/4.14/lib/ppx_inline_test/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_log/types -I /home/opam/.opam/4.14/lib/ppx_module_timer/runtime -I /home/opam/.opam/4.14/lib/ppx_sexp_conv/runtime-lib -I /home/opam/.opam/4.14/lib/ppx_stable_witness/runtime -I /home/opam/.opam/4.14/lib/ppx_stable_witness/stable_witness -I /home/opam/.opam/4.14/lib/re -I /home/opam/.opam/4.14/lib/rresult -I /home/opam/.opam/4.14/lib/seq -I /home/opam/.opam/4.14/lib/sexplib -I /home/opam/.opam/4.14/lib/sexplib/unix -I /home/opam/.opam/4.14/lib/sexplib0 -I /home/opam/.opam/4.14/lib/spawn -I /home/opam/.opam/4.14/lib/splittable_random -I /home/opam/.opam/4.14/lib/stdio -I /home/opam/.opam/4.14/lib/stringext -I /home/opam/.opam/4.14/lib/time_now -I /home/opam/.opam/4.14/lib/typerep -I /home/opam/.opam/4.14/lib/tyxml -I /home/opam/.opam/4.14/lib/tyxml/functor -I /home/opam/.opam/4.14/lib/uri -I /home/opam/.opam/4.14/lib/uutf -I /home/opam/.opam/4.14/lib/variantslib -I /home/opam/.opam/4.14/lib/vg -I /home/opam/.opam/4.14/lib/vg/pdf -I /home/opam/.opam/4.14/lib/zip -I croquis -o pwm_stub.o -c pwm_stub.c)
- In file included from pwm_stub.c:3:
- pwm_stub.c: In function 'biotk_pwm_scan':
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:277:36: warning: array subscript has type 'char' [-Wchar-subscripts]
- 277 | #define Byte(x, i) (((char *) (x)) [i]) /* Also an l-value. */
- | ~~~~~~~~~~~~~~~~^~~~
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:303:37: note: in definition of macro 'Double_val'
- 303 | #define Double_val(v) (* (double *)(v))
- | ^
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:337:29: note: in expansion of macro 'Double_flat_field'
- 337 | #define Double_field(v,i) Double_flat_field(v,i)
- | ^~~~~~~~~~~~~~~~~
- pwm_stub.c:32:16: note: in expansion of macro 'Double_field'
- 32 | score += Double_field(Field(mat, j), char_tab[Byte(seq, i + j)]);
- | ^~~~~~~~~~~~
- pwm_stub.c:32:53: note: in expansion of macro 'Byte'
- 32 | score += Double_field(Field(mat, j), char_tab[Byte(seq, i + j)]);
- | ^~~~
- pwm_stub.c: In function 'biotk_opt_pwm_scan':
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:277:36: warning: array subscript has type 'char' [-Wchar-subscripts]
- 277 | #define Byte(x, i) (((char *) (x)) [i]) /* Also an l-value. */
- | ~~~~~~~~~~~~~~~~^~~~
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:303:37: note: in definition of macro 'Double_val'
- 303 | #define Double_val(v) (* (double *)(v))
- | ^
- /home/opam/.opam/4.14/lib/ocaml/caml/mlvalues.h:337:29: note: in expansion of macro 'Double_flat_field'
- 337 | #define Double_field(v,i) Double_flat_field(v,i)
- | ^~~~~~~~~~~~~~~~~
- pwm_stub.c:87:16: note: in expansion of macro 'Double_field'
- 87 | score += Double_field(Field(mat, j), char_tab[Byte(seq, i + j)]);
- | ^~~~~~~~~~~~
- pwm_stub.c:87:53: note: in expansion of macro 'Byte'
- 87 | score += Double_field(Field(mat, j), char_tab[Byte(seq, i + j)]);
- | ^~~~
-> compiled biotk.0.3
-> removed biotk.0.3
-> installed biotk.0.3
Done.
# To update the current shell environment, run: eval $(opam env)
2026-01-24 11:19.41 ---> saved as "20f08837ef5e262c22e10a74f0980d79ab54a1d30c8c3eb3bd3a496867841cb6"
Job succeeded
2026-01-24 11:19.48: Job succeeded