- github
- ocaml
- opam-repository
- 0e6673
- compilers,5.4,menhirLib.20260203,revdeps,biotk.0.3
(not at the head of any monitored branch or PR)
2026-02-03 17:05.55: New job: test biotk.0.3 with menhirLib.20260203, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29331/head (0e6673ac97ae0f63da331269732670199dbab85e)
on debian-13-ocaml-5.4/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29331/head" && git reset --hard 0e6673ac
git fetch origin master
git merge --no-edit 01e12bc089eafb9e81d496cb6a8286b7a4d19aa2
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-5.4@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn menhirLib.20260203 20260203
RUN opam reinstall menhirLib.20260203; \
res=$?; \
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 "$pkg" != 'menhirLib.20260203' && partial_fails="$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: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-02-03 17:05.55: Using cache hint "ocaml/opam:debian-13-ocaml-5.4@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30-menhirLib.20260203-biotk.0.3-0e6673ac97ae0f63da331269732670199dbab85e"
2026-02-03 17:05.55: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-5.4@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn menhirLib.20260203 20260203"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall menhirLib.20260203;\
\n res=$?;\
\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 \"$pkg\" != 'menhirLib.20260203' && partial_fails=\"$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"))
)
2026-02-03 17:05.55: Waiting for resource in pool OCluster
2026-02-04 08:24.37: Waiting for worker…
2026-02-04 08:29.54: Got resource from pool OCluster
Building on toxis.caelum.ci.dev
All commits already cached
Updating files: 59% (11568/19338)
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Updating files: 100% (19338/19338), done.
HEAD is now at 01e12bc089 Merge pull request #29329 from vincent-botbol/catala-lsp.1.1.1
Updating 01e12bc089..0e6673ac97
Fast-forward
packages/menhir/menhir.20260203/opam | 32 ++++++++++++++++++++++++++++++
packages/menhirCST/menhirCST.20260203/opam | 30 ++++++++++++++++++++++++++++
packages/menhirGLR/menhirGLR.20260203/opam | 30 ++++++++++++++++++++++++++++
packages/menhirLib/menhirLib.20260203/opam | 31 +++++++++++++++++++++++++++++
packages/menhirSdk/menhirSdk.20260203/opam | 31 +++++++++++++++++++++++++++++
5 files changed, 154 insertions(+)
create mode 100644 packages/menhir/menhir.20260203/opam
create mode 100644 packages/menhirCST/menhirCST.20260203/opam
create mode 100644 packages/menhirGLR/menhirGLR.20260203/opam
create mode 100644 packages/menhirLib/menhirLib.20260203/opam
create mode 100644 packages/menhirSdk/menhirSdk.20260203/opam
(from ocaml/opam:debian-13-ocaml-5.4@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30)
Unable to find image 'ocaml/opam:debian-13-ocaml-5.4@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30' locally
docker.io/ocaml/opam@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30: Pulling from ocaml/opam
2ca1bfae7ba8: Already exists
e4d8ee4b2a38: Already exists
1d3116276f8e: Already exists
75b74a4d1ac0: Already exists
b6ccadbb02b4: Already exists
8cbf8e460264: Already exists
3315611f76bf: Already exists
504308973b3d: Already exists
d88808e698ae: Already exists
64194555da04: Already exists
bcae218e4dec: Already exists
0678004b187f: Already exists
608c27b1299a: Already exists
2d112e543012: Already exists
7515eb74eee1: Already exists
c57ccaf32dad: Already exists
1ad18dadc94d: Already exists
e597bdf2ce86: Already exists
895287036913: Already exists
669157da4bb1: Already exists
05dacbfea855: Already exists
c07f56eefed9: Already exists
4f4fb700ef54: Already exists
8d67afca45c4: Already exists
eaf56bb8bbcb: Already exists
3eb319385d03: Already exists
7e47d6bb7bc1: Already exists
dc066cdb4877: Already exists
3bd4cfbaf252: Already exists
e1cd4fc2a870: Already exists
c620a639b37a: Already exists
2765b1030b2e: Already exists
4e076d3d484c: Already exists
8fe2e737bcaf: Already exists
29a5f2a84735: Already exists
829846ac5653: Already exists
6cf201ca8833: Already exists
7f975caeb23f: Already exists
de5cd6b102fb: Already exists
8ce740230729: Already exists
29df89ae24a1: Already exists
5f9ff71ade5a: Pulling fs layer
59de40c91df3: Pulling fs layer
7f91a7dda691: Pulling fs layer
b8e10fccad65: Pulling fs layer
ee553cace8aa: Pulling fs layer
aa2d5ced7bb3: Pulling fs layer
5e65ef4e9b3c: Pulling fs layer
b8e10fccad65: Waiting
ee553cace8aa: Waiting
aa2d5ced7bb3: Waiting
59de40c91df3: Verifying Checksum
59de40c91df3: Download complete
5f9ff71ade5a: Verifying Checksum
5f9ff71ade5a: Download complete
7f91a7dda691: Verifying Checksum
7f91a7dda691: Download complete
5f9ff71ade5a: Pull complete
59de40c91df3: Pull complete
ee553cace8aa: Download complete
7f91a7dda691: Pull complete
aa2d5ced7bb3: Verifying Checksum
aa2d5ced7bb3: Download complete
5e65ef4e9b3c: Verifying Checksum
5e65ef4e9b3c: Download complete
b8e10fccad65: Verifying Checksum
b8e10fccad65: Download complete
b8e10fccad65: Pull complete
ee553cace8aa: Pull complete
aa2d5ced7bb3: Pull complete
5e65ef4e9b3c: Pull complete
Digest: sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30
Status: Downloaded newer image for ocaml/opam@sha256:7d9e98c625428dd7d1e2d0b79c4d9482fc6055a5b9600ca51f0c1d06a0604c30
2026-02-04 08:30.01 ---> using "d2c0f8ca6b78229a8736a1c58474579f9e8dd739d9f76726c83ac55b93330b8d" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-02-04 08:30.01 ---> using "69810ef06594f572558730216193bfcbf6d78c5dd6cd0123071b1bf3727eef69" 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
2026-02-04 08:30.01 ---> using "34638688fbfc2a101caaf841695d6077234ab6e7dc6819616e0b36882b03e972" 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 5.4
# invariant ["ocaml-base-compiler" {>= "5.4.0"}]
# compiler-packages ocaml-base-compiler.5.4.0, ocaml-compiler.5.4.0, ocaml-options-vanilla.1
# ocaml:native true
# ocaml:native-tools true
# ocaml:native-dynlink true
# ocaml:stubsdir /home/opam/.opam/5.4/lib/ocaml/stublibs:/home/opam/.opam/5.4/lib/ocaml
# ocaml:preinstalled false
# ocaml:compiler 5.4.0
2026-02-04 08:30.01 ---> using "b8c647d533a6cd445fb2824b35edcf53d5803abb85b8cd96436b13acc7e1f83c" 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/"))
2026-02-04 08:30.01 ---> using "e439e20016b1e5f6d830d3315d5f4c75b40b8430d7ab6b8dd9d289523fbd8158" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-02-04 08:30.03 ---> using "2902ede0320e7695c0eab5dfc90fa1eb05beb4ab1e3aead1e6de4e3f6a97e157" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-02-04 08:30.03 ---> using "edfa3174992b06d7c4dc3dc9d6c48e50f82d267655b177b398950b9fef583581" 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 [98.8 kB]
- Fetched 190 kB in 0s (1334 kB/s)
- Reading package lists...
-
2026-02-04 08:30.03 ---> using "62b46dd8a7b67d1f7ec9a31dc676ee134f8be67f32752ece5e3e9ed73c7b9c57" from cache
/home/opam: (run (shell "opam pin add -k version -yn menhirLib.20260203 20260203"))
menhirLib is now pinned to version 20260203
2026-02-04 08:30.03 ---> using "03834d8938bf2009495f3002891224bf475913662337dffb63af576648b21dbf" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall menhirLib.20260203;\
\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 \"$pkg\" != 'menhirLib.20260203' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
menhirLib.20260203 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 2 packages
- install dune 3.21.0 [required by menhirLib]
- install menhirLib 20260203 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.21.0 (cached)
-> retrieved menhirLib.20260203 (cached)
-> installed dune.3.21.0
-> installed menhirLib.20260203
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-04 08:30.03 ---> using "f2f25bf231821c04f0c381e399ec990638b3925de380847f51e65aa480eb26fe" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall biotk.0.3;\
\n res=$?;\
\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 105 packages
- install angstrom 0.16.1 [required by biotk]
- install angstrom-unix 0.16.1 [required by biotk]
- install base v0.17.3 [required by core, ppx_csv_conv]
- install base_bigstring v0.17.0 [required by core]
- install base_quickcheck v0.17.1 [required by core]
- install bigstringaf 0.10.0 [required by angstrom]
- install bin_prot v0.17.0-1 [required by core]
- install binning 0.0.0 [required by biotk]
- install biotk 0.3
- install camlzip 1.13 [required by biotk]
- install capitalization v0.17.0 [required by ppx_string_conv]
- 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 v0.17.1 [required by biotk]
- install core_kernel v0.17.0 [required by core_unix]
- install core_unix v0.17.1 [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 v0.17.0 [required by ppx_csv_conv]
- install dune-configurator 3.21.0 [required by gsl]
- install expect_test_helpers_core v0.17.0 [required by core_unix]
- install fieldslib v0.17.0 [required by core]
- install fmt 0.11.0 [required by biotk]
- install gel v0.17.0 [required by ppx_diff]
- install gg 1.0.0 [required by vg]
- install gsl 1.25.1 [required by biotk]
- install int_repr v0.17.0 [required by base_bigstring, core_kernel]
- install jane-street-headers v0.17.0 [required by core, core_unix]
- install jst-config v0.17.0 [required by core, core_unix]
- install num 1.6 [required by csvfields]
- install ocaml-compiler-libs v0.17.0 [required by ppxlib]
- install ocaml-syntax-shims 1.0.0 [required by angstrom]
- install ocaml_intrinsics_kernel v0.17.1 [required by base]
- 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 v0.17.0 [required by sexplib]
- install ppx_assert v0.17.0 [required by core]
- install ppx_base v0.17.0 [required by core]
- install ppx_bench v0.17.1 [required by ppx_jane]
- install ppx_bin_prot v0.17.1 [required by ppx_jane]
- install ppx_cold v0.17.0 [required by ppx_base]
- install ppx_compare v0.17.0 [required by ppx_diff]
- install ppx_conv_func v0.17.0 [required by ppx_csv_conv]
- install ppx_csv_conv v0.17.0 [required by biotk]
- install ppx_custom_printf v0.17.0 [required by ppx_jane]
- install ppx_derivers 1.2.1 [required by ppx_deriving]
- install ppx_deriving 6.1.1 [required by biotk]
- install ppx_diff v0.17.1 [required by core]
- install ppx_disable_unused_warnings v0.17.0 [required by ppx_jane]
- install ppx_enumerate v0.17.0 [required by ppx_diff]
- install ppx_expect v0.17.3 [required by ppx_jane]
- install ppx_fields_conv v0.17.0 [required by ppx_csv_conv]
- install ppx_fixed_literal v0.17.0 [required by ppx_jane]
- install ppx_globalize v0.17.2 [required by ppx_base]
- install ppx_hash v0.17.0 [required by core]
- install ppx_here v0.17.0 [required by ppx_jane]
- install ppx_ignore_instrumentation v0.17.0 [required by ppx_jane]
- install ppx_inline_test v0.17.1 [required by core]
- install ppx_jane v0.17.0 [required by core, core_unix]
- install ppx_let v0.17.1 [required by ppx_jane]
- install ppx_log v0.17.0 [required by ppx_jane]
- install ppx_module_timer v0.17.0 [required by ppx_jane]
- install ppx_optcomp v0.17.1 [required by core, core_unix]
- install ppx_optional v0.17.0 [required by ppx_jane]
- install ppx_pipebang v0.17.0 [required by ppx_jane]
- install ppx_sexp_conv v0.17.1 [required by core]
- install ppx_sexp_message v0.17.0 [required by core]
- install ppx_sexp_value v0.17.0 [required by ppx_jane]
- install ppx_stable v0.17.1 [required by ppx_jane]
- install ppx_stable_witness v0.17.0 [required by ppx_jane]
- install ppx_string v0.17.0 [required by ppx_jane]
- install ppx_string_conv v0.17.0 [required by ppx_jane]
- install ppx_tydi v0.17.1 [required by ppx_jane]
- install ppx_typerep_conv v0.17.1 [required by ppx_jane]
- install ppx_variants_conv v0.17.1 [required by ppx_jane]
- install ppxlib 0.37.0 [required by ppx_csv_conv, ppx_deriving]
- install ppxlib_jane v0.17.4 [required by ppx_diff]
- 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 v0.17.0 [required by expect_test_helpers_core]
- install sexplib v0.17.0 [required by core, core_unix]
- install sexplib0 v0.17.0 [required by base]
- install spawn v0.17.0 [required by core_unix]
- install splittable_random v0.17.0 [required by core]
- install stdio v0.17.0 [required by core]
- install stdlib-shims 0.3.0 [required by ppxlib]
- install stringext 1.6.0 [required by uri]
- install time_now v0.17.0 [required by core]
- install timezone v0.17.0 [required by core_unix]
- install topkg 1.1.1 [required by rresult, fmt, otfm, vg]
- install typerep v0.17.1 [required by core]
- install tyxml 4.6.0 [required by biotk]
- install uopt v0.17.0 [required by core_unix]
- install uri 4.4.0 [required by biotk]
- install uutf 1.0.4 [required by otfm, tyxml]
- install variantslib v0.17.0 [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%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20654 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+deb13u1) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
-> retrieved base.v0.17.3 (cached)
-> retrieved base_bigstring.v0.17.0 (cached)
-> retrieved base_quickcheck.v0.17.1 (cached)
-> retrieved bigstringaf.0.10.0 (cached)
-> retrieved bin_prot.v0.17.0-1 (cached)
-> retrieved binning.0.0.0 (cached)
-> installed binning.0.0.0
-> retrieved biotk.0.3 (cached)
-> retrieved camlzip.1.13 (cached)
-> retrieved capitalization.v0.17.0 (cached)
-> retrieved cmdliner.2.1.0 (cached)
-> retrieved core.v0.17.1 (cached)
-> installed conf-pkg-config.4
-> retrieved core_kernel.v0.17.0 (cached)
-> installed conf-gsl.2
-> retrieved core_unix.v0.17.1 (cached)
-> installed conf-zlib.1
-> retrieved cppo.1.8.0 (cached)
-> retrieved crunch.4.0.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved csvfields.v0.17.0 (cached)
-> installed csexp.1.5.2
-> retrieved dune-configurator.3.21.0 (cached)
-> installed cppo.1.8.0
-> retrieved expect_test_helpers_core.v0.17.0 (cached)
-> retrieved fieldslib.v0.17.0 (cached)
-> retrieved fmt.0.11.0 (cached)
-> retrieved gel.v0.17.0 (cached)
-> retrieved gg.1.0.0 (cached)
-> retrieved gsl.1.25.1 (cached)
-> retrieved int_repr.v0.17.0 (cached)
-> retrieved jane-street-headers.v0.17.0 (cached)
-> retrieved jst-config.v0.17.0 (cached)
-> retrieved num.1.6 (cached)
-> retrieved ocaml-compiler-libs.v0.17.0 (cached)
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocaml_intrinsics_kernel.v0.17.1 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> installed jane-street-headers.v0.17.0
-> retrieved otfm.0.4.0 (cached)
-> retrieved parsexp.v0.17.0 (cached)
-> retrieved ppx_assert.v0.17.0 (cached)
-> retrieved ppx_base.v0.17.0 (cached)
-> retrieved ppx_bench.v0.17.1 (cached)
-> retrieved ppx_bin_prot.v0.17.1 (cached)
-> retrieved ppx_cold.v0.17.0 (cached)
-> retrieved ppx_compare.v0.17.0 (cached)
-> retrieved ppx_conv_func.v0.17.0 (cached)
-> retrieved ppx_csv_conv.v0.17.0 (cached)
-> retrieved ppx_custom_printf.v0.17.0 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppx_deriving.6.1.1 (cached)
-> retrieved ppx_diff.v0.17.1 (cached)
-> retrieved ppx_disable_unused_warnings.v0.17.0 (cached)
-> retrieved ppx_enumerate.v0.17.0 (cached)
-> retrieved ppx_expect.v0.17.3 (cached)
-> retrieved ppx_fields_conv.v0.17.0 (cached)
-> installed ocaml_intrinsics_kernel.v0.17.1
-> installed ppx_derivers.1.2.1
-> retrieved ppx_fixed_literal.v0.17.0 (cached)
-> retrieved ppx_globalize.v0.17.2 (cached)
-> retrieved ppx_hash.v0.17.0 (cached)
-> retrieved ppx_here.v0.17.0 (cached)
-> retrieved ppx_ignore_instrumentation.v0.17.0 (cached)
-> retrieved ppx_inline_test.v0.17.1 (cached)
-> retrieved ppx_jane.v0.17.0 (cached)
-> retrieved ppx_let.v0.17.1 (cached)
-> retrieved ppx_log.v0.17.0 (cached)
-> retrieved ppx_module_timer.v0.17.0 (cached)
-> retrieved ppx_optcomp.v0.17.1 (cached)
-> retrieved ppx_optional.v0.17.0 (cached)
-> retrieved ppx_pipebang.v0.17.0 (cached)
-> retrieved ppx_sexp_conv.v0.17.1 (cached)
-> retrieved ppx_sexp_message.v0.17.0 (cached)
-> retrieved ppx_sexp_value.v0.17.0 (cached)
-> retrieved ppx_stable.v0.17.1 (cached)
-> retrieved ppx_stable_witness.v0.17.0 (cached)
-> retrieved ppx_string.v0.17.0 (cached)
-> retrieved ppx_string_conv.v0.17.0 (cached)
-> retrieved ppx_tydi.v0.17.1 (cached)
-> retrieved ppx_typerep_conv.v0.17.1 (cached)
-> retrieved ppx_variants_conv.v0.17.1 (cached)
-> retrieved ppxlib.0.37.0 (cached)
-> retrieved ppxlib_jane.v0.17.4 (cached)
-> retrieved ptime.1.2.0 (cached)
-> retrieved re.1.14.0 (cached)
-> retrieved result.1.5 (cached)
-> retrieved rresult.0.7.0 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexp_pretty.v0.17.0 (cached)
-> retrieved sexplib.v0.17.0 (cached)
-> retrieved sexplib0.v0.17.0 (cached)
-> retrieved spawn.v0.17.0 (cached)
-> retrieved splittable_random.v0.17.0 (cached)
-> retrieved stdio.v0.17.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved stringext.1.6.0 (cached)
-> retrieved time_now.v0.17.0 (cached)
-> retrieved timezone.v0.17.0 (cached)
-> retrieved topkg.1.1.1 (cached)
-> retrieved typerep.v0.17.1 (cached)
-> retrieved tyxml.4.6.0 (cached)
-> retrieved uopt.v0.17.0 (cached)
-> retrieved uri.4.4.0 (cached)
-> retrieved uutf.1.0.4 (cached)
-> retrieved variantslib.v0.17.0 (cached)
-> installed ocaml-compiler-libs.v0.17.0
-> retrieved vg.0.9.5 (cached)
-> installed result.1.5
-> installed ocaml-syntax-shims.1.0.0
-> installed spawn.v0.17.0
-> installed stringext.1.6.0
-> retrieved zlib.0.8 (cached)
-> installed sexplib0.v0.17.0
-> installed stdlib-shims.0.3.0
-> installed dune-configurator.3.21.0
-> installed zlib.0.8
-> installed cmdliner.2.1.0
-> installed bigstringaf.0.10.0
-> installed num.1.6
-> installed re.1.14.0
-> installed angstrom.0.16.1
-> installed parsexp.v0.17.0
-> installed angstrom-unix.0.16.1
-> installed ocamlfind.1.9.8
-> installed sexplib.v0.17.0
-> installed gsl.1.25.1
-> installed camlzip.1.13
-> installed uri.4.4.0
-> installed ocamlbuild.0.16.1
-> installed base.v0.17.3
-> installed variantslib.v0.17.0
-> installed fieldslib.v0.17.0
-> installed stdio.v0.17.0
-> installed typerep.v0.17.1
-> 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 gg.1.0.0
-> installed crunch.4.0.0
-> installed otfm.0.4.0
-> installed tyxml.4.6.0
-> installed vg.0.9.5
-> installed ppxlib.0.37.0
-> installed ppx_tydi.v0.17.1
-> installed ppx_cold.v0.17.0
-> installed ppx_optcomp.v0.17.1
-> installed ppx_variants_conv.v0.17.1
-> installed ppx_here.v0.17.0
-> installed ppx_disable_unused_warnings.v0.17.0
-> installed ppx_pipebang.v0.17.0
-> installed ppxlib_jane.v0.17.4
-> installed ppx_stable_witness.v0.17.0
-> installed ppx_typerep_conv.v0.17.1
-> installed ppx_ignore_instrumentation.v0.17.0
-> installed ppx_conv_func.v0.17.0
-> installed ppx_stable.v0.17.1
-> installed ppx_fields_conv.v0.17.0
-> installed ppx_fixed_literal.v0.17.0
-> installed ppx_deriving.6.1.1
-> installed ppx_enumerate.v0.17.0
-> installed ppx_globalize.v0.17.2
-> installed ppx_compare.v0.17.0
-> installed ppx_optional.v0.17.0
-> installed ppx_let.v0.17.1
-> installed ppx_sexp_conv.v0.17.1
-> installed ppx_hash.v0.17.0
-> installed ppx_assert.v0.17.0
-> installed ppx_sexp_message.v0.17.0
-> installed ppx_sexp_value.v0.17.0
-> installed ppx_base.v0.17.0
-> installed ppx_custom_printf.v0.17.0
-> installed capitalization.v0.17.0
-> installed jst-config.v0.17.0
-> installed sexp_pretty.v0.17.0
-> installed ppx_string.v0.17.0
-> installed bin_prot.v0.17.0-1
-> installed time_now.v0.17.0
-> installed ppx_bin_prot.v0.17.1
-> installed ppx_string_conv.v0.17.0
-> installed ppx_module_timer.v0.17.0
-> installed ppx_inline_test.v0.17.1
-> installed ppx_bench.v0.17.1
-> installed ppx_expect.v0.17.3
-> installed splittable_random.v0.17.0
-> installed base_quickcheck.v0.17.1
-> installed ppx_log.v0.17.0
-> installed ppx_jane.v0.17.0
-> installed uopt.v0.17.0
-> installed gel.v0.17.0
-> installed int_repr.v0.17.0
-> installed base_bigstring.v0.17.0
-> installed ppx_diff.v0.17.1
-> installed core.v0.17.1
-> installed csvfields.v0.17.0
-> installed timezone.v0.17.0
-> installed expect_test_helpers_core.v0.17.0
-> installed ppx_csv_conv.v0.17.0
-> installed core_kernel.v0.17.0
-> installed core_unix.v0.17.1
-> installed biotk.0.3
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-04 08:34.59 ---> saved as "2928233bd8f27c42077c83acdc3b18440a5773b697074e1d571b08ca0de9aaa3"
/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 12 packages
- install async v0.17.0 [required by delimited_parsing]
- install async_kernel v0.17.0 [required by async]
- install async_log v0.17.0 [required by async]
- install async_rpc_kernel v0.17.0 [required by async]
- install async_unix v0.17.0 [required by async]
- install core_bench v0.17.0 [required by biotk]
- install core_extended v0.17.0 [required by core_bench]
- install cstruct 6.2.0 [required by async_unix]
- install delimited_parsing v0.17.0 [required by core_bench]
- install protocol_version_header v0.17.0 [required by async_rpc_kernel]
- install record_builder v0.17.0 [required by core_extended]
- install textutils v0.17.0 [required by core_bench]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved async.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved async_kernel.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved async_log.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved async_rpc_kernel.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved async_unix.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved biotk.0.3 (https://opam.ocaml.org/cache)
-> retrieved core_bench.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved core_extended.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved cstruct.6.2.0 (https://opam.ocaml.org/cache)
-> retrieved delimited_parsing.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved protocol_version_header.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved record_builder.v0.17.0 (https://opam.ocaml.org/cache)
-> retrieved textutils.v0.17.0 (https://opam.ocaml.org/cache)
-> installed cstruct.6.2.0
-> installed record_builder.v0.17.0
-> installed protocol_version_header.v0.17.0
-> installed textutils.v0.17.0
-> removed biotk.0.3
-> installed async_kernel.v0.17.0
-> installed core_extended.v0.17.0
-> installed async_rpc_kernel.v0.17.0
-> installed async_unix.v0.17.0
-> installed async_log.v0.17.0
-> installed async.v0.17.0
-> installed delimited_parsing.v0.17.0
-> installed core_bench.v0.17.0
-> installed biotk.0.3
Done.
# To update the current shell environment, run: eval $(opam env)
2026-02-04 08:37.02 ---> saved as "461c2a1409e389829f4e2b71275345f09874e14b52812cc13a85732eedb299ac"
/home/opam: (run (shell "opam reinstall --with-test --verbose biotk.0.3;\
\n res=$?;\
\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" "71" "@install" "@runtest" (CWD=/home/opam/.opam/5.4/.opam-switch/build/biotk.0.3)
- (cd _build/default/lib/croquis && /home/opam/.opam/5.4/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 -fPIC -pthread -D_FILE_OFFSET_BITS=64 -Wall -fdiagnostics-color=always -O3 -g -I /home/opam/.opam/5.4/lib/ocaml -I /home/opam/.opam/5.4/lib/angstrom -I /home/opam/.opam/5.4/lib/angstrom-unix -I /home/opam/.opam/5.4/lib/base -I /home/opam/.opam/5.4/lib/base/base_internalhash_types -I /home/opam/.opam/5.4/lib/base/md5 -I /home/opam/.opam/5.4/lib/base/shadow_stdlib -I /home/opam/.opam/5.4/lib/base_bigstring -I /home/opam/.opam/5.4/lib/base_quickcheck -I /home/opam/.opam/5.4/lib/base_quickcheck/ppx_quickcheck/runtime -I /home/opam/.opam/5.4/lib/bigstringaf -I /home/opam/.opam/5.4/lib/bin_prot -I /home/opam/.opam/5.4/lib/bin_prot/shape -I /home/opam/.opam/5.4/lib/binning -I /home/opam/.opam/5.4/lib/core -I /home/opam/.opam/5.4/lib/core/base_for_tests -I /home/opam/.opam/5.4/lib/core/command -I /home/opam/.opam/5.4/lib/core/filename_base -I /home/opam/.opam/5.4/lib/core/heap_block -I /home/opam/.opam/5.4/lib/core/univ_map -I /home/opam/.opam/5.4/lib/core/validate -I /home/opam/.opam/5.4/lib/core_kernel -I /home/opam/.opam/5.4/lib/core_kernel/binary_packing -I /home/opam/.opam/5.4/lib/core_kernel/caml_threads -I /home/opam/.opam/5.4/lib/core_kernel/caml_unix -I /home/opam/.opam/5.4/lib/core_kernel/flags -I /home/opam/.opam/5.4/lib/core_unix -I /home/opam/.opam/5.4/lib/core_unix/error_checking_mutex -I /home/opam/.opam/5.4/lib/core_unix/signal_unix -I /home/opam/.opam/5.4/lib/csvfields -I /home/opam/.opam/5.4/lib/csvfields/csvlib -I /home/opam/.opam/5.4/lib/csvfields/xml-light -I /home/opam/.opam/5.4/lib/fieldslib -I /home/opam/.opam/5.4/lib/fmt -I /home/opam/.opam/5.4/lib/gel -I /home/opam/.opam/5.4/lib/gg -I /home/opam/.opam/5.4/lib/gsl -I /home/opam/.opam/5.4/lib/int_repr -I /home/opam/.opam/5.4/lib/jane-street-headers -I /home/opam/.opam/5.4/lib/num -I /home/opam/.opam/5.4/lib/ocaml/threads -I /home/opam/.opam/5.4/lib/ocaml/unix -I /home/opam/.opam/5.4/lib/ocaml_intrinsics_kernel -I /home/opam/.opam/5.4/lib/otfm -I /home/opam/.opam/5.4/lib/parsexp -I /home/opam/.opam/5.4/lib/ppx_assert/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_bench/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_compare/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_deriving/runtime -I /home/opam/.opam/5.4/lib/ppx_diff/diffable -I /home/opam/.opam/5.4/lib/ppx_diff/diffable_cinaps -I /home/opam/.opam/5.4/lib/ppx_enumerate/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_expect/config -I /home/opam/.opam/5.4/lib/ppx_expect/config_types -I /home/opam/.opam/5.4/lib/ppx_expect/make_corrected_file -I /home/opam/.opam/5.4/lib/ppx_expect/runtime -I /home/opam/.opam/5.4/lib/ppx_hash/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_here/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_inline_test/config -I /home/opam/.opam/5.4/lib/ppx_inline_test/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_log/syntax -I /home/opam/.opam/5.4/lib/ppx_log/types -I /home/opam/.opam/5.4/lib/ppx_module_timer/runtime -I /home/opam/.opam/5.4/lib/ppx_sexp_conv/runtime-lib -I /home/opam/.opam/5.4/lib/ppx_stable_witness/runtime -I /home/opam/.opam/5.4/lib/ppx_stable_witness/stable_witness -I /home/opam/.opam/5.4/lib/ppx_string/runtime -I /home/opam/.opam/5.4/lib/ppxlib/print_diff -I /home/opam/.opam/5.4/lib/re -I /home/opam/.opam/5.4/lib/rresult -I /home/opam/.opam/5.4/lib/seq -I /home/opam/.opam/5.4/lib/sexplib -I /home/opam/.opam/5.4/lib/sexplib/unix -I /home/opam/.opam/5.4/lib/sexplib0 -I /home/opam/.opam/5.4/lib/spawn -I /home/opam/.opam/5.4/lib/splittable_random -I /home/opam/.opam/5.4/lib/stdio -I /home/opam/.opam/5.4/lib/stringext -I /home/opam/.opam/5.4/lib/time_now -I /home/opam/.opam/5.4/lib/typerep -I /home/opam/.opam/5.4/lib/tyxml -I /home/opam/.opam/5.4/lib/tyxml/functor -I /home/opam/.opam/5.4/lib/uri -I /home/opam/.opam/5.4/lib/uutf -I /home/opam/.opam/5.4/lib/variantslib -I /home/opam/.opam/5.4/lib/vg -I /home/opam/.opam/5.4/lib/vg/pdf -I /home/opam/.opam/5.4/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/5.4/lib/ocaml/caml/mlvalues.h:352:36: warning: array subscript has type 'char' [-Wchar-subscripts]
- 352 | #define Byte(x, i) (((char *) (x)) [i]) /* Also an l-value. */
- | ~~~~~~~~~~~~~~~~^~~~
- /home/opam/.opam/5.4/lib/ocaml/caml/mlvalues.h:376:37: note: in definition of macro 'Double_val'
- 376 | #define Double_val(v) (* (double *)(v))
- | ^
- /home/opam/.opam/5.4/lib/ocaml/caml/mlvalues.h:410:29: note: in expansion of macro 'Double_flat_field'
- 410 | #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/5.4/lib/ocaml/caml/mlvalues.h:352:36: warning: array subscript has type 'char' [-Wchar-subscripts]
- 352 | #define Byte(x, i) (((char *) (x)) [i]) /* Also an l-value. */
- | ~~~~~~~~~~~~~~~~^~~~
- /home/opam/.opam/5.4/lib/ocaml/caml/mlvalues.h:376:37: note: in definition of macro 'Double_val'
- 376 | #define Double_val(v) (* (double *)(v))
- | ^
- /home/opam/.opam/5.4/lib/ocaml/caml/mlvalues.h:410:29: note: in expansion of macro 'Double_flat_field'
- 410 | #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)
2026-02-04 08:37.34 ---> saved as "475f60377173b1a3703ac635354f52c4046357d3af966844fa4509a7f613fafa"
Job succeeded
2026-02-04 08:37.41: Job succeeded