Build:
- 0
2025-09-18 09:51.51: New job: test biotk.0.0.0 with dune.3.12.1, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/28542/head (94ae65678b1f98854907785aa1107fabdeec47d2)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/28542/head" && git reset --hard 94ae6567
git fetch origin master
git merge --no-edit 151ffce963e54519dd5d1280848f631d38db358e
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn dune.3.12.1 3.12.1
RUN opam reinstall dune.3.12.1; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'dune.3.12.1' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall biotk.0.0.0; \
res=$?; \
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-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'biotk.0.0.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test biotk.0.0.0) || true
RUN opam reinstall --with-test --verbose biotk.0.0.0; \
res=$?; \
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-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'biotk.0.0.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2025-09-18 09:51.51: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc-dune.3.12.1-biotk.0.0.0-94ae65678b1f98854907785aa1107fabdeec47d2"
2025-09-18 09:51.51: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn dune.3.12.1 3.12.1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.12.1;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'dune.3.12.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall biotk.0.0.0;\
\n res=$?;\
\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-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'biotk.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test biotk.0.0.0) || true"))
(run (shell "opam reinstall --with-test --verbose biotk.0.0.0;\
\n res=$?;\
\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-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'biotk.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2025-09-18 09:51.51: Waiting for resource in pool OCluster
2025-09-18 17:41.05: Waiting for worker…
2025-09-18 17:43.50: Got resource from pool OCluster
Building on odawa.caelum.ci.dev
All commits already cached
HEAD is now at 151ffce963 Merge pull request #28412 from andersfugmann/release-ocaml-protoc-plugin-6.2.0
Updating 151ffce963..94ae65678b
Fast-forward
packages/dune/dune.3.12.1/opam | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(from ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc)
2025-09-18 17:43.51 ---> using "f2c15438f4e8107ac42e1adfbd29c5c483ff0e5aaf05ff1291b0b30470c339be" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2025-09-18 17:43.51 ---> using "8e4815ff6b482deb2badd55f707e4331a2daf52d1f97e062604f979853124597" 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
2025-09-18 17:43.51 ---> using "0309994c25db3359b71c182dd526d9cd4b87f08f6fd345755107482f61709ee3" 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 2.4.1
# 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
2025-09-18 17:43.51 ---> using "01960dce876bd083c0e115ca8b857f355a6f4a5b1589bc70acef12378d72e36e" 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/"))
2025-09-18 17:43.51 ---> using "88d8ec224acefa159471a25872197bf5efdd28e8b95159888107feac1f31a583" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2025-09-18 17:43.52 ---> using "cb2103c25b21ee4e1c59329d950656d40b52719523d4f917d56f5ec814fa100f" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2025-09-18 17:43.52 ---> using "a05965c65de41c6eff3032a5634279c228b5ac3eb5b903c6c68c60936ca1d1a4" 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 [40.4 kB]
- Fetched 131 kB in 0s (1641 kB/s)
- Reading package lists...
2025-09-18 17:43.52 ---> using "38023c57e0f91a1fd554d35e557178fc24782f93a8ea1da4e25d2c03340933a9" from cache
/home/opam: (run (shell "opam pin add -k version -yn dune.3.12.1 3.12.1"))
dune is now pinned to version 3.12.1
2025-09-18 17:43.52 ---> using "cb7452ac8f079a11102b292cd8b4ab7a95bf7ca7b6ff4bcfee9ec005ec60d9fe" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.12.1;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'dune.3.12.1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
dune.3.12.1 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 1 package
- install dune 3.12.1 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.12.1 (cached)
-> installed dune.3.12.1
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 17:43.52 ---> using "3636cd7fb69dfe196588ca0977383ce2de3c796811a263630e34d36c7ce41c8d" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall biotk.0.0.0;\
\n res=$?;\
\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-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'biotk.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
biotk.0.0.0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 92 packages
- install angstrom 0.16.1 [required by biotk]
- install angstrom-unix 0.16.1 [required by biotk]
- install base v0.14.3 [required by ppx_csv_conv]
- install base-bytes base [required by ocamlnet]
- install base64 3.5.1 [required by biocaml]
- install base_bigstring v0.14.0 [required by core_kernel]
- install base_quickcheck v0.14.1 [required by core_kernel]
- install bigstringaf 0.10.0 [required by angstrom]
- install bin_prot v0.14.1 [required by core_kernel]
- install biocaml 0.11.1 [required by biotk]
- install biotk 0.0.0
- install camlp-streams 5.0.1 [required by cfstream]
- install camlzip 1.13 [required by biocaml, ocamlnet]
- install cfstream 1.3.2 [required by biocaml]
- install conf-m4 1 [required by cfstream]
- install conf-pkg-config 4 [required by conf-zlib]
- install conf-zlib 1 [required by camlzip]
- install core v0.14.1 [required by biotk]
- install core_kernel v0.14.2 [required by biocaml]
- install cppo 1.8.0 [required by ppx_deriving]
- install csexp 1.5.2 [required by dune-configurator]
- install csvfields v0.14.0 [required by ppx_csv_conv]
- install dune-configurator 3.18.2 [required by bigstringaf]
- install fieldslib v0.14.0 [required by core_kernel]
- install fmt 0.11.0 [required by biotk]
- install gg 1.0.0 [required by vg]
- install jane-street-headers v0.14.0 [required by core_kernel]
- install jst-config v0.14.1 [required by core]
- 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 ocamlbuild 0.16.1 [required by otfm, ocamlify, fmt, etc.]
- install ocamlfind 1.9.8 [required by ppx_deriving, ocamlnet, fmt, etc.]
- install ocamlify 0.0.1 [required by biotk]
- install ocamlnet 4.1.9-2 [required by biotk]
- install octavius 1.2.2 [required by ppx_js_style]
- install otfm 0.4.0 [required by biotk]
- install parsexp v0.14.2 [required by sexplib]
- install ppx_assert v0.14.0 [required by core_kernel]
- install ppx_base v0.14.0 [required by core_kernel]
- install ppx_bench v0.14.1 [required by ppx_jane]
- install ppx_bin_prot v0.14.0 [required by ppx_jane]
- install ppx_cold v0.14.0 [required by ppx_base]
- install ppx_compare v0.14.0 [required by biocaml]
- install ppx_conv_func v0.14.0 [required by ppx_csv_conv]
- install ppx_csv_conv v0.14.0 [required by biotk]
- install ppx_custom_printf v0.14.1 [required by ppx_jane]
- install ppx_derivers 1.2.1 [required by ppx_deriving]
- install ppx_deriving 5.2.1 [required by biotk]
- install ppx_enumerate v0.14.0 [required by ppx_base]
- install ppx_expect v0.14.2 [required by ppx_jane]
- install ppx_fields_conv v0.14.2 [required by ppx_csv_conv]
- install ppx_fixed_literal v0.14.0 [required by ppx_jane]
- install ppx_hash v0.14.0 [required by core_kernel]
- install ppx_here v0.14.0 [required by ppx_jane]
- install ppx_inline_test v0.14.1 [required by core_kernel]
- install ppx_jane v0.14.0 [required by core, csvfields]
- install ppx_js_style v0.14.1 [required by ppx_base]
- install ppx_let v0.14.0 [required by ppx_jane]
- install ppx_module_timer v0.14.0 [required by ppx_jane]
- install ppx_optcomp v0.14.3 [required by core_kernel]
- install ppx_optional v0.14.0 [required by ppx_jane]
- install ppx_pipebang v0.14.0 [required by ppx_jane]
- install ppx_sexp_conv v0.14.3 [required by biocaml]
- install ppx_sexp_message v0.14.1 [required by core_kernel]
- install ppx_sexp_value v0.14.0 [required by ppx_jane]
- install ppx_stable v0.14.1 [required by ppx_jane]
- install ppx_string v0.14.1 [required by ppx_jane]
- install ppx_typerep_conv v0.14.2 [required by ppx_jane]
- install ppx_variants_conv v0.14.2 [required by ppx_jane]
- install ppxlib 0.25.1 [required by ppx_csv_conv, ppx_deriving]
- install re 1.13.2 [required by biocaml, tyxml]
- install result 1.5 [required by biotk]
- install rresult 0.7.0 [required by biotk]
- install seq base [required by tyxml]
- install sexplib v0.14.0 [required by biocaml]
- install sexplib0 v0.14.0 [required by base, sexplib]
- install spawn v0.17.0 [required by core]
- install splittable_random v0.14.0 [required by core_kernel]
- install stdio v0.14.0 [required by core_kernel]
- install stdlib-shims 0.3.0 [required by ppxlib]
- install stringext 1.6.0 [required by uri]
- install time_now v0.14.0 [required by core_kernel]
- install timezone v0.14.0 [required by core]
- install topkg 1.1.0 [required by otfm, fmt, vg]
- install typerep v0.14.0 [required by core_kernel]
- install tyxml 4.6.0 [required by biotk]
- install uri 4.4.0 [required by biocaml]
- install uutf 1.0.4 [required by otfm, tyxml]
- install variantslib v0.14.0 [required by core_kernel]
- install vg 0.9.5 [required by biotk]
- install xmlm 1.4.0 [required by biocaml]
The following system packages will first need to be installed:
m4 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" "m4" "pkg-config" "zlib1g-dev"
- Selecting previously unselected package libpkgconf3:amd64.
- (Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20622 files and directories currently installed.)
- Preparing to unpack .../0-libpkgconf3_1.8.1-4_amd64.deb ...
- Unpacking libpkgconf3:amd64 (1.8.1-4) ...
- Selecting previously unselected package m4.
- Preparing to unpack .../1-m4_1.4.19-8_amd64.deb ...
- Unpacking m4 (1.4.19-8) ...
- Selecting previously unselected package pkgconf-bin.
- Preparing to unpack .../2-pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../3-pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../4-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 .../5-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 m4 (1.4.19-8) ...
- Setting up libpkgconf3:amd64 (1.8.1-4) ...
- Setting up pkgconf-bin (1.8.1-4) ...
- Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up pkgconf:amd64 (1.8.1-4) ...
- Setting up pkg-config:amd64 (1.8.1-4) ...
- Processing triggers for libc-bin (2.41-12) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
-> retrieved base.v0.14.3 (cached)
-> retrieved base64.3.5.1 (cached)
-> retrieved base_bigstring.v0.14.0 (cached)
-> retrieved base_quickcheck.v0.14.1 (cached)
-> retrieved bigstringaf.0.10.0 (cached)
-> retrieved bin_prot.v0.14.1 (cached)
-> retrieved biocaml.0.11.1 (cached)
-> retrieved biotk.0.0.0 (cached)
-> retrieved camlp-streams.5.0.1 (cached)
-> retrieved camlzip.1.13 (cached)
-> retrieved cfstream.1.3.2 (cached)
-> retrieved core.v0.14.1 (cached)
-> installed conf-m4.1
-> installed conf-pkg-config.4
-> retrieved core_kernel.v0.14.2 (cached)
-> installed base64.3.5.1
-> installed conf-zlib.1
-> installed camlp-streams.5.0.1
-> retrieved cppo.1.8.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved csvfields.v0.14.0 (cached)
-> installed csexp.1.5.2
-> retrieved dune-configurator.3.18.2 (cached)
-> installed cppo.1.8.0
-> retrieved fieldslib.v0.14.0 (cached)
-> retrieved fmt.0.11.0 (cached)
-> retrieved gg.1.0.0 (cached)
-> retrieved jane-street-headers.v0.14.0 (cached)
-> retrieved jst-config.v0.14.1 (cached)
-> retrieved num.1.6 (cached)
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> installed jane-street-headers.v0.14.0
-> retrieved ocamlify.0.0.1 (cached)
-> retrieved ocamlnet.4.1.9-2 (cached)
-> retrieved octavius.1.2.2 (cached)
-> retrieved otfm.0.4.0 (cached)
-> retrieved parsexp.v0.14.2 (cached)
-> retrieved ppx_assert.v0.14.0 (cached)
-> retrieved ppx_base.v0.14.0 (cached)
-> retrieved ppx_bench.v0.14.1 (cached)
-> retrieved ppx_bin_prot.v0.14.0 (cached)
-> retrieved ppx_cold.v0.14.0 (cached)
-> retrieved ppx_compare.v0.14.0 (cached)
-> retrieved ppx_conv_func.v0.14.0 (cached)
-> retrieved ppx_csv_conv.v0.14.0 (cached)
-> retrieved ppx_custom_printf.v0.14.1 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppx_deriving.5.2.1 (cached)
-> retrieved ppx_enumerate.v0.14.0 (cached)
-> retrieved ppx_expect.v0.14.2 (cached)
-> installed ocaml-syntax-shims.1.0.0
-> installed ocaml-compiler-libs.v0.12.4
-> retrieved ppx_fields_conv.v0.14.2 (cached)
-> retrieved ppx_fixed_literal.v0.14.0 (cached)
-> retrieved ppx_hash.v0.14.0 (cached)
-> retrieved ppx_here.v0.14.0 (cached)
-> retrieved ppx_inline_test.v0.14.1 (cached)
-> installed dune-configurator.3.18.2
-> retrieved ppx_jane.v0.14.0 (cached)
-> installed ppx_derivers.1.2.1
-> retrieved ppx_js_style.v0.14.1 (cached)
-> retrieved ppx_let.v0.14.0 (cached)
-> retrieved ppx_module_timer.v0.14.0 (cached)
-> retrieved ppx_optcomp.v0.14.3 (cached)
-> retrieved ppx_optional.v0.14.0 (cached)
-> retrieved ppx_pipebang.v0.14.0 (cached)
-> installed num.1.6
-> retrieved ppx_sexp_conv.v0.14.3 (cached)
-> retrieved ppx_sexp_message.v0.14.1 (cached)
-> retrieved ppx_sexp_value.v0.14.0 (cached)
-> retrieved ppx_stable.v0.14.1 (cached)
-> retrieved ppx_string.v0.14.1 (cached)
-> retrieved ppx_typerep_conv.v0.14.2 (cached)
-> retrieved ppx_variants_conv.v0.14.2 (cached)
-> retrieved ppxlib.0.25.1 (cached)
-> retrieved re.1.13.2 (cached)
-> retrieved result.1.5 (cached)
-> retrieved rresult.0.7.0 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexplib.v0.14.0 (cached)
-> retrieved sexplib0.v0.14.0 (cached)
-> retrieved spawn.v0.17.0 (cached)
-> retrieved splittable_random.v0.14.0 (cached)
-> retrieved stdio.v0.14.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved stringext.1.6.0 (cached)
-> retrieved time_now.v0.14.0 (cached)
-> retrieved timezone.v0.14.0 (cached)
-> retrieved topkg.1.1.0 (cached)
-> retrieved typerep.v0.14.0 (cached)
-> retrieved tyxml.4.6.0 (cached)
-> retrieved uri.4.4.0 (cached)
-> installed bigstringaf.0.10.0
-> installed result.1.5
-> retrieved uutf.1.0.4 (cached)
-> retrieved variantslib.v0.14.0 (cached)
-> retrieved vg.0.9.5 (cached)
-> installed stdlib-shims.0.3.0
-> installed stringext.1.6.0
-> retrieved xmlm.1.4.0 (cached)
-> installed spawn.v0.17.0
-> installed octavius.1.2.2
-> installed sexplib0.v0.14.0
-> installed angstrom.0.16.1
-> installed re.1.13.2
-> installed angstrom-unix.0.16.1
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed uri.4.4.0
-> installed ocamlbuild.0.16.1
-> installed camlzip.1.13
-> installed ocamlify.0.0.1
-> installed base.v0.14.3
-> installed fieldslib.v0.14.0
-> installed variantslib.v0.14.0
-> installed stdio.v0.14.0
-> installed topkg.1.1.0
-> installed typerep.v0.14.0
-> installed rresult.0.7.0
-> installed uutf.1.0.4
-> installed parsexp.v0.14.2
-> installed fmt.0.11.0
-> installed xmlm.1.4.0
-> installed otfm.0.4.0
-> installed sexplib.v0.14.0
-> installed gg.1.0.0
-> installed ppxlib.0.25.1
-> installed tyxml.4.6.0
-> installed vg.0.9.5
-> installed ppx_optcomp.v0.14.3
-> installed ppx_conv_func.v0.14.0
-> installed ppx_here.v0.14.0
-> installed ppx_cold.v0.14.0
-> installed ppx_let.v0.14.0
-> installed ppx_enumerate.v0.14.0
-> installed ppx_fields_conv.v0.14.2
-> installed ppx_stable.v0.14.1
-> installed ppx_compare.v0.14.0
-> installed ppx_typerep_conv.v0.14.2
-> installed ppx_variants_conv.v0.14.2
-> installed ppx_pipebang.v0.14.0
-> installed ppx_fixed_literal.v0.14.0
-> installed ppx_optional.v0.14.0
-> installed ppx_js_style.v0.14.1
-> installed ppx_sexp_conv.v0.14.3
-> installed ppx_deriving.5.2.1
-> installed ppx_hash.v0.14.0
-> installed ppx_sexp_value.v0.14.0
-> installed ppx_assert.v0.14.0
-> installed ppx_sexp_message.v0.14.1
-> installed ppx_custom_printf.v0.14.1
-> installed ppx_base.v0.14.0
-> installed jst-config.v0.14.1
-> installed bin_prot.v0.14.1
-> installed ppx_string.v0.14.1
-> installed time_now.v0.14.0
-> installed ppx_bin_prot.v0.14.0
-> installed ppx_module_timer.v0.14.0
-> installed ppx_inline_test.v0.14.1
-> installed ppx_bench.v0.14.1
-> installed ppx_expect.v0.14.2
-> installed splittable_random.v0.14.0
-> installed base_quickcheck.v0.14.1
-> installed ppx_jane.v0.14.0
-> installed base_bigstring.v0.14.0
-> installed core_kernel.v0.14.2
-> installed cfstream.1.3.2
-> installed timezone.v0.14.0
-> installed core.v0.14.1
-> installed csvfields.v0.14.0
-> installed biocaml.0.11.1
-> installed ocamlnet.4.1.9-2
-> installed ppx_csv_conv.v0.14.0
-> installed biotk.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 17:45.13 ---> saved as "97f497ca4afc96d6931ae0c4b10fcc375a0178c64209c1239ee0ba5b39a8722a"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test biotk.0.0.0) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile biotk 0.0.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved biotk.0.0.0 (https://opam.ocaml.org/cache)
-> removed biotk.0.0.0
-> installed biotk.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 17:45.20 ---> saved as "01bddc66918fb8b8ebb685bb33b8aa751c2964386b056bf9cf9bbbd6d30378ba"
/home/opam: (run (shell "opam reinstall --with-test --verbose biotk.0.0.0;\
\n res=$?;\
\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-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'biotk.0.0.0' && partial_fails=\"$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 biotk 0.0.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [biotk.0.0.0: extract]
-> retrieved biotk.0.0.0 (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.0.0.0)
-> compiled biotk.0.0.0
-> removed biotk.0.0.0
-> installed biotk.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 17:45.27 ---> saved as "46d1e41d970948cbb06f95abd9228fdaa049c51651ce1c3da0da63498482acad"
Job succeeded
2025-09-18 17:45.32: Job succeeded