Build:
- 0
2026-03-11 01:09.50: New job: test phylogenetics.0.0.0 with dune.3.22.0~alpha1, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/29535/head (f5aa06af0536fd71fe2fa400c30bf2a83f6bb8de)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/29535/head" && git reset --hard f5aa06af
git fetch origin master
git merge --no-edit 3c0d72031e829cf7ddad3a74f39a8b01fe2bf302
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn dune.3.22.0~alpha1 3.22.0~alpha1
RUN opam reinstall dune.3.22.0~alpha1; \
res=$?; \
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 "$pkg" != 'dune.3.22.0~alpha1' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall phylogenetics.0.0.0; \
res=$?; \
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 "$pkg" != 'phylogenetics.0.0.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test phylogenetics.0.0.0) || true
RUN opam reinstall --with-test --verbose phylogenetics.0.0.0; \
res=$?; \
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 "$pkg" != 'phylogenetics.0.0.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2026-03-11 01:09.50: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e-dune.3.22.0~alpha1-phylogenetics.0.0.0-f5aa06af0536fd71fe2fa400c30bf2a83f6bb8de"
2026-03-11 01:09.50: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn dune.3.22.0~alpha1 3.22.0~alpha1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.22.0~alpha1;\
\n res=$?;\
\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 \"$pkg\" != 'dune.3.22.0~alpha1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall phylogenetics.0.0.0;\
\n res=$?;\
\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 \"$pkg\" != 'phylogenetics.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test phylogenetics.0.0.0) || true"))
(run (shell "opam reinstall --with-test --verbose phylogenetics.0.0.0;\
\n res=$?;\
\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 \"$pkg\" != 'phylogenetics.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2026-03-11 01:09.50: Waiting for resource in pool OCluster
2026-03-11 10:09.53: Waiting for worker…
2026-03-11 10:11.40: Got resource from pool OCluster
Building on laodoke.caelum.ci.dev
All commits already cached
Updating files: 96% (17755/18435)
Updating files: 97% (17882/18435)
Updating files: 98% (18067/18435)
Updating files: 99% (18251/18435)
Updating files: 100% (18435/18435)
Updating files: 100% (18435/18435), done.
HEAD is now at 3c0d72031e Merge pull request #29534 from filipeom/opam-publish-smtml.0.23.0
Updating 3c0d72031e..f5aa06af05
Fast-forward
.../chrome-trace/chrome-trace.3.22.0~alpha1/opam | 39 +++++++++++
.../dune-action-plugin.3.22.0~alpha1/opam | 52 +++++++++++++++
.../dune-action-trace.3.22.0~alpha1/opam | 39 +++++++++++
.../dune-build-info.3.22.0~alpha1/opam | 45 +++++++++++++
.../dune-configurator.3.22.0~alpha1/opam | 49 ++++++++++++++
packages/dune-glob/dune-glob.3.22.0~alpha1/opam | 42 ++++++++++++
.../dune-private-libs.3.22.0~alpha1/opam | 50 +++++++++++++++
.../dune-rpc-lwt/dune-rpc-lwt.3.22.0~alpha1/opam | 41 ++++++++++++
packages/dune-rpc/dune-rpc.3.22.0~alpha1/opam | 44 +++++++++++++
packages/dune-site/dune-site.3.22.0~alpha1/opam | 37 +++++++++++
packages/dune/dune.3.22.0~alpha1/opam | 75 ++++++++++++++++++++++
packages/dyn/dyn.3.22.0~alpha1/opam | 40 ++++++++++++
packages/fs-io/fs-io.3.22.0~alpha1/opam | 39 +++++++++++
packages/ocamlc-loc/ocamlc-loc.3.22.0~alpha1/opam | 43 +++++++++++++
packages/ordering/ordering.3.22.0~alpha1/opam | 38 +++++++++++
packages/stdune/stdune.3.22.0~alpha1/opam | 46 +++++++++++++
.../top-closure/top-closure.3.22.0~alpha1/opam | 38 +++++++++++
packages/xdg/xdg.3.22.0~alpha1/opam | 39 +++++++++++
18 files changed, 796 insertions(+)
create mode 100644 packages/chrome-trace/chrome-trace.3.22.0~alpha1/opam
create mode 100644 packages/dune-action-plugin/dune-action-plugin.3.22.0~alpha1/opam
create mode 100644 packages/dune-action-trace/dune-action-trace.3.22.0~alpha1/opam
create mode 100644 packages/dune-build-info/dune-build-info.3.22.0~alpha1/opam
create mode 100644 packages/dune-configurator/dune-configurator.3.22.0~alpha1/opam
create mode 100644 packages/dune-glob/dune-glob.3.22.0~alpha1/opam
create mode 100644 packages/dune-private-libs/dune-private-libs.3.22.0~alpha1/opam
create mode 100644 packages/dune-rpc-lwt/dune-rpc-lwt.3.22.0~alpha1/opam
create mode 100644 packages/dune-rpc/dune-rpc.3.22.0~alpha1/opam
create mode 100644 packages/dune-site/dune-site.3.22.0~alpha1/opam
create mode 100644 packages/dune/dune.3.22.0~alpha1/opam
create mode 100644 packages/dyn/dyn.3.22.0~alpha1/opam
create mode 100644 packages/fs-io/fs-io.3.22.0~alpha1/opam
create mode 100644 packages/ocamlc-loc/ocamlc-loc.3.22.0~alpha1/opam
create mode 100644 packages/ordering/ordering.3.22.0~alpha1/opam
create mode 100644 packages/stdune/stdune.3.22.0~alpha1/opam
create mode 100644 packages/top-closure/top-closure.3.22.0~alpha1/opam
create mode 100644 packages/xdg/xdg.3.22.0~alpha1/opam
(from ocaml/opam:debian-13-ocaml-4.14@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e)
Unable to find image 'ocaml/opam:debian-13-ocaml-4.14@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e' locally
docker.io/ocaml/opam@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e: Pulling from ocaml/opam
866771c43bf5: Already exists
1e49bea09367: Already exists
e793768537e6: Already exists
ed323d3d481a: Already exists
7df34a5cd5f1: Already exists
fd712d3eb935: Already exists
4b9fb8c99118: Already exists
9d9a01948b94: Already exists
0f1514f90b32: Already exists
e1ec5a753447: Already exists
03cc323e2f71: Already exists
c09c08ea9749: Already exists
b36b619f8e6b: Already exists
195344ca5274: Already exists
228ee78582a6: Already exists
504bde1c25b3: Already exists
9d8b1356c89f: Already exists
9d8b1356c89f: Already exists
568fb6dda155: Already exists
c499c9198aea: Already exists
048e5e358118: Already exists
871ca48eb45d: Already exists
4f4fb700ef54: Already exists
a5a2568b9df9: Already exists
068cf3106ac8: Already exists
559f54ec9b29: Already exists
798ffd96fde5: Already exists
e9a891bf80d7: Already exists
d720cfe12674: Already exists
c81c932f4a91: Already exists
79f24fa3bb11: Already exists
8c1debcd8c20: Already exists
1bb2cfea7250: Already exists
2b3d3ca75e4c: Already exists
557cacaf263c: Already exists
d10483022eef: Already exists
7b62a90d8223: Already exists
28ce8ea66e72: Already exists
d975909ea717: Already exists
5c215c69c247: Already exists
e7c082452a54: Already exists
d1a4c61b613c: Pulling fs layer
0195a6679dc6: Pulling fs layer
410dfa46d7be: Pulling fs layer
b7b221f39cbe: Pulling fs layer
b7b221f39cbe: Waiting
0195a6679dc6: Verifying Checksum
0195a6679dc6: Download complete
410dfa46d7be: Verifying Checksum
410dfa46d7be: Download complete
b7b221f39cbe: Verifying Checksum
b7b221f39cbe: Download complete
d1a4c61b613c: Verifying Checksum
d1a4c61b613c: Download complete
d1a4c61b613c: Pull complete
0195a6679dc6: Pull complete
410dfa46d7be: Pull complete
b7b221f39cbe: Pull complete
Digest: sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e
Status: Downloaded newer image for ocaml/opam@sha256:37323dc71cac48a3e4688e16b45b95486f3cc440c55ab3f83114e8973362f41e
2026-03-11 10:12.08 ---> using "32cd5b5baf995c02200cf270da597dbb25becd220af2c200c00b8b241a742195" from cache
/: (user (uid 1000) (gid 1000))
/: (workdir /home/opam)
/home/opam: (run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
2026-03-11 10:12.08 ---> using "f3ed7bdbef828c9c0b079b10505c5f05c3c9adcca11ce5bf2dac2a4183e099d8" 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
2026-03-11 10:12.08 ---> using "5bf6adb7b45bb7e0c215b8f509c71a8dae73a9a2060efcc27df9d4ef6c6d3350" from cache
/home/opam: (run (shell "opam option solver=builtin-0install && opam config report"))
Set to 'builtin-0install' the field solver in global configuration
# opam config report
# opam-version 2.5.0
# self-upgrade no
# system arch=x86_64 os=linux os-distribution=debian os-version=13
# solver builtin-0install
# install-criteria -changed,-count[avoid-version,solution]
# upgrade-criteria -count[avoid-version,solution]
# jobs 71
# repositories 1 (version-controlled)
# pinned 1 (version)
# current-switch 4.14
# invariant ["ocaml-base-compiler" {= "4.14.2"}]
# compiler-packages ocaml-base-compiler.4.14.2, ocaml-options-vanilla.1
# ocaml:native true
# ocaml:native-tools true
# ocaml:native-dynlink true
# ocaml:stubsdir /home/opam/.opam/4.14/lib/ocaml/stublibs:/home/opam/.opam/4.14/lib/ocaml
# ocaml:preinstalled false
# ocaml:compiler 4.14.2
2026-03-11 10:12.08 ---> using "0546f18fa5979677ee22eb9f2fcf19ab371564e845d317c2c70e41dd97dc22dd" 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/"))
2026-03-11 10:12.08 ---> using "0a7188cbe95f4fe0ff26694977eb8794c975bdb534078da98a06d6c7373289b4" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2026-03-11 10:12.09 ---> using "058acd97914d90fca6a329b7ff1babbb92e45a5f521e04c7114979a220f97d75" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2026-03-11 10:12.09 ---> using "a9504de0029e850164e11feaf593a22f67e6f7c5cccc92dfed09cc916f0be670" 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 [108 kB]
- Fetched 199 kB in 0s (1809 kB/s)
- Reading package lists...
-
2026-03-11 10:12.09 ---> using "fc5ea9d29c11a2b6de08c85928fd22a882efb1281fe5a3be2d5337cb56b6577e" from cache
/home/opam: (run (shell "opam pin add -k version -yn dune.3.22.0~alpha1 3.22.0~alpha1"))
dune is now pinned to version 3.22.0~alpha1
2026-03-11 10:12.09 ---> using "023c2a0e0e5efd5bf484a99a73410c324d867ace34fca4cdaff2047b39f6aa87" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall dune.3.22.0~alpha1;\
\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 \"$pkg\" != 'dune.3.22.0~alpha1' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
dune.3.22.0~alpha1 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 1 package
- install dune 3.22.0~alpha1 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.22.0~alpha1 (cached)
-> installed dune.3.22.0~alpha1
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-11 10:12.09 ---> using "7ddf5c4038e49c6780c053e6d2299b48596f42b483565b7de9e6c8e1f73bd100" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall phylogenetics.0.0.0;\
\n res=$?;\
\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 \"$pkg\" != 'phylogenetics.0.0.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
phylogenetics.0.0.0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 91 packages
- install angstrom 0.16.1 [required by angstrom-unix]
- install angstrom-unix 0.16.1 [required by phylogenetics]
- install base v0.14.3 [required by core_kernel]
- install base-bytes base [required by printbox]
- install base64 3.5.2 [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 phylogenetics]
- install camlp-streams 5.0.1 [required by cfstream]
- install camlzip 1.14 [required by biocaml]
- install cfstream 1.3.2 [required by biocaml]
- install conf-blas 1 [required by lacaml]
- install conf-gsl 2 [required by gsl]
- install conf-lapack 1 [required by lacaml]
- install conf-m4 1 [required by cfstream]
- install conf-pkg-config 4 [required by gsl]
- install conf-zlib 1 [required by camlzip]
- install core v0.14.1 [required by phylogenetics]
- 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 dune-configurator 3.22.0~alpha1 [required by gsl, lacaml]
- install fieldslib v0.14.0 [required by core_kernel]
- install gsl 1.25.1 [required by phylogenetics]
- install jane-street-headers v0.14.0 [required by core_kernel]
- install jst-config v0.14.1 [required by core]
- install lacaml 11.1.1 [required by phylogenetics]
- install menhir 20260209 [required by phylogenetics]
- install menhirCST 20260209 [required by menhir]
- install menhirGLR 20260209 [required by menhir]
- install menhirLib 20260209 [required by menhir]
- install menhirSdk 20260209 [required by menhir]
- install num 1.6 [required by sexplib]
- 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 rresult, xmlm]
- install ocamlfind 1.9.8 [required by ppx_deriving]
- install octavius 1.2.2 [required by ppx_js_style]
- install parsexp v0.14.2 [required by sexplib]
- install phylogenetics 0.0.0
- 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_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 phylogenetics]
- 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_jane]
- 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]
- 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_deriving]
- install printbox 0.5 [required by phylogenetics]
- install re 1.14.0 [required by biocaml]
- install result 1.5 [required by ppx_deriving]
- install rresult 0.7.0 [required by biocaml]
- 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 1.1.1 [required by rresult, xmlm]
- install typerep v0.14.0 [required by core_kernel]
- install uri 4.4.0 [required by biocaml]
- install variantslib v0.14.0 [required by core_kernel]
- install xmlm 1.4.0 [required by biocaml]
The following system packages will first need to be installed:
libblas-dev libgsl-dev liblapack-dev 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" "libblas-dev" "libgsl-dev" "liblapack-dev" "m4" "pkg-config" "zlib1g-dev"
- Selecting previously unselected package libblas3: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 ... 20623 files and directories currently installed.)
- Preparing to unpack .../00-libblas3_3.12.1-6_amd64.deb ...
- Unpacking libblas3:amd64 (3.12.1-6) ...
- Selecting previously unselected package libblas-dev:amd64.
- Preparing to unpack .../01-libblas-dev_3.12.1-6_amd64.deb ...
- Unpacking libblas-dev:amd64 (3.12.1-6) ...
- Selecting previously unselected package libgfortran5:amd64.
- Preparing to unpack .../02-libgfortran5_14.2.0-19_amd64.deb ...
- Unpacking libgfortran5:amd64 (14.2.0-19) ...
- Selecting previously unselected package libgslcblas0:amd64.
- Preparing to unpack .../03-libgslcblas0_2.8+dfsg-5_amd64.deb ...
- Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ...
- Selecting previously unselected package libgsl28:amd64.
- Preparing to unpack .../04-libgsl28_2.8+dfsg-5_amd64.deb ...
- Unpacking libgsl28:amd64 (2.8+dfsg-5) ...
- Selecting previously unselected package libgsl-dev.
- Preparing to unpack .../05-libgsl-dev_2.8+dfsg-5_amd64.deb ...
- Unpacking libgsl-dev (2.8+dfsg-5) ...
- Selecting previously unselected package liblapack3:amd64.
- Preparing to unpack .../06-liblapack3_3.12.1-6_amd64.deb ...
- Unpacking liblapack3:amd64 (3.12.1-6) ...
- Selecting previously unselected package liblapack-dev:amd64.
- Preparing to unpack .../07-liblapack-dev_3.12.1-6_amd64.deb ...
- Unpacking liblapack-dev:amd64 (3.12.1-6) ...
- Selecting previously unselected package libpkgconf3:amd64.
- Preparing to unpack .../08-libpkgconf3_1.8.1-4_amd64.deb ...
- Unpacking libpkgconf3:amd64 (1.8.1-4) ...
- Selecting previously unselected package m4.
- Preparing to unpack .../09-m4_1.4.19-8_amd64.deb ...
- Unpacking m4 (1.4.19-8) ...
- Selecting previously unselected package pkgconf-bin.
- Preparing to unpack .../10-pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../11-pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../12-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 .../13-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 m4 (1.4.19-8) ...
- Setting up libblas3:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
- Setting up libpkgconf3:amd64 (1.8.1-4) ...
- Setting up pkgconf-bin (1.8.1-4) ...
- Setting up libgfortran5:amd64 (14.2.0-19) ...
- Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
- Setting up libgsl28:amd64 (2.8+dfsg-5) ...
- Setting up libblas-dev:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
- Setting up liblapack3:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
- Setting up libgsl-dev (2.8+dfsg-5) ...
- Setting up pkgconf:amd64 (1.8.1-4) ...
- Setting up liblapack-dev:amd64 (3.12.1-6) ...
- update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
- 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.v0.14.3 (cached)
-> retrieved base64.3.5.2 (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 camlp-streams.5.0.1 (cached)
-> retrieved camlzip.1.14 (cached)
-> retrieved cfstream.1.3.2 (cached)
-> retrieved conf-blas.1 (cached)
-> retrieved conf-lapack.1 (cached)
-> installed base64.3.5.2
-> retrieved core.v0.14.1 (cached)
-> installed conf-m4.1
-> installed conf-pkg-config.4
-> installed conf-blas.1
-> installed conf-lapack.1
-> retrieved core_kernel.v0.14.2 (cached)
-> installed camlp-streams.5.0.1
-> installed conf-gsl.2
-> installed conf-zlib.1
-> retrieved cppo.1.8.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> installed csexp.1.5.2
-> installed cppo.1.8.0
-> retrieved dune-configurator.3.22.0~alpha1 (cached)
-> retrieved fieldslib.v0.14.0 (cached)
-> retrieved gsl.1.25.1 (cached)
-> retrieved jane-street-headers.v0.14.0 (cached)
-> retrieved jst-config.v0.14.1 (cached)
-> retrieved lacaml.11.1.1 (cached)
-> retrieved menhir.20260209, menhirCST.20260209, menhirGLR.20260209, menhirLib.20260209, menhirSdk.20260209 (cached)
-> installed jane-street-headers.v0.14.0
-> retrieved num.1.6 (cached)
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> installed menhirCST.20260209
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved octavius.1.2.2 (cached)
-> retrieved parsexp.v0.14.2 (cached)
-> retrieved phylogenetics.0.0.0 (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)
-> installed dune-configurator.3.22.0~alpha1
-> installed menhirGLR.20260209
-> installed menhirLib.20260209
-> installed menhirSdk.20260209
-> 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)
-> 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)
-> retrieved ppx_jane.v0.14.0 (cached)
-> 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)
-> installed ppx_derivers.1.2.1
-> retrieved ppx_optional.v0.14.0 (cached)
-> retrieved ppx_pipebang.v0.14.0 (cached)
-> 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)
-> installed bigstringaf.0.10.0
-> retrieved ppx_string.v0.14.1 (cached)
-> retrieved ppx_typerep_conv.v0.14.2 (cached)
-> retrieved ppx_variants_conv.v0.14.2 (cached)
-> installed ocaml-syntax-shims.1.0.0
-> retrieved ppxlib.0.25.1 (cached)
-> retrieved printbox.0.5 (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 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.1.1.1 (cached)
-> installed octavius.1.2.2
-> installed result.1.5
-> installed stdlib-shims.0.3.0
-> retrieved typerep.v0.14.0 (cached)
-> retrieved uri.4.4.0 (cached)
-> retrieved variantslib.v0.14.0 (cached)
-> retrieved xmlm.1.4.0 (cached)
-> installed angstrom.0.16.1
-> installed stringext.1.6.0
-> installed num.1.6
-> installed spawn.v0.17.0
-> installed angstrom-unix.0.16.1
-> installed sexplib0.v0.14.0
-> installed re.1.14.0
-> installed ocamlfind.1.9.8
-> installed base-bytes.base
-> installed gsl.1.25.1
-> installed uri.4.4.0
-> installed printbox.0.5
-> installed camlzip.1.14
-> installed ocamlbuild.0.16.1
-> installed base.v0.14.3
-> installed fieldslib.v0.14.0
-> installed variantslib.v0.14.0
-> installed menhir.20260209
-> installed stdio.v0.14.0
-> installed typerep.v0.14.0
-> installed lacaml.11.1.1
-> installed topkg.1.1.1
-> installed parsexp.v0.14.2
-> installed rresult.0.7.0
-> installed sexplib.v0.14.0
-> installed xmlm.1.4.0
-> installed ppxlib.0.25.1
-> installed ppx_optcomp.v0.14.3
-> installed ppx_cold.v0.14.0
-> installed ppx_here.v0.14.0
-> installed ppx_let.v0.14.0
-> installed ppx_fields_conv.v0.14.2
-> installed ppx_variants_conv.v0.14.2
-> installed ppx_enumerate.v0.14.0
-> installed ppx_stable.v0.14.1
-> installed ppx_typerep_conv.v0.14.2
-> installed ppx_compare.v0.14.0
-> installed ppx_optional.v0.14.0
-> installed ppx_fixed_literal.v0.14.0
-> installed ppx_pipebang.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 ppx_string.v0.14.1
-> installed bin_prot.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 biocaml.0.11.1
-> installed phylogenetics.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-11 10:15.19 ---> saved as "807298fe867cae903379195c8f9038ecb1b87c4bf60b40581864d274244fcb84"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test phylogenetics.0.0.0) || true"))
The following actions will be performed:
=== recompile 2 packages
- recompile phylogenetics 0.0.0
- recompile printbox 0.5 [uses uutf]
=== install 5 packages
- install alcotest 1.9.1 [required by phylogenetics]
- install astring 0.8.5 [required by alcotest]
- install cmdliner 2.1.0 [required by alcotest]
- install fmt 0.11.0 [required by alcotest]
- install uutf 1.0.4 [required by alcotest]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved alcotest.1.9.1 (https://opam.ocaml.org/cache)
-> retrieved astring.0.8.5 (https://opam.ocaml.org/cache)
-> retrieved cmdliner.2.1.0 (https://opam.ocaml.org/cache)
-> retrieved fmt.0.11.0 (https://opam.ocaml.org/cache)
-> retrieved phylogenetics.0.0.0 (https://opam.ocaml.org/cache)
-> retrieved printbox.0.5 (https://opam.ocaml.org/cache)
-> retrieved uutf.1.0.4 (https://opam.ocaml.org/cache)
-> installed astring.0.8.5
-> removed phylogenetics.0.0.0
-> removed printbox.0.5
-> installed cmdliner.2.1.0
-> installed uutf.1.0.4
-> installed fmt.0.11.0
-> installed printbox.0.5
-> installed alcotest.1.9.1
-> installed phylogenetics.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-11 10:15.49 ---> saved as "9df854f91d5605836bbfe2c64fd4626d86c8452a1dded341f3447eb47ed1c654"
/home/opam: (run (shell "opam reinstall --with-test --verbose phylogenetics.0.0.0;\
\n res=$?;\
\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 \"$pkg\" != 'phylogenetics.0.0.0' && partial_fails=\"$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 phylogenetics 0.0.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [phylogenetics.0.0.0: extract]
-> retrieved phylogenetics.0.0.0 (cached)
Processing 2/4: [phylogenetics: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "phylogenetics" "-j" "71" "@install" (CWD=/home/opam/.opam/4.14/.opam-switch/build/phylogenetics.0.0.0)
- (cd _build/default/lib && /home/opam/.opam/4.14/bin/menhir newick_parser.mly --compile-errors newick_parser.messages) > _build/default/lib/newick_parser_errors.ml
- Read 3 sample input sentences and 2 error messages.
-> compiled phylogenetics.0.0.0
-> removed phylogenetics.0.0.0
-> installed phylogenetics.0.0.0
Done.
# To update the current shell environment, run: eval $(opam env)
2026-03-11 10:16.02 ---> saved as "5cde4ea7c3cc067a32827b469b95d695d56e667bdad07ed2e3d044a156451acb"
Job succeeded
2026-03-11 10:16.14: Job succeeded