Build:
- 0
2025-09-18 12:21.25: New job: test phylogenetics.0.2.0 with re.1.14.0, using opam dev
from https://github.com/ocaml/opam-repository.git#refs/pull/28544/head (8165ebc987d9de35b2fdba552fd80e37f5bd842d)
on debian-13-ocaml-4.14/amd64
To reproduce locally:
cd $(mktemp -d)
git clone --recursive "https://github.com/ocaml/opam-repository.git" && cd "opam-repository" && git fetch origin "refs/pull/28544/head" && git reset --hard 8165ebc9
git fetch origin master
git merge --no-edit 151ffce963e54519dd5d1280848f631d38db358e
cat > ../Dockerfile <<'END-OF-DOCKERFILE'
FROM ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc
USER 1000:1000
WORKDIR /home/opam
RUN sudo ln -f /usr/bin/opam-dev /usr/bin/opam
RUN opam init --reinit -ni
RUN opam option solver=builtin-0install && opam config report
ENV OPAMDOWNLOADJOBS="1"
ENV OPAMERRLOGLEN="0"
ENV OPAMPRECISETRACKING="1"
ENV CI="true"
ENV OPAM_REPO_CI="true"
RUN rm -rf opam-repository/
COPY --chown=1000:1000 . opam-repository/
RUN opam repository set-url --strict default opam-repository/
RUN opam update --depexts || true
RUN opam pin add -k version -yn re.1.14.0 1.14.0
RUN opam reinstall re.1.14.0; \
res=$?; \
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 "$pkg" != 're.1.14.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN opam reinstall phylogenetics.0.2.0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'phylogenetics.0.2.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
RUN (opam reinstall --with-test phylogenetics.0.2.0) || true
RUN opam reinstall --with-test --verbose phylogenetics.0.2.0; \
res=$?; \
test "$res" != 31 && exit "$res"; \
export OPAMCLI=2.0; \
build_dir=$(opam var prefix)/.opam-switch/build; \
failed=$(ls "$build_dir"); \
partial_fails=""; \
for pkg in $failed; do \
if opam show -f x-ci-accept-failures: "$pkg" | grep -qF "\"debian-13\""; then \
echo "A package failed and has been disabled for CI using the 'x-ci-accept-failures' field."; \
fi; \
test "$pkg" != 'phylogenetics.0.2.0' && partial_fails="$partial_fails $pkg"; \
done; \
test "${partial_fails}" != "" && echo "opam-repo-ci detected dependencies failing: ${partial_fails}"; \
exit 1
END-OF-DOCKERFILE
docker build -f ../Dockerfile .
2025-09-18 12:21.25: Using cache hint "ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc-re.1.14.0-phylogenetics.0.2.0-8165ebc987d9de35b2fdba552fd80e37f5bd842d"
2025-09-18 12:21.25: Using OBuilder spec:
((from ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc)
(user (uid 1000) (gid 1000))
(workdir /home/opam)
(run (shell "sudo ln -f /usr/bin/opam-dev /usr/bin/opam"))
(run (network host)
(shell "opam init --reinit --config .opamrc-sandbox -ni"))
(run (shell "opam option solver=builtin-0install && opam config report"))
(env OPAMDOWNLOADJOBS 1)
(env OPAMERRLOGLEN 0)
(env OPAMPRECISETRACKING 1)
(env CI true)
(env OPAM_REPO_CI true)
(run (shell "rm -rf opam-repository/"))
(copy (src .) (dst opam-repository/))
(run (shell "opam repository set-url --strict default opam-repository/"))
(run (network host)
(shell "opam update --depexts || true"))
(run (shell "opam pin add -k version -yn re.1.14.0 1.14.0"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall re.1.14.0;\
\n res=$?;\
\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 \"$pkg\" != 're.1.14.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall phylogenetics.0.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'phylogenetics.0.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
(run (network host)
(shell "(opam reinstall --with-test phylogenetics.0.2.0) || true"))
(run (shell "opam reinstall --with-test --verbose phylogenetics.0.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'phylogenetics.0.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
)
2025-09-18 12:21.25: Waiting for resource in pool OCluster
2025-09-18 13:28.29: Waiting for worker…
2025-09-18 13:31.20: 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..8165ebc987
Fast-forward
packages/re/re.1.14.0/opam | 54 ++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)
create mode 100644 packages/re/re.1.14.0/opam
(from ocaml/opam:debian-13-ocaml-4.14@sha256:ce7583a4463e517dda39f02d53e6fd4065fe70d94a26e5f51dcceb761272b5dc)
2025-09-18 13:31.28 ---> 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 13:31.28 ---> 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 13:31.28 ---> 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 13:31.28 ---> 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 13:31.28 ---> using "88d8ec224acefa159471a25872197bf5efdd28e8b95159888107feac1f31a583" from cache
/home/opam: (copy (src .) (dst opam-repository/))
2025-09-18 13:31.29 ---> using "2daa40f8cb706c5ad638d9f505ce5440193f9c6caab6f7a1374dce811b359b23" from cache
/home/opam: (run (shell "opam repository set-url --strict default opam-repository/"))
[default] Initialised
2025-09-18 13:31.29 ---> using "c7e4a8d501560eb3ca7fc845c078f1e10620c9e07b60e1684df8a29206dc874f" 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 (1442 kB/s)
- Reading package lists...
2025-09-18 13:31.29 ---> using "bf0d21ec1484e3c2798ebb3f62e67a8d7cca2892927fadac2a00726789e47b1e" from cache
/home/opam: (run (shell "opam pin add -k version -yn re.1.14.0 1.14.0"))
re is now pinned to version 1.14.0
2025-09-18 13:31.29 ---> using "3e93ff8b91dae5836d1785da64da20f4001f9fc3eeded7d2071cf7741852d20e" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall re.1.14.0;\
\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 \"$pkg\" != 're.1.14.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
re.1.14.0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 2 packages
- install dune 3.20.2 [required by re]
- install re 1.14.0 (pinned)
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved dune.3.20.2 (cached)
-> retrieved re.1.14.0 (cached)
-> installed dune.3.20.2
-> installed re.1.14.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 13:31.29 ---> using "3bdffe64ac10ca97ac896c7a816dde89b5172193da7b76c72d478fa5566dafe0" from cache
/home/opam: (run (cache (opam-archives (target /home/opam/.opam/download-cache)))
(network host)
(shell "opam reinstall phylogenetics.0.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'phylogenetics.0.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
phylogenetics.0.2.0 is not installed. Install it? [Y/n] y
The following actions will be performed:
=== install 107 packages
- install angstrom 0.16.1 [required by angstrom-unix, biotk]
- install angstrom-unix 0.16.1 [required by phylogenetics]
- install base v0.15.1 [required by core_kernel, core, ppx_csv_conv]
- install base_bigstring v0.15.0 [required by core]
- install base_quickcheck v0.15.0 [required by core]
- install bigstringaf 0.10.0 [required by angstrom]
- install bin_prot v0.15.0 [required by core]
- install binning 0.0.0 [required by phylogenetics]
- install biotk 0.2.0 [required by phylogenetics]
- install camlzip 1.13 [required by biotk]
- install cmdliner 1.3.0 [required by fmt, crunch, uucp]
- install conf-blas 1 [required by lacaml]
- install conf-gsl 2 [required by gsl]
- install conf-lapack 1 [required by lacaml]
- install conf-pkg-config 4 [required by gsl]
- install conf-zlib 1 [required by camlzip, zlib]
- install core v0.15.1 [required by phylogenetics]
- install core_kernel v0.15.0 [required by biotk]
- install core_unix v0.15.2 [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 v0.15.1 [required by ppx_csv_conv]
- install dune-configurator 3.20.2 [required by lacaml]
- install expect_test_helpers_core v0.15.0 [required by core_unix]
- install fieldslib v0.15.0 [required by core]
- install fmt 0.11.0 [required by biotk]
- install gg 1.0.0 [required by vg]
- install gsl 1.25.1 [required by phylogenetics]
- install int_repr v0.15.0 [required by core_kernel]
- install jane-street-headers v0.15.0 [required by core, core_unix]
- install jst-config v0.15.1 [required by core, core_unix]
- install lacaml 11.1.1 [required by phylogenetics]
- install menhir 20250912 [required by phylogenetics]
- install menhirCST 20250912 [required by menhir]
- install menhirLib 20250912 [required by menhir]
- install menhirSdk 20250912 [required by menhir]
- install num 1.6 [required by csvfields]
- install ocaml-compiler-libs v0.12.4 [required by ppxlib]
- install ocaml-syntax-shims 1.0.0 [required by angstrom]
- install ocaml_intrinsics v0.15.2 [required by core_unix]
- install ocamlbuild 0.16.1 [required by vg, otfm, fmt, etc.]
- install ocamlfind 1.9.8 [required by vg, ppx_deriving, fmt, etc.]
- install otfm 0.4.0 [required by biotk]
- install parsexp v0.15.0 [required by sexplib]
- install phylogenetics 0.2.0
- install ppx_assert v0.15.0 [required by core]
- install ppx_base v0.15.0 [required by core]
- install ppx_bench v0.15.1 [required by ppx_jane]
- install ppx_bin_prot v0.15.0 [required by ppx_jane]
- install ppx_cold v0.15.0 [required by ppx_base]
- install ppx_compare v0.15.0 [required by ppx_base, bin_prot]
- install ppx_conv_func v0.15.0 [required by ppx_csv_conv]
- install ppx_csv_conv v0.15.0 [required by biotk]
- install ppx_custom_printf v0.15.0 [required by ppx_jane]
- install ppx_derivers 1.2.1 [required by ppx_deriving]
- install ppx_deriving 6.0.3 [required by phylogenetics]
- install ppx_disable_unused_warnings v0.15.0 [required by ppx_jane]
- install ppx_enumerate v0.15.0 [required by ppx_base]
- install ppx_expect v0.15.1 [required by ppx_jane]
- install ppx_fields_conv v0.15.0 [required by ppx_csv_conv]
- install ppx_fixed_literal v0.15.0 [required by ppx_jane]
- install ppx_hash v0.15.0 [required by core]
- install ppx_here v0.15.0 [required by ppx_jane]
- install ppx_ignore_instrumentation v0.15.0 [required by ppx_jane]
- install ppx_inline_test v0.15.1 [required by core]
- install ppx_jane v0.15.0 [required by core_kernel, core, core_unix]
- install ppx_let v0.15.0 [required by ppx_jane]
- install ppx_log v0.15.0 [required by ppx_jane]
- install ppx_module_timer v0.15.0 [required by ppx_jane]
- install ppx_optcomp v0.15.0 [required by ppx_jane]
- install ppx_optional v0.15.0 [required by ppx_jane]
- install ppx_pipebang v0.15.0 [required by ppx_jane]
- install ppx_sexp_conv v0.15.1 [required by core]
- install ppx_sexp_message v0.15.0 [required by core]
- install ppx_sexp_value v0.15.0 [required by ppx_jane]
- install ppx_stable v0.15.0 [required by ppx_jane]
- install ppx_string v0.15.0 [required by ppx_jane]
- install ppx_typerep_conv v0.15.0 [required by ppx_jane]
- install ppx_variants_conv v0.15.0 [required by ppx_jane]
- install ppxlib 0.35.0 [required by ppx_csv_conv, ppx_deriving]
- install printbox 0.12 [required by phylogenetics]
- install printbox-text 0.12 [required by phylogenetics]
- install ptime 1.2.0 [required by crunch]
- install result 1.5 [required by biotk]
- install rresult 0.7.0 [required by biotk]
- install seq base [required by tyxml]
- install sexp_pretty v0.15.1 [required by expect_test_helpers_core]
- install sexplib v0.15.1 [required by core, core_unix]
- install sexplib0 v0.15.1 [required by base]
- install spawn v0.17.0 [required by core_unix]
- install splittable_random v0.15.0 [required by core]
- install stdio v0.15.0 [required by core]
- install stdlib-shims 0.3.0 [required by ppxlib]
- install stringext 1.6.0 [required by uri]
- install time_now v0.15.0 [required by core]
- install timezone v0.15.0 [required by core_unix]
- install topkg 1.1.0 [required by vg, otfm, fmt, etc.]
- install typerep v0.15.0 [required by core]
- install tyxml 4.6.0 [required by biotk]
- install uri 4.4.0 [required by biotk]
- install uucp 17.0.0 [required by printbox-text]
- install uutf 1.0.4 [required by printbox-text]
- install variantslib v0.15.0 [required by core]
- install vg 0.9.5 [required by biotk]
- install yojson 3.0.0 [required by phylogenetics]
- install zlib 0.8 [required by biotk]
The following system packages will first need to be installed:
libblas-dev libgsl-dev liblapack-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" "libblas-dev" "libgsl-dev" "liblapack-dev" "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 ... 20622 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 pkgconf-bin.
- Preparing to unpack .../09-pkgconf-bin_1.8.1-4_amd64.deb ...
- Unpacking pkgconf-bin (1.8.1-4) ...
- Selecting previously unselected package pkgconf:amd64.
- Preparing to unpack .../10-pkgconf_1.8.1-4_amd64.deb ...
- Unpacking pkgconf:amd64 (1.8.1-4) ...
- Selecting previously unselected package pkg-config:amd64.
- Preparing to unpack .../11-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 .../12-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 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) ...
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
-> retrieved base.v0.15.1 (cached)
-> retrieved base_bigstring.v0.15.0 (cached)
-> retrieved base_quickcheck.v0.15.0 (cached)
-> retrieved bigstringaf.0.10.0 (cached)
-> retrieved bin_prot.v0.15.0 (cached)
-> retrieved binning.0.0.0 (cached)
-> retrieved biotk.0.2.0 (cached)
-> installed binning.0.0.0
-> retrieved camlzip.1.13 (cached)
-> retrieved cmdliner.1.3.0 (cached)
-> retrieved conf-blas.1 (cached)
-> retrieved conf-lapack.1 (cached)
-> retrieved core.v0.15.1 (cached)
-> installed conf-pkg-config.4
-> installed conf-blas.1
-> installed conf-lapack.1
-> retrieved core_kernel.v0.15.0 (cached)
-> installed conf-gsl.2
-> installed conf-zlib.1
-> retrieved core_unix.v0.15.2 (cached)
-> retrieved cppo.1.8.0 (cached)
-> retrieved crunch.4.0.0 (cached)
-> retrieved csexp.1.5.2 (cached)
-> retrieved csvfields.v0.15.1 (cached)
-> installed csexp.1.5.2
-> retrieved dune-configurator.3.20.2 (cached)
-> retrieved expect_test_helpers_core.v0.15.0 (cached)
-> retrieved fieldslib.v0.15.0 (cached)
-> retrieved fmt.0.11.0 (cached)
-> retrieved gg.1.0.0 (cached)
-> retrieved gsl.1.25.1 (cached)
-> retrieved int_repr.v0.15.0 (cached)
-> retrieved jane-street-headers.v0.15.0 (cached)
-> retrieved jst-config.v0.15.1 (cached)
-> retrieved lacaml.11.1.1 (cached)
-> installed cmdliner.1.3.0
-> installed cppo.1.8.0
-> installed jane-street-headers.v0.15.0
-> retrieved menhir.20250912, menhirCST.20250912, menhirLib.20250912, menhirSdk.20250912 (cached)
-> retrieved num.1.6 (cached)
-> installed dune-configurator.3.20.2
-> retrieved ocaml-compiler-libs.v0.12.4 (cached)
-> installed menhirCST.20250912
-> retrieved ocaml-syntax-shims.1.0.0 (cached)
-> retrieved ocaml_intrinsics.v0.15.2 (cached)
-> retrieved ocamlbuild.0.16.1 (cached)
-> retrieved ocamlfind.1.9.8 (cached)
-> retrieved otfm.0.4.0 (cached)
-> retrieved parsexp.v0.15.0 (cached)
-> retrieved phylogenetics.0.2.0 (cached)
-> retrieved ppx_assert.v0.15.0 (cached)
-> retrieved ppx_base.v0.15.0 (cached)
-> retrieved ppx_bench.v0.15.1 (cached)
-> retrieved ppx_bin_prot.v0.15.0 (cached)
-> installed menhirSdk.20250912
-> retrieved ppx_cold.v0.15.0 (cached)
-> retrieved ppx_compare.v0.15.0 (cached)
-> retrieved ppx_conv_func.v0.15.0 (cached)
-> retrieved ppx_csv_conv.v0.15.0 (cached)
-> retrieved ppx_custom_printf.v0.15.0 (cached)
-> retrieved ppx_derivers.1.2.1 (cached)
-> retrieved ppx_deriving.6.0.3 (cached)
-> installed menhirLib.20250912
-> installed bigstringaf.0.10.0
-> installed ppx_derivers.1.2.1
-> retrieved ppx_disable_unused_warnings.v0.15.0 (cached)
-> retrieved ppx_enumerate.v0.15.0 (cached)
-> retrieved ppx_expect.v0.15.1 (cached)
-> retrieved ppx_fields_conv.v0.15.0 (cached)
-> retrieved ppx_fixed_literal.v0.15.0 (cached)
-> retrieved ppx_hash.v0.15.0 (cached)
-> retrieved ppx_here.v0.15.0 (cached)
-> retrieved ppx_ignore_instrumentation.v0.15.0 (cached)
-> retrieved ppx_inline_test.v0.15.1 (cached)
-> retrieved ppx_jane.v0.15.0 (cached)
-> retrieved ppx_let.v0.15.0 (cached)
-> retrieved ppx_log.v0.15.0 (cached)
-> retrieved ppx_module_timer.v0.15.0 (cached)
-> retrieved ppx_optcomp.v0.15.0 (cached)
-> retrieved ppx_optional.v0.15.0 (cached)
-> retrieved ppx_pipebang.v0.15.0 (cached)
-> retrieved ppx_sexp_conv.v0.15.1 (cached)
-> retrieved ppx_sexp_message.v0.15.0 (cached)
-> retrieved ppx_sexp_value.v0.15.0 (cached)
-> retrieved ppx_stable.v0.15.0 (cached)
-> retrieved ppx_string.v0.15.0 (cached)
-> retrieved ppx_typerep_conv.v0.15.0 (cached)
-> retrieved ppx_variants_conv.v0.15.0 (cached)
-> installed ocaml-syntax-shims.1.0.0
-> installed ocaml_intrinsics.v0.15.2
-> retrieved ppxlib.0.35.0 (cached)
-> installed ocaml-compiler-libs.v0.12.4
-> retrieved printbox.0.12, printbox-text.0.12 (cached)
-> retrieved ptime.1.2.0 (cached)
-> retrieved result.1.5 (cached)
-> retrieved rresult.0.7.0 (cached)
-> retrieved seq.base (cached)
-> installed seq.base
-> retrieved sexp_pretty.v0.15.1 (cached)
-> installed num.1.6
-> retrieved sexplib.v0.15.1 (cached)
-> installed angstrom.0.16.1
-> retrieved sexplib0.v0.15.1 (cached)
-> retrieved spawn.v0.17.0 (cached)
-> retrieved splittable_random.v0.15.0 (cached)
-> retrieved stdio.v0.15.0 (cached)
-> retrieved stdlib-shims.0.3.0 (cached)
-> retrieved stringext.1.6.0 (cached)
-> retrieved time_now.v0.15.0 (cached)
-> retrieved timezone.v0.15.0 (cached)
-> installed printbox.0.12
-> retrieved topkg.1.1.0 (cached)
-> installed result.1.5
-> retrieved typerep.v0.15.0 (cached)
-> installed angstrom-unix.0.16.1
-> retrieved tyxml.4.6.0 (cached)
-> installed stdlib-shims.0.3.0
-> retrieved uri.4.4.0 (cached)
-> installed stringext.1.6.0
-> installed spawn.v0.17.0
-> installed sexplib0.v0.15.1
-> retrieved uucp.17.0.0 (cached)
-> retrieved uutf.1.0.4 (cached)
-> retrieved variantslib.v0.15.0 (cached)
-> retrieved vg.0.9.5 (cached)
-> retrieved yojson.3.0.0 (cached)
-> retrieved zlib.0.8 (cached)
-> installed gsl.1.25.1
-> installed zlib.0.8
-> installed ocamlfind.1.9.8
-> installed uri.4.4.0
-> installed yojson.3.0.0
-> installed camlzip.1.13
-> installed lacaml.11.1.1
-> installed ocamlbuild.0.16.1
-> installed base.v0.15.1
-> installed fieldslib.v0.15.0
-> installed variantslib.v0.15.0
-> installed stdio.v0.15.0
-> installed typerep.v0.15.0
-> installed parsexp.v0.15.0
-> installed sexplib.v0.15.1
-> installed topkg.1.1.0
-> installed rresult.0.7.0
-> installed uutf.1.0.4
-> installed fmt.0.11.0
-> installed ptime.1.2.0
-> installed crunch.4.0.0
-> installed gg.1.0.0
-> installed otfm.0.4.0
-> installed menhir.20250912
-> installed tyxml.4.6.0
-> installed ppxlib.0.35.0
-> installed vg.0.9.5
-> installed ppx_optcomp.v0.15.0
-> installed ppx_conv_func.v0.15.0
-> installed ppx_disable_unused_warnings.v0.15.0
-> installed ppx_cold.v0.15.0
-> installed ppx_enumerate.v0.15.0
-> installed ppx_fields_conv.v0.15.0
-> installed ppx_here.v0.15.0
-> installed ppx_compare.v0.15.0
-> installed ppx_variants_conv.v0.15.0
-> installed ppx_typerep_conv.v0.15.0
-> installed ppx_stable.v0.15.0
-> installed ppx_pipebang.v0.15.0
-> installed ppx_ignore_instrumentation.v0.15.0
-> installed ppx_optional.v0.15.0
-> installed ppx_fixed_literal.v0.15.0
-> installed ppx_sexp_conv.v0.15.1
-> installed ppx_deriving.6.0.3
-> installed ppx_let.v0.15.0
-> installed ppx_hash.v0.15.0
-> installed ppx_sexp_value.v0.15.0
-> installed ppx_assert.v0.15.0
-> installed ppx_sexp_message.v0.15.0
-> installed ppx_custom_printf.v0.15.0
-> installed ppx_base.v0.15.0
-> installed ppx_log.v0.15.0
-> installed jst-config.v0.15.1
-> installed sexp_pretty.v0.15.1
-> installed bin_prot.v0.15.0
-> installed ppx_string.v0.15.0
-> installed time_now.v0.15.0
-> installed ppx_bin_prot.v0.15.0
-> installed ppx_module_timer.v0.15.0
-> installed ppx_inline_test.v0.15.1
-> installed ppx_bench.v0.15.1
-> installed ppx_expect.v0.15.1
-> installed splittable_random.v0.15.0
-> installed base_quickcheck.v0.15.0
-> installed uucp.17.0.0
-> installed printbox-text.0.12
-> installed ppx_jane.v0.15.0
-> installed int_repr.v0.15.0
-> installed base_bigstring.v0.15.0
-> installed core.v0.15.1
-> installed csvfields.v0.15.1
-> installed expect_test_helpers_core.v0.15.0
-> installed timezone.v0.15.0
-> installed ppx_csv_conv.v0.15.0
-> installed core_kernel.v0.15.0
-> installed core_unix.v0.15.2
-> installed biotk.0.2.0
-> installed phylogenetics.0.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 13:33.00 ---> saved as "3289aad9b1da8e3c85f1c659708ad441f95da83557824ee09edf87d9545831ce"
/home/opam: (run (network host)
(shell "(opam reinstall --with-test phylogenetics.0.2.0) || true"))
The following actions will be performed:
=== recompile 1 package
- recompile phylogenetics 0.2.0
=== install 2 packages
- install alcotest 1.9.0 [required by phylogenetics]
- install astring 0.8.5 [required by alcotest]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> retrieved alcotest.1.9.0 (https://opam.ocaml.org/cache)
-> retrieved astring.0.8.5 (https://opam.ocaml.org/cache)
-> retrieved phylogenetics.0.2.0 (https://opam.ocaml.org/cache)
-> removed phylogenetics.0.2.0
-> installed astring.0.8.5
-> installed alcotest.1.9.0
-> installed phylogenetics.0.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 13:33.15 ---> saved as "2d98d9c012bda869ddddf172783f8777de0c3ff7f559c8b0a6052f86ee5aec6b"
/home/opam: (run (shell "opam reinstall --with-test --verbose phylogenetics.0.2.0;\
\n res=$?;\
\n test \"$res\" != 31 && exit \"$res\";\
\n export OPAMCLI=2.0;\
\n build_dir=$(opam var prefix)/.opam-switch/build;\
\n failed=$(ls \"$build_dir\");\
\n partial_fails=\"\";\
\n for pkg in $failed; do\
\n if opam show -f x-ci-accept-failures: \"$pkg\" | grep -qF \"\\\"debian-13\\\"\"; then\
\n echo \"A package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\";\
\n fi;\
\n test \"$pkg\" != 'phylogenetics.0.2.0' && partial_fails=\"$partial_fails $pkg\";\
\n done;\
\n test \"${partial_fails}\" != \"\" && echo \"opam-repo-ci detected dependencies failing: ${partial_fails}\";\
\n exit 1"))
The following actions will be performed:
=== recompile 1 package
- recompile phylogenetics 0.2.0
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/4: [phylogenetics.0.2.0: extract]
-> retrieved phylogenetics.0.2.0 (cached)
Processing 2/4: [phylogenetics: dune build]
+ /home/opam/.opam/opam-init/hooks/sandbox.sh "build" "dune" "build" "-p" "phylogenetics" "-j" "255" "@install" "@runtest" (CWD=/home/opam/.opam/4.14/.opam-switch/build/phylogenetics.0.2.0)
- (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.
- (cd _build/default/app && ./test_app.exe -q)
- Testing `All tests'.
- This run has ID `2QRMVZI1'.
-
- [OK] Sequence 0 of_string.
- [OK] Alignment 0 of_string_list.
- [OK] Alignment 1 of_fasta.
- [OK] Alignment 2 get_base.
- [OK] Phylogenetic_tree 0 of_preorder.
- [OK] Zipper 0 of_tree (check subtrees).
- [OK] Zipper 1 of_tree (check lengths).
- [OK] Zipper 2 of_tree and back to_tree.
- [OK] Zipper 3 of_tree_dir, move_left and ba...
- [OK] Zipper 4 goto vs several moves.
- [OK] Models 0 JC69 exponential.
- [OK] Models 1 K80 exponential.
- [SKIP] Felsenstein 0 test against bppml JC69 trees...
- [SKIP] Felsenstein 1 test against bppml JC69 trees...
- [SKIP] Felsenstein 2 test against bppml JC69 trees...
- [SKIP] Felsenstein 3 test against bppml JC69 trees...
- [SKIP] Felsenstein 4 test against bppml K80(kappa=...
- [SKIP] Felsenstein 5 test against bppml K80(kappa=...
- [SKIP] Felsenstein 6 test against bppml K80(kappa=...
- [SKIP] Felsenstein 7 test against bppml K80(kappa=...
- [SKIP] Felsenstein 8 test against bppml K80(kappa=...
- [SKIP] Felsenstein 9 test against bppml K80(kappa=...
- [SKIP] Felsenstein 10 test against bppml K80(kappa=...
- [SKIP] Felsenstein 11 test against bppml K80(kappa=...
- [SKIP] Felsenstein 12 test against bppml JC69 trees...
- [SKIP] Felsenstein 13 test against bppml JC69 trees...
- [SKIP] Felsenstein 14 test against bppml JC69 trees...
- [SKIP] Felsenstein 15 test against bppml JC69 trees...
- [SKIP] Felsenstein 16 test against bppml K80(kappa=...
- [SKIP] Felsenstein 17 test against bppml K80(kappa=...
- [SKIP] Felsenstein 18 test against bppml K80(kappa=...
- [SKIP] Felsenstein 19 test against bppml K80(kappa=...
- [SKIP] Rejection_sampling 0 Specific branch length on tin...
- [SKIP] MCMC 0 Specific branch length on tin...
- [OK] Newick 0 just_parse_test1.
- [OK] Newick 1 just_parse_test2.
- [OK] PhyloCTMC 0 Felsenstein vs Phylo_ctmc.
- [OK] PhyloCTMC 1 Cond. lik. simple vs ambiguous.
-
- Full test results in `~/.opam/4.14/.opam-switch/build/phylogenetics.0.2.0/_build/default/app/_build/_tests/All tests'.
- Test Successful in 0.021s. 16 tests run.
-> compiled phylogenetics.0.2.0
-> removed phylogenetics.0.2.0
-> installed phylogenetics.0.2.0
Done.
# To update the current shell environment, run: eval $(opam env)
2025-09-18 13:33.27 ---> saved as "60acd2d6a72f88e9994612dd5950c07b49f3a661bb0a72439ebf33915a6b9d17"
Job succeeded
2025-09-18 13:33.32: Job succeeded