Building on thyme
(from windows-server-2022-amd64-ocaml-5.3)
2026-02-05 13:01.17 ---> using "1d6ffeb5a52124df73b2e951323e99615c52ca4f9bdf0f65039be6146fabdaab" from cache
/: (user (uid 1000) (gid 1000))
/: (env OPAMPRECISETRACKING 1)
/: (env OPAMUTF8 never)
/: (env OPAMEXTERNALSOLVER builtin-0install)
/: (env OPAMCRITERIA +removed)
/: (env CI true)
/: (env OPAM_HEALTH_CHECK_CI true)
/: (run (shell "ln -f /usr/bin/opam-dev.exe /usr/bin/opam.exe"))
2026-02-05 13:01.17 ---> using "75bf3fbea1cbc65a9803f40104651d67c546cddf5606f6a4af6db8fca92eb5c0" from cache
/: (run (network host)
(shell "rm -rf ~/opam-repository && git clone -q 'https://github.com/ocaml/opam-repository' ~/opam-repository && git -C ~/opam-repository checkout -q 8e585b27038b7cc0badd118b2a64ccad8e4c7a5e"))
2026-02-05 13:01.17 ---> using "8a65e32b47e5f5a64f427d0c81ed5103879a61b8d64d8e40001877721503ef2b" from cache
/: (run (shell "rm -rf ~/.opam && opam init -ya --bare ~/opam-repository"))
User configuration:
[NOTE] Make sure that ~\.bash_profile is well sourced in your ~/.bashrc.
Updating ~\.bash_profile.
Added 9 lines after line 1 in ~\.bash_profile.
2026-02-05 13:01.17 ---> using "293540611dffb126dc531ef91ab2e6530071ab5ea9dffcab777e4f62de074c93" from cache
/: (run (cache (opam-archives (target "c:\\Users\\opam\\AppData\\Local\\opam\\download-cache")))
(network host)
(shell "opam switch create --repositories=default '4.14' '4.14.2'"))
<><> Installing new switch packages <><><><><><><><><><><><><><><><><><><><><><>
Switch invariant: ["ocaml-base-compiler" {= "4.14.2"} | "ocaml-system" {= "4.14.2"}]
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
-> installed arch-x86_64.1
-> installed base-bigarray.base
-> installed base-threads.base
-> installed base-unix.base
-> installed host-arch-x86_64.1
-> installed host-system-mingw.1
-> retrieved flexdll.0.44 (cached)
-> retrieved ocaml-config.3 (cached)
-> installed flexdll.0.44
-> installed ocaml-options-vanilla.1
-> retrieved mingw-w64-shims.0.2.0 (cached)
-> installed conf-mingw-w64-gcc-x86_64.1
-> installed ocaml-env-mingw64.1
-> installed system-mingw.1
-> retrieved ocaml-base-compiler.4.14.2 (cached)
-> installed mingw-w64-shims.0.2.0
-> installed ocaml-base-compiler.4.14.2
-> installed ocaml-config.3
-> installed ocaml.4.14.2
Done.
# To update the current shell environment, run: eval $(opam env --switch=4.14)
2026-02-05 13:01.17 ---> using "760ee651c109b148a38e848a0883027a3b8784a85792f7cc55e92c8bbfe74ca5" from cache
/: (run (network host)
(shell "opam update --depexts"))
2026-02-05 13:01.17 ---> using "3a993158c6ed121079e7ac5ad3d35ddbe822946d02a3cec105aeacac9ea62822" from cache
/: (run (cache (opam-archives (target "c:\\Users\\opam\\AppData\\Local\\opam\\download-cache")))
(network host)
(shell "opam remove -y phylogenetics.0.1.0\
\nopam install -vy phylogenetics.0.1.0\
\nres=$?\
\nif [ $res = 31 ]; then\
\n if opam show -f x-ci-accept-failures: phylogenetics.0.1.0 | grep -q 'windows-server-2022-amd64-ocaml-5.3'; then\
\n echo \"This package failed and has been disabled for CI using the 'x-ci-accept-failures' field.\"\
\n exit 69\
\n fi\
\nfi \
\n\
\n\
\nexit $res"))
Nothing to do.
[NOTE] phylogenetics.0.1.0 is not installed.
The following actions will be performed:
=== recompile 1 package
- recompile mingw-w64-shims 0.2.0 [uses conf-mingw-w64-gcc-i686]
=== install 94 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 1.13 [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-mingw-w64-gcc-i686 1 [required by conf-mingw-w64-zlib-i686]
- install conf-mingw-w64-zlib-i686 1 [required by conf-zlib]
- install conf-mingw-w64-zlib-x86_64 1 [required by conf-zlib]
- 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 3.20.2 [required by phylogenetics]
- install dune-configurator 3.20.2 [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 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 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 0.1.0
- 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:
m4 mingw64-i686-gcc-core mingw64-i686-zlib mingw64-x86_64-zlib
<><> Handling external dependencies <><><><><><><><><><><><><><><><><><><><><><>
opam believes some required external dependencies are missing. opam can:
> 1. Run C:\Users\opam\AppData\Local\opam\.cygwin\setup-x86_64.exe to install them (may need root/sudo access)
2. Display the recommended C:\Users\opam\AppData\Local\opam\.cygwin\setup-x86_64.exe 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
+ C:\Users\opam\AppData\Local\opam\.cygwin\setup-x86_64.exe "--root" "C:\\cygwin64" "--quiet-mode" "unattended" "--no-shortcuts" "--no-startmenu" "--no-desktop" "--no-admin" "--no-version-check" "--no-write-registry" "--packages" "m4,mingw64-i686-gcc-core,mingw64-i686-zlib,mingw64-x86_64-zlib"
- Starting cygwin install, version 2.935
- User has backup/restore rights
- User has symlink creation right
- Current Directory: C:\Windows\system32
- root: C:\cygwin64 system
- Changing gid to Administrators
- Selected local directory: C:\Windows\system32
- net: Preconfig
- site: https://cygwin.mirror.constant.com/
- solving: 5 tasks, update: no, use test packages: no
- solving: 10 tasks, update: no, use test packages: no
- Augmented Transaction List:
- 0 install gettext-locale-alias 0.26-1
- 1 install m4 1.4.20-1
- 2 install mingw64-i686-binutils 2.45.1-1
- 3 install mingw64-i686-windows-default-manifest 6.4-1
- 4 install mingw64-i686-winpthreads 13.0.0-1
- 5 install mingw64-i686-zlib 1.3.1-1
- 6 install mingw64-x86_64-zlib 1.3.1-1
- 7 install mingw64-i686-headers 13.0.0-1
- 8 install mingw64-i686-runtime 13.0.0-1
- 9 install mingw64-i686-gcc-core 13.4.0-1
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/gettext/gettext-locale-alias/gettext-locale-alias-0.26-1-x86_64.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/m4/m4-1.4.20-1-x86_64.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/mingw64-i686-binutils/mingw64-i686-binutils-2.45.1-1-x86_64.tar.zst
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-windows-default-manifest/mingw64-i686-windows-default-manifest-6.4-1.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-winpthreads/mingw64-i686-winpthreads-13.0.0-1-noarch.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-zlib/mingw64-i686-zlib-1.3.1-1.tar.zst
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-x86_64-zlib/mingw64-x86_64-zlib-1.3.1-1.tar.zst
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-headers/mingw64-i686-headers-13.0.0-1-noarch.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-runtime/mingw64-i686-runtime-13.0.0-1-noarch.tar.xz
- Downloaded C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/mingw64-i686-gcc/mingw64-i686-gcc-core/mingw64-i686-gcc-core-13.4.0-1-x86_64.tar.zst
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/gettext/gettext-locale-alias/gettext-locale-alias-0.26-1-x86_64.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/m4/m4-1.4.20-1-x86_64.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/mingw64-i686-binutils/mingw64-i686-binutils-2.45.1-1-x86_64.tar.zst
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-windows-default-manifest/mingw64-i686-windows-default-manifest-6.4-1.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-winpthreads/mingw64-i686-winpthreads-13.0.0-1-noarch.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-zlib/mingw64-i686-zlib-1.3.1-1.tar.zst
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-x86_64-zlib/mingw64-x86_64-zlib-1.3.1-1.tar.zst
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-headers/mingw64-i686-headers-13.0.0-1-noarch.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/noarch/release/mingw64-i686-runtime/mingw64-i686-runtime-13.0.0-1-noarch.tar.xz
- Extracting from file://C:\Windows\system32/https%3a%2f%2fcygwin.mirror.constant.com%2f/x86_64/release/mingw64-i686-gcc/mingw64-i686-gcc-core/mingw64-i686-gcc-core-13.4.0-1-x86_64.tar.zst
- running: C:\cygwin64\bin\dash.exe "/etc/postinstall/0p_000_autorebase.dash"
- running: C:\cygwin64\bin\dash.exe "/etc/postinstall/0p_update-info-dir.dash"
- running: C:\cygwin64\bin\dash.exe "/etc/postinstall/zp_man-db-update-index.dash"
- Ending cygwin install
- NOTE: you should run 'diskperf -y' to enable the disk statistics
- NOTE: you should run 'diskperf -y' to enable the disk statistics
<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Processing 1/281: [angstrom.0.16.1, angstrom-unix.0.16.1: extract]
Processing 2/281: [angstrom.0.16.1, angstrom-unix.0.16.1: extract] [base.v0.14.3: extract]
Processing 3/281: [angstrom.0.16.1, angstrom-unix.0.16.1: extract] [base.v0.14.3: extract]
Processing 4/281: [angstrom.0.16.1, angstrom-unix.0.16.1: extract] [base.v0.14.3: extract] [base64.3.5.2: http]
-> retrieved angstrom.0.16.1, angstrom-unix.0.16.1 (cached)
Processing 4/281: [base.v0.14.3: extract] [base64.3.5.2: http]
Processing 5/281: [base.v0.14.3: extract] [base64.3.5.2: http] [base_bigstring.v0.14.0: extract]
Processing 5/281: [base.v0.14.3: extract] [base64.3.5.2: extract] [base_bigstring.v0.14.0: extract]
Processing 5/281: [base.v0.14.3/fix-mpopcnt.patch: dl] [base64.3.5.2: extract] [base_bigstring.v0.14.0: extract]
-> retrieved base64.3.5.2 (https://github.com/mirage/ocaml-base64/releases/download/v3.5.2/base64-3.5.2.tbz)
Processing 5/281: [base.v0.14.3/fix-mpopcnt.patch: dl] [base_bigstring.v0.14.0: extract]
Processing 6/281: [base.v0.14.3/fix-mpopcnt.patch: dl] [base_bigstring.v0.14.0: extract] [base_quickcheck.v0.14.1: extract]
-> retrieved base.v0.14.3 (cached)
Processing 6/281: [base_bigstring.v0.14.0: extract] [base_quickcheck.v0.14.1: extract]
Processing 7/281: [base_bigstring.v0.14.0: extract] [base_quickcheck.v0.14.1: extract] [bigstringaf.0.10.0: extract]
-> retrieved base_bigstring.v0.14.0 (cached)
Processing 7/281: [base_quickcheck.v0.14.1: extract] [bigstringaf.0.10.0: extract]
Processing 8/281: [base_quickcheck.v0.14.1: extract] [bigstringaf.0.10.0: extract] [bin_prot.v0.14.1: extract]
-> retrieved base_quickcheck.v0.14.1 (cached)
Processing 8/281: [bigstringaf.0.10.0: extract] [bin_prot.v0.14.1: extract]
Processing 9/281: [bigstringaf.0.10.0: extract] [bin_prot.v0.14.1: extract] [biocaml.0.11.1: extract]
-> retrieved bigstringaf.0.10.0 (cached)
Processing 9/281: [bin_prot.v0.14.1: extract] [biocaml.0.11.1: extract]
Processing 10/281: [bin_prot.v0.14.1: extract] [biocaml.0.11.1: extract] [camlp-streams.5.0.1: extract]
-> retrieved bin_prot.v0.14.1 (cached)
Processing 10/281: [biocaml.0.11.1: extract] [camlp-streams.5.0.1: extract]
Processing 11/281: [biocaml.0.11.1: extract] [camlp-streams.5.0.1: extract] [camlzip.1.13: extract]
-> retrieved biocaml.0.11.1 (cached)
Processing 11/281: [camlp-streams.5.0.1: extract] [camlzip.1.13: extract]
Processing 12/281: [camlp-streams.5.0.1: extract] [camlzip.1.13: extract] [cfstream.1.3.2: extract]
-> retrieved camlp-streams.5.0.1 (cached)
Processing 12/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
-> retrieved conf-blas.1 (cached)
Processing 13/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 14/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
-> retrieved conf-lapack.1 (cached)
Processing 15/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 16/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 17/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 18/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 19/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 20/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 21/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract]
Processing 22/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract]
Processing 23/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh]
Processing 24/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh]
Processing 25/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4]
Processing 26/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc]
Processing 27/281: [camlzip.1.13: extract] [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved camlzip.1.13 (cached)
Processing 27/281: [cfstream.1.3.2: extract] [core.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 28/281: [cfstream.1.3.2: extract] [core.v0.14.1: extract] [core_kernel.v0.14.2: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved cfstream.1.3.2 (cached)
Processing 28/281: [core.v0.14.1: extract] [core_kernel.v0.14.2: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 29/281: [core.v0.14.1: extract] [core_kernel.v0.14.2: extract] [cppo.1.8.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved core.v0.14.1 (cached)
Processing 29/281: [core_kernel.v0.14.2: extract] [cppo.1.8.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 30/281: [core_kernel.v0.14.2: extract] [cppo.1.8.0: extract] [csexp.1.5.2: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved core_kernel.v0.14.2 (cached)
Processing 30/281: [cppo.1.8.0: extract] [csexp.1.5.2: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 31/281: [cppo.1.8.0: extract] [csexp.1.5.2: extract] [dune.3.20.2, dune-configurator.3.20.2: http] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved cppo.1.8.0 (cached)
Processing 31/281: [csexp.1.5.2: extract] [dune.3.20.2, dune-configurator.3.20.2: http] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 32/281: [csexp.1.5.2: extract] [dune.3.20.2, dune-configurator.3.20.2: http] [fieldslib.v0.14.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved csexp.1.5.2 (cached)
Processing 32/281: [dune.3.20.2, dune-configurator.3.20.2: http] [fieldslib.v0.14.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 33/281: [dune.3.20.2, dune-configurator.3.20.2: http] [fieldslib.v0.14.0: extract] [gsl.1.25.1: http] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 33/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [fieldslib.v0.14.0: extract] [gsl.1.25.1: http] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved fieldslib.v0.14.0 (cached)
Processing 33/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: http] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 34/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: http] [jane-street-headers.v0.14.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 34/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jane-street-headers.v0.14.0: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved jane-street-headers.v0.14.0 (cached)
Processing 34/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 35/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-blas: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
+ C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1/test-win.sh (CWD=C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-blas.1)
- /usr/lib/gcc/x86_64-w64-mingw32/13/../../../../x86_64-w64-mingw32/bin/ld: cannot find
: No such file or directory
[ERROR] The compilation of conf-blas.1 failed at "C:\\Users\\opam\\AppData\\Local\\opam\\4.14\\.opam-switch\\build\\conf-blas.1/test-win.sh".
- /usr/lib/gcc/x86_64-w64-mingw32/13/../../../../x86_64-w64-mingw32/bin/ld: cannot find -lblas: No such file or directory
- collect2: error: ld returned 1 exit status
Processing 35/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 36/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-lapack: C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
+ C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1/test-win.sh (CWD=C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-lapack.1)
- /usr/lib/gcc/x86_64-w64-mingw32/13/../../../../x86_64-w64-mingw32/bin/ld: cannot find
: No such file or directory
- /usr/lib/gcc/x86_64-w64-mingw32/13/../../../../x86_64-w64-mingw32/bin/ld: cannot find -llapack: No such file or directory
- collect2: error: ld returned 1 exit status
[ERROR] The compilation of conf-lapack.1 failed at "C:\\Users\\opam\\AppData\\Local\\opam\\4.14\\.opam-switch\\build\\conf-lapack.1/test-win.sh".
Processing 36/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 37/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-m4: sh echo | m4] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
+ C:\cygwin64\bin\sh.exe "-exc" "echo | m4" (CWD=C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-m4.1)
- + echo
- + m4
-
-> compiled conf-m4.1
Processing 37/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> installed conf-m4.1
Processing 38/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [jst-config.v0.14.1: extract] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
-> retrieved jst-config.v0.14.1 (cached)
Processing 38/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
Processing 39/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [lacaml.11.1.1: http] [conf-mingw-w64-gcc-i686: i686-w64-mingw32-gcc] [conf-pkg-config: pkgconf]
+ C:\cygwin64\bin\i686-w64-mingw32-gcc.exe "--version" (CWD=C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-mingw-w64-gcc-i686.1)
- i686-w64-mingw32-gcc (GCC) 13.4.0
- Copyright (C) 2023 Free Software Foundation, Inc.
- This is free software; see the source for copying conditions. There is NO
- warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
-> compiled conf-mingw-w64-gcc-i686.1
Processing 39/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [lacaml.11.1.1: http] [conf-pkg-config: pkgconf]
-> installed conf-mingw-w64-gcc-i686.1
Processing 40/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [lacaml.11.1.1: http] [conf-pkg-config: pkgconf]
Processing 40/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [gsl.1.25.1: extract] [lacaml.11.1.1: extract] [conf-pkg-config: pkgconf]
-> retrieved gsl.1.25.1 (https://github.com/mmottl/gsl-ocaml/releases/download/1.25.1/gsl-1.25.1.tbz)
Processing 40/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [lacaml.11.1.1: extract] [conf-pkg-config: pkgconf]
Processing 41/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [lacaml.11.1.1: extract] [menhir.20250912, menhirCST.20250912, menhirLib.20250912, menhirSdk.20250912: http] [conf-pkg-config: pkgconf]
-> retrieved lacaml.11.1.1 (https://github.com/mmottl/lacaml/releases/download/11.1.1/lacaml-11.1.1.tbz)
Processing 41/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912, menhirCST.20250912, menhirLib.20250912, menhirSdk.20250912: http] [conf-pkg-config: pkgconf]
Processing 42/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912, menhirCST.20250912, menhirLib.20250912, menhirSdk.20250912: http] [mingw-w64-shims.0.2.0: extract] [conf-pkg-config: pkgconf]
Processing 42/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [mingw-w64-shims.0.2.0: extract] [conf-pkg-config: pkgconf]
-> retrieved mingw-w64-shims.0.2.0 (cached)
Processing 42/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [conf-pkg-config: pkgconf]
Processing 43/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [num.1.6: http] [conf-pkg-config: pkgconf]
+ C:\cygwin64\bin\pkgconf.exe "--version" (CWD=C:\Users\opam\AppData\Local\opam\4.14\.opam-switch\build\conf-pkg-config.4)
- 2.5.1
-> compiled conf-pkg-config.4
Processing 43/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [num.1.6: http]
-> removed mingw-w64-shims.0.2.0
Processing 44/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [num.1.6: http]
-> installed conf-pkg-config.4
Processing 45/281: [dune.3.20.2, dune-configurator.3.20.2: extract] [menhir.20250912 + 3 others: extract] [num.1.6: http]
#=== ERROR while compiling conf-gsl.2 =========================================#
"pkg-config": command not found.
<><> Error report <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
+- The following actions were aborted
| - fetch ocaml-compiler-libs v0.12.4
| - fetch ocaml-syntax-shims 1.0.0
| - fetch ocamlbuild 0.16.1
| - fetch ocamlfind 1.9.8
| - fetch octavius 1.2.2
| - fetch parsexp v0.14.2
| - fetch phylogenetics 0.1.0
| - fetch ppx_assert v0.14.0
| - fetch ppx_base v0.14.0
| - fetch ppx_bench v0.14.1
| - fetch ppx_bin_prot v0.14.0
| - fetch ppx_cold v0.14.0
| - fetch ppx_compare v0.14.0
| - fetch ppx_custom_printf v0.14.1
| - fetch ppx_derivers 1.2.1
| - fetch ppx_deriving 5.2.1
| - fetch ppx_enumerate v0.14.0
| - fetch ppx_expect v0.14.2
| - fetch ppx_fields_conv v0.14.2
| - fetch ppx_fixed_literal v0.14.0
| - fetch ppx_hash v0.14.0
| - fetch ppx_here v0.14.0
| - fetch ppx_inline_test v0.14.1
| - fetch ppx_jane v0.14.0
| - fetch ppx_js_style v0.14.1
| - fetch ppx_let v0.14.0
| - fetch ppx_module_timer v0.14.0
| - fetch ppx_optcomp v0.14.3
| - fetch ppx_optional v0.14.0
| - fetch ppx_pipebang v0.14.0
| - fetch ppx_sexp_conv v0.14.3
| - fetch ppx_sexp_message v0.14.1
| - fetch ppx_sexp_value v0.14.0
| - fetch ppx_stable v0.14.1
| - fetch ppx_string v0.14.1
| - fetch ppx_typerep_conv v0.14.2
| - fetch ppx_variants_conv v0.14.2
| - fetch ppxlib 0.25.1
| - fetch printbox 0.5
| - fetch re 1.14.0
| - fetch result 1.5
| - fetch rresult 0.7.0
| - fetch sexplib v0.14.0
| - fetch sexplib0 v0.14.0
| - fetch spawn v0.17.0
| - fetch splittable_random v0.14.0
| - fetch stdio v0.14.0
| - fetch stdlib-shims 0.3.0
| - fetch stringext 1.6.0
| - fetch time_now v0.14.0
| - fetch timezone v0.14.0
| - fetch topkg 1.1.1
| - fetch typerep v0.14.0
| - fetch uri 4.4.0
| - fetch variantslib v0.14.0
| - fetch xmlm 1.4.0
| - install angstrom 0.16.1
| - install angstrom-unix 0.16.1
| - install base v0.14.3
| - install base-bytes base
| - install base64 3.5.2
| - install base_bigstring v0.14.0
| - install base_quickcheck v0.14.1
| - install bigstringaf 0.10.0
| - install bin_prot v0.14.1
| - install biocaml 0.11.1
| - install camlp-streams 5.0.1
| - install camlzip 1.13
| - install cfstream 1.3.2
| - install conf-mingw-w64-zlib-i686 1
| - install conf-mingw-w64-zlib-x86_64 1
| - install conf-zlib 1
| - install core v0.14.1
| - install core_kernel v0.14.2
| - install cppo 1.8.0
| - install csexp 1.5.2
| - install fieldslib v0.14.0
| - install gsl 1.25.1
| - install jane-street-headers v0.14.0
| - install jst-config v0.14.1
| - install lacaml 11.1.1
| - install mingw-w64-shims 0.2.0
| - install ocaml-compiler-libs v0.12.4
| - install ocaml-syntax-shims 1.0.0
| - install ocamlbuild 0.16.1
| - install ocamlfind 1.9.8
| - install octavius 1.2.2
| - install parsexp v0.14.2
| - install phylogenetics 0.1.0
| - install ppx_assert v0.14.0
| - install ppx_base v0.14.0
| - install ppx_bench v0.14.1
| - install ppx_bin_prot v0.14.0
| - install ppx_cold v0.14.0
| - install ppx_compare v0.14.0
| - install ppx_custom_printf v0.14.1
| - install ppx_derivers 1.2.1
| - install ppx_deriving 5.2.1
| - install ppx_enumerate v0.14.0
| - install ppx_expect v0.14.2
| - install ppx_fields_conv v0.14.2
| - install ppx_fixed_literal v0.14.0
| - install ppx_hash v0.14.0
| - install ppx_here v0.14.0
| - install ppx_inline_test v0.14.1
| - install ppx_jane v0.14.0
| - install ppx_js_style v0.14.1
| - install ppx_let v0.14.0
| - install ppx_module_timer v0.14.0
| - install ppx_optcomp v0.14.3
| - install ppx_optional v0.14.0
| - install ppx_pipebang v0.14.0
| - install ppx_sexp_conv v0.14.3
| - install ppx_sexp_message v0.14.1
| - install ppx_sexp_value v0.14.0
| - install ppx_stable v0.14.1
| - install ppx_string v0.14.1
| - install ppx_typerep_conv v0.14.2
| - install ppx_variants_conv v0.14.2
| - install ppxlib 0.25.1
| - install printbox 0.5
| - install re 1.14.0
| - install result 1.5
| - install rresult 0.7.0
| - install sexplib v0.14.0
| - install sexplib0 v0.14.0
| - install spawn v0.17.0
| - install splittable_random v0.14.0
| - install stdio v0.14.0
| - install stdlib-shims 0.3.0
| - install stringext 1.6.0
| - install time_now v0.14.0
| - install timezone v0.14.0
| - install topkg 1.1.1
| - install typerep v0.14.0
| - install uri 4.4.0
| - install variantslib v0.14.0
| - install xmlm 1.4.0
+-
+- The following actions failed
| - fetch dune.3.20.2, dune-configurator.3.20.2
| - fetch menhir.20250912, menhirCST.20250912, menhirLib.20250912, menhirSdk.20250912
| - fetch num 1.6
| - build conf-gsl 2
+-
+- The following changes have been performed (the rest was aborted)
| - remove mingw-w64-shims 0.2.0
| - install conf-blas 1
| - install conf-lapack 1
| - install conf-m4 1
| - install conf-mingw-w64-gcc-i686 1
| - install conf-pkg-config 4
+-
# To update the current shell environment, run: eval $(opam env)
The former state can be restored with:
C:\cygwin64\bin\opam.exe switch import "C:\\Users\\opam\\AppData\\Local\\opam\\4.14\\.opam-switch\\backup\\state-20260205130342.export"
'C:\cygwin64\bin\opam.exe install -vy phylogenetics.0.1.0' failed.
"opam remove -y phylogenetics.0.1.0
opam install -vy phylogenetics.0.1.0
res=$?
if [ $res = 31 ]; then
if opam show -f x-ci-accept-failures: phylogenetics.0.1.0 | grep -q 'windows-server-2022-amd64-ocaml-5.3'; then
echo "This package failed and has been disabled for CI using the 'x-ci-accept-failures' field."
exit 69
fi
fi
exit $res" failed with exit status 31
Failed: Build failed
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