Closed github-actions[bot] closed 3 months ago
The centralized nightlies job failed on Wednesday (2024-05-15) in run 9088948929
I was expecting TileDB-GO to fail since it failed while I was troubleshooting other things yesterday. However, the TileDB-VCF-Py failure was unexpected.
First there was a test failure:
=========================== short test summary info ============================
FAILED tests/test_tiledbvcf.py::test_ingest_with_stats - assert (1, 8) == (3, 8)
At index 0 diff: 1 != 3
Full diff:
(
- 3,
? ^
+ 1,
? ^
8,
)
============ 1 failed, 51 passed, 2 skipped, 159 warnings in 31.83s ============
I restarted it, but the second time it failed the configuration step during the build:
Building wheels for collected packages: tiledbvcf
Building wheel for tiledbvcf (pyproject.toml): started
Running command Building wheel for tiledbvcf (pyproject.toml)
*** scikit-build-core 0.9.4 using CMake 3.29.3 (wheel)
*** Configuring CMake...
loading initial cache file build/cp311-cp311-linux_x86_64/CMakeInit.txt
-- The CXX compiler identification is GNU 11.4.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Searching for libtiledbvcf in /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/apis/python/../../dist/lib;/home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/apis/python/dist_links/dist/lib;/home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledbvcf/lib/
-- Found libtiledbvcf: /home/runner/work/centralized-tiledb-nightlies/centralized-tiledb-nightlies/install-libtiledbvcf/lib/libtiledbvcf.so
CMake Error at CMakeLists.txt:114 (find_package):
By not providing "FindTileDB.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "TileDB", but
CMake did not find one.
Could not find a package configuration file provided by "TileDB" with any
of the following names:
TileDBConfig.cmake
tiledb-config.cmake
Add the installation prefix of "TileDB" to CMAKE_PREFIX_PATH or set
"TileDB_DIR" to a directory containing one of the above files. If "TileDB"
provides a separate development package or SDK, be sure it has been
installed.
-- Configuring incomplete, errors occurred!
*** CMake configuration failed
error: subprocess-exited-with-error
The first attempt with the test failure used libtiledb 42dbf36 and TileDB-VCF 1416d09.
The second attempt with the configuration failure also used libtiledb 42dbf36 but this time used TileDB-VCF 87e332c. This included 2 additional PRs, https://github.com/TileDB-Inc/TileDB-VCF/pull/719 and https://github.com/TileDB-Inc/TileDB-VCF/pull/720.
The centralized nightlies job failed on Wednesday (2024-05-15) in run 9105398398
The libtiledbvcf tests failed, but this was just fixed upstream in https://github.com/TileDB-Inc/TileDB-VCF/commit/7bc5d5dddc467f19842157725cabf6b53b05e8d9 (https://github.com/TileDB-Inc/TileDB-VCF/pull/722)
The TileDB-GO build failed again. A PR with a fix has been opened in https://github.com/TileDB-Inc/TileDB-Go/pull/313. However, this is incompatible with the current release branch, so we can't merge it yet. Thus to fix the nightlies, I am going to temporarily switch to using the branch smr/sc-47198/update-array-deserialize-params.
After changing the TileDB-GO branch in https://github.com/jdblischak/centralized-tiledb-nightlies/commit/be2ce9603c7a88434e62316f5f66941c71c0c187, both TileDB-GO and and libtiledbvcf passed. Thus I am going to close this Issue.
However, note that now both TileDB-Py and TileDB-SOMA-R are failing their tests. I'll let the pipeline open a new Issue tonight to address these.
now both TileDB-Py and TileDB-SOMA-R are failing their tests
https://github.com/TileDB-Inc/TileDB-Py/pull/1970 https://github.com/single-cell-data/TileDB-SOMA/pull/2573
The centralized nightlies job failed on Tuesday (2024-05-14) in run 9088948929