The centralized nightlies job failed on Tuesday (2024-05-14)

[github-actions]

The centralized nightlies job failed on Tuesday (2024-05-14) in run 9088948929

[github-actions]

The centralized nightlies job failed on Wednesday (2024-05-15) in run 9088948929

[jdblischak]

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

[jdblischak]

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, TileDB-Inc/TileDB-VCF#719 and TileDB-Inc/TileDB-VCF#720.

[github-actions]

The centralized nightlies job failed on Wednesday (2024-05-15) in run 9105398398

[jdblischak]

The libtiledbvcf tests failed, but this was just fixed upstream in TileDB-Inc/TileDB-VCF@7bc5d5d (TileDB-Inc/TileDB-VCF#722)

[jdblischak]

The TileDB-GO build failed again. A PR with a fix has been opened in TileDB-Inc/TileDB-Go#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.

Also see TileDB-Inc/TileDB-Go#314

[jdblischak]

After changing the TileDB-GO branch in jdblischak@be2ce96, 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.

[johnkerl]

now both TileDB-Py and TileDB-SOMA-R are failing their tests

TileDB-Inc/TileDB-Py#1970
single-cell-data/TileDB-SOMA#2573