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Nightly feedstock build failed #230
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Documenting the errors:
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Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
As expected, the R build continues to fail due to C++20 compilation issues. Today I did another experiment. I purposefully skipped the R client build in order to query the status of the Python build with C++20. Note that this build used the commit single-cell-data/TileDB-SOMA@ea3cd1a that was merged earlier this morning. First the good news:
But then the bad news:
The backtrace is super long (600+ lines) and only ends because Python core dumps. Below is the beginning and end of the backtrace. Note that I've also replaced the long conda installation path with
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I searched for the error message from the failed R package build on linux-64: From what I could find, I think we may need to define |
@jdblischak I agree this is probably |
And for tinkering with the feedstock recipe and/or scripts, you can start from the branch nightly-build. It gets overwritten every night, so if you want your experiments to persist beyond a day, I recommend creating a new branch. |
@jdblischak I believe this will be fixed by #231 which addresses precisely this problem. I'm looking at #231 (comment) and trying to decide what to sequence to make this all work ... 🤔 |
Re #231 (comment) I may be confused but I think we just need to merge #231 to address that bit. |
@jdblischak sorry, I need to sync with you tomorrow ... |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
I already tried applying your commit to update |
OK I'm entirely confused. I'll need to sit down and pencil-and-paper out the repro steps I need to follow to make this happen interactively, debug, and fix. Sorry for the delay. |
Today I setting The results:
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I created a dedicated branch for troubleshooting the C++20 compilation errors https://github.com/TileDB-Inc/tiledbsoma-feedstock/tree/troubleshoot-cpp20 It pulls from the main branch of TileDB-SOMA (to mimic the nightly builds). I applied your fix from #231 and also updated the macOS SDK to 13.3 To troubleshoot, you can either push commits directly to this branch (or you can spin off your own branch if you'd prefer). Once we have a working feedstock build, then I'll worry about fixing the setup scripts for the nightly build. |
Thanks @jdblischak ! I'll check my notes on how to 'drive' a branch interactively rather than waiting for the nightlies (which is how I usually interact with this repo) |
Quick update. This didn't fix the osx-arm64 build of r-tiledbsoma. And I can tell why now. Despite having conda install version 13.3 of the macOS SDK, the compiler is still passed |
Also, another interesting development. After updating the macOS SDK to 13.3, the error message from the failed import test for Python is more informative: import: 'tiledbsoma'
Traceback (most recent call last):
File "/Users/runner/miniforge3/conda-bld/tiledbsoma_1732303363846/test_tmp/run_test.py", line 2, in <module>
import tiledbsoma
File "$PREFIX/lib/python3.9/site-packages/tiledbsoma/__init__.py", line 166, in <module>
from ._experiment import Experiment
File "$PREFIX/lib/python3.9/site-packages/tiledbsoma/_experiment.py", line 18, in <module>
from ._query import ExperimentAxisQuery
File "$PREFIX/lib/python3.9/site-packages/tiledbsoma/_query.py", line 48, in <module>
from somacore.query.query import (
ImportError: cannot import name 'Numpyable' from 'somacore.query.query' ($PREFIX/lib/python3.9/site-packages/somacore/query/query.py) |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
@jdblischak re
So we do need (at least) an update to |
Closing the loop on 'how to drive': @jdblischak established in Slack:
That's it! I'd failed to realize how much autorun/trigger logic the inestimable John B has set up for this ✨ |
Addendum:
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Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
1 similar comment
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
7 similar comments
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Good news, locally I had a successful build. Resetting the CXXFLAGS to empty for both |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
@XanthosXanthopoulos Awesome! Thanks for working on this. It's great to see progress being made. Looking at your branch xan/cpp20-experiments, it looks like as of 762936e you have successfully compiled r-tiledbsoma for linux-64 and osx-64 (build log). So the remaining to-do items are:
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Ι will work on tiledbsoma-py today. For macos the min version bump is necessary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
14 similar comments
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
1 similar comment
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary |
Nightly feedstock build failure for tiledbsoma-feedstock at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=43&_a=summary
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