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Nightly feedstock build failed #108

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github-actions bot opened this issue Jul 10, 2024 · 32 comments · Fixed by TileDB-Inc/TileDB-Py#2009
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Nightly feedstock build failed #108

github-actions bot opened this issue Jul 10, 2024 · 32 comments · Fixed by TileDB-Inc/TileDB-Py#2009
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@ihnorton @jdblischak @shaunrd0 @kounelisagis @KiterLuc
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary
@jdblischak
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Looks like a real error:

building 'tiledb.cc' extension
creating build/temp.linux-x86_64-cpython-310/tiledb/cc
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev2.2024_07_09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -I$PREFIX/include -I$PREFIX/lib/python3.10/site-packages/pybind11/include -I$PREFIX/lib/python3.10/site-packages/numpy/core/include -I$PREFIX/lib/python3.10/site-packages/numpy/core/include -I$PREFIX/include/python3.10 -c tiledb/cc/array.cc -o build/temp.linux-x86_64-cpython-310/tiledb/cc/array.o -fvisibility=hidden -g0 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev2.2024_07_09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c++17 -Wno-deprecated-declarations -fvisibility=hidden
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev2.2024_07_09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -I$PREFIX/include -I$PREFIX/lib/python3.10/site-packages/pybind11/include -I$PREFIX/lib/python3.10/site-packages/numpy/core/include -I$PREFIX/lib/python3.10/site-packages/numpy/core/include -I$PREFIX/include/python3.10 -c tiledb/cc/attribute.cc -o build/temp.linux-x86_64-cpython-310/tiledb/cc/attribute.o -fvisibility=hidden -g0 -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev2.2024_07_09 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c++17 -Wno-deprecated-declarations -fvisibility=hidden
tiledb/cc/attribute.cc: In lambda function:
tiledb/cc/attribute.cc:110:48: error: 'class tiledb::Attribute' has no member named 'dump'
  110 |       .def("_dump", [](Attribute &attr) { attr.dump(); });
      |                                                ^~~~
error: command '/home/conda/feedstock_root/build_artifacts/tiledb-py_1720580993389/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

@KiterLuc
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@kounelisagis This is after merging your PR.

@jdblischak
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xref: TileDB-Inc/TileDB#5026

This was referenced Jul 10, 2024
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@kounelisagis
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To be fixed by TileDB-Inc/TileDB#5179

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@github-actions GitHub Actions
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@github-actions GitHub Actions
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@github-actions GitHub Actions
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@jdblischak
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There was a new error for tiledb-py-feedstock that started last night:

$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev3.2024_07_16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -I$PREFIX/include -I$PREFIX/lib/python3.9/site-packages/pybind11/include -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/include/python3.9 -c tiledb/libtiledb.cpp -o build/temp.linux-x86_64-cpython-39/tiledb/libtiledb.o -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev3.2024_07_16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c++17 -Wno-deprecated-declarations
In file included from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721185799040/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721185799040/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721185799040/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from tiledb/libtiledb.cpp:775:
/home/conda/feedstock_root/build_artifacts/tiledb-py_1721185799040/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
tiledb/libtiledb.pyx: In function 'PyObject* __pyx_pf_6tiledb_9libtiledb_5Array_32delete_fragments(__pyx_obj_6tiledb_9libtiledb_Array*, PyObject*, PyObject*, PyObject*)':
tiledb/libtiledb.pyx:1342:18: error: 'tiledb_array_delete_fragments' was not declared in this scope; did you mean 'tiledb_array_delete_fragments_v2'?
 1342 |             rc = tiledb_array_delete_fragments(
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                  tiledb_array_delete_fragments_v2
error: command '/home/conda/feedstock_root/build_artifacts/tiledb-py_1721185799040/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

@KiterLuc
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@teo-tsirpanis we missed this?

@teo-tsirpanis
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This codepath is deprecated and warns. We must change it to throw. I am working on it.

The Python API has migrated in TileDB-Inc/TileDB-Py#1958, this was the only usage and intended as a transitional measure.

@teo-tsirpanis teo-tsirpanis mentioned this issue Jul 17, 2024
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Nightly feedstock build failure for tiledbfeedstock_CI at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=4&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@teo-tsirpanis
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https://github.com/TileDB-Inc/tiledb-feedstock/blob/main/recipe/lz4-fix.patch fails to apply. It is no longer needed.

@jdblischak
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https://github.com/TileDB-Inc/tiledb-feedstock/blob/main/recipe/lz4-fix.patch fails to apply. It is no longer needed.

@teo-tsirpanis thanks for the quick diagnosis! I'll send a PR to fix this for the nightly build (I've done this before in #99)

This was referenced Jul 18, 2024
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Nightly feedstock build failure for tiledbfeedstock_CI at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=4&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@jdblischak
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Nothing new here. These are the same failures from Wednesday night. I broke the setup job, so no new builds ran last night (#110, #112). I chose a good time to break it since Azure was down last night anyways (conda-forge/status#184)

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@jdblischak
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tiledb-py-feedstock is still failing. Waiting on this upstream PR to be merged: TileDB-Inc/TileDB-Py#2009

$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev3.2024_07_21 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -fPIC -I$PREFIX/include -I$PREFIX/lib/python3.9/site-packages/pybind11/include -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/lib/python3.9/site-packages/numpy/core/include -I$PREFIX/include/python3.9 -c tiledb/libtiledb.cpp -o build/temp.linux-x86_64-cpython-39/tiledb/libtiledb.o -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/tiledb-py-0.30.3.dev3.2024_07_21 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -std=c++17 -Wno-deprecated-declarations
In file included from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721618389794/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960,
                 from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721618389794/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /home/conda/feedstock_root/build_artifacts/tiledb-py_1721618389794/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from tiledb/libtiledb.cpp:775:
/home/conda/feedstock_root/build_artifacts/tiledb-py_1721618389794/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
tiledb/libtiledb.pyx: In function 'PyObject* __pyx_pf_6tiledb_9libtiledb_5Array_32delete_fragments(__pyx_obj_6tiledb_9libtiledb_Array*, PyObject*, PyObject*, PyObject*)':
tiledb/libtiledb.pyx:1342:18: error: 'tiledb_array_delete_fragments' was not declared in this scope; did you mean 'tiledb_array_delete_fragments_v2'?
 1342 |             rc = tiledb_array_delete_fragments(
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                  tiledb_array_delete_fragments_v2
error: command '/home/conda/feedstock_root/build_artifacts/tiledb-py_1721618389794/_build_env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

@teo-tsirpanis
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Yes.

@jdblischak
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Also note that tiledb-py-feedstock is going to fail tonight since the PR to migrate to scikit-build-core (TileDB-Inc/TileDB-Py#1988) was just merged in TileDB-Inc/TileDB-Py@1ff19ef. We'll have to temporarily update the nightly branch to match conda-forge/tiledb-py-feedstock#224

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@jdblischak
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The tiledb-py-feedstock builds all failed because in #114 I used the jinja2 syntax {{PYTHON }} instead of the env var syntax $PYTHON or %PYTHON%

@jdblischak jdblischak mentioned this issue Jul 23, 2024
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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

@jdblischak
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tiledb-py-feedstock is back to failing as expected due to the use of deprecated APIs

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Nightly feedstock build failure for TileDB-Py%20Feedstock%20Testing at https://dev.azure.com/TileDB-Inc/CI/_build?definitionId=5&_a=summary

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Remove deprecated Array.delete_fragments code path. TileDB-Inc/TileDB-Py
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@ihnorton @jdblischak @teo-tsirpanis @shaunrd0 @kounelisagis @KiterLuc