2023-09-23T22:11:49,314 Created temporary directory: /tmp/pip-build-tracker-ehjo9l69
2023-09-23T22:11:49,315 Initialized build tracking at /tmp/pip-build-tracker-ehjo9l69
2023-09-23T22:11:49,315 Created build tracker: /tmp/pip-build-tracker-ehjo9l69
2023-09-23T22:11:49,316 Entered build tracker: /tmp/pip-build-tracker-ehjo9l69
2023-09-23T22:11:49,316 Created temporary directory: /tmp/pip-wheel-h3eao8ll
2023-09-23T22:11:49,319 Created temporary directory: /tmp/pip-ephem-wheel-cache-50jj1xr7
2023-09-23T22:11:49,341 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-23T22:11:49,344 2 location(s) to search for versions of hg38genome:
2023-09-23T22:11:49,344 * https://pypi.org/simple/hg38genome/
2023-09-23T22:11:49,344 * https://www.piwheels.org/simple/hg38genome/
2023-09-23T22:11:49,345 Fetching project page and analyzing links: https://pypi.org/simple/hg38genome/
2023-09-23T22:11:49,346 Getting page https://pypi.org/simple/hg38genome/
2023-09-23T22:11:49,348 Found index url https://pypi.org/simple/
2023-09-23T22:11:49,599 Fetched page https://pypi.org/simple/hg38genome/ as application/vnd.pypi.simple.v1+json
2023-09-23T22:11:49,601   Skipping link: No binaries permitted for hg38genome: https://files.pythonhosted.org/packages/5e/a3/aff794f9c8ba2e6966956316359ec5eeace1e3863e90c58791b981b9d7a8/hg38genome-1.0.0-cp310-cp310-macosx_13_0_x86_64.whl (from https://pypi.org/simple/hg38genome/) (requires-python:>=3.10,<4.0)
2023-09-23T22:11:49,602   Found link https://files.pythonhosted.org/packages/5b/b9/19304a5b457915528a2e903dcf5f8c80dd56674dcbb157298ac17f21a17c/hg38genome-1.0.0.tar.gz (from https://pypi.org/simple/hg38genome/) (requires-python:>=3.10,<4.0), version: 1.0.0
2023-09-23T22:11:49,603   Skipping link: No binaries permitted for hg38genome: https://files.pythonhosted.org/packages/48/90/1d0982676ea038152d538999ec3b08767449f2b169ce21cd18cd6915569f/hg38genome-1.0.1-cp310-cp310-macosx_13_0_x86_64.whl (from https://pypi.org/simple/hg38genome/) (requires-python:>=3.10,<4.0)
2023-09-23T22:11:49,604   Found link https://files.pythonhosted.org/packages/9e/ff/ea8fba6573ccf1bf9bb65b80933435bfc3b8cf17103d507bfefbcaabc46d/hg38genome-1.0.1.tar.gz (from https://pypi.org/simple/hg38genome/) (requires-python:>=3.10,<4.0), version: 1.0.1
2023-09-23T22:11:49,605 Fetching project page and analyzing links: https://www.piwheels.org/simple/hg38genome/
2023-09-23T22:11:49,606 Getting page https://www.piwheels.org/simple/hg38genome/
2023-09-23T22:11:49,607 Found index url https://www.piwheels.org/simple/
2023-09-23T22:11:49,778 Fetched page https://www.piwheels.org/simple/hg38genome/ as text/html
2023-09-23T22:11:49,780 Skipping link: not a file: https://www.piwheels.org/simple/hg38genome/
2023-09-23T22:11:49,780 Skipping link: not a file: https://pypi.org/simple/hg38genome/
2023-09-23T22:11:49,799 Given no hashes to check 1 links for project 'hg38genome': discarding no candidates
2023-09-23T22:11:49,817 Collecting hg38genome==1.0.0
2023-09-23T22:11:49,819   Created temporary directory: /tmp/pip-unpack-v700gskf
2023-09-23T22:11:50,506   Downloading hg38genome-1.0.0.tar.gz (46.6 MB)
2023-09-23T22:12:09,140   Added hg38genome==1.0.0 from https://files.pythonhosted.org/packages/5b/b9/19304a5b457915528a2e903dcf5f8c80dd56674dcbb157298ac17f21a17c/hg38genome-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-ehjo9l69'
2023-09-23T22:12:09,150   Created temporary directory: /tmp/pip-build-env-vexlhs_n
2023-09-23T22:12:09,155   Installing build dependencies: started
2023-09-23T22:12:09,156   Running command pip subprocess to install build dependencies
2023-09-23T22:12:10,296   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-23T22:12:10,756   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-23T22:12:11,258   Collecting poetry-core>=1.0.0
2023-09-23T22:12:11,295     Using cached https://www.piwheels.org/simple/poetry-core/poetry_core-1.7.0-py3-none-any.whl (426 kB)
2023-09-23T22:12:12,747   Collecting cython>=0.29.32
2023-09-23T22:12:12,752     Obtaining dependency information for cython>=0.29.32 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata
2023-09-23T22:12:12,758     Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-23T22:12:13,486     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2023-09-23T22:12:13,494     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2023-09-23T22:12:13,500     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2023-09-23T22:12:13,507     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2023-09-23T22:12:13,514     Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11)
2023-09-23T22:12:13,894   Collecting numpy>=1.23.5
2023-09-23T22:12:14,861     Using cached https://www.piwheels.org/simple/numpy/numpy-1.25.2-cp311-cp311-linux_armv7l.whl (12.5 MB)
2023-09-23T22:12:16,024   Collecting pandas>=1.5.2
2023-09-23T22:12:18,710     Using cached https://www.piwheels.org/simple/pandas/pandas-2.0.0-cp311-cp311-linux_armv7l.whl (38.5 MB)
2023-09-23T22:12:21,203   Collecting setuptools>=65.5.0
2023-09-23T22:12:21,204     Obtaining dependency information for setuptools>=65.5.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata
2023-09-23T22:12:21,209     Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
2023-09-23T22:12:21,368   Collecting ailist>=2.1.0
2023-09-23T22:12:21,509     Downloading ailist-2.1.0.tar.gz (522 kB)
2023-09-23T22:12:21,608        ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 522.2/522.2 kB 5.8 MB/s eta 0:00:00
2023-09-23T22:12:21,828     Installing build dependencies: started
2023-09-23T22:12:21,829     Running command pip subprocess to install build dependencies
2023-09-23T22:12:23,414     Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-23T22:12:23,906     Collecting poetry-core>=1.0.0
2023-09-23T22:12:23,941       Using cached https://www.piwheels.org/simple/poetry-core/poetry_core-1.7.0-py3-none-any.whl (426 kB)
2023-09-23T22:12:25,327     Collecting cython>=0.29.32
2023-09-23T22:12:25,328       Obtaining dependency information for cython>=0.29.32 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata
2023-09-23T22:12:25,333       Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-23T22:12:26,447     Collecting numpy>=1.23.5
2023-09-23T22:12:27,348       Using cached https://www.piwheels.org/simple/numpy/numpy-1.25.2-cp311-cp311-linux_armv7l.whl (12.5 MB)
2023-09-23T22:12:28,516     Collecting pandas>=1.5.2
2023-09-23T22:12:31,197       Using cached https://www.piwheels.org/simple/pandas/pandas-2.0.0-cp311-cp311-linux_armv7l.whl (38.5 MB)
2023-09-23T22:12:33,671     Collecting setuptools>=65.5.0
2023-09-23T22:12:33,672       Obtaining dependency information for setuptools>=65.5.0 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata
2023-09-23T22:12:33,677       Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB)
2023-09-23T22:12:34,471     Collecting python-dateutil>=2.8.2 (from pandas>=1.5.2)
2023-09-23T22:12:34,507       Using cached https://www.piwheels.org/simple/python-dateutil/python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
2023-09-23T22:12:34,833     Collecting pytz>=2020.1 (from pandas>=1.5.2)
2023-09-23T22:12:34,890       Using cached https://www.piwheels.org/simple/pytz/pytz-2023.3.post1-py3-none-any.whl (502 kB)
2023-09-23T22:12:35,025     Collecting tzdata>=2022.1 (from pandas>=1.5.2)
2023-09-23T22:12:35,055       Using cached https://www.piwheels.org/simple/tzdata/tzdata-2023.3-py2.py3-none-any.whl (341 kB)
2023-09-23T22:12:35,376     Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=1.5.2)
2023-09-23T22:12:35,389       Using cached https://www.piwheels.org/simple/six/six-1.16.0-py2.py3-none-any.whl (11 kB)
2023-09-23T22:12:35,446     Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB)
2023-09-23T22:12:35,490     Using cached setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-23T22:12:37,475     Installing collected packages: pytz, tzdata, six, setuptools, poetry-core, numpy, cython, python-dateutil, pandas
2023-09-23T22:13:23,319     Successfully installed cython-3.0.2 numpy-1.25.2 pandas-2.0.0 poetry-core-1.7.0 python-dateutil-2.8.2 pytz-2023.3.post1 setuptools-68.2.2 six-1.16.0 tzdata-2023.3
2023-09-23T22:13:24,016     Installing build dependencies: finished with status 'done'
2023-09-23T22:13:24,018     Getting requirements to build wheel: started
2023-09-23T22:13:24,020     Running command Getting requirements to build wheel
2023-09-23T22:13:24,382     Getting requirements to build wheel: finished with status 'done'
2023-09-23T22:13:24,387     Preparing metadata (pyproject.toml): started
2023-09-23T22:13:24,388     Running command Preparing metadata (pyproject.toml)
2023-09-23T22:13:25,263     Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-23T22:13:25,758   Collecting python-dateutil>=2.8.2 (from pandas>=1.5.2)
2023-09-23T22:13:25,785     Using cached https://www.piwheels.org/simple/python-dateutil/python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
2023-09-23T22:13:26,080   Collecting pytz>=2020.1 (from pandas>=1.5.2)
2023-09-23T22:13:26,116     Using cached https://www.piwheels.org/simple/pytz/pytz-2023.3.post1-py3-none-any.whl (502 kB)
2023-09-23T22:13:26,264   Collecting tzdata>=2022.1 (from pandas>=1.5.2)
2023-09-23T22:13:29,967     Using cached https://www.piwheels.org/simple/tzdata/tzdata-2023.3-py2.py3-none-any.whl (341 kB)
2023-09-23T22:13:30,331   Collecting cython>=0.29.32
2023-09-23T22:13:30,332     Obtaining dependency information for cython>=0.29.32 from https://files.pythonhosted.org/packages/3f/d6/9eed523aeaca42acbaa3e6d3850edae780dc7f8da9df1bf6a2ceb851839c/Cython-0.29.36-py2.py3-none-any.whl.metadata
2023-09-23T22:13:30,338     Using cached Cython-0.29.36-py2.py3-none-any.whl.metadata (3.1 kB)
2023-09-23T22:13:30,404   Collecting pandas>=1.5.2
2023-09-23T22:13:33,193     Using cached https://www.piwheels.org/simple/pandas/pandas-1.5.2-cp311-cp311-linux_armv7l.whl (37.6 MB)
2023-09-23T22:13:35,638   Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=1.5.2)
2023-09-23T22:13:35,658     Using cached https://www.piwheels.org/simple/six/six-1.16.0-py2.py3-none-any.whl (11 kB)
2023-09-23T22:13:35,725   Using cached setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-23T22:13:35,762   Using cached Cython-0.29.36-py2.py3-none-any.whl (988 kB)
2023-09-23T22:13:36,760   Building wheels for collected packages: ailist
2023-09-23T22:13:36,766     Building wheel for ailist (pyproject.toml): started
2023-09-23T22:13:36,767     Running command Building wheel for ailist (pyproject.toml)
2023-09-23T22:13:56,519     Compiling ailist/Interval_core.pyx because it changed.
2023-09-23T22:13:56,519     Compiling ailist/AIList_core.pyx because it changed.
2023-09-23T22:13:56,520     Compiling ailist/LabeledIntervalArray_core.pyx because it changed.
2023-09-23T22:13:56,522     Compiling ailist/array_query_core.pyx because it changed.
2023-09-23T22:13:56,522     [1/4] Cythonizing ailist/AIList_core.pyx
2023-09-23T22:13:56,523     [2/4] Cythonizing ailist/Interval_core.pyx
2023-09-23T22:13:56,524     [3/4] Cythonizing ailist/LabeledIntervalArray_core.pyx
2023-09-23T22:13:56,525     [4/4] Cythonizing ailist/array_query_core.pyx
2023-09-23T22:13:56,965     In file included from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-09-23T22:13:56,966                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-09-23T22:13:56,967                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-09-23T22:13:56,968                      from ailist/Interval_core.c:1183:
2023-09-23T22:13:56,969     /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-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]
2023-09-23T22:13:56,970        17 | #warning "Using deprecated NumPy API, disable it with " \
2023-09-23T22:13:56,971           |  ^~~~~~~
2023-09-23T22:14:07,041     In file included from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-09-23T22:14:07,041                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-09-23T22:14:07,042                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-09-23T22:14:07,043                      from ailist/AIList_core.c:1202:
2023-09-23T22:14:07,044     /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-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]
2023-09-23T22:14:07,045        17 | #warning "Using deprecated NumPy API, disable it with " \
2023-09-23T22:14:07,045           |  ^~~~~~~
2023-09-23T22:15:08,397     In file included from ailist/AIList_core.c:1224:
2023-09-23T22:15:08,398     ailist/src/ailist/ailist_ops.c: In function ‘ailist_subtract_intervals’:
2023-09-23T22:15:08,399     ailist/src/ailist/ailist_ops.c:64:30: warning: ‘iv_end’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-23T22:15:08,400        64 |     if (start < end && start >= iv_end)
2023-09-23T22:15:08,401           |                        ~~~~~~^~~~~~~~~
2023-09-23T22:15:08,401     ailist/src/ailist/ailist_ops.c:28:14: note: ‘iv_end’ was declared here
2023-09-23T22:15:08,402        28 |     uint32_t iv_end;
2023-09-23T22:15:08,403           |              ^~~~~~
2023-09-23T22:15:15,231     In file included from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-09-23T22:15:15,232                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-09-23T22:15:15,232                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-09-23T22:15:15,233                      from ailist/LabeledIntervalArray_core.c:1225:
2023-09-23T22:15:15,234     /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-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]
2023-09-23T22:15:15,235        17 | #warning "Using deprecated NumPy API, disable it with " \
2023-09-23T22:15:15,236           |  ^~~~~~~
2023-09-23T22:15:15,336     In file included from ailist/LabeledIntervalArray_core.c:1253:
2023-09-23T22:15:15,337     ailist/src/labeled_aiarray/labeled_augmented_array.c: In function ‘get_label’:
2023-09-23T22:15:15,338     ailist/src/labeled_aiarray/labeled_augmented_array.c:85:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2023-09-23T22:15:15,339        85 |         return k == kh_end(h)? -1 : kh_val(h, k);
2023-09-23T22:15:15,340           |                                ^~
2023-09-23T22:16:44,421     In file included from ailist/LabeledIntervalArray_core.c:1247:
2023-09-23T22:16:44,421     ailist/src/ailist/ailist_ops.c: In function ‘ailist_subtract_intervals’:
2023-09-23T22:16:44,423     ailist/src/ailist/ailist_ops.c:64:30: warning: ‘iv_end’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-23T22:16:44,424        64 |     if (start < end && start >= iv_end)
2023-09-23T22:16:44,425           |                        ~~~~~~^~~~~~~~~
2023-09-23T22:16:44,426     ailist/src/ailist/ailist_ops.c:28:14: note: ‘iv_end’ was declared here
2023-09-23T22:16:44,427        28 |     uint32_t iv_end;
2023-09-23T22:16:44,427           |              ^~~~~~
2023-09-23T22:17:08,930     In file included from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-09-23T22:17:08,931                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-09-23T22:17:08,932                      from /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-09-23T22:17:08,933                      from ailist/array_query_core.c:1183:
2023-09-23T22:17:08,934     /tmp/pip-build-env-j622kads/overlay/local/lib/python3.11/dist-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]
2023-09-23T22:17:08,935        17 | #warning "Using deprecated NumPy API, disable it with " \
2023-09-23T22:17:08,936           |  ^~~~~~~
2023-09-23T22:17:14,143     fatal: not a git repository (or any of the parent directories): .git
2023-09-23T22:17:16,492     Building wheel for ailist (pyproject.toml): finished with status 'done'
2023-09-23T22:17:16,645     Created wheel for ailist: filename=ailist-2.1.0-cp311-cp311-manylinux_2_36_armv7l.whl size=3853574 sha256=8763d2fc5cfe6a7da1b724e2e1aa45df94a925549372d62667ce50fb79e3dbc2
2023-09-23T22:17:16,646     Stored in directory: /home/piwheels/.cache/pip/wheels/42/27/51/b353b9c67d5c5e9f7d8adc1eeb8ff643fc572fe87635ed4834
2023-09-23T22:17:16,656   Successfully built ailist
2023-09-23T22:17:18,347   Installing collected packages: pytz, six, setuptools, poetry-core, numpy, cython, python-dateutil, pandas, ailist
2023-09-23T22:17:31,928     Creating /tmp/pip-build-env-vexlhs_n/overlay/local/bin
2023-09-23T22:17:31,930     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/f2py to 755
2023-09-23T22:17:31,932     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/f2py3 to 755
2023-09-23T22:17:31,934     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/f2py3.11 to 755
2023-09-23T22:17:34,539     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/cygdb to 755
2023-09-23T22:17:34,542     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/cython to 755
2023-09-23T22:17:34,545     changing mode of /tmp/pip-build-env-vexlhs_n/overlay/local/bin/cythonize to 755
2023-09-23T22:18:00,618   Successfully installed ailist-2.1.0 cython-0.29.36 numpy-1.25.2 pandas-1.5.2 poetry-core-1.7.0 python-dateutil-2.8.2 pytz-2023.3.post1 setuptools-68.2.2 six-1.16.0
2023-09-23T22:18:03,205   Installing build dependencies: finished with status 'done'
2023-09-23T22:18:03,208   Getting requirements to build wheel: started
2023-09-23T22:18:03,209   Running command Getting requirements to build wheel
2023-09-23T22:18:03,569   Getting requirements to build wheel: finished with status 'done'
2023-09-23T22:18:03,572   Created temporary directory: /tmp/pip-modern-metadata-hooqa01f
2023-09-23T22:18:03,574   Preparing metadata (pyproject.toml): started
2023-09-23T22:18:03,575   Running command Preparing metadata (pyproject.toml)
2023-09-23T22:18:04,486   Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-23T22:18:04,490   Source in /tmp/pip-wheel-h3eao8ll/hg38genome_22145356a4d24a0894afc2aff5853f12 has version 1.0.0, which satisfies requirement hg38genome==1.0.0 from https://files.pythonhosted.org/packages/5b/b9/19304a5b457915528a2e903dcf5f8c80dd56674dcbb157298ac17f21a17c/hg38genome-1.0.0.tar.gz
2023-09-23T22:18:04,491   Removed hg38genome==1.0.0 from https://files.pythonhosted.org/packages/5b/b9/19304a5b457915528a2e903dcf5f8c80dd56674dcbb157298ac17f21a17c/hg38genome-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-ehjo9l69'
2023-09-23T22:18:04,497 Created temporary directory: /tmp/pip-unpack-gzkn146z
2023-09-23T22:18:04,498 Created temporary directory: /tmp/pip-unpack-m1q3b5g2
2023-09-23T22:18:04,507 Building wheels for collected packages: hg38genome
2023-09-23T22:18:04,511   Created temporary directory: /tmp/pip-wheel-j8fwfwop
2023-09-23T22:18:04,511   Destination directory: /tmp/pip-wheel-j8fwfwop
2023-09-23T22:18:04,513   Building wheel for hg38genome (pyproject.toml): started
2023-09-23T22:18:04,515   Running command Building wheel for hg38genome (pyproject.toml)
2023-09-23T22:18:13,028   Compiling hg38genome/kmers/kmer_reader.pyx because it depends on /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/array_query_core.pxd.
2023-09-23T22:18:13,029   [1/1] Cythonizing hg38genome/kmers/kmer_reader.pyx
2023-09-23T22:18:13,472   In file included from /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
2023-09-23T22:18:13,473                    from /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
2023-09-23T22:18:13,473                    from /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
2023-09-23T22:18:13,474                    from hg38genome/kmers/kmer_reader.c:828:
2023-09-23T22:18:13,474   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-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]
2023-09-23T22:18:13,476      17 | #warning "Using deprecated NumPy API, disable it with " \
2023-09-23T22:18:13,477         |  ^~~~~~~
2023-09-23T22:18:13,579   In file included from hg38genome/kmers/kmer_reader.c:859:
2023-09-23T22:18:13,580   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/src/labeled_aiarray/labeled_augmented_array.c: In function ‘get_label’:
2023-09-23T22:18:13,580   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/src/labeled_aiarray/labeled_augmented_array.c:85:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2023-09-23T22:18:13,581      85 |         return k == kh_end(h)? -1 : kh_val(h, k);
2023-09-23T22:18:13,582         |                                ^~
2023-09-23T22:18:13,632   In file included from hg38genome/kmers/kmer_reader.c:882:
2023-09-23T22:18:13,632   hg38genome/kmers/interval_kmer.c: In function ‘add_kmer’:
2023-09-23T22:18:13,633   hg38genome/kmers/interval_kmer.c:94:13: warning: unused variable ‘ret_name’ [-Wunused-variable]
2023-09-23T22:18:13,634      94 |         int ret_name = kh_name_set(khStrInt, h, kmer_name, kc->n_kmers);
2023-09-23T22:18:13,635         |             ^~~~~~~~
2023-09-23T22:18:13,636   hg38genome/kmers/interval_kmer.c: In function ‘get_kmer’:
2023-09-23T22:18:13,636   hg38genome/kmers/interval_kmer.c:121:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare]
2023-09-23T22:18:13,637     121 |         return k == kh_end(h)? -1 : kh_val(h, k);
2023-09-23T22:18:13,637         |                                ^~
2023-09-23T22:18:13,638   hg38genome/kmers/interval_kmer.c: In function ‘interval_kmer_count’:
2023-09-23T22:18:13,638   hg38genome/kmers/interval_kmer.c:164:22: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2023-09-23T22:18:13,639     164 |         char *name = p->name;
2023-09-23T22:18:13,639         |                      ^
2023-09-23T22:18:13,640   hg38genome/kmers/interval_kmer.c:185:85: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-23T22:18:13,640     185 |                 if ((p->ail->interval_list[i].end - p->ail->interval_list[i].start) < last_n)
2023-09-23T22:18:13,641         |                                                                                     ^
2023-09-23T22:18:13,641   hg38genome/kmers/interval_kmer.c: In function ‘gc_content’:
2023-09-23T22:18:13,642   hg38genome/kmers/interval_kmer.c:228:22: warning: passing argument 1 of ‘chrom_in’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2023-09-23T22:18:13,643     228 |         if (chrom_in(name, tb->cl->chrom, tb->hdr->nChroms) == 0)
2023-09-23T22:18:13,643         |                      ^~~~
2023-09-23T22:18:13,644   hg38genome/kmers/interval_kmer.c:9:20: note: expected ‘char *’ but argument is of type ‘const char *’
2023-09-23T22:18:13,645       9 | int chrom_in(char *chrom, char **chrom_list, size_t n_chroms)
2023-09-23T22:18:13,645         |              ~~~~~~^~~~~
2023-09-23T22:18:13,646   hg38genome/kmers/interval_kmer.c:234:53: warning: passing argument 2 of ‘twobitChromLen’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2023-09-23T22:18:13,647     234 |         if (iter->intv->i->end > twobitChromLen(tb, name))
2023-09-23T22:18:13,648         |                                                     ^~~~
2023-09-23T22:18:13,648   In file included from hg38genome/kmers/interval_kmer.c:4:
2023-09-23T22:18:13,649   hg38genome/kmers/2bit.h:106:43: note: expected ‘char *’ but argument is of type ‘const char *’
2023-09-23T22:18:13,650     106 | uint32_t twobitChromLen(TwoBit *tb, char *chrom);
2023-09-23T22:18:13,651         |                                     ~~~~~~^~~~~
2023-09-23T22:18:13,652   hg38genome/kmers/interval_kmer.c:240:40: warning: passing argument 2 of ‘twobitSequence’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
2023-09-23T22:18:13,653     240 |         char *seq = twobitSequence(tb, name, iter->intv->i->start, iter->intv->i->end);
2023-09-23T22:18:13,653         |                                        ^~~~
2023-09-23T22:18:13,654   hg38genome/kmers/2bit.h:118:40: note: expected ‘char *’ but argument is of type ‘const char *’
2023-09-23T22:18:13,655     118 | char *twobitSequence(TwoBit *tb, char *chrom, uint32_t start, uint32_t end);
2023-09-23T22:18:13,656         |                                  ~~~~~~^~~~~
2023-09-23T22:18:13,656   In file included from hg38genome/kmers/kmer_reader.c:883:
2023-09-23T22:18:13,657   hg38genome/kmers/2bit.c: In function ‘bytes2bases’:
2023-09-23T22:18:13,658   hg38genome/kmers/2bit.c:96:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2023-09-23T22:18:13,659      96 |     for(offset=0; offset<remainder; offset++) {
2023-09-23T22:18:13,659         |                         ^
2023-09-23T22:18:13,660   hg38genome/kmers/2bit.c: In function ‘twobitBasesWorker’:
2023-09-23T22:18:13,661   hg38genome/kmers/2bit.c:311:20: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-23T22:18:13,661     311 |         if(maskIdx != -1 && start + i + 4 >= maskStart) {
2023-09-23T22:18:13,662         |                    ^~
2023-09-23T22:18:13,700   hg38genome/kmers/kmer_reader.c: In function ‘__pyx_pf_10hg38genome_5kmers_11kmer_reader_read_kmers’:
2023-09-23T22:18:13,703   hg38genome/kmers/kmer_reader.c:3268:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2023-09-23T22:18:13,704    3268 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
2023-09-23T22:18:13,704         |                                 ^
2023-09-23T22:18:32,996   In file included from hg38genome/kmers/kmer_reader.c:853:
2023-09-23T22:18:32,996   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/src/ailist/ailist_ops.c: In function ‘ailist_subtract_intervals’:
2023-09-23T22:18:32,997   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/src/ailist/ailist_ops.c:64:30: warning: ‘iv_end’ may be used uninitialized [-Wmaybe-uninitialized]
2023-09-23T22:18:32,997      64 |     if (start < end && start >= iv_end)
2023-09-23T22:18:32,998         |                        ~~~~~~^~~~~~~~~
2023-09-23T22:18:32,999   /tmp/pip-build-env-vexlhs_n/overlay/local/lib/python3.11/dist-packages/ailist/src/ailist/ailist_ops.c:28:14: note: ‘iv_end’ was declared here
2023-09-23T22:18:32,999      28 |     uint32_t iv_end;
2023-09-23T22:18:33,000         |              ^~~~~~
2023-09-23T22:18:40,566   fatal: not a git repository (or any of the parent directories): .git
2023-09-23T22:18:49,686   Building wheel for hg38genome (pyproject.toml): finished with status 'done'
2023-09-23T22:18:50,876   Created wheel for hg38genome: filename=hg38genome-1.0.0-cp311-cp311-manylinux_2_36_armv7l.whl size=47248362 sha256=7ab26062635503187b11d628f17d759d551b14b2e699df67b32d48a04c9e28ee
2023-09-23T22:18:50,877   Stored in directory: /tmp/pip-ephem-wheel-cache-50jj1xr7/wheels/72/ec/ba/418b21f6fe0f5bf6e51c7f222667020f49ae74a69860f0a232
2023-09-23T22:18:50,928 Successfully built hg38genome
2023-09-23T22:18:53,918 Removed build tracker: '/tmp/pip-build-tracker-ehjo9l69'