2026-01-08T05:27:55,225 Created temporary directory: /tmp/pip-ephem-wheel-cache-2i8oyo7z 2026-01-08T05:27:55,227 Created temporary directory: /tmp/pip-build-tracker-g1_uhyid 2026-01-08T05:27:55,228 Initialized build tracking at /tmp/pip-build-tracker-g1_uhyid 2026-01-08T05:27:55,229 Created build tracker: /tmp/pip-build-tracker-g1_uhyid 2026-01-08T05:27:55,229 Entered build tracker: /tmp/pip-build-tracker-g1_uhyid 2026-01-08T05:27:55,230 Created temporary directory: /tmp/pip-wheel-168mr9v1 2026-01-08T05:27:55,233 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-08T05:27:55,235 Created temporary directory: /tmp/pip-ephem-wheel-cache-m5pw0yun 2026-01-08T05:27:55,257 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-08T05:27:55,261 2 location(s) to search for versions of aldy: 2026-01-08T05:27:55,261 * https://pypi.org/simple/aldy/ 2026-01-08T05:27:55,261 * https://www.piwheels.org/simple/aldy/ 2026-01-08T05:27:55,262 Fetching project page and analyzing links: https://pypi.org/simple/aldy/ 2026-01-08T05:27:55,262 Getting page https://pypi.org/simple/aldy/ 2026-01-08T05:27:55,264 Found index url https://pypi.org/simple 2026-01-08T05:27:55,481 Fetched page https://pypi.org/simple/aldy/ as application/vnd.pypi.simple.v1+json 2026-01-08T05:27:55,487 Found link https://files.pythonhosted.org/packages/f3/56/784a829c0c2a294b9bdd158c5a0dc4227d878859319c2523f8eaa152ba5b/aldy-1.2.tar.gz (from https://pypi.org/simple/aldy/), version: 1.2 2026-01-08T05:27:55,488 Found link https://files.pythonhosted.org/packages/0b/1f/542b32f7a4ceb79eb616f270b003891428871d838c411e15bb17916952c6/aldy-2.0.tar.gz (from https://pypi.org/simple/aldy/), version: 2.0 2026-01-08T05:27:55,489 Found link https://files.pythonhosted.org/packages/79/d4/f42e18b2bca8994ed0246a180feeaeeae2e972390b49095dfb84aa4e4911/aldy-2.1.tar.gz (from https://pypi.org/simple/aldy/), version: 2.1 2026-01-08T05:27:55,489 Found link https://files.pythonhosted.org/packages/c9/68/d3f6f322dbd13a3b7500d06239857616b2e6e11256b736494563068cdea9/aldy-2.2.tar.gz (from https://pypi.org/simple/aldy/), version: 2.2 2026-01-08T05:27:55,490 Found link https://files.pythonhosted.org/packages/fe/e4/755eab1c0e23e224434b0b8baa7fa43da142e31320da81b828203b2b447f/aldy-2.2.3.tar.gz (from https://pypi.org/simple/aldy/), version: 2.2.3 2026-01-08T05:27:55,491 Found link https://files.pythonhosted.org/packages/cd/ae/40fdb3bc55c1438e3e099c700a742ff09a77f9f5597bb5ba95c5b8bc58e6/aldy-2.2.6.tar.gz (from https://pypi.org/simple/aldy/), version: 2.2.6 2026-01-08T05:27:55,491 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/c3/73/7747ac768306e140693252cab2859a6afbdb5e165568036e422b2e545509/aldy-3.0-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,492 Found link https://files.pythonhosted.org/packages/a1/78/0d015db68e842c1f133c0dde67c548b77d00c1431c52b2e806c8d628ded5/aldy-3.0.tar.gz (from https://pypi.org/simple/aldy/), version: 3.0 2026-01-08T05:27:55,492 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/09/c7/6f3ca14b1705092104fd63fb1d07a31095191d83d4a2bbb43aa11c064c97/aldy-3.1-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,493 Found link https://files.pythonhosted.org/packages/bb/b0/cbc3535d7c61e8d1c1876d77e1eaf7402c2470dc0c2d9eb9c5f7e7e6fa56/aldy-3.1.tar.gz (from https://pypi.org/simple/aldy/), version: 3.1 2026-01-08T05:27:55,494 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/ab/29/1a07d40d00c27b3b55b04bd19f31ee27feb3ff30cd2c4905c711084e9f87/aldy-3.2-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,494 Found link https://files.pythonhosted.org/packages/2f/9f/7da2ae87297a21d4d251698a8ff22dd4ef8fa9c8e844eb072109e6533273/aldy-3.2.tar.gz (from https://pypi.org/simple/aldy/), version: 3.2 2026-01-08T05:27:55,495 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/e0/86/d5c21106a02d6db3d309ba7c99cc5f3e58b410208f9c679b0979465e3588/aldy-3.3-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,496 Found link https://files.pythonhosted.org/packages/de/ba/f25b53a1016eaad2e823e95ccc98f5cadfe1f0113baf81aab81d2612b365/aldy-3.3.tar.gz (from https://pypi.org/simple/aldy/), version: 3.3 2026-01-08T05:27:55,496 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/87/5c/5096e5c1ed16f8c34c46d15b531f80ffd2082136c9af8278a66095d7e37e/aldy-4.0-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,497 Found link https://files.pythonhosted.org/packages/fc/6f/b4c6cea869941fb936b5d93ceb5227518cc1b8e460f0997e99528da2a811/aldy-4.0.tar.gz (from https://pypi.org/simple/aldy/), version: 4.0 2026-01-08T05:27:55,498 Skipping link: No binaries permitted for aldy: https://files.pythonhosted.org/packages/33/3a/934e6463765c946b6ccbcc43f325dd2941e5b6f88d77ac8ffce401582a1e/aldy-4.1-py3-none-any.whl (from https://pypi.org/simple/aldy/) 2026-01-08T05:27:55,498 Found link https://files.pythonhosted.org/packages/8e/0c/51dec884fd0af2405a30a0cd8bc13b1f8fd1152147308abc50db9375573f/aldy-4.1.tar.gz (from https://pypi.org/simple/aldy/), version: 4.1 2026-01-08T05:27:55,499 Found link https://files.pythonhosted.org/packages/43/f2/26409c567093220facd854f45c83279930003ec783ccb4ba4b09953240d2/aldy-4.2.tar.gz (from https://pypi.org/simple/aldy/), version: 4.2 2026-01-08T05:27:55,499 Found link https://files.pythonhosted.org/packages/67/d5/6ee433f995bf0024bbdac932202eb04e143ac44bf9d6c25aeafa00b6a8ae/aldy-4.2.1.tar.gz (from https://pypi.org/simple/aldy/), version: 4.2.1 2026-01-08T05:27:55,500 Found link https://files.pythonhosted.org/packages/46/89/949e7d96044f6ef935a5a06fdd37ad17803b1d043c0b65bc5d70355c8153/aldy-4.3.tar.gz (from https://pypi.org/simple/aldy/), version: 4.3 2026-01-08T05:27:55,500 Found link https://files.pythonhosted.org/packages/21/1d/3b5fb99a220a6acc9c24e73e372355a23de09c8bfc1de3e37812ee9c6360/aldy-4.3.1.tar.gz (from https://pypi.org/simple/aldy/), version: 4.3.1 2026-01-08T05:27:55,501 Found link https://files.pythonhosted.org/packages/07/0c/3e27752e5a88136f8cc014640ee4ae63c5c21d10b80fd632e60711d34723/aldy-4.4.tar.gz (from https://pypi.org/simple/aldy/), version: 4.4 2026-01-08T05:27:55,502 Found link https://files.pythonhosted.org/packages/b3/b6/d40fe3766e2e8f0b09e459ae105d78cd0ff931a4e00d2434c900d13b9bb7/aldy-4.5.tar.gz (from https://pypi.org/simple/aldy/), version: 4.5 2026-01-08T05:27:55,502 Found link https://files.pythonhosted.org/packages/7b/07/b15810a543a6e092a272cf71906cd194f08464f3327533036cc561380789/aldy-4.6.tar.gz (from https://pypi.org/simple/aldy/), version: 4.6 2026-01-08T05:27:55,503 Found link https://files.pythonhosted.org/packages/5c/ca/edf1f447c93870d4acb2b261d6db4bde31edfa8f4dc3e17967fb86cba29d/aldy-4.7.tar.gz (from https://pypi.org/simple/aldy/), version: 4.7 2026-01-08T05:27:55,503 Found link https://files.pythonhosted.org/packages/30/2b/94096c061b0e8cb0cad39fa6c4375ec5f2d976e59aa7219b83bc3f604cce/aldy-4.8.tar.gz (from https://pypi.org/simple/aldy/), version: 4.8 2026-01-08T05:27:55,504 Found link https://files.pythonhosted.org/packages/de/88/ba6eb3c61c6dc8ce13665322bb99fdceaea287808cee0f69184f0ae02720/aldy-4.8.1.tar.gz (from https://pypi.org/simple/aldy/), version: 4.8.1 2026-01-08T05:27:55,505 Found link https://files.pythonhosted.org/packages/87/97/99a9f315589ede7250934353d0eaac84dcebac8c148be42a1b34f72a4178/aldy-4.8.2.tar.gz (from https://pypi.org/simple/aldy/), version: 4.8.2 2026-01-08T05:27:55,505 Found link https://files.pythonhosted.org/packages/04/3f/bf9d14f357c482d13adf323935b44e6e61af4a878a14117ac94cfcee7299/aldy-4.8.3.tar.gz (from https://pypi.org/simple/aldy/), version: 4.8.3 2026-01-08T05:27:55,506 Fetching project page and analyzing links: https://www.piwheels.org/simple/aldy/ 2026-01-08T05:27:55,507 Getting page https://www.piwheels.org/simple/aldy/ 2026-01-08T05:27:55,508 Found index url https://www.piwheels.org/simple 2026-01-08T05:27:55,841 Fetched page https://www.piwheels.org/simple/aldy/ as text/html 2026-01-08T05:27:55,846 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-4.1-py3-none-any.whl#sha256=7ae78bf5799d17e32d2199307656c46d30cc4dd96291eb02b4ce7187e4350f33 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,846 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-4.0-py3-none-any.whl#sha256=a1788c2f762151608452c6f2e3abe0a9a280cc8e80159174fc33ea286b5886c9 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,847 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-3.3-py3-none-any.whl#sha256=8236cab87aa389bf7b611844163a1973ba0f689c8224e958bde10e899bd0f9e3 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,847 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-3.2-py3-none-any.whl#sha256=7f63da713d5182a0172e2b048d665adaa10a9889edd97a2a6a495878129f63a3 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,848 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-3.1-py3-none-any.whl#sha256=2f8b45fd60f8b0b20d801578ade67ddcc1a1ff997eb0df2308769448402909c9 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,848 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-3.0-py3-none-any.whl#sha256=a068b6007a6827ebf7a0395c4207751730ab6da5bc36ff83c472c563016c5ffc (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,848 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-2.2.6-py3-none-any.whl#sha256=7b7d2312861ec659d3cd55e6cea3072b6bee33118dabad166a45ded9b80a43e6 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,849 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-2.2.3-py3-none-any.whl#sha256=686960a5258382ddbae8cbdf991b56a760e5717b3c4687c0aea51f006edcf32f (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,850 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-2.2-py3-none-any.whl#sha256=73d7399e905db8cba77cc25646636b0f8f80173bc7a40987359d05c223e5837e (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,850 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-2.1-py3-none-any.whl#sha256=c5811f8933970804d32480b40f7119204a6cd1d407067c80e40a84bfaffd4e58 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,851 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-2.0-py3-none-any.whl#sha256=acd11ffdd277b20703496942a1664b6b2f2f73da9dbcaf0e7bf0d5aa7a05ffb2 (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,851 Skipping link: No binaries permitted for aldy: https://archive1.piwheels.org/simple/aldy/aldy-1.2-py3-none-any.whl#sha256=adbc108b51952fdd4f75ea1243f2cdd914cd4520afa6be062e550c9a40948dfb (from https://www.piwheels.org/simple/aldy/) 2026-01-08T05:27:55,852 Skipping link: not a file: https://www.piwheels.org/simple/aldy/ 2026-01-08T05:27:55,853 Skipping link: not a file: https://pypi.org/simple/aldy/ 2026-01-08T05:27:55,874 Given no hashes to check 1 links for project 'aldy': discarding no candidates 2026-01-08T05:27:55,893 Collecting aldy==4.8.3 2026-01-08T05:27:55,895 Created temporary directory: /tmp/pip-unpack-cit243h8 2026-01-08T05:27:56,128 Downloading aldy-4.8.3.tar.gz (12.2 MB) 2026-01-08T05:27:59,020 Added aldy==4.8.3 from https://files.pythonhosted.org/packages/04/3f/bf9d14f357c482d13adf323935b44e6e61af4a878a14117ac94cfcee7299/aldy-4.8.3.tar.gz to build tracker '/tmp/pip-build-tracker-g1_uhyid' 2026-01-08T05:27:59,025 Created temporary directory: /tmp/pip-build-env-6z9t1zb0 2026-01-08T05:27:59,029 Installing build dependencies: started 2026-01-08T05:27:59,031 Running command pip subprocess to install build dependencies 2026-01-08T05:28:00,148 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-08T05:28:00,806 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-08T05:28:00,829 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-08T05:28:02,557 Collecting setuptools 2026-01-08T05:28:02,649 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-08T05:28:02,940 Collecting wheel 2026-01-08T05:28:02,956 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-08T05:28:04,961 Collecting cython 2026-01-08T05:28:05,752 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-01-08T05:28:06,338 Collecting pysam 2026-01-08T05:28:07,825 Using cached https://archive1.piwheels.org/simple/pysam/pysam-0.23.3-cp311-cp311-linux_armv7l.whl (18.4 MB) 2026-01-08T05:28:11,305 Installing collected packages: wheel, setuptools, pysam, cython 2026-01-08T05:28:11,541 Creating /tmp/pip-build-env-6z9t1zb0/overlay/local/bin 2026-01-08T05:28:11,543 changing mode of /tmp/pip-build-env-6z9t1zb0/overlay/local/bin/wheel to 755 2026-01-08T05:28:21,754 changing mode of /tmp/pip-build-env-6z9t1zb0/overlay/local/bin/cygdb to 755 2026-01-08T05:28:21,756 changing mode of /tmp/pip-build-env-6z9t1zb0/overlay/local/bin/cython to 755 2026-01-08T05:28:21,758 changing mode of /tmp/pip-build-env-6z9t1zb0/overlay/local/bin/cythonize to 755 2026-01-08T05:28:21,792 Successfully installed cython-3.2.4 pysam-0.23.3 setuptools-80.9.0 wheel-0.45.1 2026-01-08T05:28:22,193 Installing build dependencies: finished with status 'done' 2026-01-08T05:28:22,212 Getting requirements to build wheel: started 2026-01-08T05:28:22,213 Running command Getting requirements to build wheel 2026-01-08T05:28:47,604 Compiling aldy/indelpost/variant.pyx because it changed. 2026-01-08T05:28:47,605 Compiling aldy/indelpost/utilities.pyx because it changed. 2026-01-08T05:28:47,605 Compiling aldy/indelpost/pileup.pyx because it changed. 2026-01-08T05:28:47,606 Compiling aldy/indelpost/varaln.pyx because it changed. 2026-01-08T05:28:47,606 Compiling aldy/indelpost/contig.pyx because it changed. 2026-01-08T05:28:47,607 Compiling aldy/indelpost/local_reference.pyx because it changed. 2026-01-08T05:28:47,608 Compiling aldy/indelpost/softclip.pyx because it changed. 2026-01-08T05:28:47,608 Compiling aldy/indelpost/localn.pyx because it changed. 2026-01-08T05:28:47,609 Compiling aldy/indelpost/gappedaln.pyx because it changed. 2026-01-08T05:28:47,609 Compiling aldy/indelpost/sswpy.pyx because it changed. 2026-01-08T05:28:47,610 [ 1/10] Cythonizing aldy/indelpost/contig.pyx 2026-01-08T05:28:47,610 [ 2/10] Cythonizing aldy/indelpost/gappedaln.pyx 2026-01-08T05:28:47,611 [ 3/10] Cythonizing aldy/indelpost/local_reference.pyx 2026-01-08T05:28:47,611 [ 4/10] Cythonizing aldy/indelpost/localn.pyx 2026-01-08T05:28:47,612 [ 5/10] Cythonizing aldy/indelpost/pileup.pyx 2026-01-08T05:28:47,612 [ 6/10] Cythonizing aldy/indelpost/softclip.pyx 2026-01-08T05:28:47,613 [ 7/10] Cythonizing aldy/indelpost/sswpy.pyx 2026-01-08T05:28:47,614 [ 8/10] Cythonizing aldy/indelpost/utilities.pyx 2026-01-08T05:28:47,614 [ 9/10] Cythonizing aldy/indelpost/varaln.pyx 2026-01-08T05:28:47,615 [10/10] Cythonizing aldy/indelpost/variant.pyx 2026-01-08T05:28:47,635 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2026-01-08T05:28:47,636 warnings.warn(msg) 2026-01-08T05:28:47,636 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2026-01-08T05:28:47,637 warnings.warn(msg) 2026-01-08T05:28:47,694 running egg_info 2026-01-08T05:28:47,702 writing aldy.egg-info/PKG-INFO 2026-01-08T05:28:47,705 writing dependency_links to aldy.egg-info/dependency_links.txt 2026-01-08T05:28:47,707 writing entry points to aldy.egg-info/entry_points.txt 2026-01-08T05:28:47,708 writing requirements to aldy.egg-info/requires.txt 2026-01-08T05:28:47,710 writing top-level names to aldy.egg-info/top_level.txt 2026-01-08T05:28:47,771 reading manifest file 'aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:47,801 reading manifest template 'MANIFEST.in' 2026-01-08T05:28:47,806 warning: no files found matching 'aldy/tests/resources/*.json' 2026-01-08T05:28:47,810 warning: no files found matching 'aldy/tests/resources/*.vcf' 2026-01-08T05:28:47,814 adding license file 'LICENSE.rst' 2026-01-08T05:28:47,832 writing manifest file 'aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:48,744 Getting requirements to build wheel: finished with status 'done' 2026-01-08T05:28:48,747 Created temporary directory: /tmp/pip-modern-metadata-52d4rhcs 2026-01-08T05:28:48,750 Preparing metadata (pyproject.toml): started 2026-01-08T05:28:48,751 Running command Preparing metadata (pyproject.toml) 2026-01-08T05:28:50,842 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2026-01-08T05:28:50,842 warnings.warn(msg) 2026-01-08T05:28:50,843 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2026-01-08T05:28:50,843 warnings.warn(msg) 2026-01-08T05:28:50,901 running dist_info 2026-01-08T05:28:50,916 creating /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info 2026-01-08T05:28:50,917 writing /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/PKG-INFO 2026-01-08T05:28:50,920 writing dependency_links to /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/dependency_links.txt 2026-01-08T05:28:50,922 writing entry points to /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/entry_points.txt 2026-01-08T05:28:50,923 writing requirements to /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/requires.txt 2026-01-08T05:28:50,924 writing top-level names to /tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/top_level.txt 2026-01-08T05:28:50,926 writing manifest file '/tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:50,964 reading manifest file '/tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:50,966 reading manifest template 'MANIFEST.in' 2026-01-08T05:28:50,971 warning: no files found matching 'aldy/tests/resources/*.json' 2026-01-08T05:28:50,975 warning: no files found matching 'aldy/tests/resources/*.vcf' 2026-01-08T05:28:50,979 adding license file 'LICENSE.rst' 2026-01-08T05:28:50,985 writing manifest file '/tmp/pip-modern-metadata-52d4rhcs/aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:50,987 creating '/tmp/pip-modern-metadata-52d4rhcs/aldy-4.8.3.dist-info' 2026-01-08T05:28:51,199 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-08T05:28:51,205 Source in /tmp/pip-wheel-168mr9v1/aldy_f85e5c9fccaa4e50a9469d3240808d8a has version 4.8.3, which satisfies requirement aldy==4.8.3 from https://files.pythonhosted.org/packages/04/3f/bf9d14f357c482d13adf323935b44e6e61af4a878a14117ac94cfcee7299/aldy-4.8.3.tar.gz 2026-01-08T05:28:51,206 Removed aldy==4.8.3 from https://files.pythonhosted.org/packages/04/3f/bf9d14f357c482d13adf323935b44e6e61af4a878a14117ac94cfcee7299/aldy-4.8.3.tar.gz from build tracker '/tmp/pip-build-tracker-g1_uhyid' 2026-01-08T05:28:51,212 Created temporary directory: /tmp/pip-unpack-1w7ybfv6 2026-01-08T05:28:51,213 Building wheels for collected packages: aldy 2026-01-08T05:28:51,218 Created temporary directory: /tmp/pip-wheel-i6jkk94o 2026-01-08T05:28:51,218 Destination directory: /tmp/pip-wheel-i6jkk94o 2026-01-08T05:28:51,221 Building wheel for aldy (pyproject.toml): started 2026-01-08T05:28:51,222 Running command Building wheel for aldy (pyproject.toml) 2026-01-08T05:28:53,316 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2026-01-08T05:28:53,317 warnings.warn(msg) 2026-01-08T05:28:53,317 /tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require' 2026-01-08T05:28:53,318 warnings.warn(msg) 2026-01-08T05:28:53,376 running bdist_wheel 2026-01-08T05:28:53,400 running build 2026-01-08T05:28:53,400 running build_py 2026-01-08T05:28:53,414 creating build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,416 copying aldy/query.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,418 copying aldy/common.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,420 copying aldy/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,422 copying aldy/version.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,424 copying aldy/profile.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,426 copying aldy/cn.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,429 copying aldy/gene.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,432 copying aldy/__main__.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,434 copying aldy/diplotype.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,436 copying aldy/minor.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,439 copying aldy/solutions.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,441 copying aldy/coverage.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,444 copying aldy/major.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,446 copying aldy/lpinterface.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,448 copying aldy/genotype.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,451 copying aldy/sam.py -> build/lib.linux-armv7l-cpython-311/aldy 2026-01-08T05:28:53,454 creating build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,455 copying aldy/indelpost/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,457 copying aldy/indelpost/consensus.py -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,460 copying aldy/indelpost/version.py -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,462 copying aldy/indelpost/alleles.py -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,465 creating build/lib.linux-armv7l-cpython-311/aldy/resources 2026-01-08T05:28:53,466 copying aldy/resources/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/resources 2026-01-08T05:28:53,468 creating build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,469 copying aldy/tests/test_major_synthetic.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,472 copying aldy/tests/test_gene.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,474 copying aldy/tests/test_query.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,477 copying aldy/tests/test_diplotype_real.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,479 copying aldy/tests/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,480 copying aldy/tests/test_cn_synthetic.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,483 copying aldy/tests/test_diplotype_synthetic.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,484 copying aldy/tests/test_full.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,487 copying aldy/tests/test_major_real.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,489 copying aldy/tests/test_cn_real.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,492 copying aldy/tests/test_minor_synthetic.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,494 copying aldy/tests/conftest.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,496 copying aldy/tests/test_minor_real.py -> build/lib.linux-armv7l-cpython-311/aldy/tests 2026-01-08T05:28:53,499 creating build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:53,500 copying aldy/resources/genes/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:53,502 creating build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:53,503 copying aldy/resources/profiles/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:53,505 creating build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:53,506 copying aldy/tests/resources/__init__.py -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:53,508 running egg_info 2026-01-08T05:28:53,523 writing aldy.egg-info/PKG-INFO 2026-01-08T05:28:53,526 writing dependency_links to aldy.egg-info/dependency_links.txt 2026-01-08T05:28:53,527 writing entry points to aldy.egg-info/entry_points.txt 2026-01-08T05:28:53,528 writing requirements to aldy.egg-info/requires.txt 2026-01-08T05:28:53,529 writing top-level names to aldy.egg-info/top_level.txt 2026-01-08T05:28:53,545 reading manifest file 'aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:53,554 reading manifest template 'MANIFEST.in' 2026-01-08T05:28:53,559 warning: no files found matching 'aldy/tests/resources/*.json' 2026-01-08T05:28:53,563 warning: no files found matching 'aldy/tests/resources/*.vcf' 2026-01-08T05:28:53,567 adding license file 'LICENSE.rst' 2026-01-08T05:28:53,575 writing manifest file 'aldy.egg-info/SOURCES.txt' 2026-01-08T05:28:53,585 copying aldy/indelpost/contig.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,631 copying aldy/indelpost/contig.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,633 copying aldy/indelpost/contig.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,636 copying aldy/indelpost/gappedaln.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,672 copying aldy/indelpost/gappedaln.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,675 copying aldy/indelpost/local_reference.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,704 copying aldy/indelpost/local_reference.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,706 copying aldy/indelpost/local_reference.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,708 copying aldy/indelpost/localn.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,750 copying aldy/indelpost/localn.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,753 copying aldy/indelpost/pileup.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,822 copying aldy/indelpost/pileup.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,824 copying aldy/indelpost/pileup.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,827 copying aldy/indelpost/softclip.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,848 copying aldy/indelpost/softclip.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,851 copying aldy/indelpost/sse2neon.h -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,862 copying aldy/indelpost/ssw.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,865 copying aldy/indelpost/ssw.h -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,868 copying aldy/indelpost/sswpy.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,891 copying aldy/indelpost/sswpy.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,893 copying aldy/indelpost/utilities.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,961 copying aldy/indelpost/utilities.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,963 copying aldy/indelpost/utilities.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:53,966 copying aldy/indelpost/varaln.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,033 copying aldy/indelpost/varaln.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,035 copying aldy/indelpost/varaln.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,039 copying aldy/indelpost/variant.c -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,098 copying aldy/indelpost/variant.pxd -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,100 copying aldy/indelpost/variant.pyx -> build/lib.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,103 copying aldy/resources/LICENSE.rst -> build/lib.linux-armv7l-cpython-311/aldy/resources 2026-01-08T05:28:54,106 copying aldy/resources/genes/abcg2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,111 copying aldy/resources/genes/cacna1s.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,115 copying aldy/resources/genes/cftr.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,128 copying aldy/resources/genes/comt.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,131 copying aldy/resources/genes/cyp1a1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,134 copying aldy/resources/genes/cyp1a2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,138 copying aldy/resources/genes/cyp2a13.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,141 copying aldy/resources/genes/cyp2a6.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,144 copying aldy/resources/genes/cyp2b6.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,148 copying aldy/resources/genes/cyp2c19.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,153 copying aldy/resources/genes/cyp2c8.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,156 copying aldy/resources/genes/cyp2c9.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,160 copying aldy/resources/genes/cyp2d6.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,167 copying aldy/resources/genes/cyp2e1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,170 copying aldy/resources/genes/cyp2f1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,173 copying aldy/resources/genes/cyp2j2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,176 copying aldy/resources/genes/cyp2r1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,179 copying aldy/resources/genes/cyp2s1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,182 copying aldy/resources/genes/cyp2w1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,185 copying aldy/resources/genes/cyp3a4.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,189 copying aldy/resources/genes/cyp3a43.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,195 copying aldy/resources/genes/cyp3a5.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,198 copying aldy/resources/genes/cyp3a7.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,202 copying aldy/resources/genes/cyp4f2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,205 copying aldy/resources/genes/dpyd.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,235 copying aldy/resources/genes/g6pd.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,238 copying aldy/resources/genes/gstm1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,241 copying aldy/resources/genes/gstp1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,244 copying aldy/resources/genes/ifnl3.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,247 copying aldy/resources/genes/mt-rnr1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,249 copying aldy/resources/genes/nat1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,253 copying aldy/resources/genes/nat2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,256 copying aldy/resources/genes/nudt15.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,259 copying aldy/resources/genes/ryr1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,270 copying aldy/resources/genes/slco1b1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,278 copying aldy/resources/genes/tpmt.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,281 copying aldy/resources/genes/ugt1a1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,286 copying aldy/resources/genes/ugt2b7.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,290 copying aldy/resources/genes/vkorc1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/genes 2026-01-08T05:28:54,293 copying aldy/resources/profiles/10x.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,295 copying aldy/resources/profiles/illumina.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,298 copying aldy/resources/profiles/pacbio-hifi-targeted-twist.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,301 copying aldy/resources/profiles/pacbio-hifi-targeted.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,303 copying aldy/resources/profiles/pgx1.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,306 copying aldy/resources/profiles/pgx2.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,309 copying aldy/resources/profiles/pgx3.yml -> build/lib.linux-armv7l-cpython-311/aldy/resources/profiles 2026-01-08T05:28:54,311 copying aldy/tests/resources/HARD.dump.tar.gz -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,373 copying aldy/tests/resources/HG03166.pb.bam -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,423 copying aldy/tests/resources/HG03166.pb.bam.bai -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,427 copying aldy/tests/resources/INS.dump.tar.gz -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,457 copying aldy/tests/resources/NA07000_SLCO1B1.vcf.gz -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,461 copying aldy/tests/resources/NA07000_SLCO1B1.vcf.gz.tbi -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,464 copying aldy/tests/resources/NA10860.bai -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,467 copying aldy/tests/resources/NA10860.bam -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,496 copying aldy/tests/resources/NA10860.out.expected -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,499 copying aldy/tests/resources/NA10860.profile -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,501 copying aldy/tests/resources/NA10860.profile.hg38 -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,504 copying aldy/tests/resources/NA10860.vcf.expected -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,507 copying aldy/tests/resources/NA10860_hg38.bai -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,510 copying aldy/tests/resources/NA10860_hg38.bam -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,551 copying aldy/tests/resources/cyp2d6.test.yml -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,555 copying aldy/tests/resources/toy.yml -> build/lib.linux-armv7l-cpython-311/aldy/tests/resources 2026-01-08T05:28:54,560 running build_ext 2026-01-08T05:28:54,568 building 'aldy.indelpost.variant' extension 2026-01-08T05:28:54,569 creating build/temp.linux-armv7l-cpython-311/aldy/indelpost 2026-01-08T05:28:54,571 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/variant.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/variant.o -Wno-unused-function 2026-01-08T05:29:16,007 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/variant.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/variant.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:29:16,145 building 'aldy.indelpost.utilities' extension 2026-01-08T05:29:16,146 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/utilities.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/utilities.o -Wno-unused-function 2026-01-08T05:29:49,395 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/utilities.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/utilities.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:29:49,549 building 'aldy.indelpost.pileup' extension 2026-01-08T05:29:49,549 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/pileup.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/pileup.o -Wno-unused-function 2026-01-08T05:30:33,986 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/pileup.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/pileup.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:30:34,417 building 'aldy.indelpost.varaln' extension 2026-01-08T05:30:34,418 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/varaln.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/varaln.o -Wno-unused-function 2026-01-08T05:31:12,754 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/varaln.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/varaln.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:31:12,972 building 'aldy.indelpost.contig' extension 2026-01-08T05:31:12,973 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/contig.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/contig.o -Wno-unused-function 2026-01-08T05:31:33,158 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/contig.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/contig.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:31:33,301 building 'aldy.indelpost.local_reference' extension 2026-01-08T05:31:33,302 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/local_reference.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/local_reference.o -Wno-unused-function 2026-01-08T05:31:40,165 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/local_reference.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/local_reference.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:31:40,277 building 'aldy.indelpost.softclip' extension 2026-01-08T05:31:40,278 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/softclip.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/softclip.o -Wno-unused-function 2026-01-08T05:31:47,963 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/softclip.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/softclip.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:31:48,075 building 'aldy.indelpost.localn' extension 2026-01-08T05:31:48,076 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/localn.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/localn.o -Wno-unused-function 2026-01-08T05:32:10,340 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/localn.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/localn.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:32:10,468 building 'aldy.indelpost.gappedaln' extension 2026-01-08T05:32:10,469 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/htslib -I/tmp/pip-build-env-6z9t1zb0/overlay/local/lib/python3.11/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -c aldy/indelpost/gappedaln.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/gappedaln.o -Wno-unused-function 2026-01-08T05:32:27,409 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/aldy/indelpost/gappedaln.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/aldy/indelpost/gappedaln.cpython-311-arm-linux-gnueabihf.so 2026-01-08T05:32:27,528 building 'aldy.indelpost.sswpy' extension 2026-01-08T05:32:27,529 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ialdy/indelpost -I/usr/include/python3.11 -c aldy/indelpost/ssw.c -o build/temp.linux-armv7l-cpython-311/aldy/indelpost/ssw.o -Wno-unused-function 2026-01-08T05:32:27,663 In file included from aldy/indelpost/ssw.c:74: 2026-01-08T05:32:27,664 aldy/indelpost/ssw.h:21:10: fatal error: emmintrin.h: No such file or directory 2026-01-08T05:32:27,664 21 | #include 2026-01-08T05:32:27,665 | ^~~~~~~~~~~~~ 2026-01-08T05:32:27,665 compilation terminated. 2026-01-08T05:32:27,669 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2026-01-08T05:32:27,830 ERROR: [present-rich] Building wheel for aldy (pyproject.toml) exited with 1 2026-01-08T05:32:27,846 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmp3q7mqnat[/] 2026-01-08T05:32:27,846 [bold magenta]cwd[/]: /tmp/pip-wheel-168mr9v1/aldy_f85e5c9fccaa4e50a9469d3240808d8a 2026-01-08T05:32:27,847 Building wheel for aldy (pyproject.toml): finished with status 'error' 2026-01-08T05:32:27,849 ERROR: Failed building wheel for aldy 2026-01-08T05:32:27,852 Failed to build aldy 2026-01-08T05:32:27,853 ERROR: Failed to build one or more wheels 2026-01-08T05:32:27,854 Exception information: 2026-01-08T05:32:27,854 Traceback (most recent call last): 2026-01-08T05:32:27,854 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2026-01-08T05:32:27,854 status = run_func(*args) 2026-01-08T05:32:27,854 ^^^^^^^^^^^^^^^ 2026-01-08T05:32:27,854 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2026-01-08T05:32:27,854 return func(self, options, args) 2026-01-08T05:32:27,854 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2026-01-08T05:32:27,854 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2026-01-08T05:32:27,854 raise CommandError("Failed to build one or more wheels") 2026-01-08T05:32:27,854 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2026-01-08T05:32:27,859 Removed build tracker: '/tmp/pip-build-tracker-g1_uhyid'