2025-09-07T23:52:23,149 Created temporary directory: /tmp/pip-build-tracker-af79grqi 2025-09-07T23:52:23,150 Initialized build tracking at /tmp/pip-build-tracker-af79grqi 2025-09-07T23:52:23,150 Created build tracker: /tmp/pip-build-tracker-af79grqi 2025-09-07T23:52:23,150 Entered build tracker: /tmp/pip-build-tracker-af79grqi 2025-09-07T23:52:23,150 Created temporary directory: /tmp/pip-wheel-2u1u2qzb 2025-09-07T23:52:23,154 Created temporary directory: /tmp/pip-ephem-wheel-cache-yu98batm 2025-09-07T23:52:23,209 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-07T23:52:23,212 2 location(s) to search for versions of biom-format: 2025-09-07T23:52:23,212 * https://pypi.org/simple/biom-format/ 2025-09-07T23:52:23,212 * https://www.piwheels.org/simple/biom-format/ 2025-09-07T23:52:23,212 Fetching project page and analyzing links: https://pypi.org/simple/biom-format/ 2025-09-07T23:52:23,212 Getting page https://pypi.org/simple/biom-format/ 2025-09-07T23:52:23,213 Found index url https://pypi.org/simple/ 2025-09-07T23:52:23,365 Fetched page https://pypi.org/simple/biom-format/ as application/vnd.pypi.simple.v1+json 2025-09-07T23:52:23,384 Found link https://files.pythonhosted.org/packages/e8/a0/0b4947cd716f8923410be46d0473442e906e80fd605d1f900667224878a9/biom-format-1.2.0-dev.tar.gz (from https://pypi.org/simple/biom-format/), version: 1.2.0-dev 2025-09-07T23:52:23,384 Found link https://files.pythonhosted.org/packages/5d/a6/50855b83db9932d78ff10721d90f79725729040db8117ce2c5a1e50c3a75/biom-format-1.3.0.tar.gz (from https://pypi.org/simple/biom-format/), version: 1.3.0 2025-09-07T23:52:23,385 Found link https://files.pythonhosted.org/packages/98/3b/4e80a9a5c4a3c6764aa8c0c994973e7df71eee02fc6b8cc6e1d06a64ab7e/biom-format-1.3.1.tar.gz (from https://pypi.org/simple/biom-format/), version: 1.3.1 2025-09-07T23:52:23,386 Found link https://files.pythonhosted.org/packages/ab/62/b44f747c549c2cb3408462905461ae8d0975163c927b4ac4452321368815/biom-format-2.0.0.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.0.0 2025-09-07T23:52:23,386 Found link https://files.pythonhosted.org/packages/26/14/46ce3a0c94b4e5f03473b029be7df19341c525c92d310443ca1bd935c4c1/biom-format-2.0.1.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.0.1 2025-09-07T23:52:23,387 Found link https://files.pythonhosted.org/packages/bc/8e/c937b6997062dfc70cd6fc6f53b70703dcec400e39af2d43542349f7ace6/biom-format-2.1.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1 2025-09-07T23:52:23,387 Found link https://files.pythonhosted.org/packages/40/45/a7a64146c75f00cf9889753d39a0371adf2982ee3f1eb31c28efbb5a3529/biom-format-2.1.1.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.1 2025-09-07T23:52:23,387 Found link https://files.pythonhosted.org/packages/d9/de/65d8089e4aab975658f80c4975015fb5c761fe4c37868cc317733f33d0cd/biom-format-2.1.2.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.2 2025-09-07T23:52:23,387 Found link https://files.pythonhosted.org/packages/9d/ed/1ff2ee2d16aa3edd66e8f07f11321eb9b9cd478307d87674c633ba9b081a/biom-format-2.1.3.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.3 2025-09-07T23:52:23,388 Found link https://files.pythonhosted.org/packages/2e/8e/f8575e51764697c485f7e81dfc31ff72d8b2c4b50e88c23094be65814451/biom-format-2.1.4.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.4 2025-09-07T23:52:23,388 Found link https://files.pythonhosted.org/packages/e8/74/9b7e50c29ba548cd53eb97fb9cc1f05a2cf53aa179a64f36e93282b84f79/biom-format-2.1.5.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.5 2025-09-07T23:52:23,388 Found link https://files.pythonhosted.org/packages/46/a6/fccc2f5db587d7d896b52054aa5a9f0f7fd8fb6ad23ab9a02934d4cb1739/biom-format-2.1.6.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.6 2025-09-07T23:52:23,388 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/c2/10/ed278d6263ad222b5327f127f07afaadff7dc7ae8482592b9c05500e976d/biom_format-2.1.6-cp27-cp27m-macosx_10_7_x86_64.whl (from https://pypi.org/simple/biom-format/) 2025-09-07T23:52:23,388 Found link https://files.pythonhosted.org/packages/25/92/ca4688a006b784bcc1f118c4a53e9aadc78d78abf8ff58ee11d29ac950a4/biom-format-2.1.7.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.7 2025-09-07T23:52:23,388 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/d1/84/0521b9203bb525c2d6a06905be950f29ca98e60a12dca71dfd18bffe7d92/biom_format-2.1.7-cp36-cp36m-macosx_10_7_x86_64.whl (from https://pypi.org/simple/biom-format/) 2025-09-07T23:52:23,389 Found link https://files.pythonhosted.org/packages/c1/c6/3b4284680b390a6c0a39de2fddddfe19a28d1bdceb5951713c483c147f44/biom-format-2.1.8-1.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.8-1 2025-09-07T23:52:23,389 Found link https://files.pythonhosted.org/packages/4b/50/65e535736597ce91e82a8e3e83cf1e88735368b58f99585f600b854f0bc9/biom-format-2.1.9.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.9 2025-09-07T23:52:23,389 Found link https://files.pythonhosted.org/packages/2b/8f/ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de/biom-format-2.1.10.tar.gz (from https://pypi.org/simple/biom-format/), version: 2.1.10 2025-09-07T23:52:23,390 Found link https://files.pythonhosted.org/packages/fc/3f/7eb762b52f490b810b1686fd41cd6f3f7f33c0dab29c4273c96e9a1641a2/biom-format-2.1.12.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6), version: 2.1.12 2025-09-07T23:52:23,390 Found link https://files.pythonhosted.org/packages/90/57/0a326e17005b25e56f6e25b8b1e3eae299b7f6d53af06b11c4830d631612/biom-format-2.1.13.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6), version: 2.1.13 2025-09-07T23:52:23,390 Found link https://files.pythonhosted.org/packages/8e/2c/132267e58172821fc15fa3856f53ed09b607837fe06e2bb60b230005951d/biom-format-2.1.14.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6), version: 2.1.14 2025-09-07T23:52:23,390 Found link https://files.pythonhosted.org/packages/fc/db/daf7c3872dd49acf6233873fb6f1ab7b6ca324bba25bf28fc9cf7dfd4c7b/biom-format-2.1.15.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6), version: 2.1.15 2025-09-07T23:52:23,390 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/52/9b/f3d2fcc1d0141e86e08330c7516d750662f8a3df40c7f5ef8d633fc485b1/biom_format-2.1.15-cp310-cp310-macosx_10_9_universal2.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/69/1a/8346a46e7b68aa49a7303d8cf9a12c7c08ee1d0a2142f1066c906a99def0/biom_format-2.1.15-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/ed/d4/6e42221bbbfee00aa96692583cef753a3f0b455b26854fd7111740a81999/biom_format-2.1.15-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/0b/2d/18978cf47787f2435d2d288d58c76e891b466845f670ffc14cd5455aca94/biom_format-2.1.15-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/63/ad/148ed220742d9d8995805a86877867551733a01edaf8e95a214ad36e051e/biom_format-2.1.15-cp311-cp311-macosx_10_9_universal2.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/ae/b6/da4325213838fe4d078da9f73d913838959680217d2188b240818216113d/biom_format-2.1.15-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/2e/cf/4bc7592b3c48664c4c927547983814c4708c248ff3d753b0d60ac0ad7250/biom_format-2.1.15-cp311-cp311-macosx_11_0_arm64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/7d/8a/6ea8c3bc9d61dcf46c6e7ccaf11ce07d46184a0b0e1ed31b8ec36db94e89/biom_format-2.1.15-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,391 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/ca/0d/64c1e729685aa1de049816f0972b9be78a9b8489a7b9ba1dc9ff6bc9f95e/biom_format-2.1.15-cp37-cp37m-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/93/c5/5d6c2adce1ad1288c9d13a689971582fc556c5c3b7523c20b25dec4a8ae8/biom_format-2.1.15-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/74/bb/bdf0f58bcf7a6d287e94d94b3464263b62f04068f2109a4380efda6a025d/biom_format-2.1.15-cp38-cp38-macosx_10_9_universal2.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/14/fe/dc90a6ec894343130e40fca22c7c324fbd08d5f48559d2d7730cfa768a72/biom_format-2.1.15-cp38-cp38-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/9c/36/b2dcba3e20fe23f839e9641a9e5e600a342c422ab07bc54c6383a3980deb/biom_format-2.1.15-cp38-cp38-macosx_11_0_arm64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/95/f4/65a3d3bdadff352d97e410173bcbf80ea5dfeefdf18588232d2029eac0d6/biom_format-2.1.15-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/0a/eb/5a836a2d9314e0a93db6c3cbb4f5a1019171ada3b8b0ff2e0c9bdbdcfc97/biom_format-2.1.15-cp39-cp39-macosx_10_9_universal2.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/4d/2a/9f1f3ea15f5894392ea77518f0982ebaac93b3c274c2762ea23defebf422/biom_format-2.1.15-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,392 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/c4/f0/53a3e6a04d281e67b3d2745b9a9163c6be3a11970cf5150d73037a6c3cca/biom_format-2.1.15-cp39-cp39-macosx_11_0_arm64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,393 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/50/14/4bf1e8766a9e4df3c2945e0d70f960985c0886ebcd09fd7d95bebeba9ff1/biom_format-2.1.15-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6) 2025-09-07T23:52:23,393 Found link https://files.pythonhosted.org/packages/62/88/d81eabe80aac30ba1fc5dfc7191e7825fcaf19b6564adafc0763d44873ac/biom-format-2.1.16.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.6), version: 2.1.16 2025-09-07T23:52:23,393 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/51/93/663ba9aba08fdbca7a6a4231f89305dfc6e8534b8551fbd2060222bdf995/biom_format-2.1.17-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.9) 2025-09-07T23:52:23,393 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/d9/fe/00070214677a1ba6ae6952be17c553c0a9efbb7ead7783db47d52ca05560/biom_format-2.1.17-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.9) 2025-09-07T23:52:23,393 Skipping link: No binaries permitted for biom-format: https://files.pythonhosted.org/packages/79/a1/ebdc161b7798ec751a5ee34395aac49f6e971fc1002ac909a94f259ec35a/biom_format-2.1.17-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.9) 2025-09-07T23:52:23,393 Skipping link: No binaries permitted for biom-format: 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biom-format: https://files.pythonhosted.org/packages/0f/e3/be8d4d7e6128993c024d5d794aa912cffe251f53021daa3e938554ecffc7/biom_format-2.1.17-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/biom-format/) (requires-python:>=3.9) 2025-09-07T23:52:23,396 Found link https://files.pythonhosted.org/packages/cf/63/da18b1cdb9de07f8ad07d71535eac0460d065c71312ad400f55f6c2865ae/biom_format-2.1.17.tar.gz (from https://pypi.org/simple/biom-format/) (requires-python:>=3.9), version: 2.1.17 2025-09-07T23:52:23,397 Fetching project page and analyzing links: https://www.piwheels.org/simple/biom-format/ 2025-09-07T23:52:23,397 Getting page https://www.piwheels.org/simple/biom-format/ 2025-09-07T23:52:23,398 Found index url https://www.piwheels.org/simple/ 2025-09-07T23:52:23,512 Fetched page https://www.piwheels.org/simple/biom-format/ as text/html 2025-09-07T23:52:23,538 Skipping link: No binaries permitted for biom-format: 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https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp37-cp37m-linux_armv7l.whl#sha256=7a626aba8ff823cc9f782efde594c9996cfb48f2c2b456a2ed55c88977f2d1d1 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,549 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp37-cp37m-linux_armv6l.whl#sha256=7a626aba8ff823cc9f782efde594c9996cfb48f2c2b456a2ed55c88977f2d1d1 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp35-cp35m-linux_armv7l.whl#sha256=117a559c6cc285a8c0e94138f1585e93ccef7862532d78e61d3f14d96ab4120f (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp35-cp35m-linux_armv6l.whl#sha256=117a559c6cc285a8c0e94138f1585e93ccef7862532d78e61d3f14d96ab4120f (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp34-cp34m-linux_armv6l.whl#sha256=65a3ba75376f8e5cacf4f89448fcc9ca10489d5a7203a89b71e8d9c71919fe33 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp34-cp34m-linux_armv7l.whl#sha256=65a3ba75376f8e5cacf4f89448fcc9ca10489d5a7203a89b71e8d9c71919fe33 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp39-cp39-linux_armv6l.whl#sha256=7f2584f3e1b8e8897d7c7b4fbaf097a44a847fda65a385f8bda36b9177394b68 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=7f2584f3e1b8e8897d7c7b4fbaf097a44a847fda65a385f8bda36b9177394b68 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-1.3.1-py3-none-any.whl#sha256=f0b5649cb13509667e6ca75c84e68a1ff1de6716848e8d4f9a3ca8f8ca74b8df (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-1.3.0-py3-none-any.whl#sha256=ee9d81bea91a7c7da55697863c1b003aca4d14b7f7416fcb8c22e169e54aabe6 (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,550 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-1.2.0.dev0-py3-none-any.whl#sha256=1c6e81249da6f3e19dd7594733329820632b1b6b0355abe79af180116c3b8aba (from https://www.piwheels.org/simple/biom-format/) 2025-09-07T23:52:23,551 Skipping link: not a file: https://www.piwheels.org/simple/biom-format/ 2025-09-07T23:52:23,551 Skipping link: not a file: https://pypi.org/simple/biom-format/ 2025-09-07T23:52:23,575 Given no hashes to check 1 links for project 'biom-format': discarding no candidates 2025-09-07T23:52:23,576 Collecting biom-format==2.0.0 2025-09-07T23:52:23,577 Created temporary directory: /tmp/pip-unpack-om68m_hs 2025-09-07T23:52:23,725 Downloading biom-format-2.0.0.tar.gz (831 kB) 2025-09-07T23:52:24,125 Added biom-format==2.0.0 from https://files.pythonhosted.org/packages/ab/62/b44f747c549c2cb3408462905461ae8d0975163c927b4ac4452321368815/biom-format-2.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-af79grqi' 2025-09-07T23:52:24,127 Running setup.py (path:/tmp/pip-wheel-2u1u2qzb/biom-format_a00c0c4ddfc34c8d9e163a457547b8de/setup.py) egg_info for package biom-format 2025-09-07T23:52:24,127 Created temporary directory: /tmp/pip-pip-egg-info-78u5ec20 2025-09-07T23:52:24,127 Preparing metadata (setup.py): started 2025-09-07T23:52:24,128 Running command python setup.py egg_info 2025-09-07T23:52:25,148 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:25,148 !! 2025-09-07T23:52:25,148 ******************************************************************************** 2025-09-07T23:52:25,148 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:25,148 License :: OSI Approved :: BSD License 2025-09-07T23:52:25,148 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:25,149 ******************************************************************************** 2025-09-07T23:52:25,149 !! 2025-09-07T23:52:25,149 self._finalize_license_expression() 2025-09-07T23:52:25,229 running egg_info 2025-09-07T23:52:25,295 creating /tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info 2025-09-07T23:52:25,296 writing /tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/PKG-INFO 2025-09-07T23:52:25,299 writing dependency_links to /tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/dependency_links.txt 2025-09-07T23:52:25,301 writing requirements to /tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/requires.txt 2025-09-07T23:52:25,301 writing top-level names to /tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/top_level.txt 2025-09-07T23:52:25,301 writing manifest file '/tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/SOURCES.txt' 2025-09-07T23:52:25,824 reading manifest file '/tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/SOURCES.txt' 2025-09-07T23:52:25,825 reading manifest template 'MANIFEST.in' 2025-09-07T23:52:25,841 no previously-included directories found matching 'docs/_build' 2025-09-07T23:52:25,842 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-07T23:52:25,844 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2025-09-07T23:52:25,845 warning: no previously-included files matching '.git' found anywhere in distribution 2025-09-07T23:52:25,845 adding license file 'COPYING.txt' 2025-09-07T23:52:25,860 writing manifest file '/tmp/pip-pip-egg-info-78u5ec20/biom_format.egg-info/SOURCES.txt' 2025-09-07T23:52:25,993 Preparing metadata (setup.py): finished with status 'done' 2025-09-07T23:52:25,998 Source in /tmp/pip-wheel-2u1u2qzb/biom-format_a00c0c4ddfc34c8d9e163a457547b8de has version 2.0.0, which satisfies requirement biom-format==2.0.0 from https://files.pythonhosted.org/packages/ab/62/b44f747c549c2cb3408462905461ae8d0975163c927b4ac4452321368815/biom-format-2.0.0.tar.gz 2025-09-07T23:52:25,998 Removed biom-format==2.0.0 from https://files.pythonhosted.org/packages/ab/62/b44f747c549c2cb3408462905461ae8d0975163c927b4ac4452321368815/biom-format-2.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-af79grqi' 2025-09-07T23:52:26,004 Created temporary directory: /tmp/pip-unpack-3xe704t8 2025-09-07T23:52:26,004 Created temporary directory: /tmp/pip-unpack-goq_qewk 2025-09-07T23:52:26,004 Building wheels for collected packages: biom-format 2025-09-07T23:52:26,006 Created temporary directory: /tmp/pip-wheel-29v7ogy9 2025-09-07T23:52:26,006 DEPRECATION: Building 'biom-format' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'biom-format'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-07T23:52:26,007 Building wheel for biom-format (setup.py): started 2025-09-07T23:52:26,008 Destination directory: /tmp/pip-wheel-29v7ogy9 2025-09-07T23:52:26,008 Running command python setup.py bdist_wheel 2025-09-07T23:52:27,030 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:27,030 !! 2025-09-07T23:52:27,031 ******************************************************************************** 2025-09-07T23:52:27,031 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:27,031 License :: OSI Approved :: BSD License 2025-09-07T23:52:27,031 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:27,031 ******************************************************************************** 2025-09-07T23:52:27,031 !! 2025-09-07T23:52:27,031 self._finalize_license_expression() 2025-09-07T23:52:27,057 running bdist_wheel 2025-09-07T23:52:27,567 running build 2025-09-07T23:52:27,567 running build_py 2025-09-07T23:52:27,636 creating build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,637 copying biom/util.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,637 copying biom/table.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,638 copying biom/parse.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,639 copying biom/exception.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,639 copying biom/__init__.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,640 creating build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,641 copying biom/commands/table_validator.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,641 copying biom/commands/table_summarizer.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,642 copying biom/commands/table_subsetter.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,642 copying biom/commands/table_converter.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,643 copying biom/commands/metadata_adder.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,643 copying biom/commands/installation_informer.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,644 copying biom/commands/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-07T23:52:27,645 creating build/lib.linux-armv7l-cpython-313/biom/interfaces 2025-09-07T23:52:27,645 copying biom/interfaces/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces 2025-09-07T23:52:27,646 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-07T23:52:27,646 copying biom/interfaces/optparse/output_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-07T23:52:27,646 copying biom/interfaces/optparse/input_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-07T23:52:27,647 copying biom/interfaces/optparse/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-07T23:52:27,648 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,648 copying biom/interfaces/optparse/config/validate_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,648 copying biom/interfaces/optparse/config/summarize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,649 copying biom/interfaces/optparse/config/subset_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,649 copying biom/interfaces/optparse/config/show_install_info.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,650 copying biom/interfaces/optparse/config/convert.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,650 copying biom/interfaces/optparse/config/add_metadata.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,651 copying biom/interfaces/optparse/config/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-07T23:52:27,652 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-07T23:52:27,652 copying biom/interfaces/html/output_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-07T23:52:27,652 copying biom/interfaces/html/input_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-07T23:52:27,653 copying biom/interfaces/html/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-07T23:52:27,654 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,654 copying biom/interfaces/html/config/validate_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,655 copying biom/interfaces/html/config/summarize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,655 copying biom/interfaces/html/config/show_install_info.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,656 copying biom/interfaces/html/config/convert.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,656 copying biom/interfaces/html/config/add_metadata.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,657 copying biom/interfaces/html/config/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-07T23:52:27,661 running build_ext 2025-09-07T23:52:27,981 building 'biom._filter' extension 2025-09-07T23:52:27,981 creating build/temp.linux-armv7l-cpython-313/biom 2025-09-07T23:52:27,982 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c biom/_filter.c -o build/temp.linux-armv7l-cpython-313/biom/_filter.o 2025-09-07T23:52:28,478 biom/_filter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-07T23:52:28,483 biom/_filter.c:3787:52: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-07T23:52:28,483 3787 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:52:28,483 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,483 | PyBUF_C_CONTIGUOUS 2025-09-07T23:52:28,483 biom/_filter.c:3787:52: note: each undeclared identifier is reported only once for each function it appears in 2025-09-07T23:52:28,510 biom/_filter.c:3825:52: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-07T23:52:28,510 3825 | __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-07T23:52:28,510 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,510 | PyBUF_F_CONTIGUOUS 2025-09-07T23:52:28,517 biom/_filter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-07T23:52:28,521 biom/_filter.c:4830:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:52:28,522 4830 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-07T23:52:28,522 | ^~ 2025-09-07T23:52:28,522 biom/_filter.c:511:45: note: in definition of macro ‘unlikely’ 2025-09-07T23:52:28,522 511 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-07T23:52:28,522 | ^ 2025-09-07T23:52:28,526 biom/_filter.c:4834:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-07T23:52:28,526 4834 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-07T23:52:28,527 | ^~ 2025-09-07T23:52:28,532 biom/_filter.c:4852:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-07T23:52:28,532 4852 | __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-07T23:52:28,533 | ^~ 2025-09-07T23:52:28,543 biom/_filter.c:5030:81: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-07T23:52:28,543 5030 | (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + __pyx_v_child->elsize); 2025-09-07T23:52:28,544 | ^~ 2025-09-07T23:52:28,558 biom/_filter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-07T23:52:28,563 biom/_filter.c:5851:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:52:28,564 5851 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(7, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 103, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:52:28,564 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,564 In file included from /usr/include/python3.13/Python.h:101, 2025-09-07T23:52:28,564 from biom/_filter.c:16: 2025-09-07T23:52:28,564 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:28,564 213 | PyCode_New( 2025-09-07T23:52:28,564 | ^~~~~~~~~~ 2025-09-07T23:52:28,570 biom/_filter.c:5851:241: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:52:28,570 5851 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(7, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 103, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:52:28,571 | ^~~ 2025-09-07T23:52:28,571 | | 2025-09-07T23:52:28,571 | int 2025-09-07T23:52:28,571 biom/_filter.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,571 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,571 | ^~~~~ 2025-09-07T23:52:28,571 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:52:28,571 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:28,571 | ~~~~~~~~~~^ 2025-09-07T23:52:28,577 biom/_filter.c:5851:246: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:52:28,577 5851 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(7, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 103, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:52:28,577 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,577 | | 2025-09-07T23:52:28,578 | PyObject * {aka struct _object *} 2025-09-07T23:52:28,578 biom/_filter.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,578 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,578 | ^~~~ 2025-09-07T23:52:28,578 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:52:28,578 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:28,578 | ~~~~^ 2025-09-07T23:52:28,584 biom/_filter.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:52:28,584 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,584 | ^~~~~~~~~~ 2025-09-07T23:52:28,584 biom/_filter.c:5851:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,584 5851 | __pyx_codeobj__12 = (PyObject*)__Pyx_PyCode_New(7, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__11, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 103, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 103; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-07T23:52:28,584 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,584 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:28,584 213 | PyCode_New( 2025-09-07T23:52:28,585 | ^~~~~~~~~~ 2025-09-07T23:52:28,654 biom/_filter.c: In function ‘__Pyx_ErrRestore’: 2025-09-07T23:52:28,661 biom/_filter.c:6905:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,661 6905 | tmp_type = tstate->curexc_type; 2025-09-07T23:52:28,661 | ^~ 2025-09-07T23:52:28,668 biom/_filter.c:6906:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,668 6906 | tmp_value = tstate->curexc_value; 2025-09-07T23:52:28,668 | ^~ 2025-09-07T23:52:28,675 biom/_filter.c:6907:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,675 6907 | tmp_tb = tstate->curexc_traceback; 2025-09-07T23:52:28,675 | ^~ 2025-09-07T23:52:28,682 biom/_filter.c:6908:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,682 6908 | tstate->curexc_type = type; 2025-09-07T23:52:28,682 | ^~ 2025-09-07T23:52:28,689 biom/_filter.c:6909:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,689 6909 | tstate->curexc_value = value; 2025-09-07T23:52:28,689 | ^~ 2025-09-07T23:52:28,696 biom/_filter.c:6910:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,696 6910 | tstate->curexc_traceback = tb; 2025-09-07T23:52:28,696 | ^~ 2025-09-07T23:52:28,696 biom/_filter.c: In function ‘__Pyx_ErrFetch’: 2025-09-07T23:52:28,703 biom/_filter.c:6921:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,703 6921 | *type = tstate->curexc_type; 2025-09-07T23:52:28,703 | ^~ 2025-09-07T23:52:28,710 biom/_filter.c:6922:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,710 6922 | *value = tstate->curexc_value; 2025-09-07T23:52:28,710 | ^~ 2025-09-07T23:52:28,717 biom/_filter.c:6923:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,717 6923 | *tb = tstate->curexc_traceback; 2025-09-07T23:52:28,717 | ^~ 2025-09-07T23:52:28,724 biom/_filter.c:6924:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,724 6924 | tstate->curexc_type = 0; 2025-09-07T23:52:28,724 | ^~ 2025-09-07T23:52:28,731 biom/_filter.c:6925:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,731 6925 | tstate->curexc_value = 0; 2025-09-07T23:52:28,731 | ^~ 2025-09-07T23:52:28,738 biom/_filter.c:6926:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,738 6926 | tstate->curexc_traceback = 0; 2025-09-07T23:52:28,738 | ^~ 2025-09-07T23:52:28,740 biom/_filter.c: In function ‘__Pyx_IterFinish’: 2025-09-07T23:52:28,747 biom/_filter.c:7060:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,747 7060 | PyObject* exc_type = tstate->curexc_type; 2025-09-07T23:52:28,747 | ^~ 2025-09-07T23:52:28,754 biom/_filter.c:7064:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,754 7064 | exc_value = tstate->curexc_value; 2025-09-07T23:52:28,755 | ^~ 2025-09-07T23:52:28,761 biom/_filter.c:7065:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,762 7065 | exc_tb = tstate->curexc_traceback; 2025-09-07T23:52:28,762 | ^~ 2025-09-07T23:52:28,769 biom/_filter.c:7066:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-07T23:52:28,769 7066 | tstate->curexc_type = 0; 2025-09-07T23:52:28,769 | ^~ 2025-09-07T23:52:28,776 biom/_filter.c:7067:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-07T23:52:28,776 7067 | tstate->curexc_value = 0; 2025-09-07T23:52:28,776 | ^~ 2025-09-07T23:52:28,783 biom/_filter.c:7068:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,783 7068 | tstate->curexc_traceback = 0; 2025-09-07T23:52:28,783 | ^~ 2025-09-07T23:52:28,804 biom/_filter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-07T23:52:28,814 biom/_filter.c:7188:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-07T23:52:28,814 7188 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-07T23:52:28,814 | ^~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,815 | PyDict_GET_SIZE 2025-09-07T23:52:28,838 biom/_filter.c: In function ‘__Pyx_Raise’: 2025-09-07T23:52:28,846 biom/_filter.c:7398:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,846 7398 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-07T23:52:28,846 | ^~ 2025-09-07T23:52:28,853 biom/_filter.c:7401:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-07T23:52:28,853 7401 | tstate->curexc_traceback = tb; 2025-09-07T23:52:28,853 | ^~ 2025-09-07T23:52:28,876 biom/_filter.c: In function ‘__Pyx_PyInt_As_npy_uint8’: 2025-09-07T23:52:28,884 biom/_filter.c:7845:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:28,884 7845 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:28,884 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,884 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-07T23:52:28,884 from /usr/include/python3.13/Python.h:81: 2025-09-07T23:52:28,884 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:28,885 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:28,885 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,889 biom/_filter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-07T23:52:28,896 biom/_filter.c:7971:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:28,896 7971 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:28,897 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,897 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:28,897 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:28,897 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,900 biom/_filter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-07T23:52:28,908 biom/_filter.c:8071:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-07T23:52:28,908 8071 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-07T23:52:28,908 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,908 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-07T23:52:28,909 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-07T23:52:28,909 | ^~~~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,930 biom/_filter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-07T23:52:28,938 biom/_filter.c:8570:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-07T23:52:28,938 8570 | py_code = __Pyx_PyCode_New( 2025-09-07T23:52:28,938 | ^~~~~~~ 2025-09-07T23:52:28,938 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:28,939 213 | PyCode_New( 2025-09-07T23:52:28,939 | ^~~~~~~~~~ 2025-09-07T23:52:28,947 biom/_filter.c:8584:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-07T23:52:28,947 8584 | py_line, /*int firstlineno,*/ 2025-09-07T23:52:28,947 | ^~~~~~~ 2025-09-07T23:52:28,947 | | 2025-09-07T23:52:28,947 | int 2025-09-07T23:52:28,947 biom/_filter.c:124:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,947 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,947 | ^~~~~ 2025-09-07T23:52:28,948 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-07T23:52:28,948 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:28,948 | ~~~~~~~~~~^ 2025-09-07T23:52:28,956 biom/_filter.c:8585:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-07T23:52:28,957 8585 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-07T23:52:28,957 | ^~~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,957 | | 2025-09-07T23:52:28,957 | PyObject * {aka struct _object *} 2025-09-07T23:52:28,957 biom/_filter.c:124:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,957 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,957 | ^~~~ 2025-09-07T23:52:28,957 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-07T23:52:28,957 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-07T23:52:28,957 | ~~~~^ 2025-09-07T23:52:28,966 biom/_filter.c:124:11: error: too few arguments to function ‘PyCode_New’ 2025-09-07T23:52:28,966 124 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-07T23:52:28,966 | ^~~~~~~~~~ 2025-09-07T23:52:28,966 biom/_filter.c:8570:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-07T23:52:28,966 8570 | py_code = __Pyx_PyCode_New( 2025-09-07T23:52:28,966 | ^~~~~~~~~~~~~~~~ 2025-09-07T23:52:28,967 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-07T23:52:28,967 213 | PyCode_New( 2025-09-07T23:52:28,967 | ^~~~~~~~~~ 2025-09-07T23:52:28,972 biom/_filter.c: In function ‘__Pyx_AddTraceback’: 2025-09-07T23:52:28,981 biom/_filter.c:8616:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-07T23:52:28,981 8616 | py_frame->f_lineno = py_line; 2025-09-07T23:52:28,981 | ^~ 2025-09-07T23:52:29,062 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-07T23:52:29,230 ERROR: python setup.py bdist_wheel exited with 1 2025-09-07T23:52:29,242 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-07T23:52:29,242 exec(compile('"'"''"'"''"'"' 2025-09-07T23:52:29,242 # This is -- a caller that pip uses to run setup.py 2025-09-07T23:52:29,242 # 2025-09-07T23:52:29,242 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-07T23:52:29,242 # import from `distutils.core` to work with newer packaging standards. 2025-09-07T23:52:29,242 # - It provides a clear error message when setuptools is not installed. 2025-09-07T23:52:29,242 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-07T23:52:29,242 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-07T23:52:29,242 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-07T23:52:29,242 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-07T23:52:29,242 import os, sys, tokenize, traceback 2025-09-07T23:52:29,242 2025-09-07T23:52:29,242 try: 2025-09-07T23:52:29,242 import setuptools 2025-09-07T23:52:29,242 except ImportError: 2025-09-07T23:52:29,242 print( 2025-09-07T23:52:29,242 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-07T23:52:29,242 "the build environment with exception:", 2025-09-07T23:52:29,242 file=sys.stderr, 2025-09-07T23:52:29,242 ) 2025-09-07T23:52:29,242 traceback.print_exc() 2025-09-07T23:52:29,242 sys.exit(1) 2025-09-07T23:52:29,242 2025-09-07T23:52:29,242 __file__ = %r 2025-09-07T23:52:29,242 sys.argv[0] = __file__ 2025-09-07T23:52:29,242 2025-09-07T23:52:29,242 if os.path.exists(__file__): 2025-09-07T23:52:29,242 filename = __file__ 2025-09-07T23:52:29,242 with tokenize.open(__file__) as f: 2025-09-07T23:52:29,242 setup_py_code = f.read() 2025-09-07T23:52:29,242 else: 2025-09-07T23:52:29,242 filename = "" 2025-09-07T23:52:29,242 setup_py_code = "from setuptools import setup; setup()" 2025-09-07T23:52:29,242 2025-09-07T23:52:29,242 exec(compile(setup_py_code, filename, "exec")) 2025-09-07T23:52:29,242 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-2u1u2qzb/biom-format_a00c0c4ddfc34c8d9e163a457547b8de/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-29v7ogy9[/] 2025-09-07T23:52:29,242 [bold magenta]cwd[/]: /tmp/pip-wheel-2u1u2qzb/biom-format_a00c0c4ddfc34c8d9e163a457547b8de/ 2025-09-07T23:52:29,242 Building wheel for biom-format (setup.py): finished with status 'error' 2025-09-07T23:52:29,243 ERROR: Failed building wheel for biom-format 2025-09-07T23:52:29,243 Running setup.py clean for biom-format 2025-09-07T23:52:29,244 Running command python setup.py clean 2025-09-07T23:52:30,261 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-07T23:52:30,261 !! 2025-09-07T23:52:30,262 ******************************************************************************** 2025-09-07T23:52:30,262 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-07T23:52:30,262 License :: OSI Approved :: BSD License 2025-09-07T23:52:30,262 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-07T23:52:30,262 ******************************************************************************** 2025-09-07T23:52:30,262 !! 2025-09-07T23:52:30,262 self._finalize_license_expression() 2025-09-07T23:52:30,329 running clean 2025-09-07T23:52:30,466 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:52:30,467 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-07T23:52:30,468 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-07T23:52:30,468 'build/scripts-3.13' does not exist -- can't clean it 2025-09-07T23:52:30,468 removing 'build' 2025-09-07T23:52:30,582 Failed to build biom-format 2025-09-07T23:52:30,582 ERROR: Failed to build one or more wheels 2025-09-07T23:52:30,583 Exception information: 2025-09-07T23:52:30,583 Traceback (most recent call last): 2025-09-07T23:52:30,583 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-07T23:52:30,583 status = _inner_run() 2025-09-07T23:52:30,583 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-07T23:52:30,583 return self.run(options, args) 2025-09-07T23:52:30,583 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-07T23:52:30,583 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-07T23:52:30,583 return func(self, options, args) 2025-09-07T23:52:30,583 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-07T23:52:30,583 raise CommandError("Failed to build one or more wheels") 2025-09-07T23:52:30,583 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-07T23:52:30,587 Removed build tracker: '/tmp/pip-build-tracker-af79grqi'