2025-09-08T01:41:54,061 Created temporary directory: /tmp/pip-build-tracker-rj0znx8t 2025-09-08T01:41:54,062 Initialized build tracking at /tmp/pip-build-tracker-rj0znx8t 2025-09-08T01:41:54,062 Created build tracker: /tmp/pip-build-tracker-rj0znx8t 2025-09-08T01:41:54,062 Entered build tracker: /tmp/pip-build-tracker-rj0znx8t 2025-09-08T01:41:54,062 Created temporary directory: /tmp/pip-wheel-g_iaimsd 2025-09-08T01:41:54,066 Created temporary directory: /tmp/pip-ephem-wheel-cache-v92h2rc4 2025-09-08T01:41:54,122 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T01:41:54,124 2 location(s) to search for versions of biom-format: 2025-09-08T01:41:54,124 * https://pypi.org/simple/biom-format/ 2025-09-08T01:41:54,124 * https://www.piwheels.org/simple/biom-format/ 2025-09-08T01:41:54,125 Fetching project page and analyzing links: https://pypi.org/simple/biom-format/ 2025-09-08T01:41:54,125 Getting page https://pypi.org/simple/biom-format/ 2025-09-08T01:41:54,126 Found index url https://pypi.org/simple/ 2025-09-08T01:41:54,275 Fetched page https://pypi.org/simple/biom-format/ as application/vnd.pypi.simple.v1+json 2025-09-08T01:41:54,294 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 2025-09-08T01:41:54,294 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 2025-09-08T01:41:54,295 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 2025-09-08T01:41:54,295 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 2025-09-08T01:41:54,296 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 2025-09-08T01:41:54,296 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 2025-09-08T01:41:54,297 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 2025-09-08T01:41:54,297 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 2025-09-08T01:41:54,297 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 2025-09-08T01:41:54,297 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 2025-09-08T01:41:54,297 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 2025-09-08T01:41:54,298 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 2025-09-08T01:41:54,298 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/) 2025-09-08T01:41:54,298 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 2025-09-08T01:41:54,298 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/) 2025-09-08T01:41:54,298 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 2025-09-08T01:41:54,298 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 2025-09-08T01:41:54,299 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 2025-09-08T01:41:54,299 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 2025-09-08T01:41:54,299 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 2025-09-08T01:41:54,300 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 2025-09-08T01:41:54,300 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 2025-09-08T01:41:54,300 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) 2025-09-08T01:41:54,300 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) 2025-09-08T01:41:54,300 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) 2025-09-08T01:41:54,300 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,301 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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) 2025-09-08T01:41:54,302 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 2025-09-08T01:41:54,303 Skipping link: No binaries permitted for 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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) 2025-09-08T01:41:54,306 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 2025-09-08T01:41:54,306 Fetching project page and analyzing links: https://www.piwheels.org/simple/biom-format/ 2025-09-08T01:41:54,307 Getting page https://www.piwheels.org/simple/biom-format/ 2025-09-08T01:41:54,307 Found index url https://www.piwheels.org/simple/ 2025-09-08T01:41:54,394 Fetched page https://www.piwheels.org/simple/biom-format/ as text/html 2025-09-08T01:41:54,417 Skipping link: No binaries permitted for biom-format: 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https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.1-cp34-cp34m-linux_armv7l.whl#sha256=7da34e0d1c989db527bf0c9f694424dc0c0822f5ac262a48b53b16fb2e1b0b8b (from https://www.piwheels.org/simple/biom-format/) 2025-09-08T01:41:54,432 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=d6182bef514f635438b834481309528194ee4cce9ca22cbebd602f0fd535ec3d (from https://www.piwheels.org/simple/biom-format/) 2025-09-08T01:41:54,432 Skipping link: No binaries permitted for biom-format: https://archive1.piwheels.org/simple/biom-format/biom_format-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=d6182bef514f635438b834481309528194ee4cce9ca22cbebd602f0fd535ec3d (from https://www.piwheels.org/simple/biom-format/) 2025-09-08T01:41:54,432 Skipping link: No binaries permitted for biom-format: 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/) 2025-09-08T01:41:54,432 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/) 2025-09-08T01:41:54,432 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/) 2025-09-08T01:41:54,432 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,433 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/) 2025-09-08T01:41:54,434 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/) 2025-09-08T01:41:54,434 Skipping link: not a file: https://www.piwheels.org/simple/biom-format/ 2025-09-08T01:41:54,434 Skipping link: not a file: https://pypi.org/simple/biom-format/ 2025-09-08T01:41:54,458 Given no hashes to check 1 links for project 'biom-format': discarding no candidates 2025-09-08T01:41:54,459 Collecting biom-format==2.1.4 2025-09-08T01:41:54,460 Created temporary directory: /tmp/pip-unpack-3qhq56qi 2025-09-08T01:41:54,604 Downloading biom-format-2.1.4.tar.gz (435 kB) 2025-09-08T01:41:54,759 Added biom-format==2.1.4 from https://files.pythonhosted.org/packages/2e/8e/f8575e51764697c485f7e81dfc31ff72d8b2c4b50e88c23094be65814451/biom-format-2.1.4.tar.gz to build tracker '/tmp/pip-build-tracker-rj0znx8t' 2025-09-08T01:41:54,760 Running setup.py (path:/tmp/pip-wheel-g_iaimsd/biom-format_5c32c0517ecc4396a8afbc81217e9951/setup.py) egg_info for package biom-format 2025-09-08T01:41:54,760 Created temporary directory: /tmp/pip-pip-egg-info-it3m18bp 2025-09-08T01:41:54,760 Preparing metadata (setup.py): started 2025-09-08T01:41:54,761 Running command python setup.py egg_info 2025-09-08T01:41:55,738 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:41:55,738 warnings.warn(msg) 2025-09-08T01:41:56,148 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T01:41:56,148 !! 2025-09-08T01:41:56,149 ******************************************************************************** 2025-09-08T01:41:56,149 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T01:41:56,149 License :: OSI Approved :: BSD License 2025-09-08T01:41:56,149 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T01:41:56,149 ******************************************************************************** 2025-09-08T01:41:56,149 !! 2025-09-08T01:41:56,149 self._finalize_license_expression() 2025-09-08T01:41:56,223 running egg_info 2025-09-08T01:41:56,297 creating /tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info 2025-09-08T01:41:56,297 writing /tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/PKG-INFO 2025-09-08T01:41:56,300 writing dependency_links to /tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/dependency_links.txt 2025-09-08T01:41:56,302 writing requirements to /tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/requires.txt 2025-09-08T01:41:56,302 writing top-level names to /tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/top_level.txt 2025-09-08T01:41:56,303 writing manifest file '/tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/SOURCES.txt' 2025-09-08T01:41:56,679 reading manifest file '/tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/SOURCES.txt' 2025-09-08T01:41:56,680 reading manifest template 'MANIFEST.in' 2025-09-08T01:41:56,686 no previously-included directories found matching 'docs/_build' 2025-09-08T01:41:56,686 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2025-09-08T01:41:56,687 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2025-09-08T01:41:56,688 warning: no previously-included files matching '.git' found anywhere in distribution 2025-09-08T01:41:56,688 adding license file 'COPYING.txt' 2025-09-08T01:41:56,693 writing manifest file '/tmp/pip-pip-egg-info-it3m18bp/biom_format.egg-info/SOURCES.txt' 2025-09-08T01:41:56,829 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T01:41:56,834 Source in /tmp/pip-wheel-g_iaimsd/biom-format_5c32c0517ecc4396a8afbc81217e9951 has version 2.1.4, which satisfies requirement biom-format==2.1.4 from https://files.pythonhosted.org/packages/2e/8e/f8575e51764697c485f7e81dfc31ff72d8b2c4b50e88c23094be65814451/biom-format-2.1.4.tar.gz 2025-09-08T01:41:56,834 Removed biom-format==2.1.4 from https://files.pythonhosted.org/packages/2e/8e/f8575e51764697c485f7e81dfc31ff72d8b2c4b50e88c23094be65814451/biom-format-2.1.4.tar.gz from build tracker '/tmp/pip-build-tracker-rj0znx8t' 2025-09-08T01:41:56,841 Created temporary directory: /tmp/pip-unpack-p5_reikp 2025-09-08T01:41:56,841 Created temporary directory: /tmp/pip-unpack-tjtegtdl 2025-09-08T01:41:56,841 Building wheels for collected packages: biom-format 2025-09-08T01:41:56,842 Created temporary directory: /tmp/pip-wheel-_t89h3wa 2025-09-08T01:41:56,843 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 2025-09-08T01:41:56,844 Building wheel for biom-format (setup.py): started 2025-09-08T01:41:56,845 Destination directory: /tmp/pip-wheel-_t89h3wa 2025-09-08T01:41:56,845 Running command python setup.py bdist_wheel 2025-09-08T01:41:57,739 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:41:57,739 warnings.warn(msg) 2025-09-08T01:41:58,131 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T01:41:58,131 !! 2025-09-08T01:41:58,131 ******************************************************************************** 2025-09-08T01:41:58,131 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T01:41:58,131 License :: OSI Approved :: BSD License 2025-09-08T01:41:58,132 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T01:41:58,132 ******************************************************************************** 2025-09-08T01:41:58,132 !! 2025-09-08T01:41:58,132 self._finalize_license_expression() 2025-09-08T01:41:58,132 running bdist_wheel 2025-09-08T01:41:58,503 running build 2025-09-08T01:41:58,503 running build_py 2025-09-08T01:41:58,582 creating build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,582 copying biom/util.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,583 copying biom/table.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,584 copying biom/parse.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,585 copying biom/exception.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,585 copying biom/err.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,586 copying biom/__init__.py -> build/lib.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,587 creating build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,587 copying biom/commands/table_validator.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,588 copying biom/commands/table_summarizer.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,588 copying biom/commands/table_subsetter.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,589 copying biom/commands/table_normalizer.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,589 copying biom/commands/table_converter.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,590 copying biom/commands/metadata_adder.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,590 copying biom/commands/installation_informer.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,591 copying biom/commands/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/commands 2025-09-08T01:41:58,592 creating build/lib.linux-armv7l-cpython-313/biom/interfaces 2025-09-08T01:41:58,592 copying biom/interfaces/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces 2025-09-08T01:41:58,593 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-08T01:41:58,593 copying biom/interfaces/optparse/output_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-08T01:41:58,593 copying biom/interfaces/optparse/input_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-08T01:41:58,594 copying biom/interfaces/optparse/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse 2025-09-08T01:41:58,595 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,595 copying biom/interfaces/optparse/config/validate_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,595 copying biom/interfaces/optparse/config/summarize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,596 copying biom/interfaces/optparse/config/subset_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,597 copying biom/interfaces/optparse/config/show_install_info.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,597 copying biom/interfaces/optparse/config/normalize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,598 copying biom/interfaces/optparse/config/convert.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,598 copying biom/interfaces/optparse/config/add_metadata.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,599 copying biom/interfaces/optparse/config/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/optparse/config 2025-09-08T01:41:58,599 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-08T01:41:58,599 copying biom/interfaces/html/output_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-08T01:41:58,600 copying biom/interfaces/html/input_handler.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-08T01:41:58,601 copying biom/interfaces/html/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html 2025-09-08T01:41:58,601 creating build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,602 copying biom/interfaces/html/config/validate_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,602 copying biom/interfaces/html/config/summarize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,603 copying biom/interfaces/html/config/show_install_info.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,603 copying biom/interfaces/html/config/normalize_table.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,604 copying biom/interfaces/html/config/convert.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,604 copying biom/interfaces/html/config/add_metadata.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,605 copying biom/interfaces/html/config/__init__.py -> build/lib.linux-armv7l-cpython-313/biom/interfaces/html/config 2025-09-08T01:41:58,609 running build_ext 2025-09-08T01:41:58,938 building 'biom._filter' extension 2025-09-08T01:41:58,938 creating build/temp.linux-armv7l-cpython-313/biom 2025-09-08T01:41:58,939 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 2025-09-08T01:41:59,344 biom/_filter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T01:41:59,345 biom/_filter.c:929:23: error: lvalue required as left operand of assignment 2025-09-08T01:41:59,345 929 | Py_SIZE(list) = len+1; 2025-09-08T01:41:59,345 | ^ 2025-09-08T01:41:59,434 biom/_filter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T01:41:59,438 biom/_filter.c:3468:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T01:41:59,438 3468 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:41:59,439 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,439 | PyBUF_C_CONTIGUOUS 2025-09-08T01:41:59,439 biom/_filter.c:3468:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T01:41:59,465 biom/_filter.c:3508:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T01:41:59,465 3508 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:41:59,465 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,466 | PyBUF_F_CONTIGUOUS 2025-09-08T01:41:59,473 biom/_filter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T01:41:59,478 biom/_filter.c:4514:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:41:59,478 4514 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T01:41:59,478 | ^~ 2025-09-08T01:41:59,478 biom/_filter.c:424:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:41:59,478 424 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:41:59,478 | ^ 2025-09-08T01:41:59,483 biom/_filter.c:4518:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:41:59,483 4518 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T01:41:59,484 | ^~ 2025-09-08T01:41:59,489 biom/_filter.c:4536:31: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T01:41:59,490 4536 | if (unlikely(__pyx_v_descr->fields == Py_None)) { 2025-09-08T01:41:59,490 | ^~ 2025-09-08T01:41:59,490 biom/_filter.c:424:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:41:59,490 424 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:41:59,490 | ^ 2025-09-08T01:41:59,495 biom/_filter.c:4540:51: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T01:41:59,495 4540 | __pyx_t_3 = __Pyx_PyDict_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-08T01:41:59,495 | ^~ 2025-09-08T01:41:59,506 biom/_filter.c:4721:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T01:41:59,506 4721 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T01:41:59,507 | ^~ 2025-09-08T01:41:59,521 biom/_filter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T01:41:59,527 biom/_filter.c:5533:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:41:59,527 5533 | __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(7, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__10, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 89, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:41:59,527 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,528 In file included from /usr/include/python3.13/Python.h:101, 2025-09-08T01:41:59,528 from biom/_filter.c:24: 2025-09-08T01:41:59,528 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:41:59,528 213 | PyCode_New( 2025-09-08T01:41:59,528 | ^~~~~~~~~~ 2025-09-08T01:41:59,534 biom/_filter.c:5533:241: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:41:59,535 5533 | __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(7, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__10, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 89, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:41:59,535 | ^~ 2025-09-08T01:41:59,535 | | 2025-09-08T01:41:59,535 | int 2025-09-08T01:41:59,535 biom/_filter.c:78:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,535 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,535 | ^~~~~ 2025-09-08T01:41:59,535 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:41:59,535 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:41:59,536 | ~~~~~~~~~~^ 2025-09-08T01:41:59,542 biom/_filter.c:5533:245: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:41:59,542 5533 | __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(7, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__10, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 89, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:41:59,542 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,542 | | 2025-09-08T01:41:59,542 | PyObject * {aka struct _object *} 2025-09-08T01:41:59,542 biom/_filter.c:78:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,543 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,543 | ^~~~ 2025-09-08T01:41:59,543 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:41:59,543 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:41:59,543 | ~~~~^ 2025-09-08T01:41:59,549 biom/_filter.c:78:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:41:59,550 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,550 | ^~~~~~~~~~ 2025-09-08T01:41:59,550 biom/_filter.c:5533:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,550 5533 | __pyx_codeobj__11 = (PyObject*)__Pyx_PyCode_New(7, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__10, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_home_jorge_code_forks_biom_form, __pyx_n_s_filter, 89, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:41:59,550 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,550 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:41:59,550 213 | PyCode_New( 2025-09-08T01:41:59,550 | ^~~~~~~~~~ 2025-09-08T01:41:59,620 biom/_filter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T01:41:59,627 biom/_filter.c:6540:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,627 6540 | tmp_type = tstate->curexc_type; 2025-09-08T01:41:59,627 | ^~ 2025-09-08T01:41:59,634 biom/_filter.c:6541:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,634 6541 | tmp_value = tstate->curexc_value; 2025-09-08T01:41:59,634 | ^~ 2025-09-08T01:41:59,641 biom/_filter.c:6542:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,641 6542 | tmp_tb = tstate->curexc_traceback; 2025-09-08T01:41:59,642 | ^~ 2025-09-08T01:41:59,648 biom/_filter.c:6543:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,649 6543 | tstate->curexc_type = type; 2025-09-08T01:41:59,649 | ^~ 2025-09-08T01:41:59,655 biom/_filter.c:6544:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,656 6544 | tstate->curexc_value = value; 2025-09-08T01:41:59,656 | ^~ 2025-09-08T01:41:59,662 biom/_filter.c:6545:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,663 6545 | tstate->curexc_traceback = tb; 2025-09-08T01:41:59,663 | ^~ 2025-09-08T01:41:59,663 biom/_filter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T01:41:59,670 biom/_filter.c:6556:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,670 6556 | *type = tstate->curexc_type; 2025-09-08T01:41:59,670 | ^~ 2025-09-08T01:41:59,677 biom/_filter.c:6557:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,677 6557 | *value = tstate->curexc_value; 2025-09-08T01:41:59,677 | ^~ 2025-09-08T01:41:59,684 biom/_filter.c:6558:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,684 6558 | *tb = tstate->curexc_traceback; 2025-09-08T01:41:59,684 | ^~ 2025-09-08T01:41:59,691 biom/_filter.c:6559:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,691 6559 | tstate->curexc_type = 0; 2025-09-08T01:41:59,692 | ^~ 2025-09-08T01:41:59,698 biom/_filter.c:6560:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,698 6560 | tstate->curexc_value = 0; 2025-09-08T01:41:59,699 | ^~ 2025-09-08T01:41:59,705 biom/_filter.c:6561:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,706 6561 | tstate->curexc_traceback = 0; 2025-09-08T01:41:59,706 | ^~ 2025-09-08T01:41:59,706 biom/_filter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T01:41:59,713 biom/_filter.c:6581:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,713 6581 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T01:41:59,713 | ^~ 2025-09-08T01:41:59,720 biom/_filter.c:6585:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,720 6585 | exc_value = tstate->curexc_value; 2025-09-08T01:41:59,720 | ^~ 2025-09-08T01:41:59,727 biom/_filter.c:6586:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,727 6586 | exc_tb = tstate->curexc_traceback; 2025-09-08T01:41:59,727 | ^~ 2025-09-08T01:41:59,735 biom/_filter.c:6587:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:41:59,735 6587 | tstate->curexc_type = 0; 2025-09-08T01:41:59,735 | ^~ 2025-09-08T01:41:59,743 biom/_filter.c:6588:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:41:59,743 6588 | tstate->curexc_value = 0; 2025-09-08T01:41:59,743 | ^~ 2025-09-08T01:41:59,751 biom/_filter.c:6589:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,751 6589 | tstate->curexc_traceback = 0; 2025-09-08T01:41:59,752 | ^~ 2025-09-08T01:41:59,773 biom/_filter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T01:41:59,783 biom/_filter.c:6806:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T01:41:59,783 6806 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T01:41:59,783 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,784 | PyDict_GET_SIZE 2025-09-08T01:41:59,806 biom/_filter.c: In function ‘__Pyx_Raise’: 2025-09-08T01:41:59,813 biom/_filter.c:7022:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,814 7022 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T01:41:59,814 | ^~ 2025-09-08T01:41:59,821 biom/_filter.c:7025:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:41:59,821 7025 | tstate->curexc_traceback = tb; 2025-09-08T01:41:59,821 | ^~ 2025-09-08T01:41:59,828 biom/_filter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T01:41:59,835 biom/_filter.c:7162:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:41:59,835 7162 | py_code = __Pyx_PyCode_New( 2025-09-08T01:41:59,835 | ^~~~~~~ 2025-09-08T01:41:59,835 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:41:59,835 213 | PyCode_New( 2025-09-08T01:41:59,835 | ^~~~~~~~~~ 2025-09-08T01:41:59,842 biom/_filter.c:7176:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:41:59,842 7176 | py_line, 2025-09-08T01:41:59,842 | ^~~~~~~ 2025-09-08T01:41:59,842 | | 2025-09-08T01:41:59,842 | int 2025-09-08T01:41:59,842 biom/_filter.c:78:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,843 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,843 | ^~~~~ 2025-09-08T01:41:59,843 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:41:59,843 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:41:59,843 | ~~~~~~~~~~^ 2025-09-08T01:41:59,850 biom/_filter.c:7177:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:41:59,850 7177 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T01:41:59,850 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,850 | | 2025-09-08T01:41:59,851 | PyObject * {aka struct _object *} 2025-09-08T01:41:59,851 biom/_filter.c:78:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,851 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,851 | ^~~~ 2025-09-08T01:41:59,851 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:41:59,851 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:41:59,851 | ~~~~^ 2025-09-08T01:41:59,858 biom/_filter.c:78:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:41:59,858 78 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:41:59,858 | ^~~~~~~~~~ 2025-09-08T01:41:59,859 biom/_filter.c:7162:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:41:59,859 7162 | py_code = __Pyx_PyCode_New( 2025-09-08T01:41:59,859 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,859 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:41:59,859 213 | PyCode_New( 2025-09-08T01:41:59,859 | ^~~~~~~~~~ 2025-09-08T01:41:59,862 biom/_filter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T01:41:59,869 biom/_filter.c:7205:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:41:59,869 7205 | py_frame->f_lineno = py_line; 2025-09-08T01:41:59,869 | ^~ 2025-09-08T01:41:59,879 biom/_filter.c: In function ‘__Pyx_PyInt_As_npy_uint8’: 2025-09-08T01:41:59,886 biom/_filter.c:7420:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:41:59,886 7420 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:41:59,886 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,886 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T01:41:59,886 from /usr/include/python3.13/Python.h:81: 2025-09-08T01:41:59,886 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:41:59,887 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:41:59,887 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,891 biom/_filter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T01:41:59,899 biom/_filter.c:7807:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:41:59,899 7807 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:41:59,900 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,900 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:41:59,900 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:41:59,900 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,903 biom/_filter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T01:41:59,911 biom/_filter.c:7928:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:41:59,911 7928 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:41:59,911 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,911 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:41:59,912 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:41:59,912 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:41:59,999 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T01:42:00,173 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T01:42:00,185 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T01:42:00,185 exec(compile('"'"''"'"''"'"' 2025-09-08T01:42:00,185 # This is -- a caller that pip uses to run setup.py 2025-09-08T01:42:00,185 # 2025-09-08T01:42:00,185 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T01:42:00,185 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T01:42:00,185 # - It provides a clear error message when setuptools is not installed. 2025-09-08T01:42:00,185 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T01:42:00,185 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T01:42:00,185 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T01:42:00,185 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T01:42:00,185 import os, sys, tokenize, traceback 2025-09-08T01:42:00,185 2025-09-08T01:42:00,185 try: 2025-09-08T01:42:00,185 import setuptools 2025-09-08T01:42:00,185 except ImportError: 2025-09-08T01:42:00,185 print( 2025-09-08T01:42:00,185 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T01:42:00,185 "the build environment with exception:", 2025-09-08T01:42:00,185 file=sys.stderr, 2025-09-08T01:42:00,185 ) 2025-09-08T01:42:00,185 traceback.print_exc() 2025-09-08T01:42:00,185 sys.exit(1) 2025-09-08T01:42:00,185 2025-09-08T01:42:00,185 __file__ = %r 2025-09-08T01:42:00,185 sys.argv[0] = __file__ 2025-09-08T01:42:00,185 2025-09-08T01:42:00,185 if os.path.exists(__file__): 2025-09-08T01:42:00,185 filename = __file__ 2025-09-08T01:42:00,185 with tokenize.open(__file__) as f: 2025-09-08T01:42:00,185 setup_py_code = f.read() 2025-09-08T01:42:00,185 else: 2025-09-08T01:42:00,185 filename = "" 2025-09-08T01:42:00,185 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T01:42:00,185 2025-09-08T01:42:00,185 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T01:42:00,185 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-g_iaimsd/biom-format_5c32c0517ecc4396a8afbc81217e9951/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-_t89h3wa[/] 2025-09-08T01:42:00,185 [bold magenta]cwd[/]: /tmp/pip-wheel-g_iaimsd/biom-format_5c32c0517ecc4396a8afbc81217e9951/ 2025-09-08T01:42:00,185 Building wheel for biom-format (setup.py): finished with status 'error' 2025-09-08T01:42:00,186 ERROR: Failed building wheel for biom-format 2025-09-08T01:42:00,187 Running setup.py clean for biom-format 2025-09-08T01:42:00,188 Running command python setup.py clean 2025-09-08T01:42:01,075 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:42:01,075 warnings.warn(msg) 2025-09-08T01:42:01,471 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-08T01:42:01,471 !! 2025-09-08T01:42:01,471 ******************************************************************************** 2025-09-08T01:42:01,471 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-08T01:42:01,471 License :: OSI Approved :: BSD License 2025-09-08T01:42:01,471 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-08T01:42:01,472 ******************************************************************************** 2025-09-08T01:42:01,472 !! 2025-09-08T01:42:01,472 self._finalize_license_expression() 2025-09-08T01:42:01,546 running clean 2025-09-08T01:42:01,692 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:42:01,692 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:42:01,694 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T01:42:01,694 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T01:42:01,694 removing 'build' 2025-09-08T01:42:01,830 Failed to build biom-format 2025-09-08T01:42:01,831 ERROR: Failed to build one or more wheels 2025-09-08T01:42:01,832 Exception information: 2025-09-08T01:42:01,832 Traceback (most recent call last): 2025-09-08T01:42:01,832 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T01:42:01,832 status = _inner_run() 2025-09-08T01:42:01,832 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T01:42:01,832 return self.run(options, args) 2025-09-08T01:42:01,832 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T01:42:01,832 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T01:42:01,832 return func(self, options, args) 2025-09-08T01:42:01,832 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T01:42:01,832 raise CommandError("Failed to build one or more wheels") 2025-09-08T01:42:01,832 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T01:42:01,836 Removed build tracker: '/tmp/pip-build-tracker-rj0znx8t'