2025-03-28T13:19:21,755 Disabling truststore because Python version isn't 3.10+ 2025-03-28T13:19:22,276 Created temporary directory: /tmp/pip-build-tracker-y8rfnyik 2025-03-28T13:19:22,277 Initialized build tracking at /tmp/pip-build-tracker-y8rfnyik 2025-03-28T13:19:22,277 Created build tracker: /tmp/pip-build-tracker-y8rfnyik 2025-03-28T13:19:22,277 Entered build tracker: /tmp/pip-build-tracker-y8rfnyik 2025-03-28T13:19:22,278 Created temporary directory: /tmp/pip-wheel-g_el_6fn 2025-03-28T13:19:22,283 Created temporary directory: /tmp/pip-ephem-wheel-cache-lp3bn1ul 2025-03-28T13:19:22,326 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-03-28T13:19:22,329 2 location(s) to search for versions of kssdtree: 2025-03-28T13:19:22,329 * https://pypi.org/simple/kssdtree/ 2025-03-28T13:19:22,329 * https://www.piwheels.org/simple/kssdtree/ 2025-03-28T13:19:22,330 Fetching project page and analyzing links: https://pypi.org/simple/kssdtree/ 2025-03-28T13:19:22,330 Getting page https://pypi.org/simple/kssdtree/ 2025-03-28T13:19:22,332 Found index url https://pypi.org/simple/ 2025-03-28T13:19:22,428 Fetched page https://pypi.org/simple/kssdtree/ as application/vnd.pypi.simple.v1+json 2025-03-28T13:19:22,432 Found link https://files.pythonhosted.org/packages/d5/1e/9e5c5945a44bb40002d1c259f734a531999fa6e87db89fe7c7ddcfc583cc/kssdtree-1.1.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.1 2025-03-28T13:19:22,432 Found link https://files.pythonhosted.org/packages/9a/4c/6516f734f5860e4b30f9091aaac5811663bfae72c4de4ae6566c89192767/kssdtree-1.1.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.2 2025-03-28T13:19:22,432 Found link https://files.pythonhosted.org/packages/a4/cd/f2954686c636e853cc3fda197c459195377b78288874cf7d68218a8bdbf4/kssdtree-1.1.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.3 2025-03-28T13:19:22,433 Found link https://files.pythonhosted.org/packages/20/ea/b0301924e3f7d367cbb7b8da66837dba9af2a332bf56ed35e03a33faee76/kssdtree-1.1.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.4 2025-03-28T13:19:22,433 Found link https://files.pythonhosted.org/packages/41/65/ed35110b84bc0dd02b9add0104f10160754d2ea0882191767d512146a884/kssdtree-1.1.6.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.6 2025-03-28T13:19:22,433 Found link https://files.pythonhosted.org/packages/cd/4b/d886cbcc573ff0969da7d9c756049925b86141e60ee6708dfbbe0644d008/kssdtree-1.1.7.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.7 2025-03-28T13:19:22,434 Found link https://files.pythonhosted.org/packages/7e/8a/a62c8adc92df69ab8cb242827ee64a3e2b6d5c89b83425785dd00605af17/kssdtree-1.1.8.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.8 2025-03-28T13:19:22,434 Found link https://files.pythonhosted.org/packages/da/db/e458cca6427752c05428d2378ccdee631d32f760174fdaba65f73125e71b/kssdtree-1.1.9.tar.gz (from https://pypi.org/simple/kssdtree/), version: 1.1.9 2025-03-28T13:19:22,434 Found link https://files.pythonhosted.org/packages/9d/47/017180a30e73e421372377cbe6d01c5e51a5108ea2177f20ccd7d283f8d1/kssdtree-2.0.0.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.0 2025-03-28T13:19:22,434 Found link https://files.pythonhosted.org/packages/ba/39/d443cac955912a0371c93b797311cb9ec3a8d6ee0a5d7673376d826aa6b2/kssdtree-2.0.1.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.1 2025-03-28T13:19:22,435 Found link https://files.pythonhosted.org/packages/2e/32/e53c0e3735cbc913b2c96b4e0e1c1005fe816a4d71b38b80cdcfb5c67fa8/kssdtree-2.0.2.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.2 2025-03-28T13:19:22,435 Found link https://files.pythonhosted.org/packages/c0/0f/effc10c8e76dbe3b9a35a4b4d9e65a0a889ee805e10334541c3ca7ae3b94/kssdtree-2.0.3.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.3 2025-03-28T13:19:22,435 Found link https://files.pythonhosted.org/packages/fc/8d/d3790baa2f2f0a01c913005b94a82dc13ef601e7015e662ccff94bb1b458/kssdtree-2.0.4.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.4 2025-03-28T13:19:22,435 Found link https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz (from https://pypi.org/simple/kssdtree/), version: 2.0.5 2025-03-28T13:19:22,436 Fetching project page and analyzing links: https://www.piwheels.org/simple/kssdtree/ 2025-03-28T13:19:22,436 Getting page https://www.piwheels.org/simple/kssdtree/ 2025-03-28T13:19:22,437 Found index url https://www.piwheels.org/simple/ 2025-03-28T13:19:22,489 Fetched page https://www.piwheels.org/simple/kssdtree/ as text/html 2025-03-28T13:19:22,506 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.5-cp311-cp311-linux_armv6l.whl#sha256=cecf3000ed0ffcd720412023d8de2f213356363c01aa3193441c040ed34353d3 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,506 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.5-cp311-cp311-linux_armv7l.whl#sha256=cecf3000ed0ffcd720412023d8de2f213356363c01aa3193441c040ed34353d3 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,506 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp311-cp311-linux_armv6l.whl#sha256=97a69f799c2d1b7024a9033b8a1e3fc17af4748a1ed726f52397d884303eb870 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,506 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp311-cp311-linux_armv7l.whl#sha256=97a69f799c2d1b7024a9033b8a1e3fc17af4748a1ed726f52397d884303eb870 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,507 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp39-cp39-linux_armv6l.whl#sha256=00938a03bead64e58bc1928832b7952b04d844e79b41da12160490c7edbb9e9f (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,507 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.4-cp39-cp39-linux_armv7l.whl#sha256=00938a03bead64e58bc1928832b7952b04d844e79b41da12160490c7edbb9e9f (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,507 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp311-cp311-linux_armv6l.whl#sha256=d70b4b00c6bf4ff5b294b9ad2594aa1e32981df4b9869be9d13aafa0ff614bc3 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,507 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp311-cp311-linux_armv7l.whl#sha256=d70b4b00c6bf4ff5b294b9ad2594aa1e32981df4b9869be9d13aafa0ff614bc3 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,507 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp39-cp39-linux_armv6l.whl#sha256=f629766f3426bb8a83c6f4adca8b02b03cb85452c129c9694cef65efd715fabd (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,508 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.3-cp39-cp39-linux_armv7l.whl#sha256=f629766f3426bb8a83c6f4adca8b02b03cb85452c129c9694cef65efd715fabd (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,508 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,509 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.1-cp311-cp311-linux_armv6l.whl#sha256=8b8c3190a5a4a010758772e9d53c3c12436541437bc9c503bec9a8f6a007cdcc (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,509 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.1-cp311-cp311-linux_armv7l.whl#sha256=8b8c3190a5a4a010758772e9d53c3c12436541437bc9c503bec9a8f6a007cdcc (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,509 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-2.0.0-cp311-cp311-linux_armv6l.whl#sha256=16a2e46376ed2874435371fd57a97405d4b631b35c014b9e395a4528a1e655b8 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,509 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,510 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp311-cp311-linux_armv7l.whl#sha256=d4c397f5fcb0af48dbb11b9fb7d7b399cc180d65355b794a8fcc7327e9a7dde1 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,510 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv6l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,510 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.9-cp39-cp39-linux_armv7l.whl#sha256=ab11dc15aca2923fe0d60bf11deb134bed4df89280b4ce40ca8e9bf3ca46b168 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,511 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,511 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv6l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,512 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp311-cp311-linux_armv7l.whl#sha256=388a8dabd657ea83e6d22b52300337c74e9d84e506806cfd4d2a76eb98777e17 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,512 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.7-cp39-cp39-linux_armv6l.whl#sha256=e1df896451d30c12e01aceb3eb91f0f7dfe0ee6f16fd66864fdefbc21cc54856 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,512 Skipping link: No binaries permitted for kssdtree: 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(from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,513 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.6-cp39-cp39-linux_armv7l.whl#sha256=9defb70b5162efc2c0eb6e415a7e37c604aa9b248a006af86af8f59a3bce5d2b (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,513 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv6l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,513 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp37-cp37m-linux_armv7l.whl#sha256=ffef4ae0f634dd977cc2ec6798b9f36f73d788aca27bb7199f552d5513c34413 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,513 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv6l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,514 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp311-cp311-linux_armv7l.whl#sha256=64b685362c3f9027bfeafdffb6a5d58c349a76fd551eeb7b98de146827463e75 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,514 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv6l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,514 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.4-cp39-cp39-linux_armv7l.whl#sha256=34527068d84569095aefee41a353c5dfc0dfa55b68097890da9a1eca2ee9b726 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,514 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv6l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,514 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp311-cp311-linux_armv7l.whl#sha256=6b76f3b3f532934ad49a829e7bf8176af580f4687f1491c49c3f571bf081f961 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,515 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv6l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,515 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp37-cp37m-linux_armv7l.whl#sha256=d179f6c6c0ad4e0f06950e1609118b065b3476c47446325f6614bdbef5ede0d0 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,515 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv6l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,515 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.3-cp39-cp39-linux_armv7l.whl#sha256=6df2298fa80eefa823153fa0b9db67e35da72da7f88c5949f4f637872ff22c3b (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,515 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv6l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,516 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp311-cp311-linux_armv7l.whl#sha256=146b572fde14b0d0770e1c1cd90870ad6db4af293ade814fed7a49e3857f1444 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,516 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv6l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,516 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp37-cp37m-linux_armv7l.whl#sha256=8c0cc1974033765d6eeefdb635a506385b5f38e00361bd6de47ff1a83b07e12a (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,516 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv6l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,516 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.2-cp39-cp39-linux_armv7l.whl#sha256=9f3fe3d3b4b4bde8b34a8f964ebde72f1efcc7833b9a0b34f6b9c8ff3ed595db (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,517 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv6l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,517 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp311-cp311-linux_armv7l.whl#sha256=29b8e7f4a3e60084db855e6d587231253771ad57184a3265922d659512e136fb (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,517 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,517 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=34b00b40f17a95b2cc5cbabd880acc2c56996457b0acd265cace6966c10b9575 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,517 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv6l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,518 Skipping link: No binaries permitted for kssdtree: https://www.piwheels.org/simple/kssdtree/kssdtree-1.1.1-cp39-cp39-linux_armv7l.whl#sha256=04471408d60c00f568404b1ab01ca89567b36a1aa50ef6041aceef07ed1e45f4 (from https://www.piwheels.org/simple/kssdtree/) 2025-03-28T13:19:22,518 Skipping link: not a file: https://www.piwheels.org/simple/kssdtree/ 2025-03-28T13:19:22,518 Skipping link: not a file: https://pypi.org/simple/kssdtree/ 2025-03-28T13:19:22,535 Given no hashes to check 1 links for project 'kssdtree': discarding no candidates 2025-03-28T13:19:22,537 Collecting kssdtree==2.0.5 2025-03-28T13:19:22,539 Created temporary directory: /tmp/pip-unpack-_q_weqnt 2025-03-28T13:19:22,554 Downloading kssdtree-2.0.5.tar.gz (113 kB) 2025-03-28T13:19:22,729 Added kssdtree==2.0.5 from https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz to build tracker '/tmp/pip-build-tracker-y8rfnyik' 2025-03-28T13:19:22,731 Running setup.py (path:/tmp/pip-wheel-g_el_6fn/kssdtree_136c60449e0b4d11b8de802e2e3552ae/setup.py) egg_info for package kssdtree 2025-03-28T13:19:22,731 Created temporary directory: /tmp/pip-pip-egg-info-uhfdlt0n 2025-03-28T13:19:22,732 Preparing metadata (setup.py): started 2025-03-28T13:19:22,733 Running command python setup.py egg_info 2025-03-28T13:19:23,900 running egg_info 2025-03-28T13:19:23,935 creating /tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info 2025-03-28T13:19:23,936 writing /tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/PKG-INFO 2025-03-28T13:19:23,940 writing dependency_links to /tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/dependency_links.txt 2025-03-28T13:19:23,942 writing requirements to /tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/requires.txt 2025-03-28T13:19:23,943 writing top-level names to /tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/top_level.txt 2025-03-28T13:19:23,944 writing manifest file '/tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/SOURCES.txt' 2025-03-28T13:19:24,082 reading manifest file '/tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/SOURCES.txt' 2025-03-28T13:19:24,084 reading manifest template 'MANIFEST.in' 2025-03-28T13:19:24,103 writing manifest file '/tmp/pip-pip-egg-info-uhfdlt0n/kssdtree.egg-info/SOURCES.txt' 2025-03-28T13:19:24,192 Preparing metadata (setup.py): finished with status 'done' 2025-03-28T13:19:24,197 Source in /tmp/pip-wheel-g_el_6fn/kssdtree_136c60449e0b4d11b8de802e2e3552ae has version 2.0.5, which satisfies requirement kssdtree==2.0.5 from https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz 2025-03-28T13:19:24,198 Removed kssdtree==2.0.5 from https://files.pythonhosted.org/packages/b5/f8/19480a4c57704944f973ebf534f9582054949cca20170a33c6f874974440/kssdtree-2.0.5.tar.gz from build tracker '/tmp/pip-build-tracker-y8rfnyik' 2025-03-28T13:19:24,204 Created temporary directory: /tmp/pip-unpack-_ew4doio 2025-03-28T13:19:24,205 Created temporary directory: /tmp/pip-unpack-05pf17v4 2025-03-28T13:19:24,205 Building wheels for collected packages: kssdtree 2025-03-28T13:19:24,209 Created temporary directory: /tmp/pip-wheel-qgtppctr 2025-03-28T13:19:24,209 Building wheel for kssdtree (setup.py): started 2025-03-28T13:19:24,210 Destination directory: /tmp/pip-wheel-qgtppctr 2025-03-28T13:19:24,210 Running command python setup.py bdist_wheel 2025-03-28T13:19:25,307 running bdist_wheel 2025-03-28T13:19:25,474 running build 2025-03-28T13:19:25,474 running build_py 2025-03-28T13:19:25,510 creating build/lib.linux-armv7l-cpython-39 2025-03-28T13:19:25,512 copying kssdtree.py -> build/lib.linux-armv7l-cpython-39 2025-03-28T13:19:25,515 copying toolutils.py -> build/lib.linux-armv7l-cpython-39 2025-03-28T13:19:25,517 running egg_info 2025-03-28T13:19:25,552 writing kssdtree.egg-info/PKG-INFO 2025-03-28T13:19:25,555 writing dependency_links to kssdtree.egg-info/dependency_links.txt 2025-03-28T13:19:25,557 writing requirements to kssdtree.egg-info/requires.txt 2025-03-28T13:19:25,558 writing top-level names to kssdtree.egg-info/top_level.txt 2025-03-28T13:19:25,594 reading manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-03-28T13:19:25,599 reading manifest template 'MANIFEST.in' 2025-03-28T13:19:25,618 writing manifest file 'kssdtree.egg-info/SOURCES.txt' 2025-03-28T13:19:25,620 running build_ext 2025-03-28T13:19:25,627 building 'kssd' extension 2025-03-28T13:19:25,628 creating build/temp.linux-armv7l-cpython-39 2025-03-28T13:19:25,630 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c co2mco.c -o build/temp.linux-armv7l-cpython-39/co2mco.o -fopenmp 2025-03-28T13:19:25,789 co2mco.c: In function ‘cdb_kmerf2kmerdb’: 2025-03-28T13:19:25,790 co2mco.c:109:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:25,790 109 | for (unsigned int i = 0; i < comp_num; i++) { 2025-03-28T13:19:25,790 | ^ 2025-03-28T13:19:25,793 co2mco.c: In function ‘co2unitllmco’: 2025-03-28T13:19:25,793 co2mco.c:191:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:25,794 191 | for (unsigned int i = 0; i < bin_sz; i++) { 2025-03-28T13:19:25,794 | ^ 2025-03-28T13:19:26,407 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_composite.c -o build/temp.linux-armv7l-cpython-39/command_composite.o -fopenmp 2025-03-28T13:19:26,704 command_composite.c: In function ‘get_species_abundance’: 2025-03-28T13:19:26,704 command_composite.c:32:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-03-28T13:19:26,705 32 | if (ref_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, ref_dstat_fpath); 2025-03-28T13:19:26,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,705 command_composite.c:34:34: warning: ‘%s’ directive argument is null [-Wformat-overflow=] 2025-03-28T13:19:26,705 34 | if (qry_dstat_fpath == NULL) fprintf(stderr, "cannot find %s under %s ", co_dstat, qry_dstat_fpath); 2025-03-28T13:19:26,705 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,706 command_composite.c:64:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:26,707 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-03-28T13:19:26,707 | ^ 2025-03-28T13:19:26,707 command_composite.c:64:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2025-03-28T13:19:26,707 64 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, skch_prefix, c); 2025-03-28T13:19:26,707 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,708 command_composite.c:70:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:26,708 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-03-28T13:19:26,708 | ^ 2025-03-28T13:19:26,708 command_composite.c:70:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2025-03-28T13:19:26,708 70 | sprintf(tmpfname, "%s/%s.%d", composite_opt->refdir, idx_prefix, c); 2025-03-28T13:19:26,709 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,709 command_composite.c:76:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:26,709 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-03-28T13:19:26,709 | ^ 2025-03-28T13:19:26,709 command_composite.c:76:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2025-03-28T13:19:26,710 76 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, skch_prefix, c); 2025-03-28T13:19:26,710 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,710 command_composite.c:82:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:26,710 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-03-28T13:19:26,710 | ^ 2025-03-28T13:19:26,711 command_composite.c:82:13: note: ‘sprintf’ output 4 or more bytes (assuming 259) into a destination of size 256 2025-03-28T13:19:26,711 82 | sprintf(tmpfname, "%s/%s.%d", composite_opt->qrydir, idx_prefix, c); 2025-03-28T13:19:26,711 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,711 command_composite.c:88:37: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:26,711 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-03-28T13:19:26,711 | ^ 2025-03-28T13:19:26,712 command_composite.c:88:13: note: ‘sprintf’ output 6 or more bytes (assuming 261) into a destination of size 256 2025-03-28T13:19:26,712 88 | sprintf(tmpfname, "%s/%s.%d.a", composite_opt->qrydir, skch_prefix, c); 2025-03-28T13:19:26,712 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:26,951 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist.c -o build/temp.linux-armv7l-cpython-39/command_dist.o -fopenmp 2025-03-28T13:19:27,144 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-03-28T13:19:27,145 command_dist.c:677:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,145 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,145 | ~~^ 2025-03-28T13:19:27,145 | | 2025-03-28T13:19:27,145 | long unsigned int 2025-03-28T13:19:27,145 | %u 2025-03-28T13:19:27,145 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,146 | ~~~~~~~ 2025-03-28T13:19:27,146 | | 2025-03-28T13:19:27,146 | size_t {aka unsigned int} 2025-03-28T13:19:27,146 command_dist.c:677:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,146 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,146 | ~~^ 2025-03-28T13:19:27,146 | | 2025-03-28T13:19:27,146 | long unsigned int 2025-03-28T13:19:27,146 | %u 2025-03-28T13:19:27,147 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,147 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-03-28T13:19:27,147 | ~~~~~~~~~ 2025-03-28T13:19:27,147 | | 2025-03-28T13:19:27,147 | size_t {aka unsigned int} 2025-03-28T13:19:27,147 command_dist.c:677:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-03-28T13:19:27,147 677 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,148 | ~~^ 2025-03-28T13:19:27,148 | | 2025-03-28T13:19:27,148 | long unsigned int 2025-03-28T13:19:27,148 | %u 2025-03-28T13:19:27,148 678 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,148 679 | maplength, (size_t) b * unitsz_distf_mapped); 2025-03-28T13:19:27,148 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,149 | | 2025-03-28T13:19:27,149 | unsigned int 2025-03-28T13:19:27,149 command_dist.c:715:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-03-28T13:19:27,150 715 | for (int n = 0; n < fco_pos[k + 1] - fco_pos[k]; n++) { 2025-03-28T13:19:27,150 | ^ 2025-03-28T13:19:27,156 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-03-28T13:19:27,157 command_dist.c:863:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,157 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-03-28T13:19:27,157 | ~~^ ~~~~~~~ 2025-03-28T13:19:27,157 | | | 2025-03-28T13:19:27,157 | long unsigned int size_t {aka unsigned int} 2025-03-28T13:19:27,157 | %u 2025-03-28T13:19:27,158 command_dist.c:863:93: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,158 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-03-28T13:19:27,158 | ~~^ 2025-03-28T13:19:27,159 | | 2025-03-28T13:19:27,159 | long unsigned int 2025-03-28T13:19:27,159 | %u 2025-03-28T13:19:27,159 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-03-28T13:19:27,159 | ~~~~~~~~~ 2025-03-28T13:19:27,159 | | 2025-03-28T13:19:27,159 | size_t {aka unsigned int} 2025-03-28T13:19:27,160 command_dist.c:863:98: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-03-28T13:19:27,160 863 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%d\tbatch_qrynum=%d\t%lu\t%lu\n", disf_sz, 2025-03-28T13:19:27,160 | ~~^ 2025-03-28T13:19:27,160 | | 2025-03-28T13:19:27,160 | long unsigned int 2025-03-28T13:19:27,160 | %u 2025-03-28T13:19:27,161 864 | mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, maplength, 2025-03-28T13:19:27,161 865 | (size_t) b * unitsz_distf_mapped); 2025-03-28T13:19:27,161 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,161 | | 2025-03-28T13:19:27,161 | unsigned int 2025-03-28T13:19:27,162 command_dist.c:810:13: warning: unused variable ‘fco_pos’ [-Wunused-variable] 2025-03-28T13:19:27,162 810 | size_t *fco_pos = malloc(sizeof(size_t) * (co_dstat_readin.infile_num + 1)); 2025-03-28T13:19:27,162 | ^~~~~~~ 2025-03-28T13:19:27,162 command_dist.c:809:17: warning: unused variable ‘cbd_fcode_stat’ [-Wunused-variable] 2025-03-28T13:19:27,162 809 | struct stat cbd_fcode_stat; 2025-03-28T13:19:27,163 | ^~~~~~~~~~~~~~ 2025-03-28T13:19:27,163 command_dist.c:808:31: warning: unused variable ‘cbd_fcode_comp_index_fp’ [-Wunused-variable] 2025-03-28T13:19:27,163 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-03-28T13:19:27,163 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,163 command_dist.c:808:11: warning: unused variable ‘cbd_fcode_comp_fp’ [-Wunused-variable] 2025-03-28T13:19:27,164 808 | FILE *cbd_fcode_comp_fp, *cbd_fcode_comp_index_fp; 2025-03-28T13:19:27,164 | ^~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,169 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-03-28T13:19:27,170 command_dist.c:1018:27: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,171 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,171 | ~~^ 2025-03-28T13:19:27,171 | | 2025-03-28T13:19:27,171 | long unsigned int 2025-03-28T13:19:27,171 | %u 2025-03-28T13:19:27,171 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,171 | ~~~~~~~ 2025-03-28T13:19:27,171 | | 2025-03-28T13:19:27,172 | size_t {aka unsigned int} 2025-03-28T13:19:27,172 command_dist.c:1018:92: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:27,173 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,173 | ~~^ 2025-03-28T13:19:27,173 | | 2025-03-28T13:19:27,173 | long unsigned int 2025-03-28T13:19:27,173 | %u 2025-03-28T13:19:27,173 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,173 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-03-28T13:19:27,173 | ~~~~~~~~~ 2025-03-28T13:19:27,173 | | 2025-03-28T13:19:27,174 | size_t {aka unsigned int} 2025-03-28T13:19:27,174 command_dist.c:1018:97: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 8 has type ‘unsigned int’ [-Wformat=] 2025-03-28T13:19:27,174 1018 | printf("disf_sz=%lu\trefnum=%d\tqrynum=%d\tnum_mapping_distf=%dbnum_infile=%d\t\t%lu\t%lu\tflag1:Ok\n", 2025-03-28T13:19:27,174 | ~~^ 2025-03-28T13:19:27,175 | | 2025-03-28T13:19:27,175 | long unsigned int 2025-03-28T13:19:27,175 | %u 2025-03-28T13:19:27,175 1019 | disf_sz, mco_dstat_readin.infile_num, co_dstat_readin.infile_num, num_mapping_distf, bnum_infile, 2025-03-28T13:19:27,175 1020 | maplength, (size_t) b * unitsz_distf_mapped); 2025-03-28T13:19:27,175 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,175 | | 2025-03-28T13:19:27,175 | unsigned int 2025-03-28T13:19:27,176 command_dist.c:1034:27: warning: comparison of integer expressions of different signedness: ‘__off_t’ {aka ‘long int’} and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,176 1034 | if (s.st_size > sizeof(gidobj_t) * MCOMM_SZ) mco_mem = (gidobj_t *) realloc(mco_mem, s.st_size); 2025-03-28T13:19:27,176 | ^ 2025-03-28T13:19:27,179 command_dist.c: In function ‘mco_co_dist_core’: 2025-03-28T13:19:27,180 command_dist.c:1116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘gidobj_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-03-28T13:19:27,180 1116 | for (int k = 1; k < unit_arrmco[ind][0] + 1; k++) { 2025-03-28T13:19:27,180 | ^ 2025-03-28T13:19:27,185 command_dist.c: In function ‘koc_dist_print_nobin’: 2025-03-28T13:19:27,186 command_dist.c:1239:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,186 1239 | for (int rid = 0; rid < ref_num; rid++) 2025-03-28T13:19:27,186 | ^ 2025-03-28T13:19:27,188 command_dist.c:1245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,188 1245 | for (int rid = 0; rid < ref_num; rid++) { 2025-03-28T13:19:27,188 | ^ 2025-03-28T13:19:27,193 command_dist.c: In function ‘dist_print_nobin’: 2025-03-28T13:19:27,194 command_dist.c:1335:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,194 1335 | if ((N_max > NREF) || (N_max > ref_num)) { 2025-03-28T13:19:27,194 | ^ 2025-03-28T13:19:27,196 command_dist.c:1356:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,196 1356 | for (int rid = 0; rid < ref_num; rid++) { 2025-03-28T13:19:27,196 | ^ 2025-03-28T13:19:27,197 command_dist.c:1380:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,198 1380 | for (int rid = 0; rid < ref_num; rid++) 2025-03-28T13:19:27,198 | ^ 2025-03-28T13:19:27,198 command_dist.c:1382:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:27,198 1382 | for (int rid = 0; rid < ref_num; rid++) 2025-03-28T13:19:27,199 | ^ 2025-03-28T13:19:27,449 command_dist.c: In function ‘run_stageI._omp_fn.1’: 2025-03-28T13:19:27,449 command_dist.c:403:21: warning: ‘com_abund_fp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2025-03-28T13:19:27,450 403 | fwrite(tmp_mem, sizeof(unsigned short) * tmpkmerct, 1, com_abund_fp); 2025-03-28T13:19:27,450 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:27,450 command_dist.c:375:40: note: ‘com_abund_fp’ was declared here 2025-03-28T13:19:27,450 375 | FILE *com_cofp, *indexfp, *com_abund_fp; 2025-03-28T13:19:27,450 | ^~~~~~~~~~~~ 2025-03-28T13:19:28,171 command_dist.c: In function ‘get_dim_shuffle’: 2025-03-28T13:19:28,171 command_dist.c:267:36: warning: ‘%s’ directive writing up to 264 bytes into a region of size 256 [-Wformat-overflow=] 2025-03-28T13:19:28,171 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-03-28T13:19:28,171 | ^~ ~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:28,171 command_dist.c:267:9: note: ‘sprintf’ output between 6 and 270 bytes into a destination of size 256 2025-03-28T13:19:28,171 267 | sprintf(shuf_infile_name, "%s.shuf", shuf_infile_name_prefix); 2025-03-28T13:19:28,172 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:28,952 command_dist.c: In function ‘mco_cbd_co_dist’: 2025-03-28T13:19:28,952 command_dist.c:596:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:28,952 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:28,952 | ^~ ~~~~~~~~~ 2025-03-28T13:19:28,952 command_dist.c:596:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-03-28T13:19:28,953 596 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:28,953 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:28,953 command_dist.c:625:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:28,953 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:28,953 | ^~~~~~~~~~~~~~~ 2025-03-28T13:19:28,954 command_dist.c:625:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-03-28T13:19:28,954 625 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:28,954 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:28,955 command_dist.c:681:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:28,955 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-03-28T13:19:28,955 | ^~~~~~~~~~~ 2025-03-28T13:19:28,955 command_dist.c:681:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-03-28T13:19:28,955 681 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-03-28T13:19:28,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:28,956 command_dist.c:682:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:28,956 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-03-28T13:19:28,956 | ^~~~~ 2025-03-28T13:19:28,956 command_dist.c:682:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-03-28T13:19:28,956 682 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-03-28T13:19:28,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,163 command_dist.c: In function ‘mco_cbdco_nobin_dist’: 2025-03-28T13:19:29,164 command_dist.c:763:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:29,164 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:29,164 | ^~ ~~~~~~~~~ 2025-03-28T13:19:29,164 command_dist.c:763:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-03-28T13:19:29,164 763 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:29,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,165 command_dist.c:790:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,165 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:29,165 | ^~~~~~~~~~~~~~~ 2025-03-28T13:19:29,165 command_dist.c:790:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-03-28T13:19:29,166 790 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:29,166 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,166 command_dist.c:823:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,166 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-03-28T13:19:29,166 | ^~~~~~~~~~~~~ 2025-03-28T13:19:29,167 command_dist.c:823:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-03-28T13:19:29,167 823 | sprintf(distf, "%s/distance.out", distout_dir); 2025-03-28T13:19:29,167 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,168 command_dist.c:849:39: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:29,168 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-03-28T13:19:29,168 | ^ 2025-03-28T13:19:29,168 command_dist.c:849:33: note: directive argument in the range [0, 536870912] 2025-03-28T13:19:29,169 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-03-28T13:19:29,169 | ^~~~~~~~~~ 2025-03-28T13:19:29,169 command_dist.c:849:8: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-03-28T13:19:29,169 849 | sprintf(mco_index_fcode, "%s/%s.%d", refmco_dname, mco_idx_prefix, j); 2025-03-28T13:19:29,169 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,170 command_dist.c:851:34: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:29,170 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-03-28T13:19:29,170 | ^ 2025-03-28T13:19:29,170 command_dist.c:851:28: note: directive argument in the range [0, 536870912] 2025-03-28T13:19:29,170 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-03-28T13:19:29,170 | ^~~~~~~~~~ 2025-03-28T13:19:29,171 command_dist.c:851:9: note: ‘sprintf’ output 4 or more bytes (assuming 267) into a destination of size 256 2025-03-28T13:19:29,171 851 | sprintf(mco_fcode, "%s/%s.%d", refmco_dname, mco_gids_prefix, j); 2025-03-28T13:19:29,171 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,406 command_dist.c: In function ‘mco_cbd_koc_compatible_dist’: 2025-03-28T13:19:29,407 command_dist.c:927:37: warning: ‘%s’ directive writing 13 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:29,407 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:29,407 | ^~ ~~~~~~~~~ 2025-03-28T13:19:29,408 command_dist.c:927:5: note: ‘sprintf’ output between 15 and 270 bytes into a destination of size 256 2025-03-28T13:19:29,408 927 | sprintf(refmco_dstat_fpath, "%s/%s", refmco_dname, mco_dstat); 2025-03-28T13:19:29,408 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,409 command_dist.c:956:25: warning: ‘/sharedk_ct.dat’ directive writing 15 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,409 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:29,409 | ^~~~~~~~~~~~~~~ 2025-03-28T13:19:29,409 command_dist.c:956:5: note: ‘sprintf’ output between 16 and 271 bytes into a destination of size 256 2025-03-28T13:19:29,409 956 | sprintf(onedist, "%s/sharedk_ct.dat", distout_dir); 2025-03-28T13:19:29,409 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,410 command_dist.c:990:23: warning: ‘/distance.out’ directive writing 13 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,410 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-03-28T13:19:29,410 | ^~~~~~~~~~~~~ 2025-03-28T13:19:29,411 command_dist.c:990:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-03-28T13:19:29,411 990 | sprintf(distf, "%s/distance.out", distout_dir); 2025-03-28T13:19:29,411 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,412 command_dist.c:1022:41: warning: ‘/mco.index.’ directive writing 11 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,412 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-03-28T13:19:29,413 | ^~~~~~~~~~~ 2025-03-28T13:19:29,413 command_dist.c:1022:13: note: ‘sprintf’ output between 13 and 278 bytes into a destination of size 256 2025-03-28T13:19:29,413 1022 | sprintf(mco_index_fcode, "%s/mco.index.%d", refmco_dname, j); 2025-03-28T13:19:29,413 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,414 command_dist.c:1023:35: warning: ‘/mco.’ directive writing 5 bytes into a region of size between 1 and 256 [-Wformat-overflow=] 2025-03-28T13:19:29,414 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-03-28T13:19:29,414 | ^~~~~ 2025-03-28T13:19:29,414 command_dist.c:1023:13: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-03-28T13:19:29,414 1023 | sprintf(mco_fcode, "%s/mco.%d", refmco_dname, j); 2025-03-28T13:19:29,415 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,660 command_dist.c: In function ‘combine_queries’: 2025-03-28T13:19:29,661 command_dist.c:1492:41: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:29,661 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-03-28T13:19:29,661 | ^ 2025-03-28T13:19:29,662 command_dist.c:1492:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:29,662 1492 | sprintf(one_kmerct_list_name, "%s/%s", co_dir, kmerct_list_fname); 2025-03-28T13:19:29,662 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,663 command_dist.c:1499:40: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:29,663 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-03-28T13:19:29,664 | ^ 2025-03-28T13:19:29,664 command_dist.c:1499:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:29,664 1499 | sprintf(one_infilename_name, "%s/%s", co_dir, fname_fname); 2025-03-28T13:19:29,665 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:29,666 command_dist.c:1603:32: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:29,667 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-03-28T13:19:29,667 | ^~ ~~~~~~~~ 2025-03-28T13:19:29,667 command_dist.c:1603:5: note: ‘sprintf’ output between 14 and 269 bytes into a destination of size 256 2025-03-28T13:19:29,668 1603 | sprintf(one_stat_name, "%s/%s", co_dir, co_dstat); 2025-03-28T13:19:29,668 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,137 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_dist_wrapper.c -o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o -fopenmp 2025-03-28T13:19:30,302 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_set.c -o build/temp.linux-armv7l-cpython-39/command_set.o -fopenmp 2025-03-28T13:19:30,446 command_set.c: In function ‘sketch_operate’: 2025-03-28T13:19:30,446 command_set.c:178:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-03-28T13:19:30,447 178 | for(int n = 0; n < fco_pos[i+1] - fco_pos[i]; n++){ 2025-03-28T13:19:30,447 | ^ 2025-03-28T13:19:30,456 command_set.c: In function ‘combin_subset_pans’: 2025-03-28T13:19:30,456 command_set.c:457:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-03-28T13:19:30,456 457 | free(co_dstat_fpath); 2025-03-28T13:19:30,457 | ^~~~~~~~~~~~~~ 2025-03-28T13:19:30,457 In file included from kssdheaders/global_basic.h:159, 2025-03-28T13:19:30,457 from command_set.c:15: 2025-03-28T13:19:30,457 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-03-28T13:19:30,457 565 | extern void free (void *__ptr) __THROW; 2025-03-28T13:19:30,457 | ~~~~~~^~~~~ 2025-03-28T13:19:30,461 command_set.c: In function ‘grouping_genomes’: 2025-03-28T13:19:30,461 command_set.c:562:10: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2025-03-28T13:19:30,462 562 | free(co_dstat_fpath); 2025-03-28T13:19:30,462 | ^~~~~~~~~~~~~~ 2025-03-28T13:19:30,462 In file included from kssdheaders/global_basic.h:159, 2025-03-28T13:19:30,462 from command_set.c:15: 2025-03-28T13:19:30,462 /usr/include/stdlib.h:565:25: note: expected ‘void *’ but argument is of type ‘const char *’ 2025-03-28T13:19:30,462 565 | extern void free (void *__ptr) __THROW; 2025-03-28T13:19:30,463 | ~~~~~~^~~~~ 2025-03-28T13:19:30,577 command_set.c: In function ‘sketch_union’: 2025-03-28T13:19:30,577 command_set.c:71:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:30,578 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,578 | ^ 2025-03-28T13:19:30,578 command_set.c:71:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:30,578 71 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,578 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,578 command_set.c:82:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,578 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-03-28T13:19:30,579 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,579 command_set.c:82:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:30,579 82 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-03-28T13:19:30,579 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,579 command_set.c:92:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,579 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-03-28T13:19:30,580 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:30,580 command_set.c:92:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-03-28T13:19:30,580 92 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,pan_prefix,i); 2025-03-28T13:19:30,580 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,690 command_set.c: In function ‘sketch_operate’: 2025-03-28T13:19:30,691 command_set.c:153:29: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,691 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-03-28T13:19:30,691 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:30,691 command_set.c:153:9: note: ‘sprintf’ output between 7 and 272 bytes into a destination of size 256 2025-03-28T13:19:30,691 153 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, pan_prefix, c); 2025-03-28T13:19:30,691 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,692 command_set.c:155:33: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,692 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-03-28T13:19:30,692 | ^~ ~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,692 command_set.c:155:13: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-03-28T13:19:30,692 155 | sprintf(tmppath,"%s/%s.%d",set_opt.pansketchpath, uniq_pan_prefix, c); 2025-03-28T13:19:30,692 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,692 command_set.c:165:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,692 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-03-28T13:19:30,693 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,693 command_set.c:165:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:30,693 165 | sprintf(tmppath,"%s/%s.index.%d",set_opt.insketchpath,skch_prefix, c); 2025-03-28T13:19:30,693 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,693 command_set.c:169:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,693 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-03-28T13:19:30,693 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,694 command_set.c:169:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:30,694 169 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix, c); 2025-03-28T13:19:30,694 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,694 command_set.c:174:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,694 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-03-28T13:19:30,694 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,694 command_set.c:174:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:30,694 174 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix, c); 2025-03-28T13:19:30,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,695 command_set.c:187:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,695 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-03-28T13:19:30,695 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,695 command_set.c:187:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:30,695 187 | sprintf(tmppath,"%s/%s.index.%d",set_opt.outdir,skch_prefix, c); 2025-03-28T13:19:30,695 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,696 command_set.c:192:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:30,696 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,696 | ^ 2025-03-28T13:19:30,696 command_set.c:192:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:30,696 192 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,696 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,843 command_set.c: In function ‘uniq_sketch_union’: 2025-03-28T13:19:30,844 command_set.c:234:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:30,844 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,844 | ^ 2025-03-28T13:19:30,844 command_set.c:234:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:30,844 234 | sprintf(outpath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,844 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,845 command_set.c:247:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,845 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-03-28T13:19:30,845 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,845 command_set.c:247:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:30,845 247 | sprintf(outpath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,i); 2025-03-28T13:19:30,845 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,845 command_set.c:259:29: warning: ‘%s’ directive writing 8 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,846 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-03-28T13:19:30,846 | ^~ ~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,846 command_set.c:259:9: note: ‘sprintf’ output between 12 and 277 bytes into a destination of size 256 2025-03-28T13:19:30,846 259 | sprintf(outpath,"%s/%s.%d",set_opt.outdir,uniq_pan_prefix,i); 2025-03-28T13:19:30,846 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,971 command_set.c: In function ‘combin_pans’: 2025-03-28T13:19:30,971 command_set.c:297:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,971 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:30,971 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:30,971 command_set.c:297:25: note: directive argument in the range [0, 1073741823] 2025-03-28T13:19:30,972 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:30,972 | ^~~~~~~~~~ 2025-03-28T13:19:30,972 command_set.c:297:9: note: ‘sprintf’ output between 10 and 274 bytes into a destination of size 256 2025-03-28T13:19:30,972 297 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:30,972 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,972 command_set.c:300:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:30,972 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:30,973 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:30,973 command_set.c:300:25: note: directive argument in the range [0, 1073741823] 2025-03-28T13:19:30,973 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:30,973 | ^~~~~~~~~~ 2025-03-28T13:19:30,973 command_set.c:300:9: note: ‘sprintf’ output between 16 and 280 bytes into a destination of size 256 2025-03-28T13:19:30,973 300 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:30,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:30,973 command_set.c:342:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:30,974 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,974 | ^ 2025-03-28T13:19:30,974 command_set.c:342:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:30,974 342 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:30,974 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,159 command_set.c: In function ‘combin_subset_pans’: 2025-03-28T13:19:31,160 command_set.c:469:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,160 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-03-28T13:19:31,160 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:31,160 command_set.c:469:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:31,160 469 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-03-28T13:19:31,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,161 command_set.c:475:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,161 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-03-28T13:19:31,161 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:31,161 command_set.c:475:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:31,161 475 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-03-28T13:19:31,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,161 command_set.c:481:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,161 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:31,162 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:31,162 command_set.c:481:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:31,162 481 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:31,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,163 command_set.c:512:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,164 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:31,164 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:31,164 command_set.c:512:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:31,164 512 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:31,164 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,164 command_set.c:523:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:31,164 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:31,164 | ^ 2025-03-28T13:19:31,165 command_set.c:523:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:31,165 523 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:31,165 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,367 command_set.c: In function ‘grouping_genomes’: 2025-03-28T13:19:31,367 command_set.c:574:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,367 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-03-28T13:19:31,367 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:31,367 command_set.c:574:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:31,368 574 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,skch_prefix,c); 2025-03-28T13:19:31,368 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,368 command_set.c:580:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,368 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-03-28T13:19:31,368 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:31,369 command_set.c:580:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:31,369 580 | sprintf(tmppath,"%s/%s.%d",set_opt.insketchpath,idx_prefix,c); 2025-03-28T13:19:31,369 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,370 command_set.c:612:29: warning: ‘%s’ directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,370 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:31,371 | ^~ ~~~~~~~~~~~ 2025-03-28T13:19:31,371 command_set.c:612:9: note: ‘sprintf’ output between 10 and 275 bytes into a destination of size 256 2025-03-28T13:19:31,371 612 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,skch_prefix,c); 2025-03-28T13:19:31,371 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,372 command_set.c:634:29: warning: ‘%s’ directive writing 12 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 2025-03-28T13:19:31,372 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:31,372 | ^~ ~~~~~~~~~~ 2025-03-28T13:19:31,372 command_set.c:634:9: note: ‘sprintf’ output between 16 and 281 bytes into a destination of size 256 2025-03-28T13:19:31,372 634 | sprintf(tmppath,"%s/%s.%d",set_opt.outdir,idx_prefix,c); 2025-03-28T13:19:31,372 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,373 command_set.c:645:27: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 2025-03-28T13:19:31,373 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:31,373 | ^ 2025-03-28T13:19:31,373 command_set.c:645:5: note: ‘sprintf’ output 2 or more bytes (assuming 257) into a destination of size 256 2025-03-28T13:19:31,373 645 | sprintf(tmppath,"%s/%s",set_opt.outdir,co_dstat); 2025-03-28T13:19:31,374 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:31,643 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c command_shuffle.c -o build/temp.linux-armv7l-cpython-39/command_shuffle.o -fopenmp 2025-03-28T13:19:31,919 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c global_basic.c -o build/temp.linux-armv7l-cpython-39/global_basic.o -fopenmp 2025-03-28T13:19:32,061 global_basic.c: In function ‘organize_infile_list’: 2025-03-28T13:19:32,062 global_basic.c:195:20: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 2025-03-28T13:19:32,062 195 | while (isspace(*buf)) buf++; 2025-03-28T13:19:32,062 | ^~~~~~~ 2025-03-28T13:19:32,062 global_basic.c:201:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:32,062 201 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-03-28T13:19:32,063 | ~~^ 2025-03-28T13:19:32,063 | | 2025-03-28T13:19:32,063 | long unsigned int 2025-03-28T13:19:32,063 | %u 2025-03-28T13:19:32,063 202 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-03-28T13:19:32,063 | ~~~~~~~~~~~ 2025-03-28T13:19:32,063 | | 2025-03-28T13:19:32,064 | size_t {aka unsigned int} 2025-03-28T13:19:32,064 global_basic.c:233:69: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2025-03-28T13:19:32,064 233 | "the input list: %s\n %dth line: %s has %lu characters exceed the maximal allowed length %d", 2025-03-28T13:19:32,064 | ~~^ 2025-03-28T13:19:32,064 | | 2025-03-28T13:19:32,064 | long unsigned int 2025-03-28T13:19:32,064 | %u 2025-03-28T13:19:32,065 234 | list_path, file_num, buf, strlen(buf), PATHLEN); 2025-03-28T13:19:32,065 | ~~~~~~~~~~~ 2025-03-28T13:19:32,065 | | 2025-03-28T13:19:32,065 | size_t {aka unsigned int} 2025-03-28T13:19:32,743 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c iseq2comem.c -o build/temp.linux-armv7l-cpython-39/iseq2comem.o -fopenmp 2025-03-28T13:19:32,896 iseq2comem.c: In function ‘reads2mco’: 2025-03-28T13:19:32,897 iseq2comem.c:156:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,897 156 | if (base > TL) { 2025-03-28T13:19:32,897 | ^ 2025-03-28T13:19:32,897 iseq2comem.c:160:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,897 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,898 | ^~ 2025-03-28T13:19:32,898 iseq2comem.c:160:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,898 160 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,898 | ^ 2025-03-28T13:19:32,899 iseq2comem.c: In function ‘fasta2co’: 2025-03-28T13:19:32,899 iseq2comem.c:239:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,899 239 | if (base > TL) { 2025-03-28T13:19:32,899 | ^ 2025-03-28T13:19:32,900 iseq2comem.c:243:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,900 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,900 | ^~ 2025-03-28T13:19:32,900 iseq2comem.c:243:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,900 243 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,900 | ^ 2025-03-28T13:19:32,900 iseq2comem.c: In function ‘fastq2co’: 2025-03-28T13:19:32,901 iseq2comem.c:272:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2025-03-28T13:19:32,901 272 | if (M >= CT_MAX) fprintf(stderr, "fastq2co(): Occurence num should smaller than %d", (int) CT_MAX); 2025-03-28T13:19:32,901 | ^~ 2025-03-28T13:19:32,902 iseq2comem.c:318:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,902 318 | if (base > TL) { 2025-03-28T13:19:32,902 | ^ 2025-03-28T13:19:32,902 iseq2comem.c:322:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,902 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,902 | ^~ 2025-03-28T13:19:32,902 iseq2comem.c:322:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,903 322 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,903 | ^ 2025-03-28T13:19:32,903 iseq2comem.c:341:44: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,903 341 | if (!((co[n] & CT_MAX) < M)) co[n] |= CT_MAX; 2025-03-28T13:19:32,903 | ^ 2025-03-28T13:19:32,905 iseq2comem.c: In function ‘fastq2koc’: 2025-03-28T13:19:32,905 iseq2comem.c:402:18: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,905 402 | if (base > TL) { 2025-03-28T13:19:32,905 | ^ 2025-03-28T13:19:32,905 iseq2comem.c:406:26: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,905 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,905 | ^~ 2025-03-28T13:19:32,906 iseq2comem.c:406:50: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,906 406 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,906 | ^ 2025-03-28T13:19:32,911 iseq2comem.c: In function ‘mt_shortreads2koc’: 2025-03-28T13:19:32,911 iseq2comem.c:582:34: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,911 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,911 | ^~ 2025-03-28T13:19:32,911 iseq2comem.c:582:58: warning: comparison of integer expressions of different signedness: ‘llong’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:32,911 582 | if ((pfilter >= dim_end) || (pfilter < dim_start)) continue; 2025-03-28T13:19:32,912 | ^ 2025-03-28T13:19:34,075 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2025-03-28T13:19:34,137 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c mytime.c -o build/temp.linux-armv7l-cpython-39/mytime.o -fopenmp 2025-03-28T13:19:34,255 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Ikssdheaders -I/usr/include/python3.9 -c pykssd.c -o build/temp.linux-armv7l-cpython-39/pykssd.o -fopenmp 2025-03-28T13:19:34,569 pykssd.c: In function ‘py_dist_dispatch’: 2025-03-28T13:19:34,569 pykssd.c:334:13: warning: unused variable ‘state1’ [-Wunused-variable] 2025-03-28T13:19:34,570 334 | int state1 = dist_dispatch(&dist_opt_val1); 2025-03-28T13:19:34,570 | ^~~~~~ 2025-03-28T13:19:34,570 pykssd.c:396:13: warning: unused variable ‘state2’ [-Wunused-variable] 2025-03-28T13:19:34,571 396 | int state2 = dist_dispatch(&dist_opt_val2); 2025-03-28T13:19:34,571 | ^~~~~~ 2025-03-28T13:19:34,572 pykssd.c:530:13: warning: unused variable ‘state4’ [-Wunused-variable] 2025-03-28T13:19:34,573 530 | int state4 = dist_dispatch(&dist_opt_val4); 2025-03-28T13:19:34,573 | ^~~~~~ 2025-03-28T13:19:34,719 pykssd.c: In function ‘rename_file’: 2025-03-28T13:19:34,719 pykssd.c:44:15: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 2025-03-28T13:19:34,719 44 | newfile = strncpy(newfile, p1, len - suffix_len); 2025-03-28T13:19:34,719 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-03-28T13:19:34,719 pykssd.c:41:15: note: length computed here 2025-03-28T13:19:34,720 41 | int len = strlen(p1); 2025-03-28T13:19:34,720 | ^~~~~~~~~~ 2025-03-28T13:19:35,179 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/co2mco.o build/temp.linux-armv7l-cpython-39/command_composite.o build/temp.linux-armv7l-cpython-39/command_dist.o build/temp.linux-armv7l-cpython-39/command_dist_wrapper.o build/temp.linux-armv7l-cpython-39/command_set.o build/temp.linux-armv7l-cpython-39/command_shuffle.o build/temp.linux-armv7l-cpython-39/global_basic.o build/temp.linux-armv7l-cpython-39/iseq2comem.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/mytime.o build/temp.linux-armv7l-cpython-39/pykssd.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -fopenmp 2025-03-28T13:19:35,330 building 'nj' extension 2025-03-28T13:19:35,332 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c align.c -o build/temp.linux-armv7l-cpython-39/align.o 2025-03-28T13:19:35,738 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c buildtree.c -o build/temp.linux-armv7l-cpython-39/buildtree.o 2025-03-28T13:19:35,867 buildtree.c: In function ‘UPGMA_buildtree’: 2025-03-28T13:19:35,867 buildtree.c:716:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:35,867 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-03-28T13:19:35,868 | ^~ 2025-03-28T13:19:35,868 buildtree.c:716:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:35,868 716 | if (min_of_row_idx[m] == minj || min_of_row_idx[m] == mini) { 2025-03-28T13:19:35,868 | ^~ 2025-03-28T13:19:36,477 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c cluster.c -o build/temp.linux-armv7l-cpython-39/cluster.o 2025-03-28T13:19:36,801 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c distancemat.c -o build/temp.linux-armv7l-cpython-39/distancemat.o 2025-03-28T13:19:36,915 distancemat.c: In function ‘clone_DistanceMatrix’: 2025-03-28T13:19:36,916 distancemat.c:226:17: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:36,916 226 | for( i=0; i < dest->size; i++) { 2025-03-28T13:19:36,916 | ^ 2025-03-28T13:19:36,916 distancemat.c: In function ‘empty_DistanceMatrix’: 2025-03-28T13:19:36,916 distancemat.c:260:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:36,917 260 | for( i=0; i < mat->size; i++) { 2025-03-28T13:19:36,917 | ^ 2025-03-28T13:19:36,917 distancemat.c: In function ‘print_DistanceMatrix’: 2025-03-28T13:19:36,917 distancemat.c:349:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:36,917 349 | for(row=0; row < mat->size; row++) { 2025-03-28T13:19:36,917 | ^ 2025-03-28T13:19:36,918 distancemat.c: In function ‘read_phylip_DistanceMatrix’: 2025-03-28T13:19:36,918 distancemat.c:410:11: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 2025-03-28T13:19:36,918 410 | while(c = fgetc(handle)) { 2025-03-28T13:19:36,918 | ^ 2025-03-28T13:19:37,290 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c pynj.c -o build/temp.linux-armv7l-cpython-39/pynj.o 2025-03-28T13:19:37,658 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c sequence.c -o build/temp.linux-armv7l-cpython-39/sequence.o 2025-03-28T13:19:37,850 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c tree.c -o build/temp.linux-armv7l-cpython-39/tree.o 2025-03-28T13:19:38,542 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Injheaders -I/usr/include/python3.9 -c util.c -o build/temp.linux-armv7l-cpython-39/util.o 2025-03-28T13:19:38,706 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/align.o build/temp.linux-armv7l-cpython-39/buildtree.o build/temp.linux-armv7l-cpython-39/cluster.o build/temp.linux-armv7l-cpython-39/distancemat.o build/temp.linux-armv7l-cpython-39/pynj.o build/temp.linux-armv7l-cpython-39/sequence.o build/temp.linux-armv7l-cpython-39/tree.o build/temp.linux-armv7l-cpython-39/util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so 2025-03-28T13:19:38,816 building 'dnj' extension 2025-03-28T13:19:38,819 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c bytescale.c -o build/temp.linux-armv7l-cpython-39/bytescale.o -fopenmp 2025-03-28T13:19:38,883 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c dnj.c -o build/temp.linux-armv7l-cpython-39/dnj.o -fopenmp 2025-03-28T13:19:39,001 dnj.c: In function ‘minQpair’: 2025-03-28T13:19:39,002 dnj.c:70:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,002 70 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,002 | ^~~ 2025-03-28T13:19:39,003 dnj.c:126:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,003 126 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,003 | ^~~ 2025-03-28T13:19:39,004 dnj.c: In function ‘maxQpair’: 2025-03-28T13:19:39,004 dnj.c:157:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,004 157 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,004 | ^~~ 2025-03-28T13:19:39,004 dnj.c:213:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,005 213 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,005 | ^~~ 2025-03-28T13:19:39,005 dnj.c: In function ‘UPGMApair’: 2025-03-28T13:19:39,005 dnj.c:237:13: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,005 237 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,005 | ^~~ 2025-03-28T13:19:39,006 dnj.c:284:25: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,006 284 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,006 | ^~~ 2025-03-28T13:19:39,006 dnj.c:291:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,006 291 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,006 | ^~~ 2025-03-28T13:19:39,007 dnj.c: In function ‘minQrow’: 2025-03-28T13:19:39,007 dnj.c:374:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,008 374 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,008 | ^~~ 2025-03-28T13:19:39,008 dnj.c: In function ‘maxQrow’: 2025-03-28T13:19:39,009 dnj.c:435:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,009 435 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,009 | ^~~ 2025-03-28T13:19:39,010 dnj.c: In function ‘UPGMArow’: 2025-03-28T13:19:39,010 dnj.c:488:21: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,010 488 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,010 | ^~~ 2025-03-28T13:19:39,010 dnj.c:494:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,010 494 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,010 | ^~~ 2025-03-28T13:19:39,011 dnj.c: In function ‘minQ_thread’: 2025-03-28T13:19:39,011 dnj.c:553:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:39,012 553 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:39,012 | ^~~ 2025-03-28T13:19:40,175 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c filebuff.c -o build/temp.linux-armv7l-cpython-39/filebuff.o -fopenmp 2025-03-28T13:19:40,278 filebuff.c: In function ‘BuffgzFileBuff’: 2025-03-28T13:19:40,278 filebuff.c:99:47: warning: comparison of integer expressions of different signedness: ‘uInt’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:40,279 99 | if(status == Z_STREAM_END && strm->avail_out == dest->buffSize) { 2025-03-28T13:19:40,279 | ^~ 2025-03-28T13:19:40,562 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c hclust.c -o build/temp.linux-armv7l-cpython-39/hclust.o -fopenmp 2025-03-28T13:19:40,679 hclust.c: In function ‘minQ’: 2025-03-28T13:19:40,679 hclust.c:364:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:40,679 364 | while(++i < Q->n) { 2025-03-28T13:19:40,679 | ^ 2025-03-28T13:19:40,680 hclust.c:377:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:40,680 377 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:40,680 | ^~~ 2025-03-28T13:19:40,681 hclust.c: In function ‘maxQ’: 2025-03-28T13:19:40,681 hclust.c:394:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-03-28T13:19:40,681 394 | while(++i < Q->n) { 2025-03-28T13:19:40,681 | ^ 2025-03-28T13:19:40,682 hclust.c:407:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:40,682 407 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:40,682 | ^~~ 2025-03-28T13:19:42,707 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c matrix.c -o build/temp.linux-armv7l-cpython-39/matrix.o -fopenmp 2025-03-28T13:19:42,824 matrix.c: In function ‘ltdMatrix_popArrange’: 2025-03-28T13:19:42,825 matrix.c:538:9: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-03-28T13:19:42,825 538 | if(pos != n) { 2025-03-28T13:19:42,825 | ^~ 2025-03-28T13:19:43,571 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c mman.c -o build/temp.linux-armv7l-cpython-39/mman.o -fopenmp 2025-03-28T13:19:43,634 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nj.c -o build/temp.linux-armv7l-cpython-39/nj.o -fopenmp 2025-03-28T13:19:43,747 nj.c: In function ‘initQ’: 2025-03-28T13:19:43,747 nj.c:243:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:43,747 243 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:43,748 | ^~~ 2025-03-28T13:19:43,749 nj.c: In function ‘initQ_MN’: 2025-03-28T13:19:43,749 nj.c:358:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:43,749 358 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:43,749 | ^~~ 2025-03-28T13:19:43,752 nj.c: In function ‘minD’: 2025-03-28T13:19:43,753 nj.c:559:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:43,753 559 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:43,753 | ^~~ 2025-03-28T13:19:43,754 nj.c: In function ‘maxD’: 2025-03-28T13:19:43,754 nj.c:642:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:43,755 642 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:43,755 | ^~~ 2025-03-28T13:19:43,758 nj.c: In function ‘minPair’: 2025-03-28T13:19:43,758 nj.c:826:6: warning: left shift count >= width of type [-Wshift-count-overflow] 2025-03-28T13:19:43,758 826 | pos <<= sizeof(unsigned) * 8; 2025-03-28T13:19:43,758 | ^~~ 2025-03-28T13:19:45,781 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c nwck.c -o build/temp.linux-armv7l-cpython-39/nwck.o -fopenmp 2025-03-28T13:19:46,255 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pherror.c -o build/temp.linux-armv7l-cpython-39/pherror.o -fopenmp 2025-03-28T13:19:46,344 pherror.c: In function ‘cfread’: 2025-03-28T13:19:46,344 pherror.c:58:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-03-28T13:19:46,344 58 | } else if(nmemb == 0 || (nmemb == -1 && (errno & EAGAIN))) { 2025-03-28T13:19:46,345 | ^~ 2025-03-28T13:19:46,438 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c phy.c -o build/temp.linux-armv7l-cpython-39/phy.o -fopenmp 2025-03-28T13:19:47,362 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c pydnj.c -o build/temp.linux-armv7l-cpython-39/pydnj.o -fopenmp 2025-03-28T13:19:47,667 In file included from pydnj.c:11: 2025-03-28T13:19:47,668 dnjheaders/pherror.h:20: warning: "_XOPEN_SOURCE" redefined 2025-03-28T13:19:47,668 20 | #define _XOPEN_SOURCE 600 2025-03-28T13:19:47,668 | 2025-03-28T13:19:47,668 In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33, 2025-03-28T13:19:47,668 from /usr/include/limits.h:26, 2025-03-28T13:19:47,668 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:195, 2025-03-28T13:19:47,669 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/syslimits.h:7, 2025-03-28T13:19:47,669 from /usr/lib/gcc/arm-linux-gnueabihf/10/include/limits.h:34, 2025-03-28T13:19:47,669 from /usr/include/python3.9/Python.h:11, 2025-03-28T13:19:47,669 from pydnj.c:1: 2025-03-28T13:19:47,669 /usr/include/features.h:207: note: this is the location of the previous definition 2025-03-28T13:19:47,669 207 | # define _XOPEN_SOURCE 700 2025-03-28T13:19:47,669 | 2025-03-28T13:19:47,683 pydnj.c: In function ‘py_build’: 2025-03-28T13:19:47,683 pydnj.c:165:9: warning: implicit declaration of function ‘omp_get_num_procs’ [-Wimplicit-function-declaration] 2025-03-28T13:19:47,683 165 | p = omp_get_num_procs(); 2025-03-28T13:19:47,683 | ^~~~~~~~~~~~~~~~~ 2025-03-28T13:19:47,868 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c qseqs.c -o build/temp.linux-armv7l-cpython-39/qseqs.o -fopenmp 2025-03-28T13:19:48,057 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c str.c -o build/temp.linux-armv7l-cpython-39/str.o -fopenmp 2025-03-28T13:19:48,166 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c tmp.c -o build/temp.linux-armv7l-cpython-39/tmp.o -fopenmp 2025-03-28T13:19:48,351 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-Ghp7MV/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -Idnjheaders -I/usr/include/python3.9 -c vector.c -o build/temp.linux-armv7l-cpython-39/vector.o -fopenmp 2025-03-28T13:19:48,505 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/bytescale.o build/temp.linux-armv7l-cpython-39/dnj.o build/temp.linux-armv7l-cpython-39/filebuff.o build/temp.linux-armv7l-cpython-39/hclust.o build/temp.linux-armv7l-cpython-39/matrix.o build/temp.linux-armv7l-cpython-39/mman.o build/temp.linux-armv7l-cpython-39/nj.o build/temp.linux-armv7l-cpython-39/nwck.o build/temp.linux-armv7l-cpython-39/pherror.o build/temp.linux-armv7l-cpython-39/phy.o build/temp.linux-armv7l-cpython-39/pydnj.o build/temp.linux-armv7l-cpython-39/qseqs.o build/temp.linux-armv7l-cpython-39/str.o build/temp.linux-armv7l-cpython-39/tmp.o build/temp.linux-armv7l-cpython-39/vector.o -L/usr/lib -lz -o build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -fopenmp 2025-03-28T13:19:48,711 /usr/local/lib/python3.9/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-03-28T13:19:48,712 !! 2025-03-28T13:19:48,712 ******************************************************************************** 2025-03-28T13:19:48,712 Please avoid running ``setup.py`` directly. 2025-03-28T13:19:48,713 Instead, use pypa/build, pypa/installer or other 2025-03-28T13:19:48,713 standards-based tools. 2025-03-28T13:19:48,713 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-03-28T13:19:48,713 ******************************************************************************** 2025-03-28T13:19:48,714 !! 2025-03-28T13:19:48,714 self.initialize_options() 2025-03-28T13:19:48,757 installing to build/bdist.linux-armv7l/wheel 2025-03-28T13:19:48,758 running install 2025-03-28T13:19:48,797 running install_lib 2025-03-28T13:19:48,835 creating build/bdist.linux-armv7l/wheel 2025-03-28T13:19:48,837 copying build/lib.linux-armv7l-cpython-39/nj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-03-28T13:19:48,841 copying build/lib.linux-armv7l-cpython-39/kssd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-03-28T13:19:48,851 copying build/lib.linux-armv7l-cpython-39/dnj.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-03-28T13:19:48,860 copying build/lib.linux-armv7l-cpython-39/kssdtree.py -> build/bdist.linux-armv7l/wheel/. 2025-03-28T13:19:48,862 copying build/lib.linux-armv7l-cpython-39/toolutils.py -> build/bdist.linux-armv7l/wheel/. 2025-03-28T13:19:48,865 running install_egg_info 2025-03-28T13:19:48,907 Copying kssdtree.egg-info to build/bdist.linux-armv7l/wheel/./kssdtree-2.0.5-py3.9.egg-info 2025-03-28T13:19:48,919 running install_scripts 2025-03-28T13:19:48,973 creating build/bdist.linux-armv7l/wheel/kssdtree-2.0.5.dist-info/WHEEL 2025-03-28T13:19:48,976 creating '/tmp/pip-wheel-qgtppctr/kssdtree-2.0.5-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-03-28T13:19:49,054 adding 'dnj.cpython-39-arm-linux-gnueabihf.so' 2025-03-28T13:19:49,149 adding 'kssd.cpython-39-arm-linux-gnueabihf.so' 2025-03-28T13:19:49,154 adding 'kssdtree.py' 2025-03-28T13:19:49,177 adding 'nj.cpython-39-arm-linux-gnueabihf.so' 2025-03-28T13:19:49,180 adding 'toolutils.py' 2025-03-28T13:19:49,182 adding 'kssdtree-2.0.5.dist-info/METADATA' 2025-03-28T13:19:49,184 adding 'kssdtree-2.0.5.dist-info/WHEEL' 2025-03-28T13:19:49,185 adding 'kssdtree-2.0.5.dist-info/dependency_links.txt' 2025-03-28T13:19:49,186 adding 'kssdtree-2.0.5.dist-info/top_level.txt' 2025-03-28T13:19:49,187 adding 'kssdtree-2.0.5.dist-info/RECORD' 2025-03-28T13:19:49,196 removing build/bdist.linux-armv7l/wheel 2025-03-28T13:19:49,298 Building wheel for kssdtree (setup.py): finished with status 'done' 2025-03-28T13:19:49,304 Created wheel for kssdtree: filename=kssdtree-2.0.5-cp39-cp39-linux_armv7l.whl size=377599 sha256=db08595adc89347b61965ba36e918055e8a0dc5f6a2b0bdfe16133eb363412d3 2025-03-28T13:19:49,305 Stored in directory: /tmp/pip-ephem-wheel-cache-lp3bn1ul/wheels/9a/6d/c0/65bfbcc09859f52bd67af61360aa6cd35d3dd56ba83e36e44b 2025-03-28T13:19:49,318 Successfully built kssdtree 2025-03-28T13:19:49,335 Removed build tracker: '/tmp/pip-build-tracker-y8rfnyik'