2026-06-19T15:39:47,863 Created temporary directory: /tmp/pip-ephem-wheel-cache-eh5hs4ef 2026-06-19T15:39:47,865 Created temporary directory: /tmp/pip-build-tracker-fdb1tbpe 2026-06-19T15:39:47,865 Initialized build tracking at /tmp/pip-build-tracker-fdb1tbpe 2026-06-19T15:39:47,866 Created build tracker: /tmp/pip-build-tracker-fdb1tbpe 2026-06-19T15:39:47,866 Entered build tracker: /tmp/pip-build-tracker-fdb1tbpe 2026-06-19T15:39:47,867 Created temporary directory: /tmp/pip-wheel-m271zems 2026-06-19T15:39:47,870 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-06-19T15:39:47,872 Created temporary directory: /tmp/pip-ephem-wheel-cache-lo10pcyl 2026-06-19T15:39:47,894 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-06-19T15:39:47,897 2 location(s) to search for versions of biobb-structure-checking: 2026-06-19T15:39:47,897 * https://pypi.org/simple/biobb-structure-checking/ 2026-06-19T15:39:47,897 * https://www.piwheels.org/simple/biobb-structure-checking/ 2026-06-19T15:39:47,898 Fetching project page and analyzing links: https://pypi.org/simple/biobb-structure-checking/ 2026-06-19T15:39:47,899 Getting page https://pypi.org/simple/biobb-structure-checking/ 2026-06-19T15:39:47,900 Found index url https://pypi.org/simple 2026-06-19T15:39:48,129 Fetched page https://pypi.org/simple/biobb-structure-checking/ as application/vnd.pypi.simple.v1+json 2026-06-19T15:39:48,143 Skipping link: No binaries permitted for biobb-structure-checking: 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https://files.pythonhosted.org/packages/61/37/9b0ff6d7f2fa5f2a7e5ca2a614ade65edf33e3351c42b2d974896bd59932/biobb_structure_checking-3.9.9.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,192 Skipping link: 3.9.9 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/61/37/9b0ff6d7f2fa5f2a7e5ca2a614ade65edf33e3351c42b2d974896bd59932/biobb_structure_checking-3.9.9.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,192 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/a3/43/cd861c5cc8ecc3476d8ae3e474acb8f98ab0c9da99b812d19c5451d00ccf/biobb_structure_checking-3.9.10-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,193 Link requires a different Python (3.11.2 not in: '==3.7.*'): https://files.pythonhosted.org/packages/0d/31/19dc942015efa8dadb519d1a330054864eaa9178affd67cedaaa61160016/biobb_structure_checking-3.9.10.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,194 Skipping link: 3.9.10 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/0d/31/19dc942015efa8dadb519d1a330054864eaa9178affd67cedaaa61160016/biobb_structure_checking-3.9.10.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,194 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/9e/99/6a7991ad252d275113a51e1225df5e202f3b99b4ebd86940c26d86e382d3/biobb_structure_checking-3.9.11-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,195 Link requires a different Python (3.11.2 not in: '==3.7.*'): https://files.pythonhosted.org/packages/d0/ca/93e5d1f2d75b0f99a578bc7a0bb8519dc073e2905dec5a0a6e95d7e991a4/biobb_structure_checking-3.9.11.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,196 Skipping link: 3.9.11 Requires-Python ==3.7.*: https://files.pythonhosted.org/packages/d0/ca/93e5d1f2d75b0f99a578bc7a0bb8519dc073e2905dec5a0a6e95d7e991a4/biobb_structure_checking-3.9.11.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,196 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/dc/66/9aee0a636ffa94d89c495468d61607790162ec26a278ec4cabb82410c93a/biobb_structure_checking-3.10.0-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,197 Found link https://files.pythonhosted.org/packages/0c/ad/2a27428424df13356f63f38ad70411199857e08a2e2cb1aa6e1d98d58d56/biobb_structure_checking-3.10.0.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.10.0 2026-06-19T15:39:48,198 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/2f/89/ab802a1e0ae870998435b8136529c43ca8eea9a106eacd170d547c5ccc6f/biobb_structure_checking-3.10.1-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,199 Found link https://files.pythonhosted.org/packages/a8/33/9ede62a4f16048d2a24d4261cdb6489ad653385e3ef851c9cbf904346493/biobb_structure_checking-3.10.1.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.10.1 2026-06-19T15:39:48,200 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/80/97/11822214f8649f0cf944468fe32461f46dc219b9a80c804cd93e2841496b/biobb_structure_checking-3.12.0-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,201 Found link https://files.pythonhosted.org/packages/f5/c1/8fe39123366ae2b1ff9806667185da01871878a3acc419d1f02fc0713aa0/biobb_structure_checking-3.12.0.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.12.0 2026-06-19T15:39:48,202 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/e0/72/0e3893b0ed4846d2237228c73378519a122e9e782bc0536bd3fc3be79501/biobb_structure_checking-3.12.1-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,202 Found link https://files.pythonhosted.org/packages/8e/a3/9e01147d4b0244435d143bdc70f6520b01394ae4622eecd7dfcec6f1ebcf/biobb_structure_checking-3.12.1.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.12.1 2026-06-19T15:39:48,203 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/c2/19/f28556efe1a066317fbe8ac794784e072e1971ae45ef27ca460f97cc0f23/biobb_structure_checking-3.13.0-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,204 Found link https://files.pythonhosted.org/packages/af/6b/580b883d738e617b7c12ae6eb5b02fc638be22b6abf67dc263927d48be6c/biobb_structure_checking-3.13.0.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.13.0 2026-06-19T15:39:48,204 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/ab/15/5a80821e138fdb530c89d24ef8d53d2283ac666a56f7c824cfbad94fd321/biobb_structure_checking-3.13.1-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,205 Found link https://files.pythonhosted.org/packages/78/3e/74d52a0ca14ee3a3cecc97011b790982d615897af38d20f4dde1a69603aa/biobb_structure_checking-3.13.1.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.13.1 2026-06-19T15:39:48,206 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/8e/77/0c113c7d98a63754e9ddd924485eef5576699663b81389a87bd9dcd4f15e/biobb_structure_checking-3.13.2-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,207 Found link https://files.pythonhosted.org/packages/cd/e6/3016f0682abfd34b50cea655736e859990d66cd1eaeaed9c734be264988e/biobb_structure_checking-3.13.2.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.13.2 2026-06-19T15:39:48,208 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/c5/34/68dc605be1c12c5ed5e1a43dfe56e021b4c4d2cfd0bf5b131e4d80f6262a/biobb_structure_checking-3.13.3-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,209 Found link https://files.pythonhosted.org/packages/71/92/5ecd16cb8297dd88ccbfbc73bf2684eaf07aea4c9b05fba10a972c4487fd/biobb_structure_checking-3.13.3.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.7), version: 3.13.3 2026-06-19T15:39:48,209 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/42/30/c3abd1652f1ab2f01b9ea438b0398bb247f9d85e4cf193abcb38b68f4ef6/biobb_structure_checking-3.13.4-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8) 2026-06-19T15:39:48,210 Found link https://files.pythonhosted.org/packages/52/c8/fbde8e5c8502699a5f85837298acefc14a198b31d30e3d87fde18fa6f169/biobb_structure_checking-3.13.4.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8), version: 3.13.4 2026-06-19T15:39:48,211 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/93/e8/c8eddb1e4996aebc703ed6344131861d54e763184f82a3b61c4dae4c68f2/biobb_structure_checking-3.13.5-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8) 2026-06-19T15:39:48,212 Found link https://files.pythonhosted.org/packages/fb/27/8cf9b68cb39e063a373b87ba8881d888dd8b6449dfce5b6a3605f095128d/biobb_structure_checking-3.13.5.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8), version: 3.13.5 2026-06-19T15:39:48,213 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/93/46/c97cecdb5d82490f01e90458255d7afdd84d309e260f0a037757a9d898ae/biobb_structure_checking-3.15.6-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8) 2026-06-19T15:39:48,214 Found link https://files.pythonhosted.org/packages/a2/86/ac0784d3a4a544ebc2275d36dd15daad21d079c0f7105d7001b4041df045/biobb_structure_checking-3.15.6.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.8), version: 3.15.6 2026-06-19T15:39:48,214 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/c6/cc/8d41be69fa53b9774fa9c93fddbe8d36de6bbc7ddeabf7b886bb752925a3/biobb_structure_checking-3.16.1-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.9) 2026-06-19T15:39:48,215 Found link https://files.pythonhosted.org/packages/b2/8c/e3743fc9913ce678190cb90d9e6a68c7c16bfdaa07a01b0ee23e9ef571a3/biobb_structure_checking-3.16.1.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.9), version: 3.16.1 2026-06-19T15:39:48,216 Skipping link: No binaries permitted for biobb-structure-checking: https://files.pythonhosted.org/packages/26/4e/1beaeb8b504d715fe789051193dc4482954611b9676272ed22b48454a262/biobb_structure_checking-3.16.2-py3-none-any.whl (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.9) 2026-06-19T15:39:48,217 Found link https://files.pythonhosted.org/packages/3d/7a/29c141ecaf0784b3c1412fc4587a3927986a4875df396611736baa7fd69b/biobb_structure_checking-3.16.2.tar.gz (from https://pypi.org/simple/biobb-structure-checking/) (requires-python:>=3.9), version: 3.16.2 2026-06-19T15:39:48,218 Fetching project page and analyzing links: https://www.piwheels.org/simple/biobb-structure-checking/ 2026-06-19T15:39:48,218 Getting page https://www.piwheels.org/simple/biobb-structure-checking/ 2026-06-19T15:39:48,220 Found index url https://www.piwheels.org/simple 2026-06-19T15:39:48,387 Fetched page https://www.piwheels.org/simple/biobb-structure-checking/ as text/html 2026-06-19T15:39:48,398 Skipping link: No binaries permitted for biobb-structure-checking: https://www.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.16.1-py3-none-any.whl#sha256=d2a8ab8cd28ed4cd3c84f79e6724d83147a39926218ed3cea208eb52a46ace1e (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.9) 2026-06-19T15:39:48,398 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.15.6-py3-none-any.whl#sha256=c09b75b465fa7da9c888d5a32c787bef17f284d6fd4bad76e4183b5ce5c3d8f1 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.8) 2026-06-19T15:39:48,399 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.13.5-py3-none-any.whl#sha256=1ff104b980ff49db450933410402e9471cf481f034023b537a0f82a92354575e (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.8) 2026-06-19T15:39:48,400 Skipping link: No binaries permitted for biobb-structure-checking: 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2026-06-19T15:39:48,402 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.13.1-py3-none-any.whl#sha256=de3edbf57f930c8be4f5271902cb1405b7eacaeb7bb9dc99ae76bf92b228a1ac (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,402 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.13.0-py3-none-any.whl#sha256=11a150b486fad67849db97665a6878ec7ecec9331aed2342c68a50ed3a63a712 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,402 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.12.1-py3-none-any.whl#sha256=720ed6cd269f005d47297be9dba8ac1db9797d8fe331eafc136915a18c30d95b (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,403 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.12.0-py3-none-any.whl#sha256=3205b198d75f26e80e2fb59bedcfb9f1edfabcc337b5ab16a9261107e6a25a9e (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,403 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.10.1-py3-none-any.whl#sha256=8edd75d0ff29bb737e8c0eb8b0d3afaa0ce321452921e584a8f29ac11910e00a (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,404 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.10.0-py3-none-any.whl#sha256=da2a762d7c3087d3dcb50581ab75dbdef6f3b7920a674fd900f210fe66305c86 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.7) 2026-06-19T15:39:48,405 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.11-py3-none-any.whl#sha256=59a99c0fa789ccb8993b3aa8b7a39783e24f49556bdb1392ba274a12a8ae06ce (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,405 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.10-py3-none-any.whl#sha256=6229a9c090a560f835fa166f7557157dc0e21d797c8cc46d6ec94d7a23256d51 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,406 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.9-py3-none-any.whl#sha256=12ec8887f6f22b9f7b89820c514231cf98909862f4f84297fa6e6bc6a045cbad (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,406 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.8-py3-none-any.whl#sha256=71299169c8ae898cf6dc19ed8043ea82995a7f7f036411121073034b07925680 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,407 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.7-py3-none-any.whl#sha256=6fafc262b410a804dfc962bf5795fe8fc3e3f6c32b2dcdb962d43ff078ab64a0 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,408 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.6-py3-none-any.whl#sha256=06d44fa470872ecb6149b0ae2f31078e42b0f3945a75f1dfee91c88823c06597 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,408 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.5-py3-none-any.whl#sha256=582d529a2c847f6c8cfc0afd2f51699bbd60bc0f1fadbfcb277dfb363253caf7 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,409 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.4-py3-none-any.whl#sha256=59e51320caa1bdc56677fb8db25e9ce9ced398c5e4b0a026617be8844df1a6d3 (from https://www.piwheels.org/simple/biobb-structure-checking/) 2026-06-19T15:39:48,409 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.3-py3-none-any.whl#sha256=bcd1ac36892c14f7cffef48805c07dedeace4f7d94add1a5c3d57b5fc064ceaa (from https://www.piwheels.org/simple/biobb-structure-checking/) 2026-06-19T15:39:48,410 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.2-py3-none-any.whl#sha256=333b156968b057501ca2b331c021dae957bffe4a63766de01b2c69f2f6715680 (from https://www.piwheels.org/simple/biobb-structure-checking/) 2026-06-19T15:39:48,410 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.9.1-py3-none-any.whl#sha256=3e9cc73943fd2fce1e5889acfd325e4405c80017d479b9276f422c04df745f1c (from https://www.piwheels.org/simple/biobb-structure-checking/) 2026-06-19T15:39:48,411 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.8.5-py3-none-any.whl#sha256=5db5ad249dcde45660778f6b2af7511367e5d712f21a2918d0a3ef878b1ad93e (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.6) 2026-06-19T15:39:48,412 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.7.3-py3-none-any.whl#sha256=171c66ce739cf98c9e748a32426353cff168927e4955c9a89538d2c8781be485 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.6) 2026-06-19T15:39:48,412 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.7.2-py3-none-any.whl#sha256=0951c702b05d2f61693b25cab0cf3b9bd46c11381048f3ad7af6c58bb7403810 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.6) 2026-06-19T15:39:48,413 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.7.1-py3-none-any.whl#sha256=a837ba4af81fd98a21e85719e595845d693dfee2a2513c504d243809ea163825 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.6) 2026-06-19T15:39:48,413 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.7.0-py3-none-any.whl#sha256=7c51b36c5f52e0addd64f3b7ec0c3e3f6ce43d95ae8d24d452c135e2650b7242 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:>=3.5) 2026-06-19T15:39:48,414 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.5.3-py3-none-any.whl#sha256=8f9443b0614b6d0c9b895612d995e36ce8d4d35a52b9de45b0587cb6007ea104 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,415 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.5.2-py3-none-any.whl#sha256=27db7be134a0b373dd67dacc9ae5116f2f57709945749df6a2950ea91a9c83c9 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,415 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.5.0-py3-none-any.whl#sha256=9076b15d538fdac6ade33a2a1b514b8fd1d64851e84ca2941390851dc3d7372e (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,415 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.0.2-py3-none-any.whl#sha256=d9c71e4c12c116a92db4e5bfc2c869ac06b270f07d10c15f86c7db1bf0510125 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,416 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.0.1-py3-none-any.whl#sha256=4dfd2c0acabfa01f77c89c67040ff349d90f919c38e0300b3e1f1ef4bba07b97 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,417 Skipping link: No binaries permitted for biobb-structure-checking: https://archive1.piwheels.org/simple/biobb-structure-checking/biobb_structure_checking-3.0.0-py3-none-any.whl#sha256=4360463771a60a95ecbb4397df8c57f7b889dda78c87d50508629149b60726e0 (from https://www.piwheels.org/simple/biobb-structure-checking/) (requires-python:==3.7.*) 2026-06-19T15:39:48,417 Skipping link: not a file: https://www.piwheels.org/simple/biobb-structure-checking/ 2026-06-19T15:39:48,418 Skipping link: not a file: https://pypi.org/simple/biobb-structure-checking/ 2026-06-19T15:39:48,439 Given no hashes to check 1 links for project 'biobb-structure-checking': discarding no candidates 2026-06-19T15:39:48,457 Collecting biobb-structure-checking==3.16.2 2026-06-19T15:39:48,459 Created temporary directory: /tmp/pip-unpack-fv6qcqsk 2026-06-19T15:39:48,681 Downloading biobb_structure_checking-3.16.2.tar.gz (175 kB) 2026-06-19T15:39:48,941 Added biobb-structure-checking==3.16.2 from https://files.pythonhosted.org/packages/3d/7a/29c141ecaf0784b3c1412fc4587a3927986a4875df396611736baa7fd69b/biobb_structure_checking-3.16.2.tar.gz to build tracker '/tmp/pip-build-tracker-fdb1tbpe' 2026-06-19T15:39:48,942 Running setup.py (path:/tmp/pip-wheel-m271zems/biobb-structure-checking_8d1def155a8144beb9200e74fd18c6bd/setup.py) egg_info for package biobb-structure-checking 2026-06-19T15:39:48,943 Created temporary directory: /tmp/pip-pip-egg-info-tlfyoc62 2026-06-19T15:39:48,944 Preparing metadata (setup.py): started 2026-06-19T15:39:48,945 Running command python setup.py egg_info 2026-06-19T15:39:49,842 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-06-19T15:39:49,843 !! 2026-06-19T15:39:49,844 ******************************************************************************** 2026-06-19T15:39:49,844 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-06-19T15:39:49,845 License :: OSI Approved :: Apache Software License 2026-06-19T15:39:49,846 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-06-19T15:39:49,846 ******************************************************************************** 2026-06-19T15:39:49,847 !! 2026-06-19T15:39:49,848 self._finalize_license_expression() 2026-06-19T15:39:49,872 running egg_info 2026-06-19T15:39:49,899 creating /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info 2026-06-19T15:39:49,900 writing /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/PKG-INFO 2026-06-19T15:39:49,903 writing dependency_links to /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/dependency_links.txt 2026-06-19T15:39:49,905 writing entry points to /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/entry_points.txt 2026-06-19T15:39:49,906 writing requirements to /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/requires.txt 2026-06-19T15:39:49,907 writing top-level names to /tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/top_level.txt 2026-06-19T15:39:49,908 writing manifest file '/tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/SOURCES.txt' 2026-06-19T15:39:50,001 reading manifest file '/tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/SOURCES.txt' 2026-06-19T15:39:50,003 reading manifest template 'MANIFEST.in' 2026-06-19T15:39:50,016 adding license file 'LICENSE' 2026-06-19T15:39:50,020 writing manifest file '/tmp/pip-pip-egg-info-tlfyoc62/biobb_structure_checking.egg-info/SOURCES.txt' 2026-06-19T15:39:50,129 Preparing metadata (setup.py): finished with status 'done' 2026-06-19T15:39:50,133 Source in /tmp/pip-wheel-m271zems/biobb-structure-checking_8d1def155a8144beb9200e74fd18c6bd has version 3.16.2, which satisfies requirement biobb-structure-checking==3.16.2 from https://files.pythonhosted.org/packages/3d/7a/29c141ecaf0784b3c1412fc4587a3927986a4875df396611736baa7fd69b/biobb_structure_checking-3.16.2.tar.gz 2026-06-19T15:39:50,134 Removed biobb-structure-checking==3.16.2 from https://files.pythonhosted.org/packages/3d/7a/29c141ecaf0784b3c1412fc4587a3927986a4875df396611736baa7fd69b/biobb_structure_checking-3.16.2.tar.gz from build tracker '/tmp/pip-build-tracker-fdb1tbpe' 2026-06-19T15:39:50,140 Created temporary directory: /tmp/pip-unpack-z2km1pi6 2026-06-19T15:39:50,141 Building wheels for collected packages: biobb-structure-checking 2026-06-19T15:39:50,145 Created temporary directory: /tmp/pip-wheel-cwtbgdcb 2026-06-19T15:39:50,146 Building wheel for biobb-structure-checking (setup.py): started 2026-06-19T15:39:50,147 Destination directory: /tmp/pip-wheel-cwtbgdcb 2026-06-19T15:39:50,147 Running command python setup.py bdist_wheel 2026-06-19T15:39:50,990 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-06-19T15:39:50,990 !! 2026-06-19T15:39:50,991 ******************************************************************************** 2026-06-19T15:39:50,992 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-06-19T15:39:50,993 License :: OSI Approved :: Apache Software License 2026-06-19T15:39:50,994 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-06-19T15:39:50,995 ******************************************************************************** 2026-06-19T15:39:50,996 !! 2026-06-19T15:39:50,997 self._finalize_license_expression() 2026-06-19T15:39:50,998 running bdist_wheel 2026-06-19T15:39:51,128 running build 2026-06-19T15:39:51,129 running build_py 2026-06-19T15:39:51,159 creating build/lib/biobb_structure_checking 2026-06-19T15:39:51,161 copying biobb_structure_checking/structure_checking.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,164 copying biobb_structure_checking/mutation_manager.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,166 copying biobb_structure_checking/check_structure.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,168 copying biobb_structure_checking/structure_manager.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,172 copying biobb_structure_checking/constants.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,174 copying biobb_structure_checking/__init__.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,176 copying biobb_structure_checking/modeller_manager.py -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,178 creating build/lib/biobb_structure_checking/libs 2026-06-19T15:39:51,179 copying biobb_structure_checking/libs/residue_lib_manager.py -> build/lib/biobb_structure_checking/libs 2026-06-19T15:39:51,181 copying biobb_structure_checking/libs/data_lib_manager.py -> build/lib/biobb_structure_checking/libs 2026-06-19T15:39:51,183 copying biobb_structure_checking/libs/__init__.py -> build/lib/biobb_structure_checking/libs 2026-06-19T15:39:51,186 creating build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,187 copying biobb_structure_checking/commands/clashes.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,189 copying biobb_structure_checking/commands/add_hydrogen.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,191 copying biobb_structure_checking/commands/metals.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,193 copying biobb_structure_checking/commands/water.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,195 copying biobb_structure_checking/commands/sequences.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,197 copying biobb_structure_checking/commands/ligands.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,199 copying biobb_structure_checking/commands/chiral.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,201 copying biobb_structure_checking/commands/altloc.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,203 copying biobb_structure_checking/commands/chains.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,205 copying biobb_structure_checking/commands/backbone.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,207 copying biobb_structure_checking/commands/rem_hydrogen.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,209 copying biobb_structure_checking/commands/amide.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,211 copying biobb_structure_checking/commands/__init__.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,212 copying biobb_structure_checking/commands/models.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,214 copying biobb_structure_checking/commands/inscodes.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,216 copying biobb_structure_checking/commands/cistransbck.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,218 copying biobb_structure_checking/commands/mutateside.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,220 copying biobb_structure_checking/commands/chiral_bck.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,222 copying biobb_structure_checking/commands/getss.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,224 copying biobb_structure_checking/commands/fixside.py -> build/lib/biobb_structure_checking/commands 2026-06-19T15:39:51,226 creating build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,227 copying biobb_structure_checking/pdbio/mmb_server.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,229 copying biobb_structure_checking/pdbio/json_writer.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,231 copying biobb_structure_checking/pdbio/PDBIO_extended.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,233 copying biobb_structure_checking/pdbio/param_input.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,235 copying biobb_structure_checking/pdbio/__init__.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,236 copying biobb_structure_checking/pdbio/bare_builder.py -> build/lib/biobb_structure_checking/pdbio 2026-06-19T15:39:51,239 creating build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,240 copying biobb_structure_checking/modelling/utils.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,242 copying biobb_structure_checking/modelling/modelsdata.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,244 copying biobb_structure_checking/modelling/structuredata.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,247 copying biobb_structure_checking/modelling/residue_set.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,248 copying biobb_structure_checking/modelling/__init__.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,250 copying biobb_structure_checking/modelling/chainsdata.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,252 copying biobb_structure_checking/modelling/sequencedata.py -> build/lib/biobb_structure_checking/modelling 2026-06-19T15:39:51,254 running egg_info 2026-06-19T15:39:51,283 writing biobb_structure_checking.egg-info/PKG-INFO 2026-06-19T15:39:51,287 writing dependency_links to biobb_structure_checking.egg-info/dependency_links.txt 2026-06-19T15:39:51,288 writing entry points to biobb_structure_checking.egg-info/entry_points.txt 2026-06-19T15:39:51,290 writing requirements to biobb_structure_checking.egg-info/requires.txt 2026-06-19T15:39:51,291 writing top-level names to biobb_structure_checking.egg-info/top_level.txt 2026-06-19T15:39:51,325 reading manifest file 'biobb_structure_checking.egg-info/SOURCES.txt' 2026-06-19T15:39:51,330 reading manifest template 'MANIFEST.in' 2026-06-19T15:39:51,343 adding license file 'LICENSE' 2026-06-19T15:39:51,348 writing manifest file 'biobb_structure_checking.egg-info/SOURCES.txt' 2026-06-19T15:39:51,351 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'biobb_structure_checking.dat' is absent from the `packages` configuration. 2026-06-19T15:39:51,351 !! 2026-06-19T15:39:51,352 ******************************************************************************** 2026-06-19T15:39:51,353 ############################ 2026-06-19T15:39:51,353 # Package would be ignored # 2026-06-19T15:39:51,354 ############################ 2026-06-19T15:39:51,355 Python recognizes 'biobb_structure_checking.dat' as an importable package[^1], 2026-06-19T15:39:51,355 but it is absent from setuptools' `packages` configuration. 2026-06-19T15:39:51,356 This leads to an ambiguous overall configuration. If you want to distribute this 2026-06-19T15:39:51,357 package, please make sure that 'biobb_structure_checking.dat' is explicitly added 2026-06-19T15:39:51,357 to the `packages` configuration field. 2026-06-19T15:39:51,358 Alternatively, you can also rely on setuptools' discovery methods 2026-06-19T15:39:51,359 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-06-19T15:39:51,359 instead of `find_packages(...)`/`find:`). 2026-06-19T15:39:51,360 You can read more about "package discovery" on setuptools documentation page: 2026-06-19T15:39:51,362 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-06-19T15:39:51,362 If you don't want 'biobb_structure_checking.dat' to be distributed and are 2026-06-19T15:39:51,363 already explicitly excluding 'biobb_structure_checking.dat' via 2026-06-19T15:39:51,363 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-06-19T15:39:51,364 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-06-19T15:39:51,364 combination with a more fine grained `package-data` configuration. 2026-06-19T15:39:51,365 You can read more about "package data files" on setuptools documentation page: 2026-06-19T15:39:51,365 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-06-19T15:39:51,367 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-06-19T15:39:51,367 even if it does not contain any `.py` files. 2026-06-19T15:39:51,369 On the other hand, currently there is no concept of package data 2026-06-19T15:39:51,370 directory, all directories are treated like packages. 2026-06-19T15:39:51,371 ******************************************************************************** 2026-06-19T15:39:51,371 !! 2026-06-19T15:39:51,372 check.warn(importable) 2026-06-19T15:39:51,373 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'biobb_structure_checking.dat.modRes' is absent from the `packages` configuration. 2026-06-19T15:39:51,373 !! 2026-06-19T15:39:51,374 ******************************************************************************** 2026-06-19T15:39:51,375 ############################ 2026-06-19T15:39:51,375 # Package would be ignored # 2026-06-19T15:39:51,377 ############################ 2026-06-19T15:39:51,377 Python recognizes 'biobb_structure_checking.dat.modRes' as an importable package[^1], 2026-06-19T15:39:51,378 but it is absent from setuptools' `packages` configuration. 2026-06-19T15:39:51,379 This leads to an ambiguous overall configuration. If you want to distribute this 2026-06-19T15:39:51,379 package, please make sure that 'biobb_structure_checking.dat.modRes' is explicitly added 2026-06-19T15:39:51,380 to the `packages` configuration field. 2026-06-19T15:39:51,381 Alternatively, you can also rely on setuptools' discovery methods 2026-06-19T15:39:51,381 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2026-06-19T15:39:51,382 instead of `find_packages(...)`/`find:`). 2026-06-19T15:39:51,383 You can read more about "package discovery" on setuptools documentation page: 2026-06-19T15:39:51,384 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2026-06-19T15:39:51,385 If you don't want 'biobb_structure_checking.dat.modRes' to be distributed and are 2026-06-19T15:39:51,385 already explicitly excluding 'biobb_structure_checking.dat.modRes' via 2026-06-19T15:39:51,386 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2026-06-19T15:39:51,386 you can try to use `exclude_package_data`, or `include-package-data=False` in 2026-06-19T15:39:51,387 combination with a more fine grained `package-data` configuration. 2026-06-19T15:39:51,388 You can read more about "package data files" on setuptools documentation page: 2026-06-19T15:39:51,389 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2026-06-19T15:39:51,391 [^1]: For Python, any directory (with suitable naming) can be imported, 2026-06-19T15:39:51,392 even if it does not contain any `.py` files. 2026-06-19T15:39:51,393 On the other hand, currently there is no concept of package data 2026-06-19T15:39:51,393 directory, all directories are treated like packages. 2026-06-19T15:39:51,394 ******************************************************************************** 2026-06-19T15:39:51,395 !! 2026-06-19T15:39:51,395 check.warn(importable) 2026-06-19T15:39:51,397 copying biobb_structure_checking/py.typed -> build/lib/biobb_structure_checking 2026-06-19T15:39:51,398 creating build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,399 copying biobb_structure_checking/dat/ADT_prm.json -> build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,399 copying biobb_structure_checking/dat/CMIP_prm.json -> build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,400 copying biobb_structure_checking/dat/all_residues.in -> build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,400 copying biobb_structure_checking/dat/commands.hlp -> build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,401 copying biobb_structure_checking/dat/data_lib.json -> build/lib/biobb_structure_checking/dat 2026-06-19T15:39:51,401 creating build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,402 copying biobb_structure_checking/dat/modRes/modSER.json -> build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,402 copying biobb_structure_checking/dat/modRes/modTHR.json -> build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,402 copying biobb_structure_checking/dat/modRes/modTYR.json -> build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,403 copying biobb_structure_checking/dat/modRes/modres.json -> build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,403 copying biobb_structure_checking/dat/modRes/modres_phospho.json -> build/lib/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,431 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2026-06-19T15:39:51,432 !! 2026-06-19T15:39:51,433 ******************************************************************************** 2026-06-19T15:39:51,434 Please avoid running ``setup.py`` directly. 2026-06-19T15:39:51,434 Instead, use pypa/build, pypa/installer or other 2026-06-19T15:39:51,435 standards-based tools. 2026-06-19T15:39:51,436 This deprecation is overdue, please update your project and remove deprecated 2026-06-19T15:39:51,436 calls to avoid build errors in the future. 2026-06-19T15:39:51,437 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2026-06-19T15:39:51,438 ******************************************************************************** 2026-06-19T15:39:51,439 !! 2026-06-19T15:39:51,440 self.initialize_options() 2026-06-19T15:39:51,461 installing to build/bdist.linux-armv7l/wheel 2026-06-19T15:39:51,461 running install 2026-06-19T15:39:51,484 running install_lib 2026-06-19T15:39:51,511 creating build/bdist.linux-armv7l/wheel 2026-06-19T15:39:51,513 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking 2026-06-19T15:39:51,515 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/libs 2026-06-19T15:39:51,516 copying build/lib/biobb_structure_checking/libs/residue_lib_manager.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/libs 2026-06-19T15:39:51,518 copying build/lib/biobb_structure_checking/libs/data_lib_manager.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/libs 2026-06-19T15:39:51,520 copying build/lib/biobb_structure_checking/libs/__init__.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/libs 2026-06-19T15:39:51,522 copying build/lib/biobb_structure_checking/structure_checking.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,525 copying build/lib/biobb_structure_checking/mutation_manager.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,527 copying build/lib/biobb_structure_checking/check_structure.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,530 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/dat 2026-06-19T15:39:51,531 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,532 copying build/lib/biobb_structure_checking/dat/modRes/modTYR.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,535 copying build/lib/biobb_structure_checking/dat/modRes/modres_phospho.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,541 copying build/lib/biobb_structure_checking/dat/modRes/modSER.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,543 copying build/lib/biobb_structure_checking/dat/modRes/modTHR.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,545 copying build/lib/biobb_structure_checking/dat/modRes/modres.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat/modRes 2026-06-19T15:39:51,551 copying build/lib/biobb_structure_checking/dat/commands.hlp -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat 2026-06-19T15:39:51,553 copying build/lib/biobb_structure_checking/dat/ADT_prm.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat 2026-06-19T15:39:51,555 copying build/lib/biobb_structure_checking/dat/all_residues.in -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat 2026-06-19T15:39:51,562 copying build/lib/biobb_structure_checking/dat/CMIP_prm.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat 2026-06-19T15:39:51,563 copying build/lib/biobb_structure_checking/dat/data_lib.json -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/dat 2026-06-19T15:39:51,567 copying build/lib/biobb_structure_checking/structure_manager.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,570 copying build/lib/biobb_structure_checking/constants.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,573 copying build/lib/biobb_structure_checking/__init__.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,574 copying build/lib/biobb_structure_checking/py.typed -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,576 copying build/lib/biobb_structure_checking/modeller_manager.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking 2026-06-19T15:39:51,579 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/commands 2026-06-19T15:39:51,580 copying build/lib/biobb_structure_checking/commands/clashes.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,582 copying build/lib/biobb_structure_checking/commands/add_hydrogen.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,584 copying build/lib/biobb_structure_checking/commands/metals.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,586 copying build/lib/biobb_structure_checking/commands/water.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,588 copying build/lib/biobb_structure_checking/commands/sequences.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,590 copying build/lib/biobb_structure_checking/commands/ligands.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,592 copying build/lib/biobb_structure_checking/commands/chiral.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,594 copying build/lib/biobb_structure_checking/commands/altloc.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,596 copying build/lib/biobb_structure_checking/commands/chains.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,598 copying build/lib/biobb_structure_checking/commands/backbone.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,601 copying build/lib/biobb_structure_checking/commands/rem_hydrogen.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,603 copying build/lib/biobb_structure_checking/commands/amide.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,604 copying build/lib/biobb_structure_checking/commands/__init__.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,606 copying build/lib/biobb_structure_checking/commands/models.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,608 copying build/lib/biobb_structure_checking/commands/inscodes.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,610 copying build/lib/biobb_structure_checking/commands/cistransbck.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,612 copying build/lib/biobb_structure_checking/commands/mutateside.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,613 copying build/lib/biobb_structure_checking/commands/chiral_bck.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,615 copying build/lib/biobb_structure_checking/commands/getss.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,617 copying build/lib/biobb_structure_checking/commands/fixside.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/commands 2026-06-19T15:39:51,620 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/pdbio 2026-06-19T15:39:51,621 copying build/lib/biobb_structure_checking/pdbio/mmb_server.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,623 copying build/lib/biobb_structure_checking/pdbio/json_writer.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,625 copying build/lib/biobb_structure_checking/pdbio/PDBIO_extended.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,627 copying build/lib/biobb_structure_checking/pdbio/param_input.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,630 copying build/lib/biobb_structure_checking/pdbio/__init__.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,631 copying build/lib/biobb_structure_checking/pdbio/bare_builder.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/pdbio 2026-06-19T15:39:51,634 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking/modelling 2026-06-19T15:39:51,635 copying build/lib/biobb_structure_checking/modelling/utils.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,638 copying build/lib/biobb_structure_checking/modelling/modelsdata.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,640 copying build/lib/biobb_structure_checking/modelling/structuredata.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,643 copying build/lib/biobb_structure_checking/modelling/residue_set.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,645 copying build/lib/biobb_structure_checking/modelling/__init__.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,646 copying build/lib/biobb_structure_checking/modelling/chainsdata.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,649 copying build/lib/biobb_structure_checking/modelling/sequencedata.py -> build/bdist.linux-armv7l/wheel/./biobb_structure_checking/modelling 2026-06-19T15:39:51,652 running install_egg_info 2026-06-19T15:39:51,687 Copying biobb_structure_checking.egg-info to build/bdist.linux-armv7l/wheel/./biobb_structure_checking-3.16.2-py3.11.egg-info 2026-06-19T15:39:51,699 running install_scripts 2026-06-19T15:39:51,712 creating build/bdist.linux-armv7l/wheel/biobb_structure_checking-3.16.2.dist-info/WHEEL 2026-06-19T15:39:51,714 creating '/tmp/pip-wheel-cwtbgdcb/biobb_structure_checking-3.16.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-06-19T15:39:51,716 adding 'biobb_structure_checking/__init__.py' 2026-06-19T15:39:51,717 adding 'biobb_structure_checking/check_structure.py' 2026-06-19T15:39:51,720 adding 'biobb_structure_checking/constants.py' 2026-06-19T15:39:51,722 adding 'biobb_structure_checking/modeller_manager.py' 2026-06-19T15:39:51,724 adding 'biobb_structure_checking/mutation_manager.py' 2026-06-19T15:39:51,726 adding 'biobb_structure_checking/py.typed' 2026-06-19T15:39:51,729 adding 'biobb_structure_checking/structure_checking.py' 2026-06-19T15:39:51,737 adding 'biobb_structure_checking/structure_manager.py' 2026-06-19T15:39:51,739 adding 'biobb_structure_checking/commands/__init__.py' 2026-06-19T15:39:51,741 adding 'biobb_structure_checking/commands/add_hydrogen.py' 2026-06-19T15:39:51,742 adding 'biobb_structure_checking/commands/altloc.py' 2026-06-19T15:39:51,744 adding 'biobb_structure_checking/commands/amide.py' 2026-06-19T15:39:51,746 adding 'biobb_structure_checking/commands/backbone.py' 2026-06-19T15:39:51,748 adding 'biobb_structure_checking/commands/chains.py' 2026-06-19T15:39:51,749 adding 'biobb_structure_checking/commands/chiral.py' 2026-06-19T15:39:51,750 adding 'biobb_structure_checking/commands/chiral_bck.py' 2026-06-19T15:39:51,752 adding 'biobb_structure_checking/commands/cistransbck.py' 2026-06-19T15:39:51,754 adding 'biobb_structure_checking/commands/clashes.py' 2026-06-19T15:39:51,755 adding 'biobb_structure_checking/commands/fixside.py' 2026-06-19T15:39:51,757 adding 'biobb_structure_checking/commands/getss.py' 2026-06-19T15:39:51,758 adding 'biobb_structure_checking/commands/inscodes.py' 2026-06-19T15:39:51,760 adding 'biobb_structure_checking/commands/ligands.py' 2026-06-19T15:39:51,762 adding 'biobb_structure_checking/commands/metals.py' 2026-06-19T15:39:51,764 adding 'biobb_structure_checking/commands/models.py' 2026-06-19T15:39:51,765 adding 'biobb_structure_checking/commands/mutateside.py' 2026-06-19T15:39:51,767 adding 'biobb_structure_checking/commands/rem_hydrogen.py' 2026-06-19T15:39:51,769 adding 'biobb_structure_checking/commands/sequences.py' 2026-06-19T15:39:51,771 adding 'biobb_structure_checking/commands/water.py' 2026-06-19T15:39:51,773 adding 'biobb_structure_checking/dat/ADT_prm.json' 2026-06-19T15:39:51,774 adding 'biobb_structure_checking/dat/CMIP_prm.json' 2026-06-19T15:39:51,792 adding 'biobb_structure_checking/dat/all_residues.in' 2026-06-19T15:39:51,795 adding 'biobb_structure_checking/dat/commands.hlp' 2026-06-19T15:39:51,800 adding 'biobb_structure_checking/dat/data_lib.json' 2026-06-19T15:39:51,802 adding 'biobb_structure_checking/dat/modRes/modSER.json' 2026-06-19T15:39:51,804 adding 'biobb_structure_checking/dat/modRes/modTHR.json' 2026-06-19T15:39:51,805 adding 'biobb_structure_checking/dat/modRes/modTYR.json' 2026-06-19T15:39:51,818 adding 'biobb_structure_checking/dat/modRes/modres.json' 2026-06-19T15:39:51,832 adding 'biobb_structure_checking/dat/modRes/modres_phospho.json' 2026-06-19T15:39:51,834 adding 'biobb_structure_checking/libs/__init__.py' 2026-06-19T15:39:51,836 adding 'biobb_structure_checking/libs/data_lib_manager.py' 2026-06-19T15:39:51,837 adding 'biobb_structure_checking/libs/residue_lib_manager.py' 2026-06-19T15:39:51,839 adding 'biobb_structure_checking/modelling/__init__.py' 2026-06-19T15:39:51,841 adding 'biobb_structure_checking/modelling/chainsdata.py' 2026-06-19T15:39:51,843 adding 'biobb_structure_checking/modelling/modelsdata.py' 2026-06-19T15:39:51,844 adding 'biobb_structure_checking/modelling/residue_set.py' 2026-06-19T15:39:51,847 adding 'biobb_structure_checking/modelling/sequencedata.py' 2026-06-19T15:39:51,849 adding 'biobb_structure_checking/modelling/structuredata.py' 2026-06-19T15:39:51,854 adding 'biobb_structure_checking/modelling/utils.py' 2026-06-19T15:39:51,856 adding 'biobb_structure_checking/pdbio/PDBIO_extended.py' 2026-06-19T15:39:51,857 adding 'biobb_structure_checking/pdbio/__init__.py' 2026-06-19T15:39:51,858 adding 'biobb_structure_checking/pdbio/bare_builder.py' 2026-06-19T15:39:51,859 adding 'biobb_structure_checking/pdbio/json_writer.py' 2026-06-19T15:39:51,861 adding 'biobb_structure_checking/pdbio/mmb_server.py' 2026-06-19T15:39:51,863 adding 'biobb_structure_checking/pdbio/param_input.py' 2026-06-19T15:39:51,866 adding 'biobb_structure_checking-3.16.2.dist-info/licenses/LICENSE' 2026-06-19T15:39:51,868 adding 'biobb_structure_checking-3.16.2.dist-info/METADATA' 2026-06-19T15:39:51,869 adding 'biobb_structure_checking-3.16.2.dist-info/WHEEL' 2026-06-19T15:39:51,869 adding 'biobb_structure_checking-3.16.2.dist-info/entry_points.txt' 2026-06-19T15:39:51,870 adding 'biobb_structure_checking-3.16.2.dist-info/top_level.txt' 2026-06-19T15:39:51,872 adding 'biobb_structure_checking-3.16.2.dist-info/RECORD' 2026-06-19T15:39:51,875 removing build/bdist.linux-armv7l/wheel 2026-06-19T15:39:52,000 Building wheel for biobb-structure-checking (setup.py): finished with status 'done' 2026-06-19T15:39:52,004 Created wheel for biobb-structure-checking: filename=biobb_structure_checking-3.16.2-py3-none-any.whl size=198861 sha256=f712d5387abe273429e2737935ca57faeacf5fc1b873a25747efa8128b03d596 2026-06-19T15:39:52,005 Stored in directory: /tmp/pip-ephem-wheel-cache-lo10pcyl/wheels/ed/21/69/5e5ee935e9baec999131201aa5624f364c422190a311b229eb 2026-06-19T15:39:52,018 Successfully built biobb-structure-checking 2026-06-19T15:39:52,028 Removed build tracker: '/tmp/pip-build-tracker-fdb1tbpe'