2023-09-08T11:40:46,229 Created temporary directory: /tmp/pip-build-tracker-177idig_ 2023-09-08T11:40:46,230 Initialized build tracking at /tmp/pip-build-tracker-177idig_ 2023-09-08T11:40:46,231 Created build tracker: /tmp/pip-build-tracker-177idig_ 2023-09-08T11:40:46,231 Entered build tracker: /tmp/pip-build-tracker-177idig_ 2023-09-08T11:40:46,232 Created temporary directory: /tmp/pip-wheel-61944oqx 2023-09-08T11:40:46,235 Created temporary directory: /tmp/pip-ephem-wheel-cache-35tkpf0_ 2023-09-08T11:40:46,257 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T11:40:46,261 2 location(s) to search for versions of ngs-plumbing: 2023-09-08T11:40:46,261 * https://pypi.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,261 * https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,262 Fetching project page and analyzing links: https://pypi.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,262 Getting page https://pypi.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,264 Found index url https://pypi.org/simple/ 2023-09-08T11:40:46,401 Fetched page https://pypi.org/simple/ngs-plumbing/ as application/vnd.pypi.simple.v1+json 2023-09-08T11:40:46,407 Found link https://files.pythonhosted.org/packages/e2/b7/896169889e1a705a2db7fc237a9e6f4b6c39b9dd94d8671667cc3bc652d7/ngs_plumbing-0.5.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.5.1 2023-09-08T11:40:46,408 Found link https://files.pythonhosted.org/packages/17/3d/83ed952f2731054d91fcd64c58748c339c597d552ffec03922be97101240/ngs_plumbing-0.6.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.1 2023-09-08T11:40:46,408 Found link https://files.pythonhosted.org/packages/ac/f5/0d958a7591e7dfc436298e2d5902cca67e2d45634fa0d699153b1098195d/ngs_plumbing-0.6.2.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.2 2023-09-08T11:40:46,409 Found link https://files.pythonhosted.org/packages/a1/3e/24003dd7ed3790f9f9f89535a0ceea78c5f4d462986bf21fb30cd354bd58/ngs_plumbing-0.6.3.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.3 2023-09-08T11:40:46,410 Found link https://files.pythonhosted.org/packages/2e/52/d94a726f19fe9269ff371b20255c4de31de8c5c02cf59532813f4a18397a/ngs_plumbing-0.7.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.0 2023-09-08T11:40:46,411 Found link https://files.pythonhosted.org/packages/d1/ed/c91ca8009f59baffc67130f5bf50b570da150e3948598a9701448be0a2cd/ngs_plumbing-0.7.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.1 2023-09-08T11:40:46,411 Found link https://files.pythonhosted.org/packages/30/66/55853e0ec4f30f1828c1cce74f4b122847854f4aa089bacc2dc60bdaaa0f/ngs_plumbing-0.7.2.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.2 2023-09-08T11:40:46,412 Found link https://files.pythonhosted.org/packages/21/29/e2b6f24977d0d3f0d20643187bc9b46c51b6ac59cedd01f62f00bf3f1e5d/ngs_plumbing-0.7.3.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.3 2023-09-08T11:40:46,413 Found link https://files.pythonhosted.org/packages/70/39/24252c9bc4dc000d52145a2d4e791fe8b2565a4f462020465554733ba4b7/ngs_plumbing-0.7.4.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.4 2023-09-08T11:40:46,413 Found link https://files.pythonhosted.org/packages/b4/00/605467be81bb6cae9f9ae5a5228946e6215c2446ad9e131bb7737bffb7a1/ngs_plumbing-0.7.5.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.5 2023-09-08T11:40:46,414 Found link https://files.pythonhosted.org/packages/e8/5a/79b30734c953d9b024b52cb6ff7009fea49b775ac143e93bb7b0e52b15d9/ngs_plumbing-0.8.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.0 2023-09-08T11:40:46,415 Found link https://files.pythonhosted.org/packages/aa/2f/ea679e884acfd3cf0766ef7e150dcb26e8e2f5bba415c0b7317a8e514377/ngs_plumbing-0.8.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.1 2023-09-08T11:40:46,415 Found link https://files.pythonhosted.org/packages/49/b4/c14b0f4bb8d2e2c475093d83d9b2a52743953d99aa3b91290ac0422d8dff/ngs_plumbing-0.8.2.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.2 2023-09-08T11:40:46,416 Found link https://files.pythonhosted.org/packages/89/1d/5ff21faba6fb2ec2775eab5a7555163a3c4865705ba4d05e8507a1ce4398/ngs_plumbing-0.9.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.9.0 2023-09-08T11:40:46,417 Found link https://files.pythonhosted.org/packages/9b/49/7ff35e46900140f2d5b696e7240d19ac90913a4d7c3c9b0d4bab5e707d84/ngs_plumbing-0.10.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.0 2023-09-08T11:40:46,418 Found link https://files.pythonhosted.org/packages/ee/af/35e8bcebff8702993f25a6987a414dda927929c9fe39fc92af1ae2ca7668/ngs_plumbing-0.10.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.1 2023-09-08T11:40:46,418 Found link https://files.pythonhosted.org/packages/29/8e/5c1c762bc712b1d3897b92078955e71216e56d64416c76bac99e0db8880a/ngs_plumbing-0.10.2.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.2 2023-09-08T11:40:46,419 Found link https://files.pythonhosted.org/packages/9e/40/62af4356ba0ad2cc37d5adeafde4974a47f8df09fa5ca79a64c5ef7bffbb/ngs_plumbing-0.11.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.11.0 2023-09-08T11:40:46,419 Found link https://files.pythonhosted.org/packages/ff/c5/92ca8129b4f963f8dfb1812a34ba0ebd285d7b5daa81896a368b64a896a5/ngs_plumbing-0.11.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.11.1 2023-09-08T11:40:46,420 Found link https://files.pythonhosted.org/packages/86/e6/e72c4b834909bc9c0412aab091fc05b0a091b9c6861a3a0d4a9edbbce822/ngs_plumbing-0.12.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.0 2023-09-08T11:40:46,420 Found link https://files.pythonhosted.org/packages/03/8a/9db89c482934552967bf5fef88f83d894cd98708c66571d7f0762cbac990/ngs_plumbing-0.12.2.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.2 2023-09-08T11:40:46,421 Found link https://files.pythonhosted.org/packages/03/0d/4c2d5c9ad4517970df0e2f6c8827d3c10f324883326a63c7e589042dbd17/ngs_plumbing-0.12.3.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.3 2023-09-08T11:40:46,422 Found link https://files.pythonhosted.org/packages/cf/95/92f0ce68a236e33d3b4be730d315d60c17fa1968d6b64a80c27001419363/ngs_plumbing-0.12.4.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.4 2023-09-08T11:40:46,422 Found link https://files.pythonhosted.org/packages/e8/69/8a0fba8c6a02c3e7a4cff43b6aa07e2942beae6eaeda732a05560dad0b8a/ngs_plumbing-0.13.0.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.13.0 2023-09-08T11:40:46,423 Found link https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz (from https://pypi.org/simple/ngs-plumbing/), version: 0.13.1 2023-09-08T11:40:46,424 Fetching project page and analyzing links: https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,424 Getting page https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T11:40:46,426 Found index url https://www.piwheels.org/simple/ 2023-09-08T11:40:48,443 Fetched page https://www.piwheels.org/simple/ngs-plumbing/ as text/html 2023-09-08T11:40:48,473 Skipping link: No binaries permitted for ngs-plumbing: 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https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.1-cp37-cp37m-linux_armv7l.whl#sha256=59a31efe3f92b6e3284520027aadae8a52db036aa2ff85b77df7a125e57c014a (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,508 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.1-cp37-cp37m-linux_armv6l.whl#sha256=59a31efe3f92b6e3284520027aadae8a52db036aa2ff85b77df7a125e57c014a (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,509 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.1-cp35-cp35m-linux_armv6l.whl#sha256=003a0d7b9263a019f2a570436ec9cc80ec1ec49c3be27366df494aaccf90247e (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,510 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.1-cp35-cp35m-linux_armv7l.whl#sha256=003a0d7b9263a019f2a570436ec9cc80ec1ec49c3be27366df494aaccf90247e (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,511 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.0-cp311-cp311-linux_armv7l.whl#sha256=496d808191c6caaea61b098098037eee726721ebbede8f0748c51c188d112b83 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,512 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.0-cp311-cp311-linux_armv6l.whl#sha256=496d808191c6caaea61b098098037eee726721ebbede8f0748c51c188d112b83 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,512 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.0-cp39-cp39-linux_armv7l.whl#sha256=cf0f84e93c37e45f16710db8ab2155eac9521fcd6c5a1ab04a1bcdf3e6181db4 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,513 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.0-cp39-cp39-linux_armv6l.whl#sha256=cf0f84e93c37e45f16710db8ab2155eac9521fcd6c5a1ab04a1bcdf3e6181db4 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,514 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.11.0-cp37-cp37m-linux_armv7l.whl#sha256=22e03ab06b064da0d834a64791b99cce4ee229fff085a72f4d3fba4ad28dd138 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,514 Skipping link: No binaries permitted for ngs-plumbing: 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https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp311-cp311-linux_armv7l.whl#sha256=3423c2c7f9f5d3505ccda1d223070089ededd194c3f5220a9cc25db3196a02e1 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,517 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp311-cp311-linux_armv6l.whl#sha256=3423c2c7f9f5d3505ccda1d223070089ededd194c3f5220a9cc25db3196a02e1 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,518 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp39-cp39-linux_armv7l.whl#sha256=023ec78da63d56760ec9dd11589bf98c1db83b3f8bc6d04e676b2b164c2d0529 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,519 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp39-cp39-linux_armv6l.whl#sha256=023ec78da63d56760ec9dd11589bf98c1db83b3f8bc6d04e676b2b164c2d0529 (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,520 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp37-cp37m-linux_armv6l.whl#sha256=ab0ae85a7b70a74a3ac35110b1b4f5bc6349c0da0e2f7c8775115864b328ed8b (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,521 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp37-cp37m-linux_armv7l.whl#sha256=ab0ae85a7b70a74a3ac35110b1b4f5bc6349c0da0e2f7c8775115864b328ed8b (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,522 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp35-cp35m-linux_armv7l.whl#sha256=f69b4c4dff49c2e1fd3f6df87126e5e3e9ad8df06fcec43351d5174558abceed (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,522 Skipping link: No binaries permitted for ngs-plumbing: https://www.piwheels.org/simple/ngs-plumbing/ngs_plumbing-0.10.2-cp35-cp35m-linux_armv6l.whl#sha256=f69b4c4dff49c2e1fd3f6df87126e5e3e9ad8df06fcec43351d5174558abceed (from https://www.piwheels.org/simple/ngs-plumbing/) 2023-09-08T11:40:48,523 Skipping link: not a file: https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T11:40:48,524 Skipping link: not a file: https://pypi.org/simple/ngs-plumbing/ 2023-09-08T11:40:48,554 Given no hashes to check 1 links for project 'ngs-plumbing': discarding no candidates 2023-09-08T11:40:48,572 Collecting ngs-plumbing==0.11.1 2023-09-08T11:40:48,574 Created temporary directory: /tmp/pip-unpack-qblpt7mm 2023-09-08T11:40:48,790 Downloading ngs_plumbing-0.11.1.tar.gz (315 kB) 2023-09-08T11:40:48,986 Added ngs-plumbing==0.11.1 from https://files.pythonhosted.org/packages/ff/c5/92ca8129b4f963f8dfb1812a34ba0ebd285d7b5daa81896a368b64a896a5/ngs_plumbing-0.11.1.tar.gz to build tracker '/tmp/pip-build-tracker-177idig_' 2023-09-08T11:40:48,988 Running setup.py (path:/tmp/pip-wheel-61944oqx/ngs-plumbing_787f9711fc734613840defdff701c5db/setup.py) egg_info for package ngs-plumbing 2023-09-08T11:40:48,989 Created temporary directory: /tmp/pip-pip-egg-info-_8xkw_7v 2023-09-08T11:40:48,989 Preparing metadata (setup.py): started 2023-09-08T11:40:48,991 Running command python setup.py egg_info 2023-09-08T11:40:50,019 running egg_info 2023-09-08T11:40:50,021 creating /tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info 2023-09-08T11:40:50,045 writing /tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/PKG-INFO 2023-09-08T11:40:50,048 writing dependency_links to /tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/dependency_links.txt 2023-09-08T11:40:50,050 writing entry points to /tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/entry_points.txt 2023-09-08T11:40:50,051 writing top-level names to /tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/top_level.txt 2023-09-08T11:40:50,053 writing manifest file '/tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T11:40:50,152 reading manifest file '/tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T11:40:50,154 reading manifest template 'MANIFEST.in' 2023-09-08T11:40:50,157 adding license file 'COPYING' 2023-09-08T11:40:50,160 writing manifest file '/tmp/pip-pip-egg-info-_8xkw_7v/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T11:40:50,162 Warning: The Python package 'h5py' cannot be imported. 2023-09-08T11:40:50,163 Without it, capabilities related to the XSQ format cannot be used. 2023-09-08T11:40:50,273 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T11:40:50,277 Source in /tmp/pip-wheel-61944oqx/ngs-plumbing_787f9711fc734613840defdff701c5db has version 0.11.1, which satisfies requirement ngs-plumbing==0.11.1 from https://files.pythonhosted.org/packages/ff/c5/92ca8129b4f963f8dfb1812a34ba0ebd285d7b5daa81896a368b64a896a5/ngs_plumbing-0.11.1.tar.gz 2023-09-08T11:40:50,278 Removed ngs-plumbing==0.11.1 from https://files.pythonhosted.org/packages/ff/c5/92ca8129b4f963f8dfb1812a34ba0ebd285d7b5daa81896a368b64a896a5/ngs_plumbing-0.11.1.tar.gz from build tracker '/tmp/pip-build-tracker-177idig_' 2023-09-08T11:40:50,282 Created temporary directory: /tmp/pip-unpack-9difg91b 2023-09-08T11:40:50,283 Created temporary directory: /tmp/pip-unpack-tnxamtx8 2023-09-08T11:40:50,285 Building wheels for collected packages: ngs-plumbing 2023-09-08T11:40:50,289 Created temporary directory: /tmp/pip-wheel-a5of1mgc 2023-09-08T11:40:50,290 Building wheel for ngs-plumbing (setup.py): started 2023-09-08T11:40:50,291 Destination directory: /tmp/pip-wheel-a5of1mgc 2023-09-08T11:40:50,291 Running command python setup.py bdist_wheel 2023-09-08T11:40:51,270 running bdist_wheel 2023-09-08T11:40:51,362 running build 2023-09-08T11:40:51,362 running build_py 2023-09-08T11:40:51,389 creating build 2023-09-08T11:40:51,390 creating build/lib.linux-armv7l-cpython-311 2023-09-08T11:40:51,390 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,392 copying src/ngsp_string.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,393 copying src/__init__.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,395 copying src/dna_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,396 copying src/dnaqual_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,398 copying src/_libdnaqual_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,400 copying src/xsq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,401 copying src/kmers.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,403 copying src/colorspace.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,405 copying src/_libxsq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,406 copying src/_libdna_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,408 copying src/intervals.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,410 copying src/report.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,412 copying src/fastq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,414 copying src/tests.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,415 copying src/dnaqual.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,417 copying src/xsq.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,419 copying src/tapir.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,421 copying src/scons.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,423 copying src/intervals_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,424 copying src/ngsp_string_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,426 copying src/dna.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,428 copying src/fastq.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,430 copying src/fasta_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,431 copying src/fasta.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,433 copying src/xsqconvert.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,435 copying src/kmers_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T11:40:51,438 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data 2023-09-08T11:40:51,438 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run 2023-09-08T11:40:51,439 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X 2023-09-08T11:40:51,440 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result 2023-09-08T11:40:51,441 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T11:40:51,442 copying src/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T11:40:51,449 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html 2023-09-08T11:40:51,450 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T11:40:51,451 copying src/data/html/templates/xsqreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T11:40:51,453 copying src/data/html/templates/xsqlibreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T11:40:51,455 copying src/data/html/templates/fqlibreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T11:40:51,457 copying src/data/html/readqual.js -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html 2023-09-08T11:40:51,460 running build_ext 2023-09-08T11:40:51,962 building 'ngs_plumbing._libxsq' extension 2023-09-08T11:40:51,963 creating build/temp.linux-armv7l-cpython-311 2023-09-08T11:40:51,964 creating build/temp.linux-armv7l-cpython-311/src 2023-09-08T11:40:51,964 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I/usr/include/python3.11 -c src/_libxsq.c -o build/temp.linux-armv7l-cpython-311/src/_libxsq.o -Wall -O3 -march=native -funroll-loops 2023-09-08T11:40:52,329 src/_libxsq.c: In function ‘PyInit__libxsq’: 2023-09-08T11:40:52,330 src/_libxsq.c:352:17: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2023-09-08T11:40:52,332 352 | PyObject *m, *d; 2023-09-08T11:40:52,334 | ^ 2023-09-08T11:40:52,975 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/_libxsq.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libxsq.cpython-311-arm-linux-gnueabihf.so -g 2023-09-08T11:40:53,071 building 'ngs_plumbing._libdna' extension 2023-09-08T11:40:53,072 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I/usr/include/python3.11 -c src/_libdna.c -o build/temp.linux-armv7l-cpython-311/src/_libdna.o -Wall -O3 -march=native -funroll-loops 2023-09-08T11:40:53,422 src/_libdna.c: In function ‘bytes_to_bit2’: 2023-09-08T11:40:53,423 src/_libdna.c:111:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-08T11:40:53,423 111 | if (bitpos == -2) { 2023-09-08T11:40:53,424 | ^~ 2023-09-08T11:40:55,992 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/_libdna.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdna.cpython-311-arm-linux-gnueabihf.so -g 2023-09-08T11:40:56,086 building 'ngs_plumbing._libdnaqual' extension 2023-09-08T11:40:56,086 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I/usr/include/python3.11 -c src/_libdnaqual.c -o build/temp.linux-armv7l-cpython-311/src/_libdnaqual.o -Wall -O3 -march=native -funroll-loops 2023-09-08T11:40:56,647 arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/_libdnaqual.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdnaqual.cpython-311-arm-linux-gnueabihf.so -g 2023-09-08T11:40:56,764 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-08T11:40:56,765 !! 2023-09-08T11:40:56,766 ******************************************************************************** 2023-09-08T11:40:56,767 Please avoid running ``setup.py`` directly. 2023-09-08T11:40:56,767 Instead, use pypa/build, pypa/installer or other 2023-09-08T11:40:56,768 standards-based tools. 2023-09-08T11:40:56,768 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-08T11:40:56,769 ******************************************************************************** 2023-09-08T11:40:56,770 !! 2023-09-08T11:40:56,770 self.initialize_options() 2023-09-08T11:40:56,793 installing to build/bdist.linux-armv7l/wheel 2023-09-08T11:40:56,793 running install 2023-09-08T11:40:56,818 running install_lib 2023-09-08T11:40:56,842 creating build/bdist.linux-armv7l 2023-09-08T11:40:56,842 creating build/bdist.linux-armv7l/wheel 2023-09-08T11:40:56,844 creating build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,845 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libxsq.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,848 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/ngsp_string.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,850 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/__init__.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,851 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data 2023-09-08T11:40:56,853 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run 2023-09-08T11:40:56,854 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X 2023-09-08T11:40:56,855 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result 2023-09-08T11:40:56,857 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T11:40:56,858 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T11:40:56,865 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html 2023-09-08T11:40:56,867 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T11:40:56,868 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/xsqreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T11:40:56,870 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/xsqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T11:40:56,872 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/fqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T11:40:56,873 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/readqual.js -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html 2023-09-08T11:40:56,875 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,877 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdnaqual.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,879 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,881 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,883 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,885 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/kmers.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,887 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/colorspace.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,889 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libxsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,890 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,893 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/intervals.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,895 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/report.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,896 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fastq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,898 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/tests.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,899 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dnaqual.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,901 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,904 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/tapir.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,905 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/scons.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,907 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/intervals_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,909 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/ngsp_string_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,911 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dna.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,913 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fastq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,915 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fasta_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,917 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fasta.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,919 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsqconvert.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,921 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdna.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,925 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/kmers_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T11:40:56,927 running install_headers 2023-09-08T11:40:56,951 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.11.1.data 2023-09-08T11:40:56,952 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.11.1.data/headers 2023-09-08T11:40:56,953 copying src/_libdna.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.11.1.data/headers 2023-09-08T11:40:56,954 running install_egg_info 2023-09-08T11:40:57,014 running egg_info 2023-09-08T11:40:57,037 writing ngs_plumbing.egg-info/PKG-INFO 2023-09-08T11:40:57,040 writing dependency_links to ngs_plumbing.egg-info/dependency_links.txt 2023-09-08T11:40:57,041 writing entry points to ngs_plumbing.egg-info/entry_points.txt 2023-09-08T11:40:57,043 writing top-level names to ngs_plumbing.egg-info/top_level.txt 2023-09-08T11:40:57,075 reading manifest file 'ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T11:40:57,079 reading manifest template 'MANIFEST.in' 2023-09-08T11:40:57,083 adding license file 'COPYING' 2023-09-08T11:40:57,086 writing manifest file 'ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T11:40:57,088 Copying ngs_plumbing.egg-info to build/bdist.linux-armv7l/wheel/ngs_plumbing-0.11.1-py3.11.egg-info 2023-09-08T11:40:57,098 running install_scripts 2023-09-08T11:40:57,153 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.11.1.dist-info/WHEEL 2023-09-08T11:40:57,155 creating '/tmp/pip-wheel-a5of1mgc/ngs_plumbing-0.11.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-08T11:40:57,159 adding 'ngs_plumbing/__init__.py' 2023-09-08T11:40:57,183 adding 'ngs_plumbing/_libdna.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T11:40:57,187 adding 'ngs_plumbing/_libdna_test.py' 2023-09-08T11:40:57,192 adding 'ngs_plumbing/_libdnaqual.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T11:40:57,194 adding 'ngs_plumbing/_libdnaqual_test.py' 2023-09-08T11:40:57,205 adding 'ngs_plumbing/_libxsq.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T11:40:57,207 adding 'ngs_plumbing/_libxsq_test.py' 2023-09-08T11:40:57,210 adding 'ngs_plumbing/colorspace.py' 2023-09-08T11:40:57,212 adding 'ngs_plumbing/dna.py' 2023-09-08T11:40:57,214 adding 'ngs_plumbing/dna_test.py' 2023-09-08T11:40:57,215 adding 'ngs_plumbing/dnaqual.py' 2023-09-08T11:40:57,217 adding 'ngs_plumbing/dnaqual_test.py' 2023-09-08T11:40:57,219 adding 'ngs_plumbing/fasta.py' 2023-09-08T11:40:57,221 adding 'ngs_plumbing/fasta_test.py' 2023-09-08T11:40:57,223 adding 'ngs_plumbing/fastq.py' 2023-09-08T11:40:57,224 adding 'ngs_plumbing/fastq_test.py' 2023-09-08T11:40:57,226 adding 'ngs_plumbing/intervals.py' 2023-09-08T11:40:57,228 adding 'ngs_plumbing/intervals_test.py' 2023-09-08T11:40:57,229 adding 'ngs_plumbing/kmers.py' 2023-09-08T11:40:57,231 adding 'ngs_plumbing/kmers_test.py' 2023-09-08T11:40:57,233 adding 'ngs_plumbing/ngsp_string.py' 2023-09-08T11:40:57,234 adding 'ngs_plumbing/ngsp_string_test.py' 2023-09-08T11:40:57,236 adding 'ngs_plumbing/report.py' 2023-09-08T11:40:57,238 adding 'ngs_plumbing/scons.py' 2023-09-08T11:40:57,239 adding 'ngs_plumbing/tapir.py' 2023-09-08T11:40:57,241 adding 'ngs_plumbing/tests.py' 2023-09-08T11:40:57,245 adding 'ngs_plumbing/xsq.py' 2023-09-08T11:40:57,246 adding 'ngs_plumbing/xsq_test.py' 2023-09-08T11:40:57,248 adding 'ngs_plumbing/xsqconvert.py' 2023-09-08T11:40:57,250 adding 'ngs_plumbing/data/html/readqual.js' 2023-09-08T11:40:57,252 adding 'ngs_plumbing/data/html/templates/fqlibreport.html' 2023-09-08T11:40:57,253 adding 'ngs_plumbing/data/html/templates/xsqlibreport.html' 2023-09-08T11:40:57,254 adding 'ngs_plumbing/data/html/templates/xsqreport.html' 2023-09-08T11:40:57,294 adding 'ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq' 2023-09-08T11:40:57,299 adding 'ngs_plumbing-0.11.1.data/headers/_libdna.h' 2023-09-08T11:40:57,306 adding 'ngs_plumbing-0.11.1.dist-info/COPYING' 2023-09-08T11:40:57,307 adding 'ngs_plumbing-0.11.1.dist-info/METADATA' 2023-09-08T11:40:57,308 adding 'ngs_plumbing-0.11.1.dist-info/WHEEL' 2023-09-08T11:40:57,309 adding 'ngs_plumbing-0.11.1.dist-info/entry_points.txt' 2023-09-08T11:40:57,310 adding 'ngs_plumbing-0.11.1.dist-info/top_level.txt' 2023-09-08T11:40:57,311 adding 'ngs_plumbing-0.11.1.dist-info/RECORD' 2023-09-08T11:40:57,316 removing build/bdist.linux-armv7l/wheel 2023-09-08T11:40:57,328 Warning: The Python package 'h5py' cannot be imported. 2023-09-08T11:40:57,329 Without it, capabilities related to the XSQ format cannot be used. 2023-09-08T11:40:57,476 Building wheel for ngs-plumbing (setup.py): finished with status 'done' 2023-09-08T11:40:57,483 Created wheel for ngs-plumbing: filename=ngs_plumbing-0.11.1-cp311-cp311-linux_armv7l.whl size=378895 sha256=6149942e92ec7dfcd454c67fdaa389d93457e06e0fd7ddd2e96bc6d42251091d 2023-09-08T11:40:57,484 Stored in directory: /tmp/pip-ephem-wheel-cache-35tkpf0_/wheels/25/30/8e/a3cf39e7b7177d07dd04c218fe2b2bc8e6fa2773f7383ce76c 2023-09-08T11:40:57,496 Successfully built ngs-plumbing 2023-09-08T11:40:57,508 Removed build tracker: '/tmp/pip-build-tracker-177idig_'