2023-09-08T15:21:05,696 Created temporary directory: /tmp/pip-build-tracker-ylnyv6mq 2023-09-08T15:21:05,697 Initialized build tracking at /tmp/pip-build-tracker-ylnyv6mq 2023-09-08T15:21:05,698 Created build tracker: /tmp/pip-build-tracker-ylnyv6mq 2023-09-08T15:21:05,698 Entered build tracker: /tmp/pip-build-tracker-ylnyv6mq 2023-09-08T15:21:05,699 Created temporary directory: /tmp/pip-wheel-bjgiyt9b 2023-09-08T15:21:05,702 Created temporary directory: /tmp/pip-ephem-wheel-cache-7kbpm57g 2023-09-08T15:21:05,723 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T15:21:05,727 2 location(s) to search for versions of ngs-plumbing: 2023-09-08T15:21:05,727 * https://pypi.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,727 * https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,728 Fetching project page and analyzing links: https://pypi.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,729 Getting page https://pypi.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,730 Found index url https://pypi.org/simple/ 2023-09-08T15:21:05,877 Fetched page https://pypi.org/simple/ngs-plumbing/ as application/vnd.pypi.simple.v1+json 2023-09-08T15:21:05,883 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 2023-09-08T15:21:05,884 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 2023-09-08T15:21:05,885 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 2023-09-08T15:21:05,885 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 2023-09-08T15:21:05,886 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 2023-09-08T15:21:05,887 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 2023-09-08T15:21:05,888 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 2023-09-08T15:21:05,888 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 2023-09-08T15:21:05,889 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 2023-09-08T15:21:05,890 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 2023-09-08T15:21:05,891 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 2023-09-08T15:21:05,892 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 2023-09-08T15:21:05,892 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 2023-09-08T15:21:05,893 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 2023-09-08T15:21:05,894 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 2023-09-08T15:21:05,895 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 2023-09-08T15:21:05,895 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 2023-09-08T15:21:05,896 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 2023-09-08T15:21:05,896 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 2023-09-08T15:21:05,897 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 2023-09-08T15:21:05,897 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 2023-09-08T15:21:05,898 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 2023-09-08T15:21:05,898 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 2023-09-08T15:21:05,899 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 2023-09-08T15:21:05,899 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 2023-09-08T15:21:05,900 Fetching project page and analyzing links: https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,901 Getting page https://www.piwheels.org/simple/ngs-plumbing/ 2023-09-08T15:21:05,902 Found index url https://www.piwheels.org/simple/ 2023-09-08T15:21:06,594 Fetched page https://www.piwheels.org/simple/ngs-plumbing/ as text/html 2023-09-08T15:21:06,629 Skipping link: No binaries permitted for ngs-plumbing: 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2023-09-08T15:21:06,709 Given no hashes to check 1 links for project 'ngs-plumbing': discarding no candidates 2023-09-08T15:21:06,727 Collecting ngs-plumbing==0.13.1 2023-09-08T15:21:06,729 Created temporary directory: /tmp/pip-unpack-evmytrvu 2023-09-08T15:21:10,471 Downloading ngs_plumbing-0.13.1.tar.gz (341 kB) 2023-09-08T15:21:10,716 Added ngs-plumbing==0.13.1 from https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz to build tracker '/tmp/pip-build-tracker-ylnyv6mq' 2023-09-08T15:21:10,718 Running setup.py (path:/tmp/pip-wheel-bjgiyt9b/ngs-plumbing_9d503da5881e4abf9fb4be85b9c2412e/setup.py) egg_info for package ngs-plumbing 2023-09-08T15:21:10,719 Created temporary directory: /tmp/pip-pip-egg-info-pacd_zg6 2023-09-08T15:21:10,719 Preparing metadata (setup.py): started 2023-09-08T15:21:10,720 Running command python setup.py egg_info 2023-09-08T15:21:11,743 running egg_info 2023-09-08T15:21:11,745 creating /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info 2023-09-08T15:21:11,770 writing /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/PKG-INFO 2023-09-08T15:21:11,773 writing dependency_links to /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/dependency_links.txt 2023-09-08T15:21:11,775 writing entry points to /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/entry_points.txt 2023-09-08T15:21:11,776 writing requirements to /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/requires.txt 2023-09-08T15:21:11,777 writing top-level names to /tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/top_level.txt 2023-09-08T15:21:11,779 writing manifest file '/tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T15:21:11,883 reading manifest file '/tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T15:21:11,884 reading manifest template 'MANIFEST.in' 2023-09-08T15:21:11,899 adding license file 'COPYING' 2023-09-08T15:21:11,902 writing manifest file '/tmp/pip-pip-egg-info-pacd_zg6/ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T15:21:11,905 Warning: The Python package 'h5py' cannot be imported. 2023-09-08T15:21:11,906 Without it, capabilities related to the XSQ format cannot be used. 2023-09-08T15:21:12,015 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T15:21:12,019 Source in /tmp/pip-wheel-bjgiyt9b/ngs-plumbing_9d503da5881e4abf9fb4be85b9c2412e has version 0.13.1, which satisfies requirement ngs-plumbing==0.13.1 from https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz 2023-09-08T15:21:12,020 Removed ngs-plumbing==0.13.1 from https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz from build tracker '/tmp/pip-build-tracker-ylnyv6mq' 2023-09-08T15:21:12,024 Created temporary directory: /tmp/pip-unpack-6ggyvba7 2023-09-08T15:21:12,025 Created temporary directory: /tmp/pip-unpack-tybxooem 2023-09-08T15:21:12,031 Building wheels for collected packages: ngs-plumbing 2023-09-08T15:21:12,036 Created temporary directory: /tmp/pip-wheel-pwd7m8gu 2023-09-08T15:21:12,036 Building wheel for ngs-plumbing (setup.py): started 2023-09-08T15:21:12,038 Destination directory: /tmp/pip-wheel-pwd7m8gu 2023-09-08T15:21:12,038 Running command python setup.py bdist_wheel 2023-09-08T15:21:13,254 running bdist_wheel 2023-09-08T15:21:13,349 running build 2023-09-08T15:21:13,349 running build_py 2023-09-08T15:21:13,377 creating build 2023-09-08T15:21:13,377 creating build/lib.linux-armv7l-cpython-311 2023-09-08T15:21:13,378 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,380 copying src/colorspace.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,382 copying src/ngsp_string_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,384 copying src/intervals_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,386 copying src/kmers_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,388 copying src/_libxsq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,390 copying src/dna.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,392 copying src/_libdna_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,395 copying src/sampling.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,397 copying src/dnaqual.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,399 copying src/tapir.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,400 copying src/parsing_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,402 copying src/sampling_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,404 copying src/tests.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,406 copying src/_libdnaqual_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,407 copying src/report.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,409 copying src/xsq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,411 copying src/intervals.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,413 copying src/fastq.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,415 copying src/fasta.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,417 copying src/parsing.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,419 copying src/fasta_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,420 copying src/ngsp_string.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,422 copying src/kmers.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,424 copying src/dnaqual_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,426 copying src/fastq_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,427 copying src/bam.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,429 copying src/xsqconvert.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,431 copying src/xsq.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,434 copying src/__init__.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,436 copying src/scons.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,438 copying src/dna_test.py -> build/lib.linux-armv7l-cpython-311/ngs_plumbing 2023-09-08T15:21:13,441 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data 2023-09-08T15:21:13,442 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run 2023-09-08T15:21:13,442 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X 2023-09-08T15:21:13,443 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result 2023-09-08T15:21:13,444 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T15:21:13,445 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 2023-09-08T15:21:13,453 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html 2023-09-08T15:21:13,453 creating build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T15:21:13,454 copying src/data/html/templates/fqlibreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T15:21:13,456 copying src/data/html/templates/xsqlibreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T15:21:13,458 copying src/data/html/templates/xsqreport.html -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates 2023-09-08T15:21:13,460 copying src/data/html/readqual.js -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html 2023-09-08T15:21:13,462 copying src/data/reads.fq -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data 2023-09-08T15:21:13,465 copying src/data/reads.fq.gz -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data 2023-09-08T15:21:13,468 copying src/data/reads.fq.bz2 -> build/lib.linux-armv7l-cpython-311/ngs_plumbing/data 2023-09-08T15:21:13,471 running build_ext 2023-09-08T15:21:13,982 building 'ngs_plumbing._libxsq' extension 2023-09-08T15:21:13,983 creating build/temp.linux-armv7l-cpython-311 2023-09-08T15:21:13,983 creating build/temp.linux-armv7l-cpython-311/src 2023-09-08T15:21:13,985 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 -funroll-loops 2023-09-08T15:21:14,364 src/_libxsq.c: In function ‘PyInit__libxsq’: 2023-09-08T15:21:14,365 src/_libxsq.c:352:17: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 2023-09-08T15:21:14,366 352 | PyObject *m, *d; 2023-09-08T15:21:14,368 | ^ 2023-09-08T15:21:14,977 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 2023-09-08T15:21:15,072 building 'ngs_plumbing._libdna' extension 2023-09-08T15:21:15,072 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 -funroll-loops 2023-09-08T15:21:15,435 src/_libdna.c: In function ‘bytes_to_bit2’: 2023-09-08T15:21:15,436 src/_libdna.c:114:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-09-08T15:21:15,437 114 | if (bitpos == -2) { 2023-09-08T15:21:15,438 | ^~ 2023-09-08T15:21:17,113 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 2023-09-08T15:21:17,214 building 'ngs_plumbing._libdnaqual' extension 2023-09-08T15:21:17,215 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 -funroll-loops 2023-09-08T15:21:17,678 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 2023-09-08T15:21:17,795 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-08T15:21:17,796 !! 2023-09-08T15:21:17,797 ******************************************************************************** 2023-09-08T15:21:17,798 Please avoid running ``setup.py`` directly. 2023-09-08T15:21:17,799 Instead, use pypa/build, pypa/installer or other 2023-09-08T15:21:17,799 standards-based tools. 2023-09-08T15:21:17,800 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-08T15:21:17,801 ******************************************************************************** 2023-09-08T15:21:17,802 !! 2023-09-08T15:21:17,802 self.initialize_options() 2023-09-08T15:21:17,824 installing to build/bdist.linux-armv7l/wheel 2023-09-08T15:21:17,825 running install 2023-09-08T15:21:17,848 running install_lib 2023-09-08T15:21:17,873 creating build/bdist.linux-armv7l 2023-09-08T15:21:17,873 creating build/bdist.linux-armv7l/wheel 2023-09-08T15:21:17,875 creating build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,876 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/colorspace.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,879 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data 2023-09-08T15:21:17,880 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/reads.fq.gz -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data 2023-09-08T15:21:17,882 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/reads.fq.bz2 -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data 2023-09-08T15:21:17,885 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run 2023-09-08T15:21:17,886 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X 2023-09-08T15:21:17,887 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result 2023-09-08T15:21:17,889 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1 2023-09-08T15:21:17,890 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 2023-09-08T15:21:17,898 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/reads.fq -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data 2023-09-08T15:21:17,901 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html 2023-09-08T15:21:17,902 creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T15:21:17,903 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/fqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T15:21:17,905 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/xsqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T15:21:17,907 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/templates/xsqreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates 2023-09-08T15:21:17,909 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/data/html/readqual.js -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html 2023-09-08T15:21:17,911 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/ngsp_string_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,912 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/intervals_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,914 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/kmers_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,916 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libxsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,918 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdnaqual.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,920 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dna.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,923 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libxsq.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,926 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,928 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/sampling.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,930 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dnaqual.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,931 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/tapir.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,933 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/parsing_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,935 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdna.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,938 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/sampling_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,940 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/tests.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,942 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/_libdnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,944 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/report.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,946 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,947 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/intervals.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,949 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fastq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,952 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fasta.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,954 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/parsing.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,956 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fasta_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,958 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/ngsp_string.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,959 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/kmers.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,961 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,963 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/fastq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,965 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/bam.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,967 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsqconvert.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,969 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/xsq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,971 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/__init__.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,973 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/scons.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,975 copying build/lib.linux-armv7l-cpython-311/ngs_plumbing/dna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing 2023-09-08T15:21:17,977 running install_headers 2023-09-08T15:21:18,002 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data 2023-09-08T15:21:18,002 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers 2023-09-08T15:21:18,003 copying src/_libdna.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers 2023-09-08T15:21:18,005 copying src/bitpack.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers 2023-09-08T15:21:18,007 running install_egg_info 2023-09-08T15:21:18,067 running egg_info 2023-09-08T15:21:18,093 writing ngs_plumbing.egg-info/PKG-INFO 2023-09-08T15:21:18,096 writing dependency_links to ngs_plumbing.egg-info/dependency_links.txt 2023-09-08T15:21:18,098 writing entry points to ngs_plumbing.egg-info/entry_points.txt 2023-09-08T15:21:18,099 writing requirements to ngs_plumbing.egg-info/requires.txt 2023-09-08T15:21:18,100 writing top-level names to ngs_plumbing.egg-info/top_level.txt 2023-09-08T15:21:18,135 reading manifest file 'ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T15:21:18,139 reading manifest template 'MANIFEST.in' 2023-09-08T15:21:18,142 adding license file 'COPYING' 2023-09-08T15:21:18,146 writing manifest file 'ngs_plumbing.egg-info/SOURCES.txt' 2023-09-08T15:21:18,147 Copying ngs_plumbing.egg-info to build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1-py3.11.egg-info 2023-09-08T15:21:18,159 running install_scripts 2023-09-08T15:21:18,212 creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.dist-info/WHEEL 2023-09-08T15:21:18,214 creating '/tmp/pip-wheel-pwd7m8gu/ngs_plumbing-0.13.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-08T15:21:18,217 adding 'ngs_plumbing/__init__.py' 2023-09-08T15:21:18,230 adding 'ngs_plumbing/_libdna.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T15:21:18,233 adding 'ngs_plumbing/_libdna_test.py' 2023-09-08T15:21:18,236 adding 'ngs_plumbing/_libdnaqual.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T15:21:18,238 adding 'ngs_plumbing/_libdnaqual_test.py' 2023-09-08T15:21:18,245 adding 'ngs_plumbing/_libxsq.cpython-311-arm-linux-gnueabihf.so' 2023-09-08T15:21:18,247 adding 'ngs_plumbing/_libxsq_test.py' 2023-09-08T15:21:18,249 adding 'ngs_plumbing/bam.py' 2023-09-08T15:21:18,250 adding 'ngs_plumbing/colorspace.py' 2023-09-08T15:21:18,252 adding 'ngs_plumbing/dna.py' 2023-09-08T15:21:18,253 adding 'ngs_plumbing/dna_test.py' 2023-09-08T15:21:18,255 adding 'ngs_plumbing/dnaqual.py' 2023-09-08T15:21:18,256 adding 'ngs_plumbing/dnaqual_test.py' 2023-09-08T15:21:18,258 adding 'ngs_plumbing/fasta.py' 2023-09-08T15:21:18,259 adding 'ngs_plumbing/fasta_test.py' 2023-09-08T15:21:18,261 adding 'ngs_plumbing/fastq.py' 2023-09-08T15:21:18,262 adding 'ngs_plumbing/fastq_test.py' 2023-09-08T15:21:18,264 adding 'ngs_plumbing/intervals.py' 2023-09-08T15:21:18,265 adding 'ngs_plumbing/intervals_test.py' 2023-09-08T15:21:18,267 adding 'ngs_plumbing/kmers.py' 2023-09-08T15:21:18,268 adding 'ngs_plumbing/kmers_test.py' 2023-09-08T15:21:18,270 adding 'ngs_plumbing/ngsp_string.py' 2023-09-08T15:21:18,271 adding 'ngs_plumbing/ngsp_string_test.py' 2023-09-08T15:21:18,272 adding 'ngs_plumbing/parsing.py' 2023-09-08T15:21:18,274 adding 'ngs_plumbing/parsing_test.py' 2023-09-08T15:21:18,275 adding 'ngs_plumbing/report.py' 2023-09-08T15:21:18,277 adding 'ngs_plumbing/sampling.py' 2023-09-08T15:21:18,278 adding 'ngs_plumbing/sampling_test.py' 2023-09-08T15:21:18,280 adding 'ngs_plumbing/scons.py' 2023-09-08T15:21:18,282 adding 'ngs_plumbing/tapir.py' 2023-09-08T15:21:18,283 adding 'ngs_plumbing/tests.py' 2023-09-08T15:21:18,287 adding 'ngs_plumbing/xsq.py' 2023-09-08T15:21:18,288 adding 'ngs_plumbing/xsq_test.py' 2023-09-08T15:21:18,290 adding 'ngs_plumbing/xsqconvert.py' 2023-09-08T15:21:18,297 adding 'ngs_plumbing/data/reads.fq' 2023-09-08T15:21:18,298 adding 'ngs_plumbing/data/reads.fq.bz2' 2023-09-08T15:21:18,300 adding 'ngs_plumbing/data/reads.fq.gz' 2023-09-08T15:21:18,302 adding 'ngs_plumbing/data/html/readqual.js' 2023-09-08T15:21:18,304 adding 'ngs_plumbing/data/html/templates/fqlibreport.html' 2023-09-08T15:21:18,306 adding 'ngs_plumbing/data/html/templates/xsqlibreport.html' 2023-09-08T15:21:18,307 adding 'ngs_plumbing/data/html/templates/xsqreport.html' 2023-09-08T15:21:18,347 adding 'ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq' 2023-09-08T15:21:18,352 adding 'ngs_plumbing-0.13.1.data/headers/_libdna.h' 2023-09-08T15:21:18,353 adding 'ngs_plumbing-0.13.1.data/headers/bitpack.h' 2023-09-08T15:21:18,359 adding 'ngs_plumbing-0.13.1.dist-info/COPYING' 2023-09-08T15:21:18,361 adding 'ngs_plumbing-0.13.1.dist-info/METADATA' 2023-09-08T15:21:18,362 adding 'ngs_plumbing-0.13.1.dist-info/WHEEL' 2023-09-08T15:21:18,362 adding 'ngs_plumbing-0.13.1.dist-info/entry_points.txt' 2023-09-08T15:21:18,363 adding 'ngs_plumbing-0.13.1.dist-info/top_level.txt' 2023-09-08T15:21:18,365 adding 'ngs_plumbing-0.13.1.dist-info/RECORD' 2023-09-08T15:21:18,371 removing build/bdist.linux-armv7l/wheel 2023-09-08T15:21:18,386 Warning: The Python package 'h5py' cannot be imported. 2023-09-08T15:21:18,387 Without it, capabilities related to the XSQ format cannot be used. 2023-09-08T15:21:18,535 Building wheel for ngs-plumbing (setup.py): finished with status 'done' 2023-09-08T15:21:18,542 Created wheel for ngs-plumbing: filename=ngs_plumbing-0.13.1-cp311-cp311-linux_armv7l.whl size=401407 sha256=f3bd83163d3e35b32fe9dde51672ee0669e5160e874a81b62807b903a7be690b 2023-09-08T15:21:18,544 Stored in directory: /tmp/pip-ephem-wheel-cache-7kbpm57g/wheels/29/6e/3d/d7b0970688ec1c423821888ecfb6596dfe593ef191a68d5b41 2023-09-08T15:21:18,555 Successfully built ngs-plumbing 2023-09-08T15:21:18,569 Removed build tracker: '/tmp/pip-build-tracker-ylnyv6mq'