2021-07-09T16:53:05,836 Created temporary directory: /tmp/pip-ephem-wheel-cache-krt615ta
2021-07-09T16:53:05,839 Created temporary directory: /tmp/pip-req-tracker-xbps7kls
2021-07-09T16:53:05,840 Initialized build tracking at /tmp/pip-req-tracker-xbps7kls
2021-07-09T16:53:05,840 Created build tracker: /tmp/pip-req-tracker-xbps7kls
2021-07-09T16:53:05,840 Entered build tracker: /tmp/pip-req-tracker-xbps7kls
2021-07-09T16:53:05,841 Created temporary directory: /tmp/pip-wheel-_go2p00x
2021-07-09T16:53:05,877 1 location(s) to search for versions of ngs-plumbing:
2021-07-09T16:53:05,877 * https://pypi.org/simple/ngs-plumbing/
2021-07-09T16:53:05,878 Fetching project page and analyzing links: https://pypi.org/simple/ngs-plumbing/
2021-07-09T16:53:05,878 Getting page https://pypi.org/simple/ngs-plumbing/
2021-07-09T16:53:05,880 Found index url https://pypi.org/simple
2021-07-09T16:53:05,984   Found link https://files.pythonhosted.org/packages/e2/b7/896169889e1a705a2db7fc237a9e6f4b6c39b9dd94d8671667cc3bc652d7/ngs_plumbing-0.5.1.tar.gz#sha256=5d714d7b7084110838e23a6b6a9c86712b8b3cb799f900f71d2a77b2d9099489 (from https://pypi.org/simple/ngs-plumbing/), version: 0.5.1
2021-07-09T16:53:05,985   Found link https://files.pythonhosted.org/packages/17/3d/83ed952f2731054d91fcd64c58748c339c597d552ffec03922be97101240/ngs_plumbing-0.6.1.tar.gz#sha256=032f716bc46ece81b40df94000decbf6a40c2a2db50dc3b777cd22a703892112 (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.1
2021-07-09T16:53:05,985   Found link https://files.pythonhosted.org/packages/ac/f5/0d958a7591e7dfc436298e2d5902cca67e2d45634fa0d699153b1098195d/ngs_plumbing-0.6.2.tar.gz#sha256=ff8abf8c8d3d2143b3b6dd9a0be376231b8d43b98b84b72f3e356fa23488cae7 (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.2
2021-07-09T16:53:05,986   Found link https://files.pythonhosted.org/packages/a1/3e/24003dd7ed3790f9f9f89535a0ceea78c5f4d462986bf21fb30cd354bd58/ngs_plumbing-0.6.3.tar.gz#sha256=3b2e19edf320d811e73f287c26a98f7f5d1c3768b846e2f6d5d460648007b706 (from https://pypi.org/simple/ngs-plumbing/), version: 0.6.3
2021-07-09T16:53:05,986   Found link https://files.pythonhosted.org/packages/2e/52/d94a726f19fe9269ff371b20255c4de31de8c5c02cf59532813f4a18397a/ngs_plumbing-0.7.0.tar.gz#sha256=023979e150cbda59712f78dc9b0f25ddd235e424120ed62e8ff56ddb8de3732e (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.0
2021-07-09T16:53:05,987   Found link https://files.pythonhosted.org/packages/d1/ed/c91ca8009f59baffc67130f5bf50b570da150e3948598a9701448be0a2cd/ngs_plumbing-0.7.1.tar.gz#sha256=2408a41040a32967df42a909aab0c51fe7edb2e8415f10ab1afa9d338338a335 (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.1
2021-07-09T16:53:05,987   Found link https://files.pythonhosted.org/packages/30/66/55853e0ec4f30f1828c1cce74f4b122847854f4aa089bacc2dc60bdaaa0f/ngs_plumbing-0.7.2.tar.gz#sha256=06f792780c251952d1b49c2f9fa94104183d80406aa22f624af2d8671459efa4 (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.2
2021-07-09T16:53:05,987   Found link https://files.pythonhosted.org/packages/21/29/e2b6f24977d0d3f0d20643187bc9b46c51b6ac59cedd01f62f00bf3f1e5d/ngs_plumbing-0.7.3.tar.gz#sha256=722645abdf4e90991b1abfab60ad7efed0dd3730abb235c03dc72fbd29d0aa59 (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.3
2021-07-09T16:53:05,988   Found link https://files.pythonhosted.org/packages/70/39/24252c9bc4dc000d52145a2d4e791fe8b2565a4f462020465554733ba4b7/ngs_plumbing-0.7.4.tar.gz#sha256=8a8a5a5cc8f5541bfb4aaaf0d1c328d7e3125e0ad4fb0769e260ae47385b49b9 (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.4
2021-07-09T16:53:05,988   Found link https://files.pythonhosted.org/packages/b4/00/605467be81bb6cae9f9ae5a5228946e6215c2446ad9e131bb7737bffb7a1/ngs_plumbing-0.7.5.tar.gz#sha256=29daa8e4689276b00f3cacb497ebec71394e491267f4a69e4d940847cd87d1e8 (from https://pypi.org/simple/ngs-plumbing/), version: 0.7.5
2021-07-09T16:53:05,989   Found link https://files.pythonhosted.org/packages/e8/5a/79b30734c953d9b024b52cb6ff7009fea49b775ac143e93bb7b0e52b15d9/ngs_plumbing-0.8.0.tar.gz#sha256=036e23c89b6aecbb76a5508b0e53a13bc27514791258cbc6c5cf73857900c0e7 (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.0
2021-07-09T16:53:05,989   Found link https://files.pythonhosted.org/packages/aa/2f/ea679e884acfd3cf0766ef7e150dcb26e8e2f5bba415c0b7317a8e514377/ngs_plumbing-0.8.1.tar.gz#sha256=ac2fcd1c2d1c2ada3d5b494332b6ce4175dc1146dca78ec1d3dbcfc06220d199 (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.1
2021-07-09T16:53:05,990   Found link https://files.pythonhosted.org/packages/49/b4/c14b0f4bb8d2e2c475093d83d9b2a52743953d99aa3b91290ac0422d8dff/ngs_plumbing-0.8.2.tar.gz#sha256=6abefcadea1b7c903986c58fd6ce47de3df8405d18b6d91f967cf53e5d634886 (from https://pypi.org/simple/ngs-plumbing/), version: 0.8.2
2021-07-09T16:53:05,990   Found link https://files.pythonhosted.org/packages/89/1d/5ff21faba6fb2ec2775eab5a7555163a3c4865705ba4d05e8507a1ce4398/ngs_plumbing-0.9.0.tar.gz#sha256=b13e7d9452accf6484985807dab5bae7139debfcad0d154211a2feb7ee442647 (from https://pypi.org/simple/ngs-plumbing/), version: 0.9.0
2021-07-09T16:53:05,990   Found link https://files.pythonhosted.org/packages/9b/49/7ff35e46900140f2d5b696e7240d19ac90913a4d7c3c9b0d4bab5e707d84/ngs_plumbing-0.10.0.tar.gz#sha256=115e2fb82aefdd82a6b92f83228de5a454119eb11f18480bdae02bed3fb4e715 (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.0
2021-07-09T16:53:05,991   Found link https://files.pythonhosted.org/packages/ee/af/35e8bcebff8702993f25a6987a414dda927929c9fe39fc92af1ae2ca7668/ngs_plumbing-0.10.1.tar.gz#sha256=f1669002e1dd8947c69e81cb201d0f057a1c7182cba5d245dc110f47ff4ebaea (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.1
2021-07-09T16:53:05,991   Found link https://files.pythonhosted.org/packages/29/8e/5c1c762bc712b1d3897b92078955e71216e56d64416c76bac99e0db8880a/ngs_plumbing-0.10.2.tar.gz#sha256=d3f2bfce20c6bb618690c802cbe31bde1f7df4125d6db6b9f43c15efba92aa46 (from https://pypi.org/simple/ngs-plumbing/), version: 0.10.2
2021-07-09T16:53:05,992   Found link https://files.pythonhosted.org/packages/9e/40/62af4356ba0ad2cc37d5adeafde4974a47f8df09fa5ca79a64c5ef7bffbb/ngs_plumbing-0.11.0.tar.gz#sha256=c7c4b4af6897b34a96b6fb7de9a0962258aed51ae094671c5368fe4cbe7c5afe (from https://pypi.org/simple/ngs-plumbing/), version: 0.11.0
2021-07-09T16:53:05,992   Found link https://files.pythonhosted.org/packages/ff/c5/92ca8129b4f963f8dfb1812a34ba0ebd285d7b5daa81896a368b64a896a5/ngs_plumbing-0.11.1.tar.gz#sha256=41cdd69655630abb592e37f62fa0f33c806e7a5af743fec25d8fe942e7ad9619 (from https://pypi.org/simple/ngs-plumbing/), version: 0.11.1
2021-07-09T16:53:05,993   Found link https://files.pythonhosted.org/packages/86/e6/e72c4b834909bc9c0412aab091fc05b0a091b9c6861a3a0d4a9edbbce822/ngs_plumbing-0.12.0.tar.gz#sha256=a6fcbf06a78363cf2654d4bf622615a830828f1409192027ec54e7477b213593 (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.0
2021-07-09T16:53:05,993   Found link https://files.pythonhosted.org/packages/03/8a/9db89c482934552967bf5fef88f83d894cd98708c66571d7f0762cbac990/ngs_plumbing-0.12.2.tar.gz#sha256=32510d70e77a266f70f0ca6f57714c7de21773768a5658735342a2eb3bb583e8 (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.2
2021-07-09T16:53:05,993   Found link https://files.pythonhosted.org/packages/03/0d/4c2d5c9ad4517970df0e2f6c8827d3c10f324883326a63c7e589042dbd17/ngs_plumbing-0.12.3.tar.gz#sha256=16fa80980168657040ec6d3c113abc74254ee52087b20eb4abba3cfea00d9802 (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.3
2021-07-09T16:53:05,994   Found link https://files.pythonhosted.org/packages/cf/95/92f0ce68a236e33d3b4be730d315d60c17fa1968d6b64a80c27001419363/ngs_plumbing-0.12.4.tar.gz#sha256=4533b4208fd73da36f15be93ea5ffe6863f1519674f995a1bb0114fece98c12d (from https://pypi.org/simple/ngs-plumbing/), version: 0.12.4
2021-07-09T16:53:05,994   Found link https://files.pythonhosted.org/packages/e8/69/8a0fba8c6a02c3e7a4cff43b6aa07e2942beae6eaeda732a05560dad0b8a/ngs_plumbing-0.13.0.tar.gz#sha256=18b3f47ce07c42b89e88fb52d07d22b9280aa6a8868fc1e33531b70e30618c76 (from https://pypi.org/simple/ngs-plumbing/), version: 0.13.0
2021-07-09T16:53:05,995   Found link https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz#sha256=d2bc142509080f20f4e152178c95d2284445405ed7659e7d95b69bb79b774382 (from https://pypi.org/simple/ngs-plumbing/), version: 0.13.1
2021-07-09T16:53:05,995 Skipping link: not a file: https://pypi.org/simple/ngs-plumbing/
2021-07-09T16:53:06,016 Given no hashes to check 1 links for project 'ngs-plumbing': discarding no candidates
2021-07-09T16:53:06,035 Collecting ngs-plumbing==0.12.3
2021-07-09T16:53:06,037   Created temporary directory: /tmp/pip-unpack-m9vj8l0b
2021-07-09T16:53:06,311   Downloading ngs_plumbing-0.12.3.tar.gz (327 kB)
2021-07-09T16:53:06,495   Added ngs-plumbing==0.12.3 from https://files.pythonhosted.org/packages/03/0d/4c2d5c9ad4517970df0e2f6c8827d3c10f324883326a63c7e589042dbd17/ngs_plumbing-0.12.3.tar.gz#sha256=16fa80980168657040ec6d3c113abc74254ee52087b20eb4abba3cfea00d9802 to build tracker '/tmp/pip-req-tracker-xbps7kls'
2021-07-09T16:53:06,496     Running setup.py (path:/tmp/pip-wheel-_go2p00x/ngs-plumbing_15bd857fd20b4238a7d528f385f72fe8/setup.py) egg_info for package ngs-plumbing
2021-07-09T16:53:06,497     Created temporary directory: /tmp/pip-pip-egg-info-1nmhzwqc
2021-07-09T16:53:06,497     Running command python setup.py egg_info
2021-07-09T16:53:07,333     running egg_info
2021-07-09T16:53:07,337     creating /tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info
2021-07-09T16:53:07,338     writing /tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/PKG-INFO
2021-07-09T16:53:07,341     writing dependency_links to /tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/dependency_links.txt
2021-07-09T16:53:07,343     writing entry points to /tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/entry_points.txt
2021-07-09T16:53:07,345     writing top-level names to /tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/top_level.txt
2021-07-09T16:53:07,347     writing manifest file '/tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T16:53:07,673     reading manifest file '/tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T16:53:07,675     reading manifest template 'MANIFEST.in'
2021-07-09T16:53:07,678     adding license file 'COPYING'
2021-07-09T16:53:07,682     writing manifest file '/tmp/pip-pip-egg-info-1nmhzwqc/ngs_plumbing.egg-info/SOURCES.txt'

2021-07-09T16:53:07,684     Warning: The Python package 'h5py' cannot be imported.
2021-07-09T16:53:07,684     Without it, capabilities related to the XSQ format cannot be used.
2021-07-09T16:53:07,758   Source in /tmp/pip-wheel-_go2p00x/ngs-plumbing_15bd857fd20b4238a7d528f385f72fe8 has version 0.12.3, which satisfies requirement ngs-plumbing==0.12.3 from https://files.pythonhosted.org/packages/03/0d/4c2d5c9ad4517970df0e2f6c8827d3c10f324883326a63c7e589042dbd17/ngs_plumbing-0.12.3.tar.gz#sha256=16fa80980168657040ec6d3c113abc74254ee52087b20eb4abba3cfea00d9802
2021-07-09T16:53:07,759   Removed ngs-plumbing==0.12.3 from https://files.pythonhosted.org/packages/03/0d/4c2d5c9ad4517970df0e2f6c8827d3c10f324883326a63c7e589042dbd17/ngs_plumbing-0.12.3.tar.gz#sha256=16fa80980168657040ec6d3c113abc74254ee52087b20eb4abba3cfea00d9802 from build tracker '/tmp/pip-req-tracker-xbps7kls'
2021-07-09T16:53:07,763 Created temporary directory: /tmp/pip-unpack-xynsezc7
2021-07-09T16:53:07,764 Building wheels for collected packages: ngs-plumbing
2021-07-09T16:53:07,767   Created temporary directory: /tmp/pip-wheel-hpgr9era
2021-07-09T16:53:07,768   Building wheel for ngs-plumbing (setup.py): started
2021-07-09T16:53:07,768   Destination directory: /tmp/pip-wheel-hpgr9era
2021-07-09T16:53:07,769   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-_go2p00x/ngs-plumbing_15bd857fd20b4238a7d528f385f72fe8/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-_go2p00x/ngs-plumbing_15bd857fd20b4238a7d528f385f72fe8/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-hpgr9era
2021-07-09T16:53:08,655   running bdist_wheel
2021-07-09T16:53:08,830   running build
2021-07-09T16:53:08,830   running build_py
2021-07-09T16:53:08,973   creating build
2021-07-09T16:53:08,974   creating build/lib.linux-armv7l-3.9
2021-07-09T16:53:08,974   creating build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,975   copying src/fastq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,977   copying src/dnaqual_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,979   copying src/dnaqual.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,981   copying src/_libdna_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,984   copying src/report.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,986   copying src/_libxsq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,987   copying src/__init__.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,989   copying src/dna_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,991   copying src/intervals_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,993   copying src/bam.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,995   copying src/ngsp_string_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,997   copying src/intervals.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:08,999   copying src/fastq.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,001   copying src/colorspace.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,004   copying src/kmers_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,006   copying src/tests.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,008   copying src/fasta_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,010   copying src/ngsp_string.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,012   copying src/parsing.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,014   copying src/kmers.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,017   copying src/scons.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,019   copying src/xsqconvert.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,021   copying src/dna.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,024   copying src/xsq.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,027   copying src/xsq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,028   copying src/_libdnaqual_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,031   copying src/fasta.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T16:53:09,035   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T16:53:09,035   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run
2021-07-09T16:53:09,036   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X
2021-07-09T16:53:09,037   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result
2021-07-09T16:53:09,037   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1
2021-07-09T16:53:09,039   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-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1
2021-07-09T16:53:09,051   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/html
2021-07-09T16:53:09,052   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T16:53:09,053   copying src/data/html/templates/xsqlibreport.html -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T16:53:09,056   copying src/data/html/readqual.js -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html
2021-07-09T16:53:09,058   copying src/data/reads.fq -> build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T16:53:09,064   running build_ext
2021-07-09T16:53:09,070   building 'ngs_plumbing._libxsq' extension
2021-07-09T16:53:09,071   creating build/temp.linux-armv7l-3.9
2021-07-09T16:53:09,071   creating build/temp.linux-armv7l-3.9/src
2021-07-09T16:53:09,072   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c src/_libxsq.c -o build/temp.linux-armv7l-3.9/src/_libxsq.o -Wall -O3 -funroll-loops
2021-07-09T16:53:09,551   src/_libxsq.c: In function ‘PyInit__libxsq’:
2021-07-09T16:53:09,552   src/_libxsq.c:352:17: warning: variable ‘d’ set but not used [-Wunused-but-set-variable]
2021-07-09T16:53:09,552     352 |   PyObject *m, *d;
2021-07-09T16:53:09,553         |                 ^
2021-07-09T16:53:10,291   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/_libxsq.o -o build/lib.linux-armv7l-3.9/ngs_plumbing/_libxsq.cpython-39-arm-linux-gnueabihf.so -g
2021-07-09T16:53:10,412   building 'ngs_plumbing._libdna' extension
2021-07-09T16:53:10,412   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c src/_libdna.c -o build/temp.linux-armv7l-3.9/src/_libdna.o -Wall -O3 -funroll-loops
2021-07-09T16:53:10,771   src/_libdna.c: In function ‘bytes_to_bit2’:
2021-07-09T16:53:10,771   src/_libdna.c:114:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T16:53:10,772     114 |       if (bitpos == -2) {
2021-07-09T16:53:10,772         |                  ^~
2021-07-09T16:53:12,337   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/_libdna.o -o build/lib.linux-armv7l-3.9/ngs_plumbing/_libdna.cpython-39-arm-linux-gnueabihf.so -g
2021-07-09T16:53:12,443   building 'ngs_plumbing._libdnaqual' extension
2021-07-09T16:53:12,443   arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c src/_libdnaqual.c -o build/temp.linux-armv7l-3.9/src/_libdnaqual.o -Wall -O3 -funroll-loops
2021-07-09T16:53:12,952   arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/src/_libdnaqual.o -o build/lib.linux-armv7l-3.9/ngs_plumbing/_libdnaqual.cpython-39-arm-linux-gnueabihf.so -g
2021-07-09T16:53:13,067   installing to build/bdist.linux-armv7l/wheel
2021-07-09T16:53:13,067   running install
2021-07-09T16:53:13,068   running install_lib
2021-07-09T16:53:13,072   creating build/bdist.linux-armv7l
2021-07-09T16:53:13,073   creating build/bdist.linux-armv7l/wheel
2021-07-09T16:53:13,075   creating build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,076   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fastq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,078   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,081   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dnaqual.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,083   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,085   copying build/lib.linux-armv7l-3.9/ngs_plumbing/report.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,087   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libxsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,090   copying build/lib.linux-armv7l-3.9/ngs_plumbing/__init__.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,092   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,094   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdna.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,099   copying build/lib.linux-armv7l-3.9/ngs_plumbing/intervals_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,101   copying build/lib.linux-armv7l-3.9/ngs_plumbing/bam.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,103   copying build/lib.linux-armv7l-3.9/ngs_plumbing/ngsp_string_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,105   copying build/lib.linux-armv7l-3.9/ngs_plumbing/intervals.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,108   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fastq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,110   copying build/lib.linux-armv7l-3.9/ngs_plumbing/colorspace.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,113   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdnaqual.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,115   copying build/lib.linux-armv7l-3.9/ngs_plumbing/kmers_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,117   copying build/lib.linux-armv7l-3.9/ngs_plumbing/tests.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,120   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fasta_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,122   copying build/lib.linux-armv7l-3.9/ngs_plumbing/ngsp_string.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,124   copying build/lib.linux-armv7l-3.9/ngs_plumbing/parsing.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,126   copying build/lib.linux-armv7l-3.9/ngs_plumbing/kmers.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,128   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libxsq.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,131   copying build/lib.linux-armv7l-3.9/ngs_plumbing/scons.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,133   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsqconvert.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,136   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dna.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,138   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,141   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,144   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T16:53:13,145   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/reads.fq -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T16:53:13,148   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run
2021-07-09T16:53:13,150   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X
2021-07-09T16:53:13,151   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result
2021-07-09T16:53:13,153   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1
2021-07-09T16:53:13,154   copying build/lib.linux-armv7l-3.9/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
2021-07-09T16:53:13,164   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html
2021-07-09T16:53:13,166   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T16:53:13,167   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates/xsqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T16:53:13,169   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/readqual.js -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html
2021-07-09T16:53:13,171   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,173   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fasta.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T16:53:13,175   running install_headers
2021-07-09T16:53:13,177   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3.data
2021-07-09T16:53:13,177   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3.data/headers
2021-07-09T16:53:13,178   copying src/_libdna.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3.data/headers
2021-07-09T16:53:13,180   copying src/bitpack.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3.data/headers
2021-07-09T16:53:13,182   running install_egg_info
2021-07-09T16:53:13,203   running egg_info
2021-07-09T16:53:13,204   writing ngs_plumbing.egg-info/PKG-INFO
2021-07-09T16:53:13,206   writing dependency_links to ngs_plumbing.egg-info/dependency_links.txt
2021-07-09T16:53:13,208   writing entry points to ngs_plumbing.egg-info/entry_points.txt
2021-07-09T16:53:13,209   writing top-level names to ngs_plumbing.egg-info/top_level.txt
2021-07-09T16:53:13,221   reading manifest file 'ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T16:53:13,223   reading manifest template 'MANIFEST.in'
2021-07-09T16:53:13,227   adding license file 'COPYING'
2021-07-09T16:53:13,231   writing manifest file 'ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T16:53:13,233   Copying ngs_plumbing.egg-info to build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3-py3.9.egg-info
2021-07-09T16:53:13,248   running install_scripts
2021-07-09T16:53:13,334   adding license file "COPYING" (matched pattern "COPYING*")
2021-07-09T16:53:13,341   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.12.3.dist-info/WHEEL
2021-07-09T16:53:13,344   creating '/tmp/pip-wheel-hpgr9era/ngs_plumbing-0.12.3-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-09T16:53:13,347   adding 'ngs_plumbing/__init__.py'
2021-07-09T16:53:13,367   adding 'ngs_plumbing/_libdna.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T16:53:13,370   adding 'ngs_plumbing/_libdna_test.py'
2021-07-09T16:53:13,375   adding 'ngs_plumbing/_libdnaqual.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T16:53:13,376   adding 'ngs_plumbing/_libdnaqual_test.py'
2021-07-09T16:53:13,384   adding 'ngs_plumbing/_libxsq.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T16:53:13,386   adding 'ngs_plumbing/_libxsq_test.py'
2021-07-09T16:53:13,388   adding 'ngs_plumbing/bam.py'
2021-07-09T16:53:13,389   adding 'ngs_plumbing/colorspace.py'
2021-07-09T16:53:13,392   adding 'ngs_plumbing/dna.py'
2021-07-09T16:53:13,393   adding 'ngs_plumbing/dna_test.py'
2021-07-09T16:53:13,395   adding 'ngs_plumbing/dnaqual.py'
2021-07-09T16:53:13,396   adding 'ngs_plumbing/dnaqual_test.py'
2021-07-09T16:53:13,398   adding 'ngs_plumbing/fasta.py'
2021-07-09T16:53:13,400   adding 'ngs_plumbing/fasta_test.py'
2021-07-09T16:53:13,402   adding 'ngs_plumbing/fastq.py'
2021-07-09T16:53:13,404   adding 'ngs_plumbing/fastq_test.py'
2021-07-09T16:53:13,405   adding 'ngs_plumbing/intervals.py'
2021-07-09T16:53:13,407   adding 'ngs_plumbing/intervals_test.py'
2021-07-09T16:53:13,408   adding 'ngs_plumbing/kmers.py'
2021-07-09T16:53:13,410   adding 'ngs_plumbing/kmers_test.py'
2021-07-09T16:53:13,412   adding 'ngs_plumbing/ngsp_string.py'
2021-07-09T16:53:13,414   adding 'ngs_plumbing/ngsp_string_test.py'
2021-07-09T16:53:13,415   adding 'ngs_plumbing/parsing.py'
2021-07-09T16:53:13,417   adding 'ngs_plumbing/report.py'
2021-07-09T16:53:13,418   adding 'ngs_plumbing/scons.py'
2021-07-09T16:53:13,420   adding 'ngs_plumbing/tests.py'
2021-07-09T16:53:13,424   adding 'ngs_plumbing/xsq.py'
2021-07-09T16:53:13,425   adding 'ngs_plumbing/xsq_test.py'
2021-07-09T16:53:13,427   adding 'ngs_plumbing/xsqconvert.py'
2021-07-09T16:53:13,434   adding 'ngs_plumbing/data/reads.fq'
2021-07-09T16:53:13,436   adding 'ngs_plumbing/data/html/readqual.js'
2021-07-09T16:53:13,439   adding 'ngs_plumbing/data/html/templates/xsqlibreport.html'
2021-07-09T16:53:13,485   adding 'ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq'
2021-07-09T16:53:13,490   adding 'ngs_plumbing-0.12.3.data/headers/_libdna.h'
2021-07-09T16:53:13,491   adding 'ngs_plumbing-0.12.3.data/headers/bitpack.h'
2021-07-09T16:53:13,498   adding 'ngs_plumbing-0.12.3.dist-info/COPYING'
2021-07-09T16:53:13,500   adding 'ngs_plumbing-0.12.3.dist-info/METADATA'
2021-07-09T16:53:13,501   adding 'ngs_plumbing-0.12.3.dist-info/WHEEL'
2021-07-09T16:53:13,502   adding 'ngs_plumbing-0.12.3.dist-info/entry_points.txt'
2021-07-09T16:53:13,503   adding 'ngs_plumbing-0.12.3.dist-info/top_level.txt'
2021-07-09T16:53:13,504   adding 'ngs_plumbing-0.12.3.dist-info/RECORD'
2021-07-09T16:53:13,511   removing build/bdist.linux-armv7l/wheel

2021-07-09T16:53:13,530   Warning: The Python package 'h5py' cannot be imported.
2021-07-09T16:53:13,530   Without it, capabilities related to the XSQ format cannot be used.
2021-07-09T16:53:13,630   Building wheel for ngs-plumbing (setup.py): finished with status 'done'
2021-07-09T16:53:13,637   Created wheel for ngs-plumbing: filename=ngs_plumbing-0.12.3-cp39-cp39-linux_armv7l.whl size=371318 sha256=2cf1330cfcf96b713b3c6ee1bf1c08eed14ba3b00b9a64225d4ed2262c7ffa94
2021-07-09T16:53:13,637   Stored in directory: /tmp/pip-ephem-wheel-cache-krt615ta/wheels/96/d6/fb/1193984ee091d66dd2cc477099a5c142e3f1df86aefb97a4c4
2021-07-09T16:53:13,651 Successfully built ngs-plumbing
2021-07-09T16:53:13,667 Removed build tracker: '/tmp/pip-req-tracker-xbps7kls'