2021-07-09T21:40:33,508 Created temporary directory: /tmp/pip-ephem-wheel-cache-9qoq0q04
2021-07-09T21:40:33,511 Created temporary directory: /tmp/pip-req-tracker-j8b3pbbv
2021-07-09T21:40:33,511 Initialized build tracking at /tmp/pip-req-tracker-j8b3pbbv
2021-07-09T21:40:33,511 Created build tracker: /tmp/pip-req-tracker-j8b3pbbv
2021-07-09T21:40:33,512 Entered build tracker: /tmp/pip-req-tracker-j8b3pbbv
2021-07-09T21:40:33,512 Created temporary directory: /tmp/pip-wheel-wcimebzl
2021-07-09T21:40:33,545 1 location(s) to search for versions of ngs-plumbing:
2021-07-09T21:40:33,545 * https://pypi.org/simple/ngs-plumbing/
2021-07-09T21:40:33,546 Fetching project page and analyzing links: https://pypi.org/simple/ngs-plumbing/
2021-07-09T21:40:33,546 Getting page https://pypi.org/simple/ngs-plumbing/
2021-07-09T21:40:33,548 Found index url https://pypi.org/simple
2021-07-09T21:40:33,649   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
2021-07-09T21:40:33,649   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
2021-07-09T21:40:33,650   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
2021-07-09T21:40:33,650   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
2021-07-09T21:40:33,650   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
2021-07-09T21:40:33,650   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
2021-07-09T21:40:33,651   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
2021-07-09T21:40:33,651   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
2021-07-09T21:40:33,651   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
2021-07-09T21:40:33,652   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
2021-07-09T21:40:33,652   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
2021-07-09T21:40:33,652   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
2021-07-09T21:40:33,652   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
2021-07-09T21:40:33,653   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
2021-07-09T21:40:33,653   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
2021-07-09T21:40:33,653   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
2021-07-09T21:40:33,654   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
2021-07-09T21:40:33,654   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
2021-07-09T21:40:33,654   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
2021-07-09T21:40:33,654   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
2021-07-09T21:40:33,655   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
2021-07-09T21:40:33,655   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
2021-07-09T21:40:33,655   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
2021-07-09T21:40:33,655   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
2021-07-09T21:40:33,656   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
2021-07-09T21:40:33,656 Skipping link: not a file: https://pypi.org/simple/ngs-plumbing/
2021-07-09T21:40:33,676 Given no hashes to check 1 links for project 'ngs-plumbing': discarding no candidates
2021-07-09T21:40:33,693 Collecting ngs-plumbing==0.13.1
2021-07-09T21:40:33,695   Created temporary directory: /tmp/pip-unpack-z3lprkgn
2021-07-09T21:40:33,954   Downloading ngs_plumbing-0.13.1.tar.gz (341 kB)
2021-07-09T21:40:34,178   Added ngs-plumbing==0.13.1 from https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz#sha256=d2bc142509080f20f4e152178c95d2284445405ed7659e7d95b69bb79b774382 to build tracker '/tmp/pip-req-tracker-j8b3pbbv'
2021-07-09T21:40:34,179     Running setup.py (path:/tmp/pip-wheel-wcimebzl/ngs-plumbing_98eb26bfa2064d9fb839393f64631e2c/setup.py) egg_info for package ngs-plumbing
2021-07-09T21:40:34,180     Created temporary directory: /tmp/pip-pip-egg-info-2asljghe
2021-07-09T21:40:34,180     Running command python setup.py egg_info
2021-07-09T21:40:34,954     running egg_info
2021-07-09T21:40:34,956     creating /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info
2021-07-09T21:40:34,957     writing /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/PKG-INFO
2021-07-09T21:40:34,960     writing dependency_links to /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/dependency_links.txt
2021-07-09T21:40:34,961     writing entry points to /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/entry_points.txt
2021-07-09T21:40:34,962     writing requirements to /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/requires.txt
2021-07-09T21:40:34,963     writing top-level names to /tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/top_level.txt
2021-07-09T21:40:34,965     writing manifest file '/tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T21:40:35,295     reading manifest file '/tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T21:40:35,297     reading manifest template 'MANIFEST.in'
2021-07-09T21:40:35,301     adding license file 'COPYING'
2021-07-09T21:40:35,305     writing manifest file '/tmp/pip-pip-egg-info-2asljghe/ngs_plumbing.egg-info/SOURCES.txt'

2021-07-09T21:40:35,306     Warning: The Python package 'h5py' cannot be imported.
2021-07-09T21:40:35,307     Without it, capabilities related to the XSQ format cannot be used.
2021-07-09T21:40:35,380   Source in /tmp/pip-wheel-wcimebzl/ngs-plumbing_98eb26bfa2064d9fb839393f64631e2c 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#sha256=d2bc142509080f20f4e152178c95d2284445405ed7659e7d95b69bb79b774382
2021-07-09T21:40:35,381   Removed ngs-plumbing==0.13.1 from https://files.pythonhosted.org/packages/e7/43/38c5059e87bbfc0ab7e3656de6144da6ae5df0832b2accf49f80a63abb22/ngs_plumbing-0.13.1.tar.gz#sha256=d2bc142509080f20f4e152178c95d2284445405ed7659e7d95b69bb79b774382 from build tracker '/tmp/pip-req-tracker-j8b3pbbv'
2021-07-09T21:40:35,385 Created temporary directory: /tmp/pip-unpack-_5u4a94v
2021-07-09T21:40:35,386 Building wheels for collected packages: ngs-plumbing
2021-07-09T21:40:35,391   Created temporary directory: /tmp/pip-wheel-l2eopt7d
2021-07-09T21:40:35,391   Building wheel for ngs-plumbing (setup.py): started
2021-07-09T21:40:35,391   Destination directory: /tmp/pip-wheel-l2eopt7d
2021-07-09T21:40:35,392   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-wcimebzl/ngs-plumbing_98eb26bfa2064d9fb839393f64631e2c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-wcimebzl/ngs-plumbing_98eb26bfa2064d9fb839393f64631e2c/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-l2eopt7d
2021-07-09T21:40:36,187   running bdist_wheel
2021-07-09T21:40:36,376   running build
2021-07-09T21:40:36,376   running build_py
2021-07-09T21:40:36,516   creating build
2021-07-09T21:40:36,516   creating build/lib.linux-armv7l-3.9
2021-07-09T21:40:36,517   creating build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,518   copying src/ngsp_string.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,520   copying src/scons.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,522   copying src/xsqconvert.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,524   copying src/_libdnaqual_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,526   copying src/tests.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,528   copying src/fastq.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,530   copying src/dna.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,533   copying src/kmers_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,535   copying src/parsing.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,537   copying src/dna_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,539   copying src/dnaqual.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,541   copying src/__init__.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,543   copying src/_libxsq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,545   copying src/fasta.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,548   copying src/fastq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,550   copying src/ngsp_string_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,552   copying src/xsq_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,554   copying src/parsing_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,556   copying src/intervals_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,558   copying src/dnaqual_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,560   copying src/report.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,562   copying src/colorspace.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,564   copying src/xsq.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,568   copying src/tapir.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,570   copying src/_libdna_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,572   copying src/fasta_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,574   copying src/sampling_test.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,577   copying src/sampling.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,579   copying src/bam.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,581   copying src/kmers.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,583   copying src/intervals.py -> build/lib.linux-armv7l-3.9/ngs_plumbing
2021-07-09T21:40:36,587   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T21:40:36,588   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run
2021-07-09T21:40:36,588   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X
2021-07-09T21:40:36,589   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result
2021-07-09T21:40:36,590   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1
2021-07-09T21:40:36,591   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
2021-07-09T21:40:36,610   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/html
2021-07-09T21:40:36,610   creating build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T21:40:36,612   copying src/data/html/templates/xsqreport.html -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T21:40:36,614   copying src/data/html/templates/fqlibreport.html -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T21:40:36,617   copying src/data/html/templates/xsqlibreport.html -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates
2021-07-09T21:40:36,619   copying src/data/html/readqual.js -> build/lib.linux-armv7l-3.9/ngs_plumbing/data/html
2021-07-09T21:40:36,621   copying src/data/reads.fq -> build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T21:40:36,625   copying src/data/reads.fq.gz -> build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T21:40:36,627   copying src/data/reads.fq.bz2 -> build/lib.linux-armv7l-3.9/ngs_plumbing/data
2021-07-09T21:40:36,632   running build_ext
2021-07-09T21:40:36,639   building 'ngs_plumbing._libxsq' extension
2021-07-09T21:40:36,640   creating build/temp.linux-armv7l-3.9
2021-07-09T21:40:36,640   creating build/temp.linux-armv7l-3.9/src
2021-07-09T21:40:36,641   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
2021-07-09T21:40:37,039   src/_libxsq.c: In function ‘PyInit__libxsq’:
2021-07-09T21:40:37,040   src/_libxsq.c:352:17: warning: variable ‘d’ set but not used [-Wunused-but-set-variable]
2021-07-09T21:40:37,040     352 |   PyObject *m, *d;
2021-07-09T21:40:37,041         |                 ^
2021-07-09T21:40:37,602   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
2021-07-09T21:40:37,716   building 'ngs_plumbing._libdna' extension
2021-07-09T21:40:37,716   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
2021-07-09T21:40:38,073   src/_libdna.c: In function ‘bytes_to_bit2’:
2021-07-09T21:40:38,073   src/_libdna.c:114:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-09T21:40:38,074     114 |       if (bitpos == -2) {
2021-07-09T21:40:38,074         |                  ^~
2021-07-09T21:40:39,575   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
2021-07-09T21:40:39,681   building 'ngs_plumbing._libdnaqual' extension
2021-07-09T21:40:39,682   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
2021-07-09T21:40:40,146   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
2021-07-09T21:40:40,255   installing to build/bdist.linux-armv7l/wheel
2021-07-09T21:40:40,255   running install
2021-07-09T21:40:40,257   running install_lib
2021-07-09T21:40:40,261   creating build/bdist.linux-armv7l
2021-07-09T21:40:40,261   creating build/bdist.linux-armv7l/wheel
2021-07-09T21:40:40,263   creating build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,264   copying build/lib.linux-armv7l-3.9/ngs_plumbing/ngsp_string.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,267   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdnaqual.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,269   copying build/lib.linux-armv7l-3.9/ngs_plumbing/scons.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,272   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsqconvert.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,274   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,276   copying build/lib.linux-armv7l-3.9/ngs_plumbing/tests.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,278   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fastq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,280   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dna.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,283   copying build/lib.linux-armv7l-3.9/ngs_plumbing/kmers_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,285   copying build/lib.linux-armv7l-3.9/ngs_plumbing/parsing.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,287   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libxsq.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,290   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,292   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dnaqual.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,294   copying build/lib.linux-armv7l-3.9/ngs_plumbing/__init__.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,296   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libxsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,298   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fasta.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,300   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fastq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,302   copying build/lib.linux-armv7l-3.9/ngs_plumbing/ngsp_string_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,304   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsq_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,306   copying build/lib.linux-armv7l-3.9/ngs_plumbing/parsing_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,308   copying build/lib.linux-armv7l-3.9/ngs_plumbing/intervals_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,310   copying build/lib.linux-armv7l-3.9/ngs_plumbing/dnaqual_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,312   copying build/lib.linux-armv7l-3.9/ngs_plumbing/report.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,314   copying build/lib.linux-armv7l-3.9/ngs_plumbing/colorspace.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,316   copying build/lib.linux-armv7l-3.9/ngs_plumbing/xsq.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,319   copying build/lib.linux-armv7l-3.9/ngs_plumbing/tapir.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,321   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdna_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,324   copying build/lib.linux-armv7l-3.9/ngs_plumbing/_libdna.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,329   copying build/lib.linux-armv7l-3.9/ngs_plumbing/fasta_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,331   copying build/lib.linux-armv7l-3.9/ngs_plumbing/sampling_test.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,333   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T21:40:40,335   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run
2021-07-09T21:40:40,337   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X
2021-07-09T21:40:40,338   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result
2021-07-09T21:40:40,340   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1
2021-07-09T21:40:40,341   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
2021-07-09T21:40:40,352   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/reads.fq.gz -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T21:40:40,356   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html
2021-07-09T21:40:40,357   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/readqual.js -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html
2021-07-09T21:40:40,360   creating build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T21:40:40,361   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates/xsqreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T21:40:40,364   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates/fqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T21:40:40,366   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/html/templates/xsqlibreport.html -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data/html/templates
2021-07-09T21:40:40,368   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/reads.fq -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T21:40:40,372   copying build/lib.linux-armv7l-3.9/ngs_plumbing/data/reads.fq.bz2 -> build/bdist.linux-armv7l/wheel/ngs_plumbing/data
2021-07-09T21:40:40,374   copying build/lib.linux-armv7l-3.9/ngs_plumbing/sampling.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,377   copying build/lib.linux-armv7l-3.9/ngs_plumbing/bam.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,379   copying build/lib.linux-armv7l-3.9/ngs_plumbing/kmers.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,381   copying build/lib.linux-armv7l-3.9/ngs_plumbing/intervals.py -> build/bdist.linux-armv7l/wheel/ngs_plumbing
2021-07-09T21:40:40,384   running install_headers
2021-07-09T21:40:40,386   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data
2021-07-09T21:40:40,387   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers
2021-07-09T21:40:40,388   copying src/_libdna.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers
2021-07-09T21:40:40,390   copying src/bitpack.h -> build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.data/headers
2021-07-09T21:40:40,392   running install_egg_info
2021-07-09T21:40:40,416   running egg_info
2021-07-09T21:40:40,417   writing ngs_plumbing.egg-info/PKG-INFO
2021-07-09T21:40:40,419   writing dependency_links to ngs_plumbing.egg-info/dependency_links.txt
2021-07-09T21:40:40,421   writing entry points to ngs_plumbing.egg-info/entry_points.txt
2021-07-09T21:40:40,422   writing requirements to ngs_plumbing.egg-info/requires.txt
2021-07-09T21:40:40,424   writing top-level names to ngs_plumbing.egg-info/top_level.txt
2021-07-09T21:40:40,436   reading manifest file 'ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T21:40:40,442   reading manifest template 'MANIFEST.in'
2021-07-09T21:40:40,447   adding license file 'COPYING'
2021-07-09T21:40:40,452   writing manifest file 'ngs_plumbing.egg-info/SOURCES.txt'
2021-07-09T21:40:40,454   Copying ngs_plumbing.egg-info to build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1-py3.9.egg-info
2021-07-09T21:40:40,470   running install_scripts
2021-07-09T21:40:40,551   adding license file "COPYING" (matched pattern "COPYING*")
2021-07-09T21:40:40,557   creating build/bdist.linux-armv7l/wheel/ngs_plumbing-0.13.1.dist-info/WHEEL
2021-07-09T21:40:40,560   creating '/tmp/pip-wheel-l2eopt7d/ngs_plumbing-0.13.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2021-07-09T21:40:40,563   adding 'ngs_plumbing/__init__.py'
2021-07-09T21:40:40,580   adding 'ngs_plumbing/_libdna.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T21:40:40,584   adding 'ngs_plumbing/_libdna_test.py'
2021-07-09T21:40:40,588   adding 'ngs_plumbing/_libdnaqual.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T21:40:40,589   adding 'ngs_plumbing/_libdnaqual_test.py'
2021-07-09T21:40:40,596   adding 'ngs_plumbing/_libxsq.cpython-39-arm-linux-gnueabihf.so'
2021-07-09T21:40:40,598   adding 'ngs_plumbing/_libxsq_test.py'
2021-07-09T21:40:40,599   adding 'ngs_plumbing/bam.py'
2021-07-09T21:40:40,601   adding 'ngs_plumbing/colorspace.py'
2021-07-09T21:40:40,603   adding 'ngs_plumbing/dna.py'
2021-07-09T21:40:40,605   adding 'ngs_plumbing/dna_test.py'
2021-07-09T21:40:40,607   adding 'ngs_plumbing/dnaqual.py'
2021-07-09T21:40:40,608   adding 'ngs_plumbing/dnaqual_test.py'
2021-07-09T21:40:40,610   adding 'ngs_plumbing/fasta.py'
2021-07-09T21:40:40,612   adding 'ngs_plumbing/fasta_test.py'
2021-07-09T21:40:40,614   adding 'ngs_plumbing/fastq.py'
2021-07-09T21:40:40,615   adding 'ngs_plumbing/fastq_test.py'
2021-07-09T21:40:40,617   adding 'ngs_plumbing/intervals.py'
2021-07-09T21:40:40,619   adding 'ngs_plumbing/intervals_test.py'
2021-07-09T21:40:40,620   adding 'ngs_plumbing/kmers.py'
2021-07-09T21:40:40,622   adding 'ngs_plumbing/kmers_test.py'
2021-07-09T21:40:40,624   adding 'ngs_plumbing/ngsp_string.py'
2021-07-09T21:40:40,625   adding 'ngs_plumbing/ngsp_string_test.py'
2021-07-09T21:40:40,627   adding 'ngs_plumbing/parsing.py'
2021-07-09T21:40:40,629   adding 'ngs_plumbing/parsing_test.py'
2021-07-09T21:40:40,630   adding 'ngs_plumbing/report.py'
2021-07-09T21:40:40,632   adding 'ngs_plumbing/sampling.py'
2021-07-09T21:40:40,634   adding 'ngs_plumbing/sampling_test.py'
2021-07-09T21:40:40,635   adding 'ngs_plumbing/scons.py'
2021-07-09T21:40:40,637   adding 'ngs_plumbing/tapir.py'
2021-07-09T21:40:40,638   adding 'ngs_plumbing/tests.py'
2021-07-09T21:40:40,642   adding 'ngs_plumbing/xsq.py'
2021-07-09T21:40:40,644   adding 'ngs_plumbing/xsq_test.py'
2021-07-09T21:40:40,646   adding 'ngs_plumbing/xsqconvert.py'
2021-07-09T21:40:40,654   adding 'ngs_plumbing/data/reads.fq'
2021-07-09T21:40:40,656   adding 'ngs_plumbing/data/reads.fq.bz2'
2021-07-09T21:40:40,658   adding 'ngs_plumbing/data/reads.fq.gz'
2021-07-09T21:40:40,660   adding 'ngs_plumbing/data/html/readqual.js'
2021-07-09T21:40:40,662   adding 'ngs_plumbing/data/html/templates/fqlibreport.html'
2021-07-09T21:40:40,664   adding 'ngs_plumbing/data/html/templates/xsqlibreport.html'
2021-07-09T21:40:40,665   adding 'ngs_plumbing/data/html/templates/xsqreport.html'
2021-07-09T21:40:40,707   adding 'ngs_plumbing/data/test_run/test_run_2012_01_08_Prof_X/result/lane1/test_run_2012_01_08_Prof_X_01.xsq'
2021-07-09T21:40:40,713   adding 'ngs_plumbing-0.13.1.data/headers/_libdna.h'
2021-07-09T21:40:40,714   adding 'ngs_plumbing-0.13.1.data/headers/bitpack.h'
2021-07-09T21:40:40,722   adding 'ngs_plumbing-0.13.1.dist-info/COPYING'
2021-07-09T21:40:40,723   adding 'ngs_plumbing-0.13.1.dist-info/METADATA'
2021-07-09T21:40:40,724   adding 'ngs_plumbing-0.13.1.dist-info/WHEEL'
2021-07-09T21:40:40,725   adding 'ngs_plumbing-0.13.1.dist-info/entry_points.txt'
2021-07-09T21:40:40,727   adding 'ngs_plumbing-0.13.1.dist-info/top_level.txt'
2021-07-09T21:40:40,728   adding 'ngs_plumbing-0.13.1.dist-info/RECORD'
2021-07-09T21:40:40,736   removing build/bdist.linux-armv7l/wheel

2021-07-09T21:40:40,754   Warning: The Python package 'h5py' cannot be imported.
2021-07-09T21:40:40,754   Without it, capabilities related to the XSQ format cannot be used.
2021-07-09T21:40:40,846   Building wheel for ngs-plumbing (setup.py): finished with status 'done'
2021-07-09T21:40:40,853   Created wheel for ngs-plumbing: filename=ngs_plumbing-0.13.1-cp39-cp39-linux_armv7l.whl size=395438 sha256=e84e01c6ddece267d014d3bb98cfe473f0c04288da44fc037a163a28811a0ab2
2021-07-09T21:40:40,854   Stored in directory: /tmp/pip-ephem-wheel-cache-9qoq0q04/wheels/e1/16/bb/bbfb4b3930b1b910696daf7d3187b1900dcb30f1efa77e0a22
2021-07-09T21:40:40,865 Successfully built ngs-plumbing
2021-07-09T21:40:40,880 Removed build tracker: '/tmp/pip-req-tracker-j8b3pbbv'