2021-07-29T12:20:20,974 Created temporary directory: /tmp/pip-ephem-wheel-cache-rnou_wuj
2021-07-29T12:20:20,977 Created temporary directory: /tmp/pip-req-tracker-luwdjrmt
2021-07-29T12:20:20,977 Initialized build tracking at /tmp/pip-req-tracker-luwdjrmt
2021-07-29T12:20:20,978 Created build tracker: /tmp/pip-req-tracker-luwdjrmt
2021-07-29T12:20:20,978 Entered build tracker: /tmp/pip-req-tracker-luwdjrmt
2021-07-29T12:20:20,978 Created temporary directory: /tmp/pip-wheel-4r1dbhn6
2021-07-29T12:20:21,006 WARNING: The index url "/" seems invalid, please provide a scheme.
2021-07-29T12:20:21,006 WARNING: The index url "t" seems invalid, please provide a scheme.
2021-07-29T12:20:21,007 WARNING: The index url "m" seems invalid, please provide a scheme.
2021-07-29T12:20:21,007 WARNING: The index url "p" seems invalid, please provide a scheme.
2021-07-29T12:20:21,007 Looking in indexes: https://pypi.org/simple, /, t, m, p
2021-07-29T12:20:21,010 WARNING: Location '/whatshap/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T12:20:21,010 WARNING: Location 't/whatshap/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T12:20:21,010 WARNING: Location 'm/whatshap/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T12:20:21,010 WARNING: Location 'p/whatshap/' is ignored: it is either a non-existing path or lacks a specific scheme.
2021-07-29T12:20:21,011 1 location(s) to search for versions of whatshap:
2021-07-29T12:20:21,011 * https://pypi.org/simple/whatshap/
2021-07-29T12:20:21,011 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/
2021-07-29T12:20:21,012 Getting page https://pypi.org/simple/whatshap/
2021-07-29T12:20:21,013 Found index url https://pypi.org/simple
2021-07-29T12:20:21,204   Found link https://files.pythonhosted.org/packages/35/95/43ff2304cd59ade39e64aadaeaec48e8c12bbe6262bcbbbd7b7d89487757/whatshap-0.9.tar.gz#sha256=beaadbc79e4d463b5e441b8e9a13b5345c07db3d91fb093cee1bfebfebae4442 (from https://pypi.org/simple/whatshap/), version: 0.9
2021-07-29T12:20:21,204   Found link https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz#sha256=864d4ecfc33eac7265452f5a2f468a830779afc53e723119ecac5ecf73255acc (from https://pypi.org/simple/whatshap/), version: 0.10
2021-07-29T12:20:21,205   Found link https://files.pythonhosted.org/packages/fc/dc/30559c28fb54985773fb242f5768fc206e054e44e45962a32cf4fd29a794/whatshap-0.11.tar.gz#sha256=d0367a4dd0adf288d30a9a87b565e4f141745bec3ea825cb85ac3409a593bde9 (from https://pypi.org/simple/whatshap/), version: 0.11
2021-07-29T12:20:21,205   Found link https://files.pythonhosted.org/packages/01/84/31a5ea338647d0256a4a5c57e98d7a563f387e6a47f1e26299b89e3f2da1/whatshap-0.12.tar.gz#sha256=c65060155dc901e4d4bd48077706660e5b214540d4dc20575a8b2146fb6a11f9 (from https://pypi.org/simple/whatshap/), version: 0.12
2021-07-29T12:20:21,205   Found link https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz#sha256=529646db74b2cac9f12ebd530bd7bb40cb073c367894bf66c5994c1d7f32b56a (from https://pypi.org/simple/whatshap/), version: 0.13
2021-07-29T12:20:21,206   Found link https://files.pythonhosted.org/packages/cd/d3/a63285d15b0da196a259197e46d9f61a852d1b3c94800f4a82ca4e31e307/whatshap-0.14.tar.gz#sha256=dd6076e67c5a4ce75d2510b3dbdd3c1e524124be62655f06c82f7d9fce4c5643 (from https://pypi.org/simple/whatshap/), version: 0.14
2021-07-29T12:20:21,206   Found link https://files.pythonhosted.org/packages/ec/d4/d6c19b716926895ee3def919ab23194212172ed5cf89ccb91c2949fb258d/whatshap-0.14.1.tar.gz#sha256=7b5781f1138b1830c4627451d1d5c77e7f2a3c5403510d9ab2a63f545911415b (from https://pypi.org/simple/whatshap/), version: 0.14.1
2021-07-29T12:20:21,206   Found link https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 (from https://pypi.org/simple/whatshap/), version: 0.15
2021-07-29T12:20:21,206   Found link https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz#sha256=1df54d8705fb0451cc0a640918842481087f7b741778dfb4100cc1f4f60f48fe (from https://pypi.org/simple/whatshap/), version: 0.16
2021-07-29T12:20:21,207   Found link https://files.pythonhosted.org/packages/79/11/79da12b8c23f43b00fab8a6206f75cc1cc8c1902ff30eca53c17abe2f633/whatshap-0.17.tar.gz#sha256=8ad1c66789fe5fe957b3695902dae3c3fd4e67f79b9e349b92b532e9ff618933 (from https://pypi.org/simple/whatshap/), version: 0.17
2021-07-29T12:20:21,207   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/97/19/5758de9357d2639e81f774dffd5227278df2df7f56e81f080098f00c8d5a/whatshap-0.18-cp34-cp34m-manylinux1_x86_64.whl#sha256=4a09adc24c6db3bd525667ac2559181dc94ee203a64f488dfce1ac38cbf44ba5 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4)
2021-07-29T12:20:21,207   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/d0/72/94dc654f66164a351a1a9540e28b4bdf34a81046fbf26b5955725bea2f64/whatshap-0.18-cp35-cp35m-manylinux1_x86_64.whl#sha256=1c99980629655e58a34496b0e1b1c9123dddd0797a13cf681dcf83f92a6f33e0 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4)
2021-07-29T12:20:21,207   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/0a/50/c9c89e7f3a59251a91e618165ccc2586b626643a4c59dfd8d1b32f9b6bbb/whatshap-0.18-cp36-cp36m-manylinux1_x86_64.whl#sha256=fdadadbed86cc7a7abd8f9ef3d55fe280eda957473db03dc30ad06ace6b877bd (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4)
2021-07-29T12:20:21,208   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/32/77/e9e6f3e15a89ea87b0a3ed50e99af2a375a897707eb8b4c81209af918ff0/whatshap-0.18-cp37-cp37m-manylinux1_x86_64.whl#sha256=2e189cb51c2527444dada90f8fd2355ddfe8d9d35aca386330e63bc46c2d2699 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4)
2021-07-29T12:20:21,208   Found link https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.4), version: 0.18
2021-07-29T12:20:21,208   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/0f/f5/78e5fa758144941f08b1de923889c7123e4d20368837904fc004592b6ec9/whatshap-1.0-cp36-cp36m-manylinux2010_x86_64.whl#sha256=ff945c6a0406f328771dbbc86970bd48a0327833ca8e96ad836a55ab32ae99d4 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,209   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/42/cb/53a1a2a160846a225c6184da26e8f6d6577f5af378e3a90aab728bb5b504/whatshap-1.0-cp37-cp37m-manylinux2010_x86_64.whl#sha256=78bacd81697878129a6ff39f9474792f85b95e6fde7bfa30371b87a24d5e9d3a (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,209   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/63/91/5aaa2ec02a362e784d7be43f43b1e243fa9153ef5d9ab3ada91759638444/whatshap-1.0-cp38-cp38-manylinux2010_x86_64.whl#sha256=62318377e996d1f3040cbfdb3462a3140dbdfd4113584c9000b530ca70bbf223 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,210   Found link https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.0
2021-07-29T12:20:21,210   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/8a/fb/dfaa97a9ec1fe333dcd730498376d33bc21de017760b633d8dd84f9cd9f6/whatshap-1.1-cp36-cp36m-manylinux2010_x86_64.whl#sha256=93af99ab08fac60bb3e46cde68978619f095e1b47490f59e4085f338ad715b46 (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,210   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/37/4e/a06bd339ea7179e750d49fec27caba7a6b364f608b5126105770333a6dfa/whatshap-1.1-cp37-cp37m-manylinux2010_x86_64.whl#sha256=94c04469069a87636c8aaf88d9f3e33022864de633327fedfdedd8da2bc4c6aa (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,210   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/2b/61/3000e39650a20faf011d74e41c3a6e3eea11195b1dad6cc8398665539363/whatshap-1.1-cp38-cp38-manylinux2010_x86_64.whl#sha256=7821711be901f898437a6be4993a15e77edbb59683ffa76d3dc9bc1bf855769a (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,211   Skipping link: No binaries permitted for whatshap: https://files.pythonhosted.org/packages/37/1a/f9708037de73715099098762c13e8e0681129041d41fb0ab508004ed2aa7/whatshap-1.1-cp39-cp39-manylinux2010_x86_64.whl#sha256=9e3a3169de452412c4e5cfe3220c0d51178d4811f33183e53069c57de49253ae (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6)
2021-07-29T12:20:21,211   Found link https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f (from https://pypi.org/simple/whatshap/) (requires-python:>=3.6), version: 1.1
2021-07-29T12:20:21,211 Skipping link: not a file: https://pypi.org/simple/whatshap/
2021-07-29T12:20:21,230 Given no hashes to check 1 links for project 'whatshap': discarding no candidates
2021-07-29T12:20:21,249 Collecting whatshap==1.1
2021-07-29T12:20:21,250   Created temporary directory: /tmp/pip-unpack-j8r_ix64
2021-07-29T12:20:21,684   Downloading whatshap-1.1.tar.gz (588 kB)
2021-07-29T12:20:22,235   Added whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f to build tracker '/tmp/pip-req-tracker-luwdjrmt'
2021-07-29T12:20:22,236     Running setup.py (path:/tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58/setup.py) egg_info for package whatshap
2021-07-29T12:20:22,237     Created temporary directory: /tmp/pip-pip-egg-info-yzxnwg9s
2021-07-29T12:20:22,237     Running command python setup.py egg_info
2021-07-29T12:20:25,447     running egg_info
2021-07-29T12:20:25,449     creating /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info
2021-07-29T12:20:25,449     writing /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/PKG-INFO
2021-07-29T12:20:25,452     writing dependency_links to /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/dependency_links.txt
2021-07-29T12:20:25,454     writing entry points to /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/entry_points.txt
2021-07-29T12:20:25,455     writing requirements to /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/requires.txt
2021-07-29T12:20:25,456     writing top-level names to /tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/top_level.txt
2021-07-29T12:20:25,458     writing manifest file '/tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/SOURCES.txt'
2021-07-29T12:20:25,666     reading manifest file '/tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/SOURCES.txt'
2021-07-29T12:20:25,673     writing manifest file '/tmp/pip-pip-egg-info-yzxnwg9s/whatshap.egg-info/SOURCES.txt'
2021-07-29T12:20:25,752   Source in /tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58 has version 1.1, which satisfies requirement whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f
2021-07-29T12:20:25,753   Removed whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f from build tracker '/tmp/pip-req-tracker-luwdjrmt'
2021-07-29T12:20:25,758 Created temporary directory: /tmp/pip-unpack-4nlld5_1
2021-07-29T12:20:25,759 Building wheels for collected packages: whatshap
2021-07-29T12:20:25,763   Created temporary directory: /tmp/pip-wheel-7932tftd
2021-07-29T12:20:25,764   Building wheel for whatshap (setup.py): started
2021-07-29T12:20:25,764   Destination directory: /tmp/pip-wheel-7932tftd
2021-07-29T12:20:25,764   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58/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-7932tftd
2021-07-29T12:20:26,876   running bdist_wheel
2021-07-29T12:20:26,880   running build
2021-07-29T12:20:26,880   running build_py
2021-07-29T12:20:27,023   creating build
2021-07-29T12:20:27,023   creating build/lib.linux-armv7l-3.9
2021-07-29T12:20:27,024   creating build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,025   copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,027   copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,029   copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,031   copying whatshap/utils.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,033   copying whatshap/merge.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,036   copying whatshap/timer.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,037   copying whatshap/math.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,039   copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,042   copying whatshap/threading.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,044   copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,047   copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,050   copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,053   copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,057   copying whatshap/variants.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,061   copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,062   copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,065   copying whatshap/__main__.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,067   copying whatshap/_version.py -> build/lib.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,070   creating build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,071   copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,074   copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,077   copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,080   copying whatshap/cli/phase.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,084   copying whatshap/cli/compare.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,088   copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,092   copying whatshap/cli/split.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,095   copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,097   copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,099   copying whatshap/cli/stats.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,102   copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-3.9/whatshap/cli
2021-07-29T12:20:27,108   running build_ext
2021-07-29T12:20:27,114   building 'whatshap.core' extension
2021-07-29T12:20:27,115   creating build/temp.linux-armv7l-3.9
2021-07-29T12:20:27,116   creating build/temp.linux-armv7l-3.9/src
2021-07-29T12:20:27,118   creating build/temp.linux-armv7l-3.9/src/hapchat
2021-07-29T12:20:27,119   creating build/temp.linux-armv7l-3.9/src/polyphase
2021-07-29T12:20:27,120   creating build/temp.linux-armv7l-3.9/whatshap
2021-07-29T12:20:27,120   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 -UNDEBUG -I/usr/include/python3.9 -c src/backwardcolumniterator.cpp -o build/temp.linux-armv7l-3.9/src/backwardcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:28,775   In file included from /usr/include/c++/10/cassert:44,
2021-07-29T12:20:28,775                    from src/backwardcolumniterator.cpp:1:
2021-07-29T12:20:28,775   src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’:
2021-07-29T12:20:28,775   src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:28,776     121 |  assert(k < positions->size());
2021-07-29T12:20:28,776         |         ~~^~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:28,776   src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:20:28,776     140 |     assert(active_entry < read->getVariantCount());
2021-07-29T12:20:28,776         |            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:30,332   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 -UNDEBUG -I/usr/include/python3.9 -c src/binomial.cpp -o build/temp.linux-armv7l-3.9/src/binomial.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:30,446   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 -UNDEBUG -I/usr/include/python3.9 -c src/columnindexingiterator.cpp -o build/temp.linux-armv7l-3.9/src/columnindexingiterator.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:31,562   src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’:
2021-07-29T12:20:31,562   src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:31,563      90 |  for(int j=0; j< parent->read_ids.size(); ++j) {
2021-07-29T12:20:31,563         |               ~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:31,563   src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:20:31,563      92 |   if(m != -1) {
2021-07-29T12:20:31,563         |      ~~^~~~~
2021-07-29T12:20:31,564   src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable]
2021-07-29T12:20:31,564      89 |  unsigned int s = 1;
2021-07-29T12:20:31,564         |               ^
2021-07-29T12:20:31,849   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 -UNDEBUG -I/usr/include/python3.9 -c src/columnindexingscheme.cpp -o build/temp.linux-armv7l-3.9/src/columnindexingscheme.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:32,962   src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector<unsigned int>&)’:
2021-07-29T12:20:32,962   src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:32,962      22 |   while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2021-07-29T12:20:32,963         |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:32,963   src/columnindexingscheme.cpp:22:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:32,963      22 |   while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2021-07-29T12:20:32,963         |                                                   ~^~~~~~~~~~~~~~~~
2021-07-29T12:20:32,965   src/columnindexingscheme.cpp: In member function ‘void ColumnIndexingScheme::set_next_column(const ColumnIndexingScheme*)’:
2021-07-29T12:20:32,965   src/columnindexingscheme.cpp:71:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:32,966      71 |  while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2021-07-29T12:20:32,966         |          ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:32,966   src/columnindexingscheme.cpp:71:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2021-07-29T12:20:32,966      71 |  while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2021-07-29T12:20:32,966         |                                              ~^~~~~~~~~~~~~~~~
2021-07-29T12:20:33,468   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 -UNDEBUG -I/usr/include/python3.9 -c src/columniterator.cpp -o build/temp.linux-armv7l-3.9/src/columniterator.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:35,068   In file included from /usr/include/c++/10/cassert:44,
2021-07-29T12:20:35,068                    from src/columniterator.cpp:1:
2021-07-29T12:20:35,068   src/columniterator.cpp: In member function ‘std::unique_ptr<std::vector<const Entry*> > ColumnIterator::get_next()’:
2021-07-29T12:20:35,068   src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:20:35,068     105 |    assert(list_it->active_entry < read->getVariantCount());
2021-07-29T12:20:35,069         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:35,085   src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’:
2021-07-29T12:20:35,086   src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:20:35,086     161 |     assert(active_entry < read->getVariantCount());
2021-07-29T12:20:35,086         |            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:36,702   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 -UNDEBUG -I/usr/include/python3.9 -c src/entry.cpp -o build/temp.linux-armv7l-3.9/src/entry.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:37,718   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 -UNDEBUG -I/usr/include/python3.9 -c src/genotype.cpp -o build/temp.linux-armv7l-3.9/src/genotype.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:40,120   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 -UNDEBUG -I/usr/include/python3.9 -c src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-3.9/src/genotypecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:42,901   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 -UNDEBUG -I/usr/include/python3.9 -c src/genotypedistribution.cpp -o build/temp.linux-armv7l-3.9/src/genotypedistribution.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:44,112   src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’:
2021-07-29T12:20:44,112   src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:20:44,113      55 |   if (i == best_index) continue;
2021-07-29T12:20:44,113         |       ~~^~~~~~~~~~~~~
2021-07-29T12:20:44,570   In file included from /usr/include/c++/10/vector:72,
2021-07-29T12:20:44,570                    from src/genotypedistribution.h:4,
2021-07-29T12:20:44,570                    from src/genotypedistribution.cpp:5:
2021-07-29T12:20:44,570   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
2021-07-29T12:20:44,571   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2021-07-29T12:20:44,571     426 |       vector<_Tp, _Alloc>::
2021-07-29T12:20:44,571         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:44,604   In file included from /usr/include/c++/10/vector:67,
2021-07-29T12:20:44,604                    from src/genotypedistribution.h:4,
2021-07-29T12:20:44,604                    from src/genotypedistribution.cpp:5:
2021-07-29T12:20:44,604   /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’:
2021-07-29T12:20:44,604   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-29T12:20:44,605    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T12:20:44,605         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T12:20:44,605   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-29T12:20:44,605    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T12:20:44,605         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T12:20:44,605   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2021-07-29T12:20:44,605    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T12:20:44,606         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T12:20:44,791   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 -UNDEBUG -I/usr/include/python3.9 -c src/genotypedptable.cpp -o build/temp.linux-armv7l-3.9/src/genotypedptable.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:46,907   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’:
2021-07-29T12:20:46,908   src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable]
2021-07-29T12:20:46,908      61 |     size_t column_count = input_column_iterator.get_column_count();
2021-07-29T12:20:46,908         |            ^~~~~~~~~~~~
2021-07-29T12:20:46,962   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’:
2021-07-29T12:20:46,962   src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable]
2021-07-29T12:20:46,962      91 |     unsigned int transmission_configurations = pow(4, pedigree->triple_count());
2021-07-29T12:20:46,962         |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:46,965   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’:
2021-07-29T12:20:46,966   src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2021-07-29T12:20:46,966     152 |         if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) {
2021-07-29T12:20:46,966         |                       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2021-07-29T12:20:46,969   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’:
2021-07-29T12:20:46,969   src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable]
2021-07-29T12:20:46,970     178 |     size_t k = (size_t)sqrt(input_column_iterator.get_column_count());
2021-07-29T12:20:46,970         |            ^
2021-07-29T12:20:50,695   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 -UNDEBUG -I/usr/include/python3.9 -c src/genotyper.cpp -o build/temp.linux-armv7l-3.9/src/genotyper.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:53,052   In file included from /usr/include/c++/10/vector:72,
2021-07-29T12:20:53,052                    from src/columniterator.h:4,
2021-07-29T12:20:53,052                    from src/genotyper.cpp:6:
2021-07-29T12:20:53,052   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Genotype&}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’:
2021-07-29T12:20:53,053   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
2021-07-29T12:20:53,053     426 |       vector<_Tp, _Alloc>::
2021-07-29T12:20:53,053         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:53,243   In file included from /usr/include/c++/10/vector:67,
2021-07-29T12:20:53,243                    from src/columniterator.h:4,
2021-07-29T12:20:53,243                    from src/genotyper.cpp:6:
2021-07-29T12:20:53,243   /usr/include/c++/10/bits/stl_vector.h: In function ‘void compute_genotypes(const ReadSet&, std::vector<Genotype>*, std::vector<GenotypeDistribution>*, std::vector<unsigned int>*)’:
2021-07-29T12:20:53,243   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2021-07-29T12:20:53,244    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T12:20:53,244         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T12:20:53,411   In file included from /usr/include/c++/10/vector:72,
2021-07-29T12:20:53,411                    from src/columniterator.h:4,
2021-07-29T12:20:53,411                    from src/genotyper.cpp:6:
2021-07-29T12:20:53,412   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’:
2021-07-29T12:20:53,412   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
2021-07-29T12:20:53,412     426 |       vector<_Tp, _Alloc>::
2021-07-29T12:20:53,412         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:53,524   /usr/include/c++/10/bits/vector.tcc: In function ‘void compute_polyploid_genotypes(const ReadSet&, size_t, std::vector<Genotype>*, std::vector<unsigned int>*)’:
2021-07-29T12:20:53,524   /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2021-07-29T12:20:53,524     121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2021-07-29T12:20:53,524         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:20:53,525   In file included from /usr/include/c++/10/vector:67,
2021-07-29T12:20:53,525                    from src/columniterator.h:4,
2021-07-29T12:20:53,526                    from src/genotyper.cpp:6:
2021-07-29T12:20:53,526   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2021-07-29T12:20:53,526    1198 |    _M_realloc_insert(end(), __x);
2021-07-29T12:20:53,526         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2021-07-29T12:20:53,933   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 -UNDEBUG -I/usr/include/python3.9 -c src/graycodes.cpp -o build/temp.linux-armv7l-3.9/src/graycodes.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:54,995   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 -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/balancedcombinations.cpp -o build/temp.linux-armv7l-3.9/src/hapchat/balancedcombinations.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:20:58,655   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 -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/basictypes.cpp -o build/temp.linux-armv7l-3.9/src/hapchat/basictypes.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:00,287   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 -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/binomialcoefficient.cpp -o build/temp.linux-armv7l-3.9/src/hapchat/binomialcoefficient.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:02,965   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 -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/hapchatcolumniterator.cpp -o build/temp.linux-armv7l-3.9/src/hapchat/hapchatcolumniterator.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:05,261   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 -UNDEBUG -I/usr/include/python3.9 -c src/hapchat/hapchatcore.cpp -o build/temp.linux-armv7l-3.9/src/hapchat/hapchatcore.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:07,432   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2021-07-29T12:21:07,432   src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2021-07-29T12:21:07,432     145 |   Counter counter_columns;
2021-07-29T12:21:07,432         |           ^~~~~~~~~~~~~~~
2021-07-29T12:21:07,442   src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2021-07-29T12:21:07,442   src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,442     208 |   return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2021-07-29T12:21:07,443         |                                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,580   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector<bool>&, std::vector<bool>&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’:
2021-07-29T12:21:07,581   src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable]
2021-07-29T12:21:07,581     939 |    int old_k = k_j[input_pointer];
2021-07-29T12:21:07,581         |        ^~~~~
2021-07-29T12:21:07,598   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, std::vector<std::bitset<64> >&, std::vector<unsigned int>&, const bool&)’:
2021-07-29T12:21:07,599   src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,599    1114 |          (colJ[j].get_read_id() != -1) &&
2021-07-29T12:21:07,599         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,599   src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,599    1115 |          (colQ[i].get_read_id() != -1)) {
2021-07-29T12:21:07,600         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,601   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2021-07-29T12:21:07,601   src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,601    1159 |   while(cov < column.size() && column[cov].get_read_id() != -1) {
2021-07-29T12:21:07,602         |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,606   src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2021-07-29T12:21:07,606   src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,606    1294 |          (colJ[j].get_read_id() != -1) &&
2021-07-29T12:21:07,607         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,607   src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,607    1295 |          (colQ[i].get_read_id() != -1)) {
2021-07-29T12:21:07,607         |           ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:07,609   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector<std::vector<Entry> >&, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<Cost>&, const Pointer&, const Column&, std::vector<bool>&, const Counter&)’:
2021-07-29T12:21:07,610   src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:07,610    1350 |   if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2021-07-29T12:21:07,610         |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2021-07-29T12:21:08,612   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 -UNDEBUG -I/usr/include/python3.9 -c src/indexset.cpp -o build/temp.linux-armv7l-3.9/src/indexset.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:10,199   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 -UNDEBUG -I/usr/include/python3.9 -c src/pedigree.cpp -o build/temp.linux-armv7l-3.9/src/pedigree.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:11,611   In file included from /usr/include/c++/10/cassert:44,
2021-07-29T12:21:11,612                    from src/pedigree.cpp:4:
2021-07-29T12:21:11,612   src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector<Genotype*>, std::vector<PhredGenotypeLikelihoods*>)’:
2021-07-29T12:21:11,612   src/pedigree.cpp:32:26: warning: comparison of integer expressions of different signedness: ‘std::vector<Genotype*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:21:11,612      32 |  assert(genotypes.size() == variant_count);
2021-07-29T12:21:11,612         |         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2021-07-29T12:21:11,613   src/pedigree.cpp:33:37: warning: comparison of integer expressions of different signedness: ‘std::vector<PhredGenotypeLikelihoods*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2021-07-29T12:21:11,613      33 |  assert(genotype_likelihoods.size() == variant_count);
2021-07-29T12:21:11,613         |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2021-07-29T12:21:11,622   src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’:
2021-07-29T12:21:11,622   src/pedigree.cpp:70:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2021-07-29T12:21:11,622      70 |  assert(variant_index < variant_count);
2021-07-29T12:21:11,622         |         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2021-07-29T12:21:11,622   src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’:
2021-07-29T12:21:11,623   src/pedigree.cpp:81:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2021-07-29T12:21:11,623      81 |  assert(variant_index < variant_count);
2021-07-29T12:21:11,623         |         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2021-07-29T12:21:11,634   src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’:
2021-07-29T12:21:11,635   src/pedigree.cpp:112:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
2021-07-29T12:21:11,635     112 |   for (size_t j=0; j<variant_count; ++j) {
2021-07-29T12:21:11,635         |                    ~^~~~~~~~~~~~~~
2021-07-29T12:21:13,875   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 -UNDEBUG -I/usr/include/python3.9 -c src/pedigreecolumncostcomputer.cpp -o build/temp.linux-armv7l-3.9/src/pedigreecolumncostcomputer.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:15,590   src/pedigreecolumncostcomputer.cpp: In constructor ‘PedigreeColumnCostComputer::PedigreeColumnCostComputer(const std::vector<const Entry*>&, size_t, const std::vector<unsigned int>&, const Pedigree*, const PedigreePartitions&, bool)’:
2021-07-29T12:21:15,591   src/pedigreecolumncostcomputer.cpp:25:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2021-07-29T12:21:15,591      25 |  for (unsigned int i = 0; i < (1<<pedigree_partitions.count()); ++i) {
2021-07-29T12:21:15,591         |                           ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:21:15,628   src/pedigreecolumncostcomputer.cpp: In member function ‘std::vector<PedigreeColumnCostComputer::phased_variant_t> PedigreeColumnCostComputer::get_alleles()’:
2021-07-29T12:21:15,628   src/pedigreecolumncostcomputer.cpp:119:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable]
2021-07-29T12:21:15,628     119 |  unsigned int second_best_cost = numeric_limits < unsigned int >::max();
2021-07-29T12:21:15,628         |               ^~~~~~~~~~~~~~~~
2021-07-29T12:21:16,747   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 -UNDEBUG -I/usr/include/python3.9 -c src/pedigreedptable.cpp -o build/temp.linux-armv7l-3.9/src/pedigreedptable.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:22,935   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 -UNDEBUG -I/usr/include/python3.9 -c src/pedigreepartitions.cpp -o build/temp.linux-armv7l-3.9/src/pedigreepartitions.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:24,866   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 -UNDEBUG -I/usr/include/python3.9 -c src/phredgenotypelikelihoods.cpp -o build/temp.linux-armv7l-3.9/src/phredgenotypelikelihoods.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:26,481   In file included from /usr/include/c++/10/vector:72,
2021-07-29T12:21:26,481                    from src/genotype.h:4,
2021-07-29T12:21:26,481                    from src/phredgenotypelikelihoods.h:5,
2021-07-29T12:21:26,481                    from src/phredgenotypelikelihoods.cpp:4:
2021-07-29T12:21:26,482   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’:
2021-07-29T12:21:26,482   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
2021-07-29T12:21:26,482     426 |       vector<_Tp, _Alloc>::
2021-07-29T12:21:26,482         |       ^~~~~~~~~~~~~~~~~~~
2021-07-29T12:21:26,514   /usr/include/c++/10/bits/vector.tcc: In member function ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector<Genotype>&) const’:
2021-07-29T12:21:26,515   /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
2021-07-29T12:21:26,515     121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2021-07-29T12:21:26,515         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2021-07-29T12:21:26,718   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 -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/clustereditingsolution.cpp -o build/temp.linux-armv7l-3.9/src/polyphase/clustereditingsolution.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:28,197   In file included from src/polyphase/clustereditingsolution.h:4,
2021-07-29T12:21:28,197                    from src/polyphase/clustereditingsolution.cpp:1:
2021-07-29T12:21:28,197   src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’:
2021-07-29T12:21:28,197   src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:28,198     225 |         uint64_t mask = (1UL << 63); // fill in values right-to-left
2021-07-29T12:21:28,198         |                          ~~~~^~~~~
2021-07-29T12:21:28,627   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 -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/clustereditingsolver.cpp -o build/temp.linux-armv7l-3.9/src/polyphase/clustereditingsolver.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:30,110   In file included from src/polyphase/clustereditingsolution.h:4,
2021-07-29T12:21:30,110                    from src/polyphase/clustereditingsolver.h:10,
2021-07-29T12:21:30,110                    from src/polyphase/clustereditingsolver.cpp:1:
2021-07-29T12:21:30,110   src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’:
2021-07-29T12:21:30,110   src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:30,111     225 |         uint64_t mask = (1UL << 63); // fill in values right-to-left
2021-07-29T12:21:30,111         |                          ~~~~^~~~~
2021-07-29T12:21:30,802   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 -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/edgeheap.cpp -o build/temp.linux-armv7l-3.9/src/polyphase/edgeheap.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:32,510   In file included from src/polyphase/edgeheap.h:6,
2021-07-29T12:21:32,510                    from src/polyphase/edgeheap.cpp:1:
2021-07-29T12:21:32,511   src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’:
2021-07-29T12:21:32,511   src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:32,511     225 |         uint64_t mask = (1UL << 63); // fill in values right-to-left
2021-07-29T12:21:32,511         |                          ~~~~^~~~~
2021-07-29T12:21:34,899   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 -UNDEBUG -I/usr/include/python3.9 -c src/polyphase/haplothreader.cpp -o build/temp.linux-armv7l-3.9/src/polyphase/haplothreader.o -std=c++11 -Werror=return-type -Werror=narrowing
2021-07-29T12:21:36,309   In file included from src/polyphase/haplothreader.cpp:1:
2021-07-29T12:21:36,309   src/polyphase/haplothreader.h:30:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:36,309      30 |         31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2021-07-29T12:21:36,309         |                                             ~~~~~^~~~~
2021-07-29T12:21:36,310   src/polyphase/haplothreader.h:31:14: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:36,310      31 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2021-07-29T12:21:36,310         |         ~~~~~^~~~~
2021-07-29T12:21:36,310   src/polyphase/haplothreader.h:31:26: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:36,310      31 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2021-07-29T12:21:36,310         |                     ~~~~~^~~~~
2021-07-29T12:21:36,311   src/polyphase/haplothreader.h:31:38: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:36,311      31 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2021-07-29T12:21:36,311         |                                 ~~~~~^~~~~
2021-07-29T12:21:36,311   src/polyphase/haplothreader.h:31:50: warning: left shift count >= width of type [-Wshift-count-overflow]
2021-07-29T12:21:36,311      31 |         31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2021-07-29T12:21:36,311         |                                             ~~~~~^~~~~
2021-07-29T12:21:36,312   src/polyphase/haplothreader.h:30:50: error: right operand of shift expression ‘(31 << 35)’ is greater than or equal to the precision 32 of the left operand [-fpermissive]
2021-07-29T12:21:36,312      30 |         31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2021-07-29T12:21:36,312         |                                             ~~~~~^~~~~
2021-07-29T12:21:36,740   src/polyphase/haplothreader.cpp: In member function ‘std::vector<std::vector<unsigned int> > HaploThreader::computePaths(Position, Position, const std::vector<std::vector<unsigned int> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<unsigned int> >&, const std::vector<std::unordered_map<unsigned int, unsigned int> >&, Position) const’:
2021-07-29T12:21:36,740   src/polyphase/haplothreader.cpp:253:18: warning: unused variable ‘allRows’ [-Wunused-variable]
2021-07-29T12:21:36,740     253 |         uint32_t allRows = column.size();
2021-07-29T12:21:36,741         |                  ^~~~~~~
2021-07-29T12:21:37,565   error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1
2021-07-29T12:21:37,634   Building wheel for whatshap (setup.py): finished with status 'error'
2021-07-29T12:21:37,634   ERROR: Failed building wheel for whatshap
2021-07-29T12:21:37,635   Running setup.py clean for whatshap
2021-07-29T12:21:37,635   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-4r1dbhn6/whatshap_8ac6baeff3bb42d8b0350d627f124f58/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'"'"'))' clean --all
2021-07-29T12:21:38,839   running clean
2021-07-29T12:21:38,842   removing 'build/temp.linux-armv7l-3.9' (and everything under it)
2021-07-29T12:21:38,858   removing 'build/lib.linux-armv7l-3.9' (and everything under it)
2021-07-29T12:21:38,871   'build/bdist.linux-armv7l' does not exist -- can't clean it
2021-07-29T12:21:38,872   'build/scripts-3.9' does not exist -- can't clean it
2021-07-29T12:21:38,873   removing 'build'
2021-07-29T12:21:38,934 Failed to build whatshap
2021-07-29T12:21:38,935 ERROR: Failed to build one or more wheels
2021-07-29T12:21:38,935 Exception information:
2021-07-29T12:21:38,935 Traceback (most recent call last):
2021-07-29T12:21:38,935   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main
2021-07-29T12:21:38,935     status = self.run(options, args)
2021-07-29T12:21:38,935   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper
2021-07-29T12:21:38,935     return func(self, options, args)
2021-07-29T12:21:38,935   File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run
2021-07-29T12:21:38,935     raise CommandError(
2021-07-29T12:21:38,935 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2021-07-29T12:21:38,939 Removed build tracker: '/tmp/pip-req-tracker-luwdjrmt'