2021-07-16T09:49:35,962 Created temporary directory: /tmp/pip-ephem-wheel-cache-r6mb2zuf 2021-07-16T09:49:35,964 Created temporary directory: /tmp/pip-req-tracker-9vc15zxo 2021-07-16T09:49:35,965 Initialized build tracking at /tmp/pip-req-tracker-9vc15zxo 2021-07-16T09:49:35,965 Created build tracker: /tmp/pip-req-tracker-9vc15zxo 2021-07-16T09:49:35,965 Entered build tracker: /tmp/pip-req-tracker-9vc15zxo 2021-07-16T09:49:35,966 Created temporary directory: /tmp/pip-wheel-xq4isnzx 2021-07-16T09:49:35,992 1 location(s) to search for versions of whatshap: 2021-07-16T09:49:35,992 * https://pypi.org/simple/whatshap/ 2021-07-16T09:49:35,993 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-07-16T09:49:35,993 Getting page https://pypi.org/simple/whatshap/ 2021-07-16T09:49:35,995 Found index url https://pypi.org/simple 2021-07-16T09:49:36,171 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 2021-07-16T09:49:36,171 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 2021-07-16T09:49:36,171 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 2021-07-16T09:49:36,172 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 2021-07-16T09:49:36,172 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 2021-07-16T09:49:36,172 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 2021-07-16T09:49:36,173 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 2021-07-16T09:49:36,173 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 2021-07-16T09:49:36,173 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 2021-07-16T09:49:36,173 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 2021-07-16T09:49:36,191 Skipping link: none of the wheel's tags (cp34-cp34m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,191 Skipping link: none of the wheel's tags (cp35-cp35m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,192 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,192 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux1_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,193 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 2021-07-16T09:49:36,194 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,194 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,195 Skipping link: none of the wheel's tags (cp38-cp38-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,195 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 2021-07-16T09:49:36,196 Skipping link: none of the wheel's tags (cp36-cp36m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,196 Skipping link: none of the wheel's tags (cp37-cp37m-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,197 Skipping link: none of the wheel's tags (cp38-cp38-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,197 Skipping link: none of the wheel's tags (cp39-cp39-manylinux2010_x86_64) are compatible (run pip debug --verbose to show compatible tags): 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) 2021-07-16T09:49:36,198 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 2021-07-16T09:49:36,198 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2021-07-16T09:49:36,201 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-07-16T09:49:36,219 Collecting whatshap==1.0 2021-07-16T09:49:36,221 Created temporary directory: /tmp/pip-unpack-npbmgt5f 2021-07-16T09:49:36,794 Downloading whatshap-1.0.tar.gz (579 kB) 2021-07-16T09:49:37,340 Added whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 to build tracker '/tmp/pip-req-tracker-9vc15zxo' 2021-07-16T09:49:37,341 Running setup.py (path:/tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0/setup.py) egg_info for package whatshap 2021-07-16T09:49:37,342 Created temporary directory: /tmp/pip-pip-egg-info-hw7f2jk3 2021-07-16T09:49:37,342 Running command python setup.py egg_info 2021-07-16T09:49:38,339 running egg_info 2021-07-16T09:49:38,341 creating /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info 2021-07-16T09:49:38,343 writing /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/PKG-INFO 2021-07-16T09:49:38,344 writing dependency_links to /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/dependency_links.txt 2021-07-16T09:49:38,346 writing entry points to /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/entry_points.txt 2021-07-16T09:49:38,347 writing requirements to /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/requires.txt 2021-07-16T09:49:38,348 writing top-level names to /tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/top_level.txt 2021-07-16T09:49:38,350 writing manifest file '/tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/SOURCES.txt' 2021-07-16T09:49:38,529 reading manifest file '/tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/SOURCES.txt' 2021-07-16T09:49:38,535 writing manifest file '/tmp/pip-pip-egg-info-hw7f2jk3/whatshap.egg-info/SOURCES.txt' 2021-07-16T09:49:38,609 Source in /tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0 has version 1.0, which satisfies requirement whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 2021-07-16T09:49:38,610 Removed whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 from build tracker '/tmp/pip-req-tracker-9vc15zxo' 2021-07-16T09:49:38,616 Created temporary directory: /tmp/pip-unpack-xowv11so 2021-07-16T09:49:38,617 Building wheels for collected packages: whatshap 2021-07-16T09:49:38,621 Created temporary directory: /tmp/pip-wheel-wdkfxudz 2021-07-16T09:49:38,621 Building wheel for whatshap (setup.py): started 2021-07-16T09:49:38,621 Destination directory: /tmp/pip-wheel-wdkfxudz 2021-07-16T09:49:38,621 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0/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-wdkfxudz 2021-07-16T09:49:39,627 running bdist_wheel 2021-07-16T09:49:39,631 running build 2021-07-16T09:49:39,632 running build_py 2021-07-16T09:49:39,772 creating build 2021-07-16T09:49:39,772 creating build/lib.linux-armv7l-3.9 2021-07-16T09:49:39,773 creating build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,774 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,778 copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,780 copying whatshap/variants.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,782 copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,784 copying whatshap/timer.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,785 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,788 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,789 copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,791 copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,794 copying whatshap/threading.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,796 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,798 copying whatshap/_version.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,800 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,802 copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,803 copying whatshap/utils.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,805 copying whatshap/math.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,806 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,808 copying whatshap/merge.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,811 creating build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,812 copying whatshap/cli/split.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,814 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,816 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,818 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,821 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,825 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,828 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,831 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,834 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,836 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,839 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-3.9/whatshap/cli 2021-07-16T09:49:39,844 running build_ext 2021-07-16T09:49:39,850 building 'whatshap.core' extension 2021-07-16T09:49:39,851 creating build/temp.linux-armv7l-3.9 2021-07-16T09:49:39,851 creating build/temp.linux-armv7l-3.9/src 2021-07-16T09:49:39,853 creating build/temp.linux-armv7l-3.9/src/hapchat 2021-07-16T09:49:39,854 creating build/temp.linux-armv7l-3.9/src/polyphase 2021-07-16T09:49:39,855 creating build/temp.linux-armv7l-3.9/whatshap 2021-07-16T09:49:39,855 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 2021-07-16T09:49:41,475 In file included from /usr/include/c++/10/cassert:44, 2021-07-16T09:49:41,475 from src/backwardcolumniterator.cpp:1: 2021-07-16T09:49:41,475 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2021-07-16T09:49:41,475 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:41,475 121 | assert(k < positions->size()); 2021-07-16T09:49:41,476 | ~~^~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:41,477 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:49:41,477 140 | assert(active_entry < read->getVariantCount()); 2021-07-16T09:49:41,477 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:43,026 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 2021-07-16T09:49:43,126 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 2021-07-16T09:49:44,224 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2021-07-16T09:49:44,224 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:44,225 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2021-07-16T09:49:44,225 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:44,225 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:49:44,225 92 | if(m != -1) { 2021-07-16T09:49:44,225 | ~~^~~~~ 2021-07-16T09:49:44,226 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2021-07-16T09:49:44,226 89 | unsigned int s = 1; 2021-07-16T09:49:44,226 | ^ 2021-07-16T09:49:44,504 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 2021-07-16T09:49:45,584 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2021-07-16T09:49:45,584 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:45,584 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:45,585 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:45,588 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T09:49:45,588 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2021-07-16T09:49:47,648 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:49:47,648 105 | assert(list_it->active_entry < read->getVariantCount()); 2021-07-16T09:49:47,648 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:47,666 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2021-07-16T09:49:47,666 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:49:47,666 161 | assert(active_entry < read->getVariantCount()); 2021-07-16T09:49:47,667 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:49,275 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 2021-07-16T09:49:50,264 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 2021-07-16T09:49:52,659 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 2021-07-16T09:49:55,412 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -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 2021-07-16T09:49:56,602 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2021-07-16T09:49:56,603 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:49:56,603 55 | if (i == best_index) continue; 2021-07-16T09:49:56,603 | ~~^~~~~~~~~~~~~ 2021-07-16T09:49:57,061 In file included from /usr/include/c++/10/vector:72, 2021-07-16T09:49:57,061 from src/genotypedistribution.h:4, 2021-07-16T09:49:57,061 from src/genotypedistribution.cpp:5: 2021-07-16T09:49:57,062 /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]’: 2021-07-16T09:49:57,062 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-16T09:49:57,062 426 | vector<_Tp, _Alloc>:: 2021-07-16T09:49:57,062 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:57,095 In file included from /usr/include/c++/10/vector:67, 2021-07-16T09:49:57,095 from src/genotypedistribution.h:4, 2021-07-16T09:49:57,095 from src/genotypedistribution.cpp:5: 2021-07-16T09:49:57,095 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2021-07-16T09:49:57,095 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:49:57,096 1198 | _M_realloc_insert(end(), __x); 2021-07-16T09:49:57,096 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-16T09:49:57,096 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:49:57,096 1198 | _M_realloc_insert(end(), __x); 2021-07-16T09:49:57,096 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-16T09:49:57,096 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:49:57,096 1198 | _M_realloc_insert(end(), __x); 2021-07-16T09:49:57,097 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-16T09:49:57,280 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 2021-07-16T09:49:59,397 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2021-07-16T09:49:59,398 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2021-07-16T09:49:59,398 61 | size_t column_count = input_column_iterator.get_column_count(); 2021-07-16T09:49:59,398 | ^~~~~~~~~~~~ 2021-07-16T09:49:59,452 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2021-07-16T09:49:59,452 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2021-07-16T09:49:59,452 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2021-07-16T09:49:59,452 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:49:59,456 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2021-07-16T09:49:59,456 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T09:49:59,456 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2021-07-16T09:49:59,456 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-16T09:49:59,459 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2021-07-16T09:49:59,460 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2021-07-16T09:49:59,460 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2021-07-16T09:49:59,460 | ^ 2021-07-16T09:50:03,223 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 2021-07-16T09:50:05,552 In file included from /usr/include/c++/10/vector:72, 2021-07-16T09:50:05,553 from src/columniterator.h:4, 2021-07-16T09:50:05,553 from src/genotyper.cpp:6: 2021-07-16T09:50:05,553 /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]’: 2021-07-16T09:50:05,553 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-16T09:50:05,553 426 | vector<_Tp, _Alloc>:: 2021-07-16T09:50:05,553 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T09:50:05,745 In file included from /usr/include/c++/10/vector:67, 2021-07-16T09:50:05,745 from src/columniterator.h:4, 2021-07-16T09:50:05,745 from src/genotyper.cpp:6: 2021-07-16T09:50:05,746 /usr/include/c++/10/bits/stl_vector.h: In function ‘void compute_genotypes(const ReadSet&, std::vector*, std::vector*, std::vector*)’: 2021-07-16T09:50:05,746 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:50:05,746 1198 | _M_realloc_insert(end(), __x); 2021-07-16T09:50:05,746 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-16T09:50:05,914 In file included from /usr/include/c++/10/vector:72, 2021-07-16T09:50:05,915 from src/columniterator.h:4, 2021-07-16T09:50:05,915 from src/genotyper.cpp:6: 2021-07-16T09:50:05,915 /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]’: 2021-07-16T09:50:05,915 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-16T09:50:05,915 426 | vector<_Tp, _Alloc>:: 2021-07-16T09:50:05,915 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T09:50:06,028 /usr/include/c++/10/bits/vector.tcc: In function ‘void compute_polyploid_genotypes(const ReadSet&, size_t, std::vector*, std::vector*)’: 2021-07-16T09:50:06,028 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:50:06,028 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-16T09:50:06,029 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:50:06,030 In file included from /usr/include/c++/10/vector:67, 2021-07-16T09:50:06,030 from src/columniterator.h:4, 2021-07-16T09:50:06,030 from src/genotyper.cpp:6: 2021-07-16T09:50:06,030 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:50:06,031 1198 | _M_realloc_insert(end(), __x); 2021-07-16T09:50:06,031 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-16T09:50:06,441 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 2021-07-16T09:50:07,477 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 2021-07-16T09:50:11,096 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 2021-07-16T09:50:12,725 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 2021-07-16T09:50:15,289 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 2021-07-16T09:50:17,538 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 2021-07-16T09:50:19,678 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2021-07-16T09:50:19,679 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2021-07-16T09:50:19,679 145 | Counter counter_columns; 2021-07-16T09:50:19,679 | ^~~~~~~~~~~~~~~ 2021-07-16T09:50:19,688 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2021-07-16T09:50:19,689 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,689 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2021-07-16T09:50:19,689 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,827 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2021-07-16T09:50:19,828 src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2021-07-16T09:50:19,828 939 | int old_k = k_j[input_pointer]; 2021-07-16T09:50:19,828 | ^~~~~ 2021-07-16T09:50:19,846 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector >&, std::vector >&, std::vector >&, std::vector&, const bool&)’: 2021-07-16T09:50:19,846 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,846 1114 | (colJ[j].get_read_id() != -1) && 2021-07-16T09:50:19,846 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,846 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,847 1115 | (colQ[i].get_read_id() != -1)) { 2021-07-16T09:50:19,847 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,848 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2021-07-16T09:50:19,848 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,849 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2021-07-16T09:50:19,849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,853 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2021-07-16T09:50:19,853 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,853 1294 | (colJ[j].get_read_id() != -1) && 2021-07-16T09:50:19,854 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,854 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,854 1295 | (colQ[i].get_read_id() != -1)) { 2021-07-16T09:50:19,854 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:19,856 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector >&, std::vector&, std::vector&, std::vector&, const Pointer&, const Column&, std::vector&, const Counter&)’: 2021-07-16T09:50:19,857 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:19,857 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2021-07-16T09:50:19,857 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T09:50:20,861 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 2021-07-16T09:50:22,425 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 2021-07-16T09:50:23,805 In file included from /usr/include/c++/10/cassert:44, 2021-07-16T09:50:23,805 from src/pedigree.cpp:4: 2021-07-16T09:50:23,806 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2021-07-16T09:50:23,806 src/pedigree.cpp:32:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:50:23,806 32 | assert(genotypes.size() == variant_count); 2021-07-16T09:50:23,806 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-16T09:50:23,807 src/pedigree.cpp:33:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T09:50:23,807 33 | assert(genotype_likelihoods.size() == variant_count); 2021-07-16T09:50:23,807 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-16T09:50:23,817 src/pedigree.cpp: In member function ‘const Genotype* Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2021-07-16T09:50:23,817 src/pedigree.cpp:70:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-16T09:50:23,817 70 | assert(variant_index < variant_count); 2021-07-16T09:50:23,817 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-16T09:50:23,818 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2021-07-16T09:50:23,819 src/pedigree.cpp:81:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-16T09:50:23,819 81 | assert(variant_index < variant_count); 2021-07-16T09:50:23,819 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-16T09:50:23,831 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2021-07-16T09:50:23,831 src/pedigree.cpp:112:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2021-07-16T09:50:23,831 112 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2021-07-16T09:50:27,753 src/pedigreecolumncostcomputer.cpp:25:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T09:50:27,753 25 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2021-07-16T09:50:27,790 src/pedigreecolumncostcomputer.cpp:119:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2021-07-16T09:50:27,790 119 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2021-07-16T09:50:27,790 | ^~~~~~~~~~~~~~~~ 2021-07-16T09:50:28,894 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 2021-07-16T09:50:35,074 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 2021-07-16T09:50:36,972 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 2021-07-16T09:50:38,550 In file included from /usr/include/c++/10/vector:72, 2021-07-16T09:50:38,550 from src/genotype.h:4, 2021-07-16T09:50:38,550 from src/phredgenotypelikelihoods.h:5, 2021-07-16T09:50:38,550 from src/phredgenotypelikelihoods.cpp:4: 2021-07-16T09:50:38,551 /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]’: 2021-07-16T09:50:38,551 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-16T09:50:38,551 426 | vector<_Tp, _Alloc>:: 2021-07-16T09:50:38,551 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T09:50:38,583 /usr/include/c++/10/bits/vector.tcc: In member function ‘void PhredGenotypeLikelihoods::get_genotypes(std::vector&) const’: 2021-07-16T09:50:38,583 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2021-07-16T09:50:38,583 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-16T09:50:38,583 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T09:50:38,727 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 2021-07-16T09:50:40,156 In file included from src/polyphase/clustereditingsolution.h:4, 2021-07-16T09:50:40,156 from src/polyphase/clustereditingsolution.cpp:1: 2021-07-16T09:50:40,156 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2021-07-16T09:50:40,156 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:40,156 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2021-07-16T09:50:40,156 | ~~~~^~~~~ 2021-07-16T09:50:40,585 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 2021-07-16T09:50:42,037 In file included from src/polyphase/clustereditingsolution.h:4, 2021-07-16T09:50:42,038 from src/polyphase/clustereditingsolver.h:10, 2021-07-16T09:50:42,038 from src/polyphase/clustereditingsolver.cpp:1: 2021-07-16T09:50:42,038 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2021-07-16T09:50:42,038 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:42,038 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2021-07-16T09:50:42,038 | ~~~~^~~~~ 2021-07-16T09:50:42,730 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 2021-07-16T09:50:44,171 In file included from src/polyphase/edgeheap.h:6, 2021-07-16T09:50:44,171 from src/polyphase/edgeheap.cpp:1: 2021-07-16T09:50:44,171 src/polyphase/staticsparsegraph.h: In member function ‘std::string StaticSparseGraph::int2bin(uint64_t)’: 2021-07-16T09:50:44,171 src/polyphase/staticsparsegraph.h:225:30: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:44,171 225 | uint64_t mask = (1UL << 63); // fill in values right-to-left 2021-07-16T09:50:44,171 | ~~~~^~~~~ 2021-07-16T09:50:46,486 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 2021-07-16T09:50:47,839 In file included from src/polyphase/haplothreader.cpp:1: 2021-07-16T09:50:47,840 src/polyphase/haplothreader.h:30:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:47,840 30 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2021-07-16T09:50:47,840 | ~~~~~^~~~~ 2021-07-16T09:50:47,840 src/polyphase/haplothreader.h:31:14: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:47,840 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-07-16T09:50:47,841 | ~~~~~^~~~~ 2021-07-16T09:50:47,841 src/polyphase/haplothreader.h:31:26: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:47,841 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-07-16T09:50:47,841 | ~~~~~^~~~~ 2021-07-16T09:50:47,841 src/polyphase/haplothreader.h:31:38: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:47,841 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-07-16T09:50:47,841 | ~~~~~^~~~~ 2021-07-16T09:50:47,842 src/polyphase/haplothreader.h:31:50: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-07-16T09:50:47,842 31 | 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-07-16T09:50:47,842 | ~~~~~^~~~~ 2021-07-16T09:50:47,842 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] 2021-07-16T09:50:47,843 30 | 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2021-07-16T09:50:47,843 | ~~~~~^~~~~ 2021-07-16T09:50:48,268 src/polyphase/haplothreader.cpp: In member function ‘std::vector > HaploThreader::computePaths(Position, Position, const std::vector >&, const std::vector >&, const std::vector >&, const std::vector >&, Position) const’: 2021-07-16T09:50:48,268 src/polyphase/haplothreader.cpp:253:18: warning: unused variable ‘allRows’ [-Wunused-variable] 2021-07-16T09:50:48,268 253 | uint32_t allRows = column.size(); 2021-07-16T09:50:48,269 | ^~~~~~~ 2021-07-16T09:50:49,097 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-16T09:50:49,162 Building wheel for whatshap (setup.py): finished with status 'error' 2021-07-16T09:50:49,163 ERROR: Failed building wheel for whatshap 2021-07-16T09:50:49,163 Running setup.py clean for whatshap 2021-07-16T09:50:49,164 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-xq4isnzx/whatshap_4211eaf823f94593a41a7db654e1ecd0/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 2021-07-16T09:50:50,232 running clean 2021-07-16T09:50:50,235 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-16T09:50:50,250 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-16T09:50:50,259 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-16T09:50:50,260 'build/scripts-3.9' does not exist -- can't clean it 2021-07-16T09:50:50,260 removing 'build' 2021-07-16T09:50:50,317 Failed to build whatshap 2021-07-16T09:50:50,318 ERROR: Failed to build one or more wheels 2021-07-16T09:50:50,318 Exception information: 2021-07-16T09:50:50,318 Traceback (most recent call last): 2021-07-16T09:50:50,318 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-16T09:50:50,318 status = self.run(options, args) 2021-07-16T09:50:50,318 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-16T09:50:50,318 return func(self, options, args) 2021-07-16T09:50:50,318 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-16T09:50:50,318 raise CommandError( 2021-07-16T09:50:50,318 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-16T09:50:50,322 Removed build tracker: '/tmp/pip-req-tracker-9vc15zxo'