2021-07-13T10:27:19,406 Created temporary directory: /tmp/pip-ephem-wheel-cache-v_wtyxhu 2021-07-13T10:27:19,409 Created temporary directory: /tmp/pip-req-tracker-tnrh_d5q 2021-07-13T10:27:19,409 Initialized build tracking at /tmp/pip-req-tracker-tnrh_d5q 2021-07-13T10:27:19,410 Created build tracker: /tmp/pip-req-tracker-tnrh_d5q 2021-07-13T10:27:19,410 Entered build tracker: /tmp/pip-req-tracker-tnrh_d5q 2021-07-13T10:27:19,410 Created temporary directory: /tmp/pip-wheel-fqhbdcwt 2021-07-13T10:27:19,457 1 location(s) to search for versions of whatshap: 2021-07-13T10:27:19,457 * https://pypi.org/simple/whatshap/ 2021-07-13T10:27:19,457 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-07-13T10:27:19,458 Getting page https://pypi.org/simple/whatshap/ 2021-07-13T10:27:19,459 Found index url https://pypi.org/simple 2021-07-13T10:27:19,652 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 2021-07-13T10:27:19,652 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 2021-07-13T10:27:19,653 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 2021-07-13T10:27:19,653 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 2021-07-13T10:27:19,653 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 2021-07-13T10:27:19,653 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 2021-07-13T10:27:19,654 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 2021-07-13T10:27:19,654 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 2021-07-13T10:27:19,654 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 2021-07-13T10:27:19,655 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 2021-07-13T10:27:19,672 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) 2021-07-13T10:27:19,673 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) 2021-07-13T10:27:19,673 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) 2021-07-13T10:27:19,673 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) 2021-07-13T10:27:19,674 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 2021-07-13T10:27:19,675 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) 2021-07-13T10:27:19,675 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) 2021-07-13T10:27:19,676 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) 2021-07-13T10:27:19,676 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 2021-07-13T10:27:19,677 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) 2021-07-13T10:27:19,677 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) 2021-07-13T10:27:19,678 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) 2021-07-13T10:27:19,678 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) 2021-07-13T10:27:19,679 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 2021-07-13T10:27:19,679 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2021-07-13T10:27:19,682 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-07-13T10:27:19,703 Collecting whatshap==0.16 2021-07-13T10:27:19,705 Created temporary directory: /tmp/pip-unpack-48ch_uvn 2021-07-13T10:27:20,312 Downloading whatshap-0.16.tar.gz (530 kB) 2021-07-13T10:27:20,874 Added whatshap==0.16 from https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz#sha256=1df54d8705fb0451cc0a640918842481087f7b741778dfb4100cc1f4f60f48fe to build tracker '/tmp/pip-req-tracker-tnrh_d5q' 2021-07-13T10:27:20,876 Running setup.py (path:/tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e/setup.py) egg_info for package whatshap 2021-07-13T10:27:20,876 Created temporary directory: /tmp/pip-pip-egg-info-nc52_1bl 2021-07-13T10:27:20,877 Running command python setup.py egg_info 2021-07-13T10:27:22,178 running egg_info 2021-07-13T10:27:22,181 creating /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info 2021-07-13T10:27:22,182 writing /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/PKG-INFO 2021-07-13T10:27:22,184 writing dependency_links to /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/dependency_links.txt 2021-07-13T10:27:22,186 writing entry points to /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/entry_points.txt 2021-07-13T10:27:22,187 writing requirements to /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/requires.txt 2021-07-13T10:27:22,188 writing top-level names to /tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/top_level.txt 2021-07-13T10:27:22,189 writing manifest file '/tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/SOURCES.txt' 2021-07-13T10:27:22,202 reading manifest file '/tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/SOURCES.txt' 2021-07-13T10:27:22,203 reading manifest template 'MANIFEST.in' 2021-07-13T10:27:22,206 warning: no files found matching 'whatshap/readselect.cpp' 2021-07-13T10:27:22,208 warning: no files found matching 'src/dptable.h' 2021-07-13T10:27:22,208 warning: no files found matching 'src/columncostcomputer.h' 2021-07-13T10:27:22,218 writing manifest file '/tmp/pip-pip-egg-info-nc52_1bl/whatshap.egg-info/SOURCES.txt' 2021-07-13T10:27:22,287 Source in /tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e has version 0.16, which satisfies requirement whatshap==0.16 from https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz#sha256=1df54d8705fb0451cc0a640918842481087f7b741778dfb4100cc1f4f60f48fe 2021-07-13T10:27:22,288 Removed whatshap==0.16 from https://files.pythonhosted.org/packages/3d/cb/55730a8713ecba10f6d987dbd935ba31ded92f9af1ddd250896f3c1cfc3b/whatshap-0.16.tar.gz#sha256=1df54d8705fb0451cc0a640918842481087f7b741778dfb4100cc1f4f60f48fe from build tracker '/tmp/pip-req-tracker-tnrh_d5q' 2021-07-13T10:27:22,292 Created temporary directory: /tmp/pip-unpack-me0zuf0g 2021-07-13T10:27:22,293 Building wheels for collected packages: whatshap 2021-07-13T10:27:22,296 Created temporary directory: /tmp/pip-wheel-2ywwedtx 2021-07-13T10:27:22,297 Building wheel for whatshap (setup.py): started 2021-07-13T10:27:22,297 Destination directory: /tmp/pip-wheel-2ywwedtx 2021-07-13T10:27:22,297 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e/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-2ywwedtx 2021-07-13T10:27:23,566 running bdist_wheel 2021-07-13T10:27:23,571 running build 2021-07-13T10:27:23,572 running build_py 2021-07-13T10:27:23,578 creating build 2021-07-13T10:27:23,578 creating build/lib.linux-armv7l-3.9 2021-07-13T10:27:23,579 creating build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,580 copying whatshap/stats.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,582 copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,584 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,586 copying whatshap/phase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,588 copying whatshap/timer.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,590 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,591 copying whatshap/utils.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,593 copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,594 copying whatshap/variants.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,597 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,600 copying whatshap/unphase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,602 copying whatshap/math.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,603 copying whatshap/_version.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,605 copying whatshap/genotype.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,608 copying whatshap/compare.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,611 copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,613 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,615 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,617 copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,619 copying whatshap/hapcut2vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,621 copying whatshap/haplotag.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,625 UPDATING build/lib.linux-armv7l-3.9/whatshap/_version.py 2021-07-13T10:27:23,627 set build/lib.linux-armv7l-3.9/whatshap/_version.py to '0.16' 2021-07-13T10:27:23,627 running build_ext 2021-07-13T10:27:23,633 building 'whatshap.core' extension 2021-07-13T10:27:23,634 creating build/temp.linux-armv7l-3.9 2021-07-13T10:27:23,635 creating build/temp.linux-armv7l-3.9/src 2021-07-13T10:27:23,636 creating build/temp.linux-armv7l-3.9/whatshap 2021-07-13T10:27:23,637 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 2021-07-13T10:27:25,270 In file included from /usr/include/c++/10/cassert:44, 2021-07-13T10:27:25,270 from src/backwardcolumniterator.cpp:1: 2021-07-13T10:27:25,270 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2021-07-13T10:27:25,271 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:25,271 121 | assert(k < positions->size()); 2021-07-13T10:27:25,271 | ~~^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:25,271 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:25,271 140 | assert(active_entry < read->getVariantCount()); 2021-07-13T10:27:25,271 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:26,836 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 2021-07-13T10:27:27,968 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2021-07-13T10:27:27,968 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:27,968 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2021-07-13T10:27:27,968 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:27,969 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-13T10:27:27,969 92 | if(m != -1) { 2021-07-13T10:27:27,969 | ~~^~~~~ 2021-07-13T10:27:27,969 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2021-07-13T10:27:27,969 89 | unsigned int s = 1; 2021-07-13T10:27:27,969 | ^ 2021-07-13T10:27:28,258 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 2021-07-13T10:27:29,367 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2021-07-13T10:27:29,367 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:29,367 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:29,368 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:29,371 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-13T10:27:29,371 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2021-07-13T10:27:31,472 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:31,472 105 | assert(list_it->active_entry < read->getVariantCount()); 2021-07-13T10:27:31,472 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:31,489 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2021-07-13T10:27:31,489 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:31,489 161 | assert(active_entry < read->getVariantCount()); 2021-07-13T10:27:31,490 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:33,108 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 2021-07-13T10:27:34,015 src/entry.cpp: In function ‘std::ostream& operator<<(std::ostream&, const Entry&)’: 2021-07-13T10:27:34,015 src/entry.cpp:59:40: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-13T10:27:34,015 59 | out << ',' << ((int)e.phred_score) << ')'; 2021-07-13T10:27:34,015 | ^~~ 2021-07-13T10:27:34,149 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 2021-07-13T10:27:36,926 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 2021-07-13T10:27:37,964 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2021-07-13T10:27:37,965 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:37,965 55 | if (i == best_index) continue; 2021-07-13T10:27:37,965 | ~~^~~~~~~~~~~~~ 2021-07-13T10:27:38,358 In file included from /usr/include/c++/10/vector:72, 2021-07-13T10:27:38,358 from src/genotypedistribution.h:4, 2021-07-13T10:27:38,358 from src/genotypedistribution.cpp:5: 2021-07-13T10:27:38,359 /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]’: 2021-07-13T10:27:38,359 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-13T10:27:38,359 426 | vector<_Tp, _Alloc>:: 2021-07-13T10:27:38,359 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:38,392 In file included from /usr/include/c++/10/vector:67, 2021-07-13T10:27:38,392 from src/genotypedistribution.h:4, 2021-07-13T10:27:38,392 from src/genotypedistribution.cpp:5: 2021-07-13T10:27:38,392 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2021-07-13T10:27:38,393 /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 2021-07-13T10:27:38,393 1198 | _M_realloc_insert(end(), __x); 2021-07-13T10:27:38,393 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-13T10:27:38,393 /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 2021-07-13T10:27:38,393 1198 | _M_realloc_insert(end(), __x); 2021-07-13T10:27:38,393 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-13T10:27:38,393 /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 2021-07-13T10:27:38,393 1198 | _M_realloc_insert(end(), __x); 2021-07-13T10:27:38,394 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-13T10:27:38,563 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 2021-07-13T10:27:40,689 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2021-07-13T10:27:40,689 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2021-07-13T10:27:40,689 61 | size_t column_count = input_column_iterator.get_column_count(); 2021-07-13T10:27:40,689 | ^~~~~~~~~~~~ 2021-07-13T10:27:40,743 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2021-07-13T10:27:40,743 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2021-07-13T10:27:40,743 91 | unsigned int transmission_configurations = std::pow(4, pedigree->triple_count()); 2021-07-13T10:27:40,743 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:27:40,747 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2021-07-13T10:27:40,747 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-13T10:27:40,747 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2021-07-13T10:27:40,748 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-13T10:27:40,750 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2021-07-13T10:27:40,751 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2021-07-13T10:27:40,751 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2021-07-13T10:27:40,751 | ^ 2021-07-13T10:27:44,470 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 2021-07-13T10:27:47,154 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 2021-07-13T10:27:48,211 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 2021-07-13T10:27:49,809 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 2021-07-13T10:27:51,136 In file included from /usr/include/c++/10/cassert:44, 2021-07-13T10:27:51,137 from src/pedigree.cpp:4: 2021-07-13T10:27:51,137 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2021-07-13T10:27:51,137 src/pedigree.cpp:30:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:51,137 30 | assert(genotypes.size() == variant_count); 2021-07-13T10:27:51,137 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-13T10:27:51,137 src/pedigree.cpp:31:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-13T10:27:51,138 31 | assert(genotype_likelihoods.size() == variant_count); 2021-07-13T10:27:51,138 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-13T10:27:51,146 src/pedigree.cpp: In member function ‘unsigned int Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2021-07-13T10:27:51,147 src/pedigree.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-13T10:27:51,147 68 | assert(variant_index < variant_count); 2021-07-13T10:27:51,147 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-13T10:27:51,147 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2021-07-13T10:27:51,147 src/pedigree.cpp:79:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-13T10:27:51,148 79 | assert(variant_index < variant_count); 2021-07-13T10:27:51,148 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-13T10:27:51,159 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2021-07-13T10:27:51,159 src/pedigree.cpp:110:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2021-07-13T10:27:51,159 110 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2021-07-13T10:27:54,996 src/pedigreecolumncostcomputer.cpp:24:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-13T10:27:54,996 24 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2021-07-13T10:27:55,032 src/pedigreecolumncostcomputer.cpp:118:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2021-07-13T10:27:55,032 118 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2021-07-13T10:27:55,032 | ^~~~~~~~~~~~~~~~ 2021-07-13T10:27:56,052 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 2021-07-13T10:28:02,267 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 2021-07-13T10:28:04,051 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 2021-07-13T10:28:05,290 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/read.cpp -o build/temp.linux-armv7l-3.9/src/read.o -std=c++11 2021-07-13T10:28:08,316 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/readset.cpp -o build/temp.linux-armv7l-3.9/src/readset.o -std=c++11 2021-07-13T10:28:12,883 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/transitionprobabilitycomputer.cpp -o build/temp.linux-armv7l-3.9/src/transitionprobabilitycomputer.o -std=c++11 2021-07-13T10:28:15,301 In file included from /usr/include/c++/10/vector:72, 2021-07-13T10:28:15,301 from src/vector2d.h:5, 2021-07-13T10:28:15,301 from src/transitionprobabilitycomputer.h:5, 2021-07-13T10:28:15,301 from src/transitionprobabilitycomputer.cpp:1: 2021-07-13T10:28:15,302 /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 = {long double}; _Tp = long double; _Alloc = std::allocator]’: 2021-07-13T10:28:15,302 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2021-07-13T10:28:15,302 426 | vector<_Tp, _Alloc>:: 2021-07-13T10:28:15,302 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:15,790 /usr/include/c++/10/bits/vector.tcc: In constructor ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector&)’: 2021-07-13T10:28:15,791 /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 2021-07-13T10:28:15,791 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-13T10:28:15,791 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:16,514 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 whatshap/core.cpp -o build/temp.linux-armv7l-3.9/whatshap/core.o -std=c++11 2021-07-13T10:28:19,219 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2021-07-13T10:28:19,220 whatshap/core.cpp:7281:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-13T10:28:19,220 7281 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-13T10:28:19,220 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-13T10:28:19,745 whatshap/core.cpp: In function ‘PyObject* PyInit_core()’: 2021-07-13T10:28:19,745 whatshap/core.cpp:18368:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,745 18368 | __pyx_type_8whatshap_4core_NumericSampleIds.tp_print = 0; 2021-07-13T10:28:19,745 | ^~~~~~~~ 2021-07-13T10:28:19,746 whatshap/core.cpp:18373:35: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,747 18373 | __pyx_type_8whatshap_4core_Read.tp_print = 0; 2021-07-13T10:28:19,747 | ^~~~~~~~ 2021-07-13T10:28:19,749 whatshap/core.cpp:18418:38: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,750 18418 | __pyx_type_8whatshap_4core_ReadSet.tp_print = 0; 2021-07-13T10:28:19,750 | ^~~~~~~~ 2021-07-13T10:28:19,751 whatshap/core.cpp:18423:39: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,751 18423 | __pyx_type_8whatshap_4core_Pedigree.tp_print = 0; 2021-07-13T10:28:19,751 | ^~~~~~~~ 2021-07-13T10:28:19,752 whatshap/core.cpp:18428:46: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,752 18428 | __pyx_type_8whatshap_4core_PedigreeDPTable.tp_print = 0; 2021-07-13T10:28:19,752 | ^~~~~~~~ 2021-07-13T10:28:19,753 whatshap/core.cpp:18433:55: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,753 18433 | __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_print = 0; 2021-07-13T10:28:19,754 | ^~~~~~~~ 2021-07-13T10:28:19,754 whatshap/core.cpp:18438:46: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,755 18438 | __pyx_type_8whatshap_4core_GenotypeDPTable.tp_print = 0; 2021-07-13T10:28:19,755 | ^~~~~~~~ 2021-07-13T10:28:19,756 whatshap/core.cpp:18443:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,756 18443 | __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_print = 0; 2021-07-13T10:28:19,756 | ^~~~~~~~ 2021-07-13T10:28:19,756 whatshap/core.cpp:18446:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,757 18446 | __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_print = 0; 2021-07-13T10:28:19,757 | ^~~~~~~~ 2021-07-13T10:28:19,757 whatshap/core.cpp:18449:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,757 18449 | __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_print = 0; 2021-07-13T10:28:19,758 | ^~~~~~~~ 2021-07-13T10:28:19,758 whatshap/core.cpp:18452:100: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,758 18452 | __pyx_type_8whatshap_4core___pyx_scope_struct_3___pyx_f_8whatshap_4core_format_read_source_stats.tp_print = 0; 2021-07-13T10:28:19,758 | ^~~~~~~~ 2021-07-13T10:28:19,759 whatshap/core.cpp:18455:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-13T10:28:19,759 18455 | __pyx_type_8whatshap_4core___pyx_scope_struct_4_genexpr.tp_print = 0; 2021-07-13T10:28:19,759 | ^~~~~~~~ 2021-07-13T10:28:19,790 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-13T10:28:19,790 from /usr/include/python3.9/Python.h:97, 2021-07-13T10:28:19,791 from whatshap/core.cpp:56: 2021-07-13T10:28:19,791 whatshap/core.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-13T10:28:19,791 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,791 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,791 | ^ 2021-07-13T10:28:19,791 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,791 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-13T10:28:19,791 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,792 whatshap/core.cpp:19222:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,792 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,792 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,792 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,792 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,792 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,793 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,793 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-13T10:28:19,793 | ^ 2021-07-13T10:28:19,793 whatshap/core.cpp:19222:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,793 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,793 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,794 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-13T10:28:19,794 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-13T10:28:19,794 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,795 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,795 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,795 | ^ 2021-07-13T10:28:19,795 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,795 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-13T10:28:19,795 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,795 whatshap/core.cpp:19222:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,796 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,796 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,796 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,796 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,796 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,797 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,797 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,797 | ^ 2021-07-13T10:28:19,797 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,797 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-13T10:28:19,798 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,798 whatshap/core.cpp:19222:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,798 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,798 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,798 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,798 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,798 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,799 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,799 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-13T10:28:19,799 | ^ 2021-07-13T10:28:19,799 whatshap/core.cpp:19222:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,799 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,799 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,800 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-13T10:28:19,800 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-13T10:28:19,800 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,800 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,801 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,801 | ^ 2021-07-13T10:28:19,801 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,801 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-13T10:28:19,801 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,801 whatshap/core.cpp:19222:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,801 19222 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,802 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,805 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,805 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,805 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,806 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,806 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,806 | ^ 2021-07-13T10:28:19,806 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,806 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-13T10:28:19,806 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,806 whatshap/core.cpp:19238:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,806 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,807 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,807 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,807 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,807 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,807 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,807 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-13T10:28:19,807 | ^ 2021-07-13T10:28:19,808 whatshap/core.cpp:19238:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,808 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,808 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,808 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-13T10:28:19,808 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-13T10:28:19,808 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,808 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,808 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,809 | ^ 2021-07-13T10:28:19,809 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,809 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-13T10:28:19,809 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,809 whatshap/core.cpp:19238:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,809 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,809 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,809 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,810 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,810 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,810 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,810 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,810 | ^ 2021-07-13T10:28:19,810 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,810 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-13T10:28:19,810 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,811 whatshap/core.cpp:19238:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,811 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,811 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,811 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,811 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,811 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,811 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,811 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-13T10:28:19,812 | ^ 2021-07-13T10:28:19,812 whatshap/core.cpp:19238:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,812 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,812 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,812 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-13T10:28:19,812 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-13T10:28:19,812 | ^~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,813 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,813 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-13T10:28:19,813 | ^ 2021-07-13T10:28:19,813 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-13T10:28:19,813 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-13T10:28:19,813 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,813 whatshap/core.cpp:19238:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-13T10:28:19,814 19238 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-13T10:28:19,814 | ^~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,814 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-13T10:28:19,814 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-13T10:28:19,814 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,818 whatshap/core.cpp: In function ‘PyObject* __Pyx_decode_c_bytes(const char*, Py_ssize_t, Py_ssize_t, Py_ssize_t, const char*, const char*, PyObject* (*)(const char*, Py_ssize_t, const char*))’: 2021-07-13T10:28:19,818 whatshap/core.cpp:19505:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-13T10:28:19,818 19505 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-13T10:28:19,818 | ^ 2021-07-13T10:28:19,819 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-13T10:28:19,819 from /usr/include/python3.9/Python.h:97, 2021-07-13T10:28:19,819 from whatshap/core.cpp:56: 2021-07-13T10:28:19,819 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-13T10:28:19,819 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-13T10:28:19,819 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-13T10:28:19,937 whatshap/core.cpp: In function ‘void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2021-07-13T10:28:19,937 whatshap/core.cpp:21428:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-13T10:28:19,937 21428 | tmp_type = tstate->exc_type; 2021-07-13T10:28:19,937 | ^~~~~~~~ 2021-07-13T10:28:19,937 | curexc_type 2021-07-13T10:28:19,937 whatshap/core.cpp:21429:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-13T10:28:19,937 21429 | tmp_value = tstate->exc_value; 2021-07-13T10:28:19,938 | ^~~~~~~~~ 2021-07-13T10:28:19,938 | curexc_value 2021-07-13T10:28:19,938 whatshap/core.cpp:21430:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-13T10:28:19,938 21430 | tmp_tb = tstate->exc_traceback; 2021-07-13T10:28:19,938 | ^~~~~~~~~~~~~ 2021-07-13T10:28:19,938 | curexc_traceback 2021-07-13T10:28:19,938 whatshap/core.cpp:21431:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-13T10:28:19,938 21431 | tstate->exc_type = *type; 2021-07-13T10:28:19,939 | ^~~~~~~~ 2021-07-13T10:28:19,939 | curexc_type 2021-07-13T10:28:19,939 whatshap/core.cpp:21432:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-13T10:28:19,939 21432 | tstate->exc_value = *value; 2021-07-13T10:28:19,939 | ^~~~~~~~~ 2021-07-13T10:28:19,939 | curexc_value 2021-07-13T10:28:19,939 whatshap/core.cpp:21433:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-13T10:28:19,939 21433 | tstate->exc_traceback = *tb; 2021-07-13T10:28:19,940 | ^~~~~~~~~~~~~ 2021-07-13T10:28:19,940 | curexc_traceback 2021-07-13T10:28:20,685 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-13T10:28:20,758 Building wheel for whatshap (setup.py): finished with status 'error' 2021-07-13T10:28:20,759 ERROR: Failed building wheel for whatshap 2021-07-13T10:28:20,759 Running setup.py clean for whatshap 2021-07-13T10:28:20,760 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-fqhbdcwt/whatshap_89d80cf75a1942af85882c05a83aa20e/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 2021-07-13T10:28:22,047 running clean 2021-07-13T10:28:22,049 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-13T10:28:22,060 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-13T10:28:22,067 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-13T10:28:22,068 'build/scripts-3.9' does not exist -- can't clean it 2021-07-13T10:28:22,068 removing 'build' 2021-07-13T10:28:22,137 Failed to build whatshap 2021-07-13T10:28:22,138 ERROR: Failed to build one or more wheels 2021-07-13T10:28:22,138 Exception information: 2021-07-13T10:28:22,138 Traceback (most recent call last): 2021-07-13T10:28:22,138 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-13T10:28:22,138 status = self.run(options, args) 2021-07-13T10:28:22,138 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-13T10:28:22,138 return func(self, options, args) 2021-07-13T10:28:22,138 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-13T10:28:22,138 raise CommandError( 2021-07-13T10:28:22,138 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-13T10:28:22,142 Removed build tracker: '/tmp/pip-req-tracker-tnrh_d5q'