2021-07-14T07:39:09,623 Created temporary directory: /tmp/pip-ephem-wheel-cache-muoo0b_x 2021-07-14T07:39:09,627 Created temporary directory: /tmp/pip-req-tracker-xrm3jvu_ 2021-07-14T07:39:09,627 Initialized build tracking at /tmp/pip-req-tracker-xrm3jvu_ 2021-07-14T07:39:09,628 Created build tracker: /tmp/pip-req-tracker-xrm3jvu_ 2021-07-14T07:39:09,628 Entered build tracker: /tmp/pip-req-tracker-xrm3jvu_ 2021-07-14T07:39:09,629 Created temporary directory: /tmp/pip-wheel-ji8ew16q 2021-07-14T07:39:09,664 1 location(s) to search for versions of whatshap: 2021-07-14T07:39:09,664 * https://pypi.org/simple/whatshap/ 2021-07-14T07:39:09,665 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-07-14T07:39:09,666 Getting page https://pypi.org/simple/whatshap/ 2021-07-14T07:39:09,667 Found index url https://pypi.org/simple 2021-07-14T07:39:09,869 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 2021-07-14T07:39:09,869 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 2021-07-14T07:39:09,870 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 2021-07-14T07:39:09,870 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 2021-07-14T07:39:09,871 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 2021-07-14T07:39:09,872 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 2021-07-14T07:39:09,872 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 2021-07-14T07:39:09,873 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 2021-07-14T07:39:09,873 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 2021-07-14T07:39:09,874 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 2021-07-14T07:39:09,894 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) 2021-07-14T07:39:09,894 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) 2021-07-14T07:39:09,895 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) 2021-07-14T07:39:09,896 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) 2021-07-14T07:39:09,896 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 2021-07-14T07:39:09,897 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) 2021-07-14T07:39:09,898 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) 2021-07-14T07:39:09,898 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) 2021-07-14T07:39:09,899 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 2021-07-14T07:39:09,900 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) 2021-07-14T07:39:09,901 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) 2021-07-14T07:39:09,901 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) 2021-07-14T07:39:09,902 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) 2021-07-14T07:39:09,903 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 2021-07-14T07:39:09,903 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2021-07-14T07:39:09,906 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-07-14T07:39:09,931 Collecting whatshap==0.18 2021-07-14T07:39:09,932 Created temporary directory: /tmp/pip-unpack-jymvm2b5 2021-07-14T07:39:10,240 Downloading whatshap-0.18.tar.gz (460 kB) 2021-07-14T07:39:10,680 Added whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 to build tracker '/tmp/pip-req-tracker-xrm3jvu_' 2021-07-14T07:39:10,682 Running setup.py (path:/tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7/setup.py) egg_info for package whatshap 2021-07-14T07:39:10,683 Created temporary directory: /tmp/pip-pip-egg-info-70g8ze9y 2021-07-14T07:39:10,683 Running command python setup.py egg_info 2021-07-14T07:39:15,418 running egg_info 2021-07-14T07:39:15,421 creating /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info 2021-07-14T07:39:15,423 writing /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/PKG-INFO 2021-07-14T07:39:15,425 writing dependency_links to /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/dependency_links.txt 2021-07-14T07:39:15,427 writing entry points to /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/entry_points.txt 2021-07-14T07:39:15,428 writing requirements to /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/requires.txt 2021-07-14T07:39:15,429 writing top-level names to /tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/top_level.txt 2021-07-14T07:39:15,431 writing manifest file '/tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/SOURCES.txt' 2021-07-14T07:39:15,676 reading manifest file '/tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/SOURCES.txt' 2021-07-14T07:39:15,684 writing manifest file '/tmp/pip-pip-egg-info-70g8ze9y/whatshap.egg-info/SOURCES.txt' 2021-07-14T07:39:15,789 Source in /tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7 has version 0.18, which satisfies requirement whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 2021-07-14T07:39:15,790 Removed whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 from build tracker '/tmp/pip-req-tracker-xrm3jvu_' 2021-07-14T07:39:15,798 Created temporary directory: /tmp/pip-unpack-n78te1t2 2021-07-14T07:39:15,799 Building wheels for collected packages: whatshap 2021-07-14T07:39:15,804 Created temporary directory: /tmp/pip-wheel-8bvzsfua 2021-07-14T07:39:15,805 Building wheel for whatshap (setup.py): started 2021-07-14T07:39:15,805 Destination directory: /tmp/pip-wheel-8bvzsfua 2021-07-14T07:39:15,806 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7/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-8bvzsfua 2021-07-14T07:39:17,443 running bdist_wheel 2021-07-14T07:39:17,448 running build 2021-07-14T07:39:17,448 running build_py 2021-07-14T07:39:17,595 creating build 2021-07-14T07:39:17,596 creating build/lib.linux-armv7l-3.9 2021-07-14T07:39:17,596 creating build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,597 copying whatshap/variants.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,600 copying whatshap/math.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,602 copying whatshap/genotype.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,605 copying whatshap/unphase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,607 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,609 copying whatshap/hapcut2vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,611 copying whatshap/haplotag.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,614 copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,616 copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,618 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,620 copying whatshap/compare.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,622 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,624 copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,627 copying whatshap/utils.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,629 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,631 copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,633 copying whatshap/timer.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,635 copying whatshap/stats.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,638 copying whatshap/phase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,642 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,645 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,649 running build_ext 2021-07-14T07:39:17,656 building 'whatshap.core' extension 2021-07-14T07:39:17,657 creating build/temp.linux-armv7l-3.9 2021-07-14T07:39:17,657 creating build/temp.linux-armv7l-3.9/src 2021-07-14T07:39:17,659 creating build/temp.linux-armv7l-3.9/src/hapchat 2021-07-14T07:39:17,660 creating build/temp.linux-armv7l-3.9/whatshap 2021-07-14T07:39:17,661 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 2021-07-14T07:39:19,557 In file included from /usr/include/c++/10/cassert:44, 2021-07-14T07:39:19,558 from src/backwardcolumniterator.cpp:1: 2021-07-14T07:39:19,558 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2021-07-14T07:39:19,558 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:19,558 121 | assert(k < positions->size()); 2021-07-14T07:39:19,558 | ~~^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:19,560 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:39:19,560 140 | assert(active_entry < read->getVariantCount()); 2021-07-14T07:39:19,560 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:21,326 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 2021-07-14T07:39:22,625 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2021-07-14T07:39:22,626 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:22,626 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2021-07-14T07:39:22,626 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:22,627 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:39:22,627 92 | if(m != -1) { 2021-07-14T07:39:22,627 | ~~^~~~~ 2021-07-14T07:39:22,627 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2021-07-14T07:39:22,628 89 | unsigned int s = 1; 2021-07-14T07:39:22,628 | ^ 2021-07-14T07:39:22,947 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 2021-07-14T07:39:24,233 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2021-07-14T07:39:24,234 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:24,234 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:24,235 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:24,239 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:39:24,240 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2021-07-14T07:39:26,631 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:39:26,631 105 | assert(list_it->active_entry < read->getVariantCount()); 2021-07-14T07:39:26,631 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:26,650 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2021-07-14T07:39:26,650 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:39:26,651 161 | assert(active_entry < read->getVariantCount()); 2021-07-14T07:39:26,651 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:28,514 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 src/entry.cpp -o build/temp.linux-armv7l-3.9/src/entry.o -std=c++11 -Werror=return-type 2021-07-14T07:39:29,655 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -UNDEBUG -I/usr/include/python3.9 -c src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-3.9/src/genotypecolumncostcomputer.o -std=c++11 -Werror=return-type 2021-07-14T07:39:32,833 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 2021-07-14T07:39:34,015 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2021-07-14T07:39:34,015 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:39:34,016 55 | if (i == best_index) continue; 2021-07-14T07:39:34,016 | ~~^~~~~~~~~~~~~ 2021-07-14T07:39:34,471 In file included from /usr/include/c++/10/vector:72, 2021-07-14T07:39:34,471 from src/genotypedistribution.h:4, 2021-07-14T07:39:34,471 from src/genotypedistribution.cpp:5: 2021-07-14T07:39:34,472 /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]’: 2021-07-14T07:39:34,472 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2021-07-14T07:39:34,472 426 | vector<_Tp, _Alloc>:: 2021-07-14T07:39:34,473 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:34,508 In file included from /usr/include/c++/10/vector:67, 2021-07-14T07:39:34,508 from src/genotypedistribution.h:4, 2021-07-14T07:39:34,509 from src/genotypedistribution.cpp:5: 2021-07-14T07:39:34,509 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2021-07-14T07:39:34,509 /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 2021-07-14T07:39:34,509 1198 | _M_realloc_insert(end(), __x); 2021-07-14T07:39:34,510 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-14T07:39:34,510 /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 2021-07-14T07:39:34,510 1198 | _M_realloc_insert(end(), __x); 2021-07-14T07:39:34,510 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-14T07:39:34,511 /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 2021-07-14T07:39:34,511 1198 | _M_realloc_insert(end(), __x); 2021-07-14T07:39:34,511 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-14T07:39:34,694 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 2021-07-14T07:39:37,150 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2021-07-14T07:39:37,150 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2021-07-14T07:39:37,150 61 | size_t column_count = input_column_iterator.get_column_count(); 2021-07-14T07:39:37,150 | ^~~~~~~~~~~~ 2021-07-14T07:39:37,214 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2021-07-14T07:39:37,214 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2021-07-14T07:39:37,214 91 | unsigned int transmission_configurations = pow(4, pedigree->triple_count()); 2021-07-14T07:39:37,214 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:39:37,219 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2021-07-14T07:39:37,220 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:39:37,220 152 | if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2021-07-14T07:39:37,220 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-14T07:39:37,225 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2021-07-14T07:39:37,225 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2021-07-14T07:39:37,225 178 | size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2021-07-14T07:39:37,225 | ^ 2021-07-14T07:39:41,440 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 2021-07-14T07:39:44,822 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 2021-07-14T07:39:46,204 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 2021-07-14T07:39:50,423 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 2021-07-14T07:39:52,310 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 2021-07-14T07:39:55,850 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 2021-07-14T07:39:59,145 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 2021-07-14T07:40:02,263 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2021-07-14T07:40:02,264 src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2021-07-14T07:40:02,264 145 | Counter counter_columns; 2021-07-14T07:40:02,264 | ^~~~~~~~~~~~~~~ 2021-07-14T07:40:02,274 src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2021-07-14T07:40:02,275 src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,275 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2021-07-14T07:40:02,275 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,424 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2021-07-14T07:40:02,424 src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2021-07-14T07:40:02,425 939 | int old_k = k_j[input_pointer]; 2021-07-14T07:40:02,425 | ^~~~~ 2021-07-14T07:40:02,442 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&)’: 2021-07-14T07:40:02,442 src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,443 1114 | (colJ[j].get_read_id() != -1) && 2021-07-14T07:40:02,443 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,443 src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,443 1115 | (colQ[i].get_read_id() != -1)) { 2021-07-14T07:40:02,443 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,445 src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2021-07-14T07:40:02,445 src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,445 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2021-07-14T07:40:02,445 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,450 src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2021-07-14T07:40:02,450 src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,450 1294 | (colJ[j].get_read_id() != -1) && 2021-07-14T07:40:02,450 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,450 src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,451 1295 | (colQ[i].get_read_id() != -1)) { 2021-07-14T07:40:02,451 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:02,453 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&)’: 2021-07-14T07:40:02,453 src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:02,453 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2021-07-14T07:40:02,454 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:03,590 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 2021-07-14T07:40:05,674 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 2021-07-14T07:40:07,267 In file included from /usr/include/c++/10/cassert:44, 2021-07-14T07:40:07,267 from src/pedigree.cpp:4: 2021-07-14T07:40:07,267 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2021-07-14T07:40:07,267 src/pedigree.cpp:30:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:40:07,268 30 | assert(genotypes.size() == variant_count); 2021-07-14T07:40:07,268 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-14T07:40:07,268 src/pedigree.cpp:31:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:40:07,268 31 | assert(genotype_likelihoods.size() == variant_count); 2021-07-14T07:40:07,268 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-14T07:40:07,278 src/pedigree.cpp: In member function ‘unsigned int Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2021-07-14T07:40:07,279 src/pedigree.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-14T07:40:07,279 68 | assert(variant_index < variant_count); 2021-07-14T07:40:07,279 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-14T07:40:07,279 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2021-07-14T07:40:07,279 src/pedigree.cpp:79:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-14T07:40:07,280 79 | assert(variant_index < variant_count); 2021-07-14T07:40:07,280 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-14T07:40:07,295 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2021-07-14T07:40:07,295 src/pedigree.cpp:110:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2021-07-14T07:40:07,295 110 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2021-07-14T07:40:11,742 src/pedigreecolumncostcomputer.cpp:24:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:11,742 24 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2021-07-14T07:40:11,782 src/pedigreecolumncostcomputer.cpp:118:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2021-07-14T07:40:11,782 118 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2021-07-14T07:40:11,782 | ^~~~~~~~~~~~~~~~ 2021-07-14T07:40:12,913 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 2021-07-14T07:40:19,924 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 2021-07-14T07:40:21,972 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 2021-07-14T07:40:23,382 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 -Werror=return-type 2021-07-14T07:40:26,842 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 -Werror=return-type 2021-07-14T07:40:32,957 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 -Werror=return-type 2021-07-14T07:40:36,269 In file included from /usr/include/c++/10/vector:72, 2021-07-14T07:40:36,269 from src/vector2d.h:5, 2021-07-14T07:40:36,269 from src/transitionprobabilitycomputer.h:5, 2021-07-14T07:40:36,270 from src/transitionprobabilitycomputer.cpp:1: 2021-07-14T07:40:36,270 /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]’: 2021-07-14T07:40:36,270 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2021-07-14T07:40:36,270 426 | vector<_Tp, _Alloc>:: 2021-07-14T07:40:36,271 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:36,956 /usr/include/c++/10/bits/vector.tcc: In constructor ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector&)’: 2021-07-14T07:40:36,957 /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 2021-07-14T07:40:36,957 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2021-07-14T07:40:36,957 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:37,828 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 -Werror=return-type 2021-07-14T07:40:41,481 In file included from whatshap/core.cpp:653: 2021-07-14T07:40:41,482 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2021-07-14T07:40:41,482 whatshap/../src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2021-07-14T07:40:41,482 145 | Counter counter_columns; 2021-07-14T07:40:41,482 | ^~~~~~~~~~~~~~~ 2021-07-14T07:40:41,495 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2021-07-14T07:40:41,495 whatshap/../src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,495 208 | return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2021-07-14T07:40:41,495 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,694 In file included from whatshap/core.cpp:653: 2021-07-14T07:40:41,694 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector&, std::vector&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’: 2021-07-14T07:40:41,694 whatshap/../src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2021-07-14T07:40:41,695 939 | int old_k = k_j[input_pointer]; 2021-07-14T07:40:41,695 | ^~~~~ 2021-07-14T07:40:41,720 whatshap/../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&)’: 2021-07-14T07:40:41,720 whatshap/../src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,720 1114 | (colJ[j].get_read_id() != -1) && 2021-07-14T07:40:41,720 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,721 whatshap/../src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,721 1115 | (colQ[i].get_read_id() != -1)) { 2021-07-14T07:40:41,721 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,723 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2021-07-14T07:40:41,723 whatshap/../src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,724 1159 | while(cov < column.size() && column[cov].get_read_id() != -1) { 2021-07-14T07:40:41,724 | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,730 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2021-07-14T07:40:41,730 whatshap/../src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,730 1294 | (colJ[j].get_read_id() != -1) && 2021-07-14T07:40:41,731 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,731 whatshap/../src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,731 1295 | (colQ[i].get_read_id() != -1)) { 2021-07-14T07:40:41,731 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:41,735 whatshap/../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&)’: 2021-07-14T07:40:41,735 whatshap/../src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:40:41,735 1350 | if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2021-07-14T07:40:41,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:40:42,030 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2021-07-14T07:40:42,030 whatshap/core.cpp:7460:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:40:42,030 7460 | for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-14T07:40:42,030 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-14T07:40:42,255 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’: 2021-07-14T07:40:42,256 whatshap/core.cpp:11086:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:40:42,256 11086 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-14T07:40:42,256 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-14T07:40:42,825 whatshap/core.cpp: In function ‘int __Pyx_modinit_type_init_code()’: 2021-07-14T07:40:42,826 whatshap/core.cpp:19152:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,826 19152 | __pyx_type_8whatshap_4core_NumericSampleIds.tp_print = 0; 2021-07-14T07:40:42,826 | ^~~~~~~~ 2021-07-14T07:40:42,827 whatshap/core.cpp:19160:35: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,827 19160 | __pyx_type_8whatshap_4core_Read.tp_print = 0; 2021-07-14T07:40:42,827 | ^~~~~~~~ 2021-07-14T07:40:42,831 whatshap/core.cpp:19208:38: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,832 19208 | __pyx_type_8whatshap_4core_ReadSet.tp_print = 0; 2021-07-14T07:40:42,832 | ^~~~~~~~ 2021-07-14T07:40:42,832 whatshap/core.cpp:19216:39: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,833 19216 | __pyx_type_8whatshap_4core_Pedigree.tp_print = 0; 2021-07-14T07:40:42,833 | ^~~~~~~~ 2021-07-14T07:40:42,834 whatshap/core.cpp:19224:46: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,834 19224 | __pyx_type_8whatshap_4core_PedigreeDPTable.tp_print = 0; 2021-07-14T07:40:42,834 | ^~~~~~~~ 2021-07-14T07:40:42,835 whatshap/core.cpp:19232:55: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,835 19232 | __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_print = 0; 2021-07-14T07:40:42,835 | ^~~~~~~~ 2021-07-14T07:40:42,836 whatshap/core.cpp:19240:46: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,836 19240 | __pyx_type_8whatshap_4core_GenotypeDPTable.tp_print = 0; 2021-07-14T07:40:42,837 | ^~~~~~~~ 2021-07-14T07:40:42,837 whatshap/core.cpp:19248:42: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,838 19248 | __pyx_type_8whatshap_4core_HapChatCore.tp_print = 0; 2021-07-14T07:40:42,838 | ^~~~~~~~ 2021-07-14T07:40:42,839 whatshap/core.cpp:19256:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,839 19256 | __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_print = 0; 2021-07-14T07:40:42,839 | ^~~~~~~~ 2021-07-14T07:40:42,839 whatshap/core.cpp:19262:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,840 19262 | __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_print = 0; 2021-07-14T07:40:42,840 | ^~~~~~~~ 2021-07-14T07:40:42,840 whatshap/core.cpp:19268:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,840 19268 | __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_print = 0; 2021-07-14T07:40:42,841 | ^~~~~~~~ 2021-07-14T07:40:42,841 whatshap/core.cpp:19274:100: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,841 19274 | __pyx_type_8whatshap_4core___pyx_scope_struct_3___pyx_f_8whatshap_4core_format_read_source_stats.tp_print = 0; 2021-07-14T07:40:42,842 | ^~~~~~~~ 2021-07-14T07:40:42,842 whatshap/core.cpp:19280:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-14T07:40:42,842 19280 | __pyx_type_8whatshap_4core___pyx_scope_struct_4_genexpr.tp_print = 0; 2021-07-14T07:40:42,842 | ^~~~~~~~ 2021-07-14T07:40:42,903 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T07:40:42,903 from /usr/include/python3.9/Python.h:97, 2021-07-14T07:40:42,904 from whatshap/core.cpp:63: 2021-07-14T07:40:42,904 whatshap/core.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-14T07:40:42,904 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,904 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,904 | ^ 2021-07-14T07:40:42,904 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,905 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T07:40:42,905 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,905 whatshap/core.cpp:20441:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,905 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,905 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,905 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,905 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,906 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,906 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T07:40:42,906 | ^ 2021-07-14T07:40:42,906 whatshap/core.cpp:20441:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,906 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,906 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,907 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T07:40:42,907 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T07:40:42,907 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,907 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,907 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,907 | ^ 2021-07-14T07:40:42,907 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,908 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T07:40:42,908 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,908 whatshap/core.cpp:20441:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,908 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,908 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,908 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,908 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,908 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,909 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,909 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,909 | ^ 2021-07-14T07:40:42,909 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,909 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T07:40:42,909 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,910 whatshap/core.cpp:20441:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,910 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,910 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,910 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,910 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,910 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,910 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,911 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T07:40:42,911 | ^ 2021-07-14T07:40:42,911 whatshap/core.cpp:20441:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,911 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,911 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,911 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T07:40:42,912 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T07:40:42,912 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,912 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,912 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,912 | ^ 2021-07-14T07:40:42,912 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,913 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T07:40:42,913 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,913 whatshap/core.cpp:20441:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,913 20441 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,913 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,913 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,913 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,914 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,914 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,914 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,914 | ^ 2021-07-14T07:40:42,914 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,914 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T07:40:42,914 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,915 whatshap/core.cpp:20457:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,915 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,915 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,915 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,915 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,915 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,915 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,916 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T07:40:42,916 | ^ 2021-07-14T07:40:42,916 whatshap/core.cpp:20457:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,916 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,916 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,916 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T07:40:42,916 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T07:40:42,916 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,917 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,917 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,917 | ^ 2021-07-14T07:40:42,917 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,917 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T07:40:42,917 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,917 whatshap/core.cpp:20457:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,917 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,918 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,918 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,918 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,918 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,918 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,918 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,918 | ^ 2021-07-14T07:40:42,919 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,919 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-14T07:40:42,919 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,919 whatshap/core.cpp:20457:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,919 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,919 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,919 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,919 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,920 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,920 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-14T07:40:42,920 | ^ 2021-07-14T07:40:42,920 whatshap/core.cpp:20457:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,920 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,920 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,921 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-14T07:40:42,921 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-14T07:40:42,921 | ^~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,921 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,921 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-14T07:40:42,921 | ^ 2021-07-14T07:40:42,922 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-14T07:40:42,923 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-14T07:40:42,925 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,926 whatshap/core.cpp:20457:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-14T07:40:42,927 20457 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-14T07:40:42,928 | ^~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,928 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-14T07:40:42,929 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-14T07:40:42,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:42,932 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*))’: 2021-07-14T07:40:42,933 whatshap/core.cpp:20627:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-14T07:40:42,934 20627 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-14T07:40:42,935 | ^ 2021-07-14T07:40:42,936 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-14T07:40:42,937 from /usr/include/python3.9/Python.h:97, 2021-07-14T07:40:42,938 from whatshap/core.cpp:63: 2021-07-14T07:40:42,939 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-14T07:40:42,940 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-14T07:40:42,941 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:40:45,232 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-14T07:40:45,330 Building wheel for whatshap (setup.py): finished with status 'error' 2021-07-14T07:40:45,331 ERROR: Failed building wheel for whatshap 2021-07-14T07:40:45,332 Running setup.py clean for whatshap 2021-07-14T07:40:45,332 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ji8ew16q/whatshap_a84c36883a6740318dcb4fad90956eb7/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 2021-07-14T07:40:47,167 running clean 2021-07-14T07:40:47,170 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-14T07:40:47,183 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-14T07:40:47,191 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-14T07:40:47,191 'build/scripts-3.9' does not exist -- can't clean it 2021-07-14T07:40:47,192 removing 'build' 2021-07-14T07:40:47,262 Failed to build whatshap 2021-07-14T07:40:47,263 ERROR: Failed to build one or more wheels 2021-07-14T07:40:47,264 Exception information: 2021-07-14T07:40:47,264 Traceback (most recent call last): 2021-07-14T07:40:47,264 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-14T07:40:47,264 status = self.run(options, args) 2021-07-14T07:40:47,264 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-14T07:40:47,264 return func(self, options, args) 2021-07-14T07:40:47,264 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-14T07:40:47,264 raise CommandError( 2021-07-14T07:40:47,264 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-14T07:40:47,269 Removed build tracker: '/tmp/pip-req-tracker-xrm3jvu_'