2021-07-11T20:41:48,500 Created temporary directory: /tmp/pip-ephem-wheel-cache-yilmtdk_ 2021-07-11T20:41:48,503 Created temporary directory: /tmp/pip-req-tracker-uvgei4ng 2021-07-11T20:41:48,503 Initialized build tracking at /tmp/pip-req-tracker-uvgei4ng 2021-07-11T20:41:48,504 Created build tracker: /tmp/pip-req-tracker-uvgei4ng 2021-07-11T20:41:48,504 Entered build tracker: /tmp/pip-req-tracker-uvgei4ng 2021-07-11T20:41:48,504 Created temporary directory: /tmp/pip-wheel-zx8sn8z3 2021-07-11T20:41:48,533 1 location(s) to search for versions of whatshap: 2021-07-11T20:41:48,533 * https://pypi.org/simple/whatshap/ 2021-07-11T20:41:48,533 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-07-11T20:41:48,534 Getting page https://pypi.org/simple/whatshap/ 2021-07-11T20:41:48,535 Found index url https://pypi.org/simple 2021-07-11T20:41:48,725 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 2021-07-11T20:41:48,725 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 2021-07-11T20:41:48,725 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 2021-07-11T20:41:48,726 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 2021-07-11T20:41:48,726 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 2021-07-11T20:41:48,726 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 2021-07-11T20:41:48,726 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 2021-07-11T20:41:48,727 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 2021-07-11T20:41:48,727 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 2021-07-11T20:41:48,727 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 2021-07-11T20:41:48,745 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) 2021-07-11T20:41:48,745 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) 2021-07-11T20:41:48,746 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) 2021-07-11T20:41:48,746 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) 2021-07-11T20:41:48,747 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 2021-07-11T20:41:48,748 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) 2021-07-11T20:41:48,748 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) 2021-07-11T20:41:48,749 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) 2021-07-11T20:41:48,749 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 2021-07-11T20:41:48,750 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) 2021-07-11T20:41:48,750 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) 2021-07-11T20:41:48,751 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) 2021-07-11T20:41:48,751 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) 2021-07-11T20:41:48,752 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 2021-07-11T20:41:48,752 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2021-07-11T20:41:48,755 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-07-11T20:41:48,774 Collecting whatshap==0.13 2021-07-11T20:41:48,775 Created temporary directory: /tmp/pip-unpack-_eejnkhm 2021-07-11T20:41:49,138 Downloading whatshap-0.13.tar.gz (438 kB) 2021-07-11T20:41:49,530 Added whatshap==0.13 from https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz#sha256=529646db74b2cac9f12ebd530bd7bb40cb073c367894bf66c5994c1d7f32b56a to build tracker '/tmp/pip-req-tracker-uvgei4ng' 2021-07-11T20:41:49,531 Running setup.py (path:/tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061/setup.py) egg_info for package whatshap 2021-07-11T20:41:49,532 Created temporary directory: /tmp/pip-pip-egg-info-l9w36z48 2021-07-11T20:41:49,533 Running command python setup.py egg_info 2021-07-11T20:41:50,751 running egg_info 2021-07-11T20:41:50,753 creating /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info 2021-07-11T20:41:50,754 writing /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/PKG-INFO 2021-07-11T20:41:50,757 writing dependency_links to /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/dependency_links.txt 2021-07-11T20:41:50,758 writing entry points to /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/entry_points.txt 2021-07-11T20:41:50,759 writing requirements to /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/requires.txt 2021-07-11T20:41:50,760 writing top-level names to /tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/top_level.txt 2021-07-11T20:41:50,762 writing manifest file '/tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/SOURCES.txt' 2021-07-11T20:41:50,775 reading manifest file '/tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/SOURCES.txt' 2021-07-11T20:41:50,777 reading manifest template 'MANIFEST.in' 2021-07-11T20:41:50,780 warning: no files found matching 'whatshap/readselect.cpp' 2021-07-11T20:41:50,782 warning: no files found matching 'src/dptable.h' 2021-07-11T20:41:50,782 warning: no files found matching 'src/columncostcomputer.h' 2021-07-11T20:41:50,791 writing manifest file '/tmp/pip-pip-egg-info-l9w36z48/whatshap.egg-info/SOURCES.txt' 2021-07-11T20:41:50,856 Source in /tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061 has version 0.13, which satisfies requirement whatshap==0.13 from https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz#sha256=529646db74b2cac9f12ebd530bd7bb40cb073c367894bf66c5994c1d7f32b56a 2021-07-11T20:41:50,857 Removed whatshap==0.13 from https://files.pythonhosted.org/packages/e2/f3/c71cb4bc3ba3b1234ee0c5fe729c60440164e07437695ca09c61750e0e11/whatshap-0.13.tar.gz#sha256=529646db74b2cac9f12ebd530bd7bb40cb073c367894bf66c5994c1d7f32b56a from build tracker '/tmp/pip-req-tracker-uvgei4ng' 2021-07-11T20:41:50,861 Created temporary directory: /tmp/pip-unpack-7x0z18t5 2021-07-11T20:41:50,861 Building wheels for collected packages: whatshap 2021-07-11T20:41:50,865 Created temporary directory: /tmp/pip-wheel-wjq5hu_y 2021-07-11T20:41:50,866 Building wheel for whatshap (setup.py): started 2021-07-11T20:41:50,866 Destination directory: /tmp/pip-wheel-wjq5hu_y 2021-07-11T20:41:50,866 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061/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-wjq5hu_y 2021-07-11T20:41:52,077 running bdist_wheel 2021-07-11T20:41:52,082 running build 2021-07-11T20:41:52,082 running build_py 2021-07-11T20:41:52,090 creating build 2021-07-11T20:41:52,090 creating build/lib.linux-armv7l-3.9 2021-07-11T20:41:52,091 creating build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,092 copying whatshap/unphase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,094 copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,096 copying whatshap/stats.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,098 copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,100 copying whatshap/math.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,102 copying whatshap/compare.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,105 copying whatshap/variants.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,107 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,109 copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,111 copying whatshap/_version.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,113 copying whatshap/example.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,115 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,117 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,119 copying whatshap/haplotag.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,122 copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,124 copying whatshap/timer.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,126 copying whatshap/phase.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,131 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,133 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,135 copying whatshap/hapcut2vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,139 UPDATING build/lib.linux-armv7l-3.9/whatshap/_version.py 2021-07-11T20:41:52,141 set build/lib.linux-armv7l-3.9/whatshap/_version.py to '0.13' 2021-07-11T20:41:52,141 running build_ext 2021-07-11T20:41:52,148 building 'whatshap.core' extension 2021-07-11T20:41:52,149 creating build/temp.linux-armv7l-3.9 2021-07-11T20:41:52,149 creating build/temp.linux-armv7l-3.9/src 2021-07-11T20:41:52,151 creating build/temp.linux-armv7l-3.9/whatshap 2021-07-11T20:41:52,151 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 2021-07-11T20:41:53,325 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2021-07-11T20:41:53,326 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:41:53,326 90 | for(int j=0; j< parent->read_ids.size(); ++j) { 2021-07-11T20:41:53,326 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:41:53,326 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:41:53,327 92 | if(m != -1) { 2021-07-11T20:41:53,327 | ~~^~~~~ 2021-07-11T20:41:53,327 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2021-07-11T20:41:53,327 89 | unsigned int s = 1; 2021-07-11T20:41:53,327 | ^ 2021-07-11T20:41:53,615 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 2021-07-11T20:41:54,714 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2021-07-11T20:41:54,715 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:41:54,715 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:41:54,716 22 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:41:54,718 71 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:41:54,719 71 | while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2021-07-11T20:41:56,822 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:41:56,822 105 | assert(list_it->active_entry < read->getVariantCount()); 2021-07-11T20:41:56,822 | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:41:56,839 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2021-07-11T20:41:56,839 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:41:56,839 161 | assert(active_entry < read->getVariantCount()); 2021-07-11T20:41:56,839 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:41:58,464 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 2021-07-11T20:41:59,344 src/entry.cpp: In function ‘std::ostream& operator<<(std::ostream&, const Entry&)’: 2021-07-11T20:41:59,344 src/entry.cpp:59:40: warning: control reaches end of non-void function [-Wreturn-type] 2021-07-11T20:41:59,344 59 | out << ',' << ((int)e.phred_score) << ')'; 2021-07-11T20:41:59,344 | ^~~ 2021-07-11T20:41:59,470 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/graycodes.cpp -o build/temp.linux-armv7l-3.9/src/graycodes.o -std=c++11 2021-07-11T20:42:00,533 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 2021-07-11T20:42:02,195 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 2021-07-11T20:42:03,510 In file included from /usr/include/c++/10/cassert:44, 2021-07-11T20:42:03,510 from src/pedigree.cpp:4: 2021-07-11T20:42:03,510 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2021-07-11T20:42:03,511 src/pedigree.cpp:30:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:42:03,511 30 | assert(genotypes.size() == variant_count); 2021-07-11T20:42:03,511 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-11T20:42:03,511 src/pedigree.cpp:31:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:42:03,512 31 | assert(genotype_likelihoods.size() == variant_count); 2021-07-11T20:42:03,512 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2021-07-11T20:42:03,520 src/pedigree.cpp: In member function ‘unsigned int Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2021-07-11T20:42:03,520 src/pedigree.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-11T20:42:03,520 68 | assert(variant_index < variant_count); 2021-07-11T20:42:03,520 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-11T20:42:03,522 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2021-07-11T20:42:03,522 src/pedigree.cpp:79:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2021-07-11T20:42:03,522 79 | assert(variant_index < variant_count); 2021-07-11T20:42:03,522 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2021-07-11T20:42:03,534 src/pedigree.cpp: In member function ‘std::string Pedigree::toString() const’: 2021-07-11T20:42:03,534 src/pedigree.cpp:110:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2021-07-11T20:42:03,535 110 | for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2021-07-11T20:42:07,357 src/pedigreecolumncostcomputer.cpp:24:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:42:07,357 24 | for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2021-07-11T20:42:07,394 src/pedigreecolumncostcomputer.cpp:118:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2021-07-11T20:42:07,394 118 | unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2021-07-11T20:42:07,394 | ^~~~~~~~~~~~~~~~ 2021-07-11T20:42:08,402 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 2021-07-11T20:42:14,487 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 2021-07-11T20:42:16,302 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 2021-07-11T20:42:17,532 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 2021-07-11T20:42:20,511 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 2021-07-11T20:42:24,992 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 2021-07-11T20:42:27,473 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2021-07-11T20:42:27,474 whatshap/core.cpp:6122:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T20:42:27,474 6122 | for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-11T20:42:27,474 | ~~~~~~~~~~^~~~~~~~~~~ 2021-07-11T20:42:27,814 whatshap/core.cpp: In function ‘std::vector __pyx_convert_vector_from_py_unsigned_int(PyObject*)’: 2021-07-11T20:42:27,814 whatshap/core.cpp:12476:83: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:42:27,814 12476 | __pyx_t_5 = __Pyx_PyInt_As_unsigned_int(__pyx_v_item); if (unlikely(__pyx_t_5 == -1 && PyErr_Occurred())) __PYX_ERR(2, 52, __pyx_L1_error) 2021-07-11T20:42:27,814 | ~~~~~~~~~~^~~~~ 2021-07-11T20:42:27,814 whatshap/core.cpp:515:43: note: in definition of macro ‘unlikely’ 2021-07-11T20:42:27,815 515 | #define unlikely(x) __builtin_expect(!!(x), 0) 2021-07-11T20:42:27,815 | ^ 2021-07-11T20:42:27,880 whatshap/core.cpp: In function ‘PyObject* PyInit_core()’: 2021-07-11T20:42:27,880 whatshap/core.cpp:14661:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,880 14661 | __pyx_type_8whatshap_4core_NumericSampleIds.tp_print = 0; 2021-07-11T20:42:27,880 | ^~~~~~~~ 2021-07-11T20:42:27,881 whatshap/core.cpp:14665:35: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,881 14665 | __pyx_type_8whatshap_4core_Read.tp_print = 0; 2021-07-11T20:42:27,881 | ^~~~~~~~ 2021-07-11T20:42:27,883 whatshap/core.cpp:14709:38: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,883 14709 | __pyx_type_8whatshap_4core_ReadSet.tp_print = 0; 2021-07-11T20:42:27,883 | ^~~~~~~~ 2021-07-11T20:42:27,883 whatshap/core.cpp:14713:39: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,884 14713 | __pyx_type_8whatshap_4core_Pedigree.tp_print = 0; 2021-07-11T20:42:27,884 | ^~~~~~~~ 2021-07-11T20:42:27,884 whatshap/core.cpp:14717:46: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,884 14717 | __pyx_type_8whatshap_4core_PedigreeDPTable.tp_print = 0; 2021-07-11T20:42:27,884 | ^~~~~~~~ 2021-07-11T20:42:27,885 whatshap/core.cpp:14721:55: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,885 14721 | __pyx_type_8whatshap_4core_PhredGenotypeLikelihoods.tp_print = 0; 2021-07-11T20:42:27,885 | ^~~~~~~~ 2021-07-11T20:42:27,885 whatshap/core.cpp:14725:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,885 14725 | __pyx_type_8whatshap_4core___pyx_scope_struct____iter__.tp_print = 0; 2021-07-11T20:42:27,885 | ^~~~~~~~ 2021-07-11T20:42:27,886 whatshap/core.cpp:14728:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,886 14728 | __pyx_type_8whatshap_4core___pyx_scope_struct_1___iter__.tp_print = 0; 2021-07-11T20:42:27,886 | ^~~~~~~~ 2021-07-11T20:42:27,886 whatshap/core.cpp:14731:60: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,886 14731 | __pyx_type_8whatshap_4core___pyx_scope_struct_2___iter__.tp_print = 0; 2021-07-11T20:42:27,886 | ^~~~~~~~ 2021-07-11T20:42:27,886 whatshap/core.cpp:14734:76: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,887 14734 | __pyx_type_8whatshap_4core___pyx_scope_struct_3_format_read_source_stats.tp_print = 0; 2021-07-11T20:42:27,887 | ^~~~~~~~ 2021-07-11T20:42:27,887 whatshap/core.cpp:14737:59: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2021-07-11T20:42:27,887 14737 | __pyx_type_8whatshap_4core___pyx_scope_struct_4_genexpr.tp_print = 0; 2021-07-11T20:42:27,887 | ^~~~~~~~ 2021-07-11T20:42:27,910 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-11T20:42:27,910 from /usr/include/python3.9/Python.h:97, 2021-07-11T20:42:27,910 from whatshap/core.cpp:27: 2021-07-11T20:42:27,910 whatshap/core.cpp: In function ‘int __Pyx_ParseOptionalKeywords(PyObject*, PyObject***, PyObject*, PyObject**, Py_ssize_t, const char*)’: 2021-07-11T20:42:27,911 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,911 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,911 | ^ 2021-07-11T20:42:27,911 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,911 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-11T20:42:27,911 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,912 whatshap/core.cpp:15297:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,912 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,912 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,912 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,912 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,912 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,913 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,913 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-11T20:42:27,913 | ^ 2021-07-11T20:42:27,913 whatshap/core.cpp:15297:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,913 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,913 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,913 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-11T20:42:27,914 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-11T20:42:27,914 | ^~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,914 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,914 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,914 | ^ 2021-07-11T20:42:27,914 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,914 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-11T20:42:27,914 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,915 whatshap/core.cpp:15297:22: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,915 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,915 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,915 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,915 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,915 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,915 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,916 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,916 | ^ 2021-07-11T20:42:27,916 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,916 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-11T20:42:27,916 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,916 whatshap/core.cpp:15297:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,916 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,916 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,917 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,917 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,917 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,917 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-11T20:42:27,917 | ^ 2021-07-11T20:42:27,917 whatshap/core.cpp:15297:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,918 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,918 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,918 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-11T20:42:27,918 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-11T20:42:27,918 | ^~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,918 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,918 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,918 | ^ 2021-07-11T20:42:27,919 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,919 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-11T20:42:27,919 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,919 whatshap/core.cpp:15297:52: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,919 15297 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,919 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,919 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,919 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,920 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,920 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,920 | ^ 2021-07-11T20:42:27,920 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,920 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-11T20:42:27,921 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,921 whatshap/core.cpp:15313:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,921 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,921 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,921 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,921 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,921 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,922 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,922 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-11T20:42:27,922 | ^ 2021-07-11T20:42:27,922 whatshap/core.cpp:15313:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,922 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,922 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,922 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-11T20:42:27,923 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-11T20:42:27,923 | ^~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,923 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,923 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,923 | ^ 2021-07-11T20:42:27,923 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,923 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-11T20:42:27,924 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,924 whatshap/core.cpp:15313:26: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,924 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,924 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,924 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,924 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,924 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,925 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,925 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,925 | ^ 2021-07-11T20:42:27,925 /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,925 261 | PyUnicode_WSTR_LENGTH(op) : \ 2021-07-11T20:42:27,925 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,925 whatshap/core.cpp:15313:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,925 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,926 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,926 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,926 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,926 /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,926 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ 2021-07-11T20:42:27,926 | ^ 2021-07-11T20:42:27,927 whatshap/core.cpp:15313:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,927 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,927 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,927 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-11T20:42:27,927 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-11T20:42:27,927 | ^~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,927 /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,928 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) 2021-07-11T20:42:27,928 | ^ 2021-07-11T20:42:27,928 /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 2021-07-11T20:42:27,928 264 | PyUnicode_WSTR_LENGTH(op))) 2021-07-11T20:42:27,928 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,928 whatshap/core.cpp:15313:59: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 2021-07-11T20:42:27,928 15313 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-11T20:42:27,929 | ^~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,929 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-11T20:42:27,929 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-11T20:42:27,929 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:27,930 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*))’: 2021-07-11T20:42:27,930 whatshap/core.cpp:15461:45: warning: ‘PyObject* PyUnicode_FromUnicode(const Py_UNICODE*, Py_ssize_t)’ is deprecated [-Wdeprecated-declarations] 2021-07-11T20:42:27,930 15461 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-11T20:42:27,930 | ^ 2021-07-11T20:42:27,930 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-11T20:42:27,930 from /usr/include/python3.9/Python.h:97, 2021-07-11T20:42:27,930 from whatshap/core.cpp:27: 2021-07-11T20:42:27,930 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-11T20:42:27,930 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-11T20:42:27,931 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:42:28,041 whatshap/core.cpp: In function ‘void __Pyx__ExceptionSwap(PyThreadState*, PyObject**, PyObject**, PyObject**)’: 2021-07-11T20:42:28,041 whatshap/core.cpp:17366:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-11T20:42:28,041 17366 | tmp_type = tstate->exc_type; 2021-07-11T20:42:28,041 | ^~~~~~~~ 2021-07-11T20:42:28,041 | curexc_type 2021-07-11T20:42:28,041 whatshap/core.cpp:17367:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-11T20:42:28,042 17367 | tmp_value = tstate->exc_value; 2021-07-11T20:42:28,042 | ^~~~~~~~~ 2021-07-11T20:42:28,042 | curexc_value 2021-07-11T20:42:28,042 whatshap/core.cpp:17368:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-11T20:42:28,042 17368 | tmp_tb = tstate->exc_traceback; 2021-07-11T20:42:28,042 | ^~~~~~~~~~~~~ 2021-07-11T20:42:28,043 | curexc_traceback 2021-07-11T20:42:28,043 whatshap/core.cpp:17369:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’? 2021-07-11T20:42:28,043 17369 | tstate->exc_type = *type; 2021-07-11T20:42:28,043 | ^~~~~~~~ 2021-07-11T20:42:28,043 | curexc_type 2021-07-11T20:42:28,043 whatshap/core.cpp:17370:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’? 2021-07-11T20:42:28,043 17370 | tstate->exc_value = *value; 2021-07-11T20:42:28,044 | ^~~~~~~~~ 2021-07-11T20:42:28,044 | curexc_value 2021-07-11T20:42:28,044 whatshap/core.cpp:17371:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’? 2021-07-11T20:42:28,044 17371 | tstate->exc_traceback = *tb; 2021-07-11T20:42:28,044 | ^~~~~~~~~~~~~ 2021-07-11T20:42:28,044 | curexc_traceback 2021-07-11T20:42:28,690 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-11T20:42:28,760 Building wheel for whatshap (setup.py): finished with status 'error' 2021-07-11T20:42:28,761 ERROR: Failed building wheel for whatshap 2021-07-11T20:42:28,762 Running setup.py clean for whatshap 2021-07-11T20:42:28,763 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-zx8sn8z3/whatshap_218eda4755164f8ba26d366a06579061/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 2021-07-11T20:42:30,008 running clean 2021-07-11T20:42:30,010 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-11T20:42:30,018 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-11T20:42:30,026 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-11T20:42:30,026 'build/scripts-3.9' does not exist -- can't clean it 2021-07-11T20:42:30,026 removing 'build' 2021-07-11T20:42:30,090 Failed to build whatshap 2021-07-11T20:42:30,091 ERROR: Failed to build one or more wheels 2021-07-11T20:42:30,091 Exception information: 2021-07-11T20:42:30,091 Traceback (most recent call last): 2021-07-11T20:42:30,091 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-11T20:42:30,091 status = self.run(options, args) 2021-07-11T20:42:30,091 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-11T20:42:30,091 return func(self, options, args) 2021-07-11T20:42:30,091 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-11T20:42:30,091 raise CommandError( 2021-07-11T20:42:30,091 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-11T20:42:30,094 Removed build tracker: '/tmp/pip-req-tracker-uvgei4ng'