2021-04-08T14:09:17,090 Created temporary directory: /tmp/pip-ephem-wheel-cache-wba73377 2021-04-08T14:09:17,093 Created temporary directory: /tmp/pip-req-tracker-kr79do27 2021-04-08T14:09:17,093 Initialized build tracking at /tmp/pip-req-tracker-kr79do27 2021-04-08T14:09:17,093 Created build tracker: /tmp/pip-req-tracker-kr79do27 2021-04-08T14:09:17,094 Entered build tracker: /tmp/pip-req-tracker-kr79do27 2021-04-08T14:09:17,094 Created temporary directory: /tmp/pip-wheel-fb1tk_l2 2021-04-08T14:09:17,124 1 location(s) to search for versions of whatshap: 2021-04-08T14:09:17,124 * https://pypi.org/simple/whatshap/ 2021-04-08T14:09:17,124 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-04-08T14:09:17,125 Getting page https://pypi.org/simple/whatshap/ 2021-04-08T14:09:17,127 Found index url https://pypi.org/simple 2021-04-08T14:09:17,228 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 2021-04-08T14:09:17,228 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 2021-04-08T14:09:17,229 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 2021-04-08T14:09:17,229 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 2021-04-08T14:09:17,229 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 2021-04-08T14:09:17,230 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 2021-04-08T14:09:17,230 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 2021-04-08T14:09:17,230 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 2021-04-08T14:09:17,231 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 2021-04-08T14:09:17,231 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 2021-04-08T14:09:17,245 Skipping link: none of the wheel's tags match: cp34-cp34m-manylinux1_x86_64: 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) 2021-04-08T14:09:17,246 Skipping link: none of the wheel's tags match: cp35-cp35m-manylinux1_x86_64: 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) 2021-04-08T14:09:17,246 Skipping link: none of the wheel's tags match: cp36-cp36m-manylinux1_x86_64: 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) 2021-04-08T14:09:17,247 Skipping link: none of the wheel's tags match: cp37-cp37m-manylinux1_x86_64: 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) 2021-04-08T14:09:17,247 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 2021-04-08T14:09:17,248 Skipping link: none of the wheel's tags match: cp36-cp36m-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,248 Skipping link: none of the wheel's tags match: cp37-cp37m-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,249 Skipping link: none of the wheel's tags match: cp38-cp38-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,249 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 2021-04-08T14:09:17,250 Skipping link: none of the wheel's tags match: cp36-cp36m-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,250 Skipping link: none of the wheel's tags match: cp37-cp37m-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,251 Skipping link: none of the wheel's tags match: cp38-cp38-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,251 Skipping link: none of the wheel's tags match: cp39-cp39-manylinux2010_x86_64: 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) 2021-04-08T14:09:17,252 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 2021-04-08T14:09:17,254 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-04-08T14:09:17,269 Collecting whatshap==1.1 2021-04-08T14:09:17,271 Created temporary directory: /tmp/pip-unpack-oc4t6m5n 2021-04-08T14:09:17,460 Downloading whatshap-1.1.tar.gz (588 kB) 2021-04-08T14:09:18,099 Added whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f to build tracker '/tmp/pip-req-tracker-kr79do27' 2021-04-08T14:09:18,100 Running setup.py (path:/tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42/setup.py) egg_info for package whatshap 2021-04-08T14:09:18,101 Created temporary directory: /tmp/pip-pip-egg-info-k2aeskkj 2021-04-08T14:09:18,102 Running command python setup.py egg_info 2021-04-08T14:09:22,151 running egg_info 2021-04-08T14:09:22,153 creating /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info 2021-04-08T14:09:22,154 writing /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/PKG-INFO 2021-04-08T14:09:22,157 writing dependency_links to /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/dependency_links.txt 2021-04-08T14:09:22,159 writing entry points to /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/entry_points.txt 2021-04-08T14:09:22,161 writing requirements to /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/requires.txt 2021-04-08T14:09:22,162 writing top-level names to /tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/top_level.txt 2021-04-08T14:09:22,165 writing manifest file '/tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/SOURCES.txt' 2021-04-08T14:09:22,374 reading manifest file '/tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/SOURCES.txt' 2021-04-08T14:09:22,383 writing manifest file '/tmp/pip-pip-egg-info-k2aeskkj/whatshap.egg-info/SOURCES.txt' 2021-04-08T14:09:22,457 Source in /tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42 has version 1.1, which satisfies requirement whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f 2021-04-08T14:09:22,458 Removed whatshap==1.1 from https://files.pythonhosted.org/packages/94/69/20b124a032b37c73ac56708744cbf2542cbc3e31390f261853ca5a6f62fe/whatshap-1.1.tar.gz#sha256=4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f from build tracker '/tmp/pip-req-tracker-kr79do27' 2021-04-08T14:09:22,464 Created temporary directory: /tmp/pip-unpack-_1zwc3r7 2021-04-08T14:09:22,464 Building wheels for collected packages: whatshap 2021-04-08T14:09:22,469 Created temporary directory: /tmp/pip-wheel-0w54k65n 2021-04-08T14:09:22,469 Building wheel for whatshap (setup.py): started 2021-04-08T14:09:22,470 Destination directory: /tmp/pip-wheel-0w54k65n 2021-04-08T14:09:22,470 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-0w54k65n 2021-04-08T14:09:24,085 running bdist_wheel 2021-04-08T14:09:24,089 running build 2021-04-08T14:09:24,090 running build_py 2021-04-08T14:09:24,217 creating build 2021-04-08T14:09:24,218 creating build/lib.linux-armv7l-3.7 2021-04-08T14:09:24,219 creating build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,220 copying whatshap/utils.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,222 copying whatshap/verification.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,224 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,226 copying whatshap/math.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,228 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,230 copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,233 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,235 copying whatshap/merge.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,237 copying whatshap/timer.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,239 copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,242 copying whatshap/args.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,244 copying whatshap/threading.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,247 copying whatshap/_version.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,249 copying whatshap/bam.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,251 copying whatshap/graph.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,254 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,256 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,259 copying whatshap/variants.py -> build/lib.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,264 creating build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,265 copying whatshap/cli/split.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,268 copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,270 copying whatshap/cli/compare.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,274 copying whatshap/cli/stats.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,277 copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,280 copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,283 copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,285 copying whatshap/cli/phase.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,288 copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,291 copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,294 copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-3.7/whatshap/cli 2021-04-08T14:09:24,300 running build_ext 2021-04-08T14:09:24,307 building 'whatshap.core' extension 2021-04-08T14:09:24,309 creating build/temp.linux-armv7l-3.7 2021-04-08T14:09:24,309 creating build/temp.linux-armv7l-3.7/whatshap 2021-04-08T14:09:24,311 creating build/temp.linux-armv7l-3.7/src 2021-04-08T14:09:24,312 creating build/temp.linux-armv7l-3.7/src/hapchat 2021-04-08T14:09:24,313 creating build/temp.linux-armv7l-3.7/src/polyphase 2021-04-08T14:09:24,314 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -UNDEBUG -I/usr/include/python3.7m -c whatshap/core.cpp -o build/temp.linux-armv7l-3.7/whatshap/core.o -std=c++11 -Werror=return-type -Werror=narrowing 2021-04-08T14:09:27,260 In file included from whatshap/core.cpp:733: 2021-04-08T14:09:27,260 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’: 2021-04-08T14:09:27,261 whatshap/../src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable] 2021-04-08T14:09:27,261 Counter counter_columns; 2021-04-08T14:09:27,261 ^~~~~~~~~~~~~~~ 2021-04-08T14:09:27,268 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector >&, const Pointer&, const bool&)’: 2021-04-08T14:09:27,269 whatshap/../src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,269 return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1))); 2021-04-08T14:09:27,269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,380 In file included from whatshap/core.cpp:733: 2021-04-08T14:09:27,380 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)’: 2021-04-08T14:09:27,381 whatshap/../src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable] 2021-04-08T14:09:27,381 int old_k = k_j[input_pointer]; 2021-04-08T14:09:27,381 ^~~~~ 2021-04-08T14:09:27,396 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&)’: 2021-04-08T14:09:27,397 whatshap/../src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,397 (colJ[j].get_read_id() != -1) && 2021-04-08T14:09:27,397 ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,397 whatshap/../src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,398 (colQ[i].get_read_id() != -1)) { 2021-04-08T14:09:27,398 ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,399 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’: 2021-04-08T14:09:27,399 whatshap/../src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,399 while(cov < column.size() && column[cov].get_read_id() != -1) { 2021-04-08T14:09:27,400 ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,403 whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’: 2021-04-08T14:09:27,404 whatshap/../src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,404 (colJ[j].get_read_id() != -1) && 2021-04-08T14:09:27,404 ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,404 whatshap/../src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,405 (colQ[i].get_read_id() != -1)) { 2021-04-08T14:09:27,405 ~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,407 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&)’: 2021-04-08T14:09:27,407 whatshap/../src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-04-08T14:09:27,407 if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1) 2021-04-08T14:09:27,407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-04-08T14:09:27,481 In file included from whatshap/../src/polyphase/clustereditingsolution.h:4, 2021-04-08T14:09:27,481 from whatshap/../src/polyphase/clustereditingsolver.h:10, 2021-04-08T14:09:27,481 from whatshap/core.cpp:734: 2021-04-08T14:09:27,481 whatshap/../src/polyphase/staticsparsegraph.h: In member function ‘std::__cxx11::string StaticSparseGraph::int2bin(uint64_t)’: 2021-04-08T14:09:27,482 whatshap/../src/polyphase/staticsparsegraph.h:225:33: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,482 uint64_t mask = (1UL << 63); // fill in values right-to-left 2021-04-08T14:09:27,482 ^~ 2021-04-08T14:09:27,521 In file included from whatshap/core.cpp:738: 2021-04-08T14:09:27,522 whatshap/../src/polyphase/haplothreader.h: At global scope: 2021-04-08T14:09:27,522 whatshap/../src/polyphase/haplothreader.h:30:53: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,522 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2021-04-08T14:09:27,522 ^~ 2021-04-08T14:09:27,523 whatshap/../src/polyphase/haplothreader.h:31:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,523 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-04-08T14:09:27,523 ^~ 2021-04-08T14:09:27,523 whatshap/../src/polyphase/haplothreader.h:31:29: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,523 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-04-08T14:09:27,524 ^~ 2021-04-08T14:09:27,524 whatshap/../src/polyphase/haplothreader.h:31:41: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,524 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-04-08T14:09:27,524 ^~ 2021-04-08T14:09:27,524 whatshap/../src/polyphase/haplothreader.h:31:53: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,525 31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55}; 2021-04-08T14:09:27,525 ^~ 2021-04-08T14:09:27,525 whatshap/../src/polyphase/haplothreader.h:30:50: error: right operand of shift expression ‘(31 << 35)’ is >= than the precision of the left operand [-fpermissive] 2021-04-08T14:09:27,525 31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35, 2021-04-08T14:09:27,526 ~~~~~^~~~~ 2021-04-08T14:09:27,541 In file included from whatshap/core.cpp:739: 2021-04-08T14:09:27,541 whatshap/../src/polyphase/switchflipcalculator.h:30:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,542 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2021-04-08T14:09:27,542 ^~ 2021-04-08T14:09:27,542 whatshap/../src/polyphase/switchflipcalculator.h:30:29: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,542 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2021-04-08T14:09:27,542 ^~ 2021-04-08T14:09:27,543 whatshap/../src/polyphase/switchflipcalculator.h:30:41: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,543 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2021-04-08T14:09:27,543 ^~ 2021-04-08T14:09:27,543 whatshap/../src/polyphase/switchflipcalculator.h:30:53: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,544 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2021-04-08T14:09:27,544 ^~ 2021-04-08T14:09:27,544 whatshap/../src/polyphase/switchflipcalculator.h:31:17: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,544 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2021-04-08T14:09:27,544 ^~ 2021-04-08T14:09:27,545 whatshap/../src/polyphase/switchflipcalculator.h:31:29: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,545 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2021-04-08T14:09:27,545 ^~ 2021-04-08T14:09:27,545 whatshap/../src/polyphase/switchflipcalculator.h:31:41: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,545 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2021-04-08T14:09:27,546 ^~ 2021-04-08T14:09:27,546 whatshap/../src/polyphase/switchflipcalculator.h:31:53: warning: left shift count >= width of type [-Wshift-count-overflow] 2021-04-08T14:09:27,546 15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60 2021-04-08T14:09:27,546 ^~ 2021-04-08T14:09:27,546 whatshap/../src/polyphase/switchflipcalculator.h:30:14: error: right operand of shift expression ‘(15 << 32)’ is >= than the precision of the left operand [-fpermissive] 2021-04-08T14:09:27,547 15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44, 2021-04-08T14:09:27,547 ~~~~~^~~~~ 2021-04-08T14:09:27,862 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2021-04-08T14:09:27,862 whatshap/core.cpp:9492:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-04-08T14:09:27,862 for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-04-08T14:09:27,862 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-08T14:09:28,099 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’: 2021-04-08T14:09:28,099 whatshap/core.cpp:15716:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-04-08T14:09:28,099 for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-04-08T14:09:28,099 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-08T14:09:28,523 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_20SwitchFlipCalculator_2compute_switch_flips_poly(__pyx_obj_8whatshap_4core_SwitchFlipCalculator*, PyObject*, PyObject*)’: 2021-04-08T14:09:28,524 whatshap/core.cpp:24022:30: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,524 __pyx_t_3 = (__pyx_t_2 == __pyx_v_self->ploidy); 2021-04-08T14:09:28,524 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2021-04-08T14:09:28,528 whatshap/core.cpp:24097:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,528 for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-04-08T14:09:28,529 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-08T14:09:28,532 whatshap/core.cpp:24133:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,532 for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-04-08T14:09:28,533 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-08T14:09:28,553 whatshap/core.cpp:24231:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,554 __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_switches_in_column.size()) != 0); 2021-04-08T14:09:28,554 ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-08T14:09:28,554 whatshap/core.cpp:24256:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,554 __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_flips_in_column.size()) != 0); 2021-04-08T14:09:28,555 ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-08T14:09:28,555 whatshap/core.cpp:24281:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,555 __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_perm_in_column.size()) != 0); 2021-04-08T14:09:28,555 ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-04-08T14:09:28,559 whatshap/core.cpp:24439:37: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-04-08T14:09:28,559 for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-04-08T14:09:28,559 ~~~~~~~~~~^~~~~~~~~~~ 2021-04-08T14:09:30,914 error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1 2021-04-08T14:09:30,982 Building wheel for whatshap (setup.py): finished with status 'error' 2021-04-08T14:09:30,983 ERROR: Failed building wheel for whatshap 2021-04-08T14:09:30,983 Running setup.py clean for whatshap 2021-04-08T14:09:30,984 Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-fb1tk_l2/whatshap_d875c0130b064f62b19b709796af9a42/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all 2021-04-08T14:09:32,352 running clean 2021-04-08T14:09:32,354 removing 'build/temp.linux-armv7l-3.7' (and everything under it) 2021-04-08T14:09:32,360 removing 'build/lib.linux-armv7l-3.7' (and everything under it) 2021-04-08T14:09:32,374 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-04-08T14:09:32,374 'build/scripts-3.7' does not exist -- can't clean it 2021-04-08T14:09:32,375 removing 'build' 2021-04-08T14:09:32,435 Failed to build whatshap 2021-04-08T14:09:32,435 ERROR: Failed to build one or more wheels 2021-04-08T14:09:32,436 Exception information: 2021-04-08T14:09:32,436 Traceback (most recent call last): 2021-04-08T14:09:32,436 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 189, in _main 2021-04-08T14:09:32,436 status = self.run(options, args) 2021-04-08T14:09:32,436 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 178, in wrapper 2021-04-08T14:09:32,436 return func(self, options, args) 2021-04-08T14:09:32,436 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 191, in run 2021-04-08T14:09:32,436 "Failed to build one or more wheels" 2021-04-08T14:09:32,436 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-04-08T14:09:32,439 Removed build tracker: '/tmp/pip-req-tracker-kr79do27'