2020-06-26T14:56:44,963 Created temporary directory: /tmp/pip-ephem-wheel-cache-bzv8898r
2020-06-26T14:56:44,967 Created temporary directory: /tmp/pip-req-tracker-y4ykle2r
2020-06-26T14:56:44,968 Initialized build tracking at /tmp/pip-req-tracker-y4ykle2r
2020-06-26T14:56:44,969 Created build tracker: /tmp/pip-req-tracker-y4ykle2r
2020-06-26T14:56:44,969 Entered build tracker: /tmp/pip-req-tracker-y4ykle2r
2020-06-26T14:56:44,970 Created temporary directory: /tmp/pip-wheel-2ty_nezf
2020-06-26T14:56:44,984 1 location(s) to search for versions of whatshap:
2020-06-26T14:56:44,984 * https://pypi.org/simple/whatshap/
2020-06-26T14:56:44,985 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/
2020-06-26T14:56:44,986 Getting page https://pypi.org/simple/whatshap/
2020-06-26T14:56:44,988 Found index url https://pypi.org/simple
2020-06-26T14:56:45,299   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
2020-06-26T14:56:45,299   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
2020-06-26T14:56:45,300   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
2020-06-26T14:56:45,301   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
2020-06-26T14:56:45,302   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
2020-06-26T14:56:45,303   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
2020-06-26T14:56:45,304   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
2020-06-26T14:56:45,308   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
2020-06-26T14:56:45,309   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
2020-06-26T14:56:45,310   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
2020-06-26T14:56:45,311   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,312   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,313   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,314   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,315   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
2020-06-26T14:56:45,317   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,318   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,319   Skipping link: No binaries permitted for whatshap: 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)
2020-06-26T14:56:45,321   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
2020-06-26T14:56:45,341 Given no hashes to check 1 links for project 'whatshap': discarding no candidates
2020-06-26T14:56:45,345 Using version 1.0 (newest of versions: 1.0)
2020-06-26T14:56:45,351 Collecting whatshap==1.0
2020-06-26T14:56:45,355   Created temporary directory: /tmp/pip-unpack-ct7nok2i
2020-06-26T14:56:45,438   Downloading whatshap-1.0.tar.gz (579 kB)
2020-06-26T14:56:46,959   Added whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 to build tracker '/tmp/pip-req-tracker-y4ykle2r'
2020-06-26T14:56:46,961     Running setup.py (path:/tmp/pip-wheel-2ty_nezf/whatshap/setup.py) egg_info for package whatshap
2020-06-26T14:56:46,962     Created temporary directory: /tmp/pip-pip-egg-info-mxjiei1f
2020-06-26T14:56:46,963     Running command python setup.py egg_info
2020-06-26T14:56:54,419     running egg_info
2020-06-26T14:56:54,423     creating /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info
2020-06-26T14:56:54,425     writing /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/PKG-INFO
2020-06-26T14:56:54,430     writing dependency_links to /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/dependency_links.txt
2020-06-26T14:56:54,434     writing entry points to /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/entry_points.txt
2020-06-26T14:56:54,437     writing requirements to /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/requires.txt
2020-06-26T14:56:54,439     writing top-level names to /tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/top_level.txt
2020-06-26T14:56:54,443     writing manifest file '/tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/SOURCES.txt'
2020-06-26T14:56:54,845     reading manifest file '/tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/SOURCES.txt'
2020-06-26T14:56:54,861     writing manifest file '/tmp/pip-pip-egg-info-mxjiei1f/whatshap.egg-info/SOURCES.txt'
2020-06-26T14:56:55,033   Source in /tmp/pip-wheel-2ty_nezf/whatshap has version 1.0, which satisfies requirement whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2
2020-06-26T14:56:55,035   Removed whatshap==1.0 from https://files.pythonhosted.org/packages/c0/c8/98036e04fb95249128d6b49ca61691e1d8eea484dd94611f90efb5857174/whatshap-1.0.tar.gz#sha256=fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2 from build tracker '/tmp/pip-req-tracker-y4ykle2r'
2020-06-26T14:56:55,040 Building wheels for collected packages: whatshap
2020-06-26T14:56:55,050   Created temporary directory: /tmp/pip-wheel-eogvma3x
2020-06-26T14:56:55,051   Building wheel for whatshap (setup.py): started
2020-06-26T14:56:55,052   Destination directory: /tmp/pip-wheel-eogvma3x
2020-06-26T14:56:55,052   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-2ty_nezf/whatshap/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-2ty_nezf/whatshap/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-eogvma3x
2020-06-26T14:56:57,907   running bdist_wheel
2020-06-26T14:56:57,914   running build
2020-06-26T14:56:57,915   running build_py
2020-06-26T14:56:58,194   creating build
2020-06-26T14:56:58,195   creating build/lib.linux-armv7l-3.7
2020-06-26T14:56:58,197   creating build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,199   copying whatshap/coverage.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,204   copying whatshap/_version.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,207   copying whatshap/bam.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,212   copying whatshap/utils.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,217   copying whatshap/merge.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,223   copying whatshap/timer.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,227   copying whatshap/polyphaseplots.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,233   copying whatshap/threading.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,239   copying whatshap/math.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,243   copying whatshap/vcf.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,251   copying whatshap/graph.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,255   copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,260   copying whatshap/args.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,264   copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,270   copying whatshap/verification.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,276   copying whatshap/variants.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,284   copying whatshap/__init__.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,288   copying whatshap/__main__.py -> build/lib.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,294   creating build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,296   copying whatshap/cli/stats.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,302   copying whatshap/cli/genotype.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,308   copying whatshap/cli/phase.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,317   copying whatshap/cli/haplotag.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,323   copying whatshap/cli/hapcut2vcf.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,329   copying whatshap/cli/find_snv_candidates.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,335   copying whatshap/cli/polyphase.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,345   copying whatshap/cli/compare.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,354   copying whatshap/cli/__init__.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,361   copying whatshap/cli/unphase.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,366   copying whatshap/cli/split.py -> build/lib.linux-armv7l-3.7/whatshap/cli
2020-06-26T14:56:58,377   running build_ext
2020-06-26T14:56:58,388   building 'whatshap.core' extension
2020-06-26T14:56:58,391   creating build/temp.linux-armv7l-3.7
2020-06-26T14:56:58,392   creating build/temp.linux-armv7l-3.7/whatshap
2020-06-26T14:56:58,394   creating build/temp.linux-armv7l-3.7/src
2020-06-26T14:56:58,397   creating build/temp.linux-armv7l-3.7/src/hapchat
2020-06-26T14:56:58,400   creating build/temp.linux-armv7l-3.7/src/polyphase
2020-06-26T14:56:58,401   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
2020-06-26T14:57:05,971   In file included from whatshap/core.cpp:729:
2020-06-26T14:57:05,971   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2020-06-26T14:57:05,972   whatshap/../src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2020-06-26T14:57:05,973      Counter counter_columns;
2020-06-26T14:57:05,973              ^~~~~~~~~~~~~~~
2020-06-26T14:57:05,986   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2020-06-26T14:57:05,986   whatshap/../src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:05,987      return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2020-06-26T14:57:05,988                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,234   In file included from whatshap/core.cpp:729:
2020-06-26T14:57:06,235   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::dp(const constants_t&, std::vector<bool>&, std::vector<bool>&, Counter&, Cost&, Counter&, Counter&, Counter&, Counter&, HapChatColumnIterator)’:
2020-06-26T14:57:06,236   whatshap/../src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable]
2020-06-26T14:57:06,237       int old_k = k_j[input_pointer];
2020-06-26T14:57:06,237           ^~~~~
2020-06-26T14:57:06,275   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::intersect(const Column&, const Column&, const Pointer&, std::vector<std::vector<int> >&, std::vector<std::vector<int> >&, std::vector<std::bitset<64> >&, std::vector<unsigned int>&, const bool&)’:
2020-06-26T14:57:06,276   whatshap/../src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,276             (colJ[j].get_read_id() != -1) &&
2020-06-26T14:57:06,277              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,277   whatshap/../src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,278             (colQ[i].get_read_id() != -1)) {
2020-06-26T14:57:06,279              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,279   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2020-06-26T14:57:06,280   whatshap/../src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,281      while(cov < column.size() && column[cov].get_read_id() != -1) {
2020-06-26T14:57:06,281                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,288   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2020-06-26T14:57:06,289   whatshap/../src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,290             (colJ[j].get_read_id() != -1) &&
2020-06-26T14:57:06,290              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,291   whatshap/../src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,292             (colQ[i].get_read_id() != -1)) {
2020-06-26T14:57:06,292              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,295   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::insert_col_and_update(std::vector<std::vector<Entry> >&, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<Cost>&, const Pointer&, const Column&, std::vector<bool>&, const Counter&)’:
2020-06-26T14:57:06,295   whatshap/../src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2020-06-26T14:57:06,296      if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2020-06-26T14:57:06,297                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2020-06-26T14:57:06,447   In file included from whatshap/../src/polyphase/clustereditingsolution.h:4,
2020-06-26T14:57:06,448                    from whatshap/../src/polyphase/clustereditingsolver.h:10,
2020-06-26T14:57:06,449                    from whatshap/core.cpp:730:
2020-06-26T14:57:06,449   whatshap/../src/polyphase/staticsparsegraph.h: In member function ‘std::__cxx11::string StaticSparseGraph::int2bin(uint64_t)’:
2020-06-26T14:57:06,450   whatshap/../src/polyphase/staticsparsegraph.h:225:33: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,450            uint64_t mask = (1UL << 63); // fill in values right-to-left
2020-06-26T14:57:06,451                                    ^~
2020-06-26T14:57:06,520   In file included from whatshap/core.cpp:734:
2020-06-26T14:57:06,521   whatshap/../src/polyphase/haplothreader.h: At global scope:
2020-06-26T14:57:06,522   whatshap/../src/polyphase/haplothreader.h:30:53: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,522            31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2020-06-26T14:57:06,523                                                        ^~
2020-06-26T14:57:06,524   whatshap/../src/polyphase/haplothreader.h:31:17: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,525            31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2020-06-26T14:57:06,525                    ^~
2020-06-26T14:57:06,526   whatshap/../src/polyphase/haplothreader.h:31:29: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,526            31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2020-06-26T14:57:06,527                                ^~
2020-06-26T14:57:06,528   whatshap/../src/polyphase/haplothreader.h:31:41: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,528            31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2020-06-26T14:57:06,529                                            ^~
2020-06-26T14:57:06,529   whatshap/../src/polyphase/haplothreader.h:31:53: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,530            31UL << 40, 31UL << 45, 31UL << 50, 31UL << 55};
2020-06-26T14:57:06,530                                                        ^~
2020-06-26T14:57:06,531   whatshap/../src/polyphase/haplothreader.h:30:50: error: right operand of shift expression ‘(31 << 35)’ is >= than the precision of the left operand [-fpermissive]
2020-06-26T14:57:06,531            31UL << 20, 31UL << 25, 31UL << 30, 31UL << 35,
2020-06-26T14:57:06,532                                                ~~~~~^~~~~
2020-06-26T14:57:06,560   In file included from whatshap/core.cpp:735:
2020-06-26T14:57:06,561   whatshap/../src/polyphase/switchflipcalculator.h:30:17: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,561            15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2020-06-26T14:57:06,562                    ^~
2020-06-26T14:57:06,562   whatshap/../src/polyphase/switchflipcalculator.h:30:29: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,563            15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2020-06-26T14:57:06,564                                ^~
2020-06-26T14:57:06,564   whatshap/../src/polyphase/switchflipcalculator.h:30:41: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,565            15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2020-06-26T14:57:06,566                                            ^~
2020-06-26T14:57:06,566   whatshap/../src/polyphase/switchflipcalculator.h:30:53: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,567            15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2020-06-26T14:57:06,567                                                        ^~
2020-06-26T14:57:06,568   whatshap/../src/polyphase/switchflipcalculator.h:31:17: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,568            15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2020-06-26T14:57:06,569                    ^~
2020-06-26T14:57:06,569   whatshap/../src/polyphase/switchflipcalculator.h:31:29: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,570            15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2020-06-26T14:57:06,570                                ^~
2020-06-26T14:57:06,571   whatshap/../src/polyphase/switchflipcalculator.h:31:41: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,571            15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2020-06-26T14:57:06,572                                            ^~
2020-06-26T14:57:06,573   whatshap/../src/polyphase/switchflipcalculator.h:31:53: warning: left shift count >= width of type [-Wshift-count-overflow]
2020-06-26T14:57:06,573            15UL << 48, 15UL << 52, 15UL << 56, 15UL << 60
2020-06-26T14:57:06,574                                                        ^~
2020-06-26T14:57:06,574   whatshap/../src/polyphase/switchflipcalculator.h:30:14: error: right operand of shift expression ‘(15 << 32)’ is >= than the precision of the left operand [-fpermissive]
2020-06-26T14:57:06,575            15UL << 32, 15UL << 36, 15UL << 40, 15UL << 44,
2020-06-26T14:57:06,576            ~~~~~^~~~~
2020-06-26T14:57:07,061   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’:
2020-06-26T14:57:07,062   whatshap/core.cpp:8090:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2020-06-26T14:57:07,063      for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2020-06-26T14:57:07,064                          ~~~~~~~~~~^~~~~~~~~~~
2020-06-26T14:57:07,564   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’:
2020-06-26T14:57:07,565   whatshap/core.cpp:14314:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2020-06-26T14:57:07,566      for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2020-06-26T14:57:07,567                          ~~~~~~~~~~^~~~~~~~~~~
2020-06-26T14:57:08,547   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_20SwitchFlipCalculator_2compute_switch_flips_poly(__pyx_obj_8whatshap_4core_SwitchFlipCalculator*, PyObject*, PyObject*)’:
2020-06-26T14:57:08,548   whatshap/core.cpp:22620:30: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,548          __pyx_t_3 = (__pyx_t_2 == __pyx_v_self->ploidy);
2020-06-26T14:57:08,549                       ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
2020-06-26T14:57:08,556   whatshap/core.cpp:22695:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,556        for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2020-06-26T14:57:08,557                            ~~~~~~~~~~^~~~~~~~~~~
2020-06-26T14:57:08,563   whatshap/core.cpp:22731:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,564        for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2020-06-26T14:57:08,565                            ~~~~~~~~~~^~~~~~~~~~~
2020-06-26T14:57:08,575   whatshap/core.cpp:22829:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,576          __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_switches_in_column.size()) != 0);
2020-06-26T14:57:08,576                         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-06-26T14:57:08,577   whatshap/core.cpp:22854:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector<std::vector<unsigned int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,578          __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_flips_in_column.size()) != 0);
2020-06-26T14:57:08,578                         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-06-26T14:57:08,579   whatshap/core.cpp:22879:39: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘std::vector<std::vector<unsigned int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,579          __pyx_t_15 = ((__pyx_v_num_vars == __pyx_v_perm_in_column.size()) != 0);
2020-06-26T14:57:08,580                         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-06-26T14:57:08,585   whatshap/core.cpp:23037:37: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
2020-06-26T14:57:08,586          for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
2020-06-26T14:57:08,587                              ~~~~~~~~~~^~~~~~~~~~~
2020-06-26T14:57:13,911   error: command 'arm-linux-gnueabihf-gcc' failed with exit status 1
2020-06-26T14:57:14,072   Building wheel for whatshap (setup.py): finished with status 'error'
2020-06-26T14:57:14,073   ERROR: Failed building wheel for whatshap
2020-06-26T14:57:14,074   Running setup.py clean for whatshap
2020-06-26T14:57:14,075   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-2ty_nezf/whatshap/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-2ty_nezf/whatshap/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
2020-06-26T14:57:16,893   running clean
2020-06-26T14:57:16,898   removing 'build/temp.linux-armv7l-3.7' (and everything under it)
2020-06-26T14:57:16,907   removing 'build/lib.linux-armv7l-3.7' (and everything under it)
2020-06-26T14:57:16,931   'build/bdist.linux-armv7l' does not exist -- can't clean it
2020-06-26T14:57:16,932   'build/scripts-3.7' does not exist -- can't clean it
2020-06-26T14:57:16,933   removing 'build'
2020-06-26T14:57:17,069 Failed to build whatshap
2020-06-26T14:57:17,070 ERROR: Failed to build one or more wheels
2020-06-26T14:57:17,071 Exception information:
2020-06-26T14:57:17,071 Traceback (most recent call last):
2020-06-26T14:57:17,071   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 188, in _main
2020-06-26T14:57:17,071     status = self.run(options, args)
2020-06-26T14:57:17,071   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 185, in wrapper
2020-06-26T14:57:17,071     return func(self, options, args)
2020-06-26T14:57:17,071   File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 189, in run
2020-06-26T14:57:17,071     "Failed to build one or more wheels"
2020-06-26T14:57:17,071 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2020-06-26T14:57:17,078 Removed build tracker: '/tmp/pip-req-tracker-y4ykle2r'