2021-07-10T17:11:45,164 Created temporary directory: /tmp/pip-ephem-wheel-cache-oxbf5al7 2021-07-10T17:11:45,172 Created temporary directory: /tmp/pip-req-tracker-qafriutv 2021-07-10T17:11:45,172 Initialized build tracking at /tmp/pip-req-tracker-qafriutv 2021-07-10T17:11:45,172 Created build tracker: /tmp/pip-req-tracker-qafriutv 2021-07-10T17:11:45,172 Entered build tracker: /tmp/pip-req-tracker-qafriutv 2021-07-10T17:11:45,173 Created temporary directory: /tmp/pip-wheel-j5npusoh 2021-07-10T17:11:45,202 1 location(s) to search for versions of whatshap: 2021-07-10T17:11:45,202 * https://pypi.org/simple/whatshap/ 2021-07-10T17:11:45,203 Fetching project page and analyzing links: https://pypi.org/simple/whatshap/ 2021-07-10T17:11:45,203 Getting page https://pypi.org/simple/whatshap/ 2021-07-10T17:11:45,205 Found index url https://pypi.org/simple 2021-07-10T17:11:45,396 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 2021-07-10T17:11:45,397 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 2021-07-10T17:11:45,397 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 2021-07-10T17:11:45,398 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 2021-07-10T17:11:45,398 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 2021-07-10T17:11:45,398 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 2021-07-10T17:11:45,398 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 2021-07-10T17:11:45,399 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 2021-07-10T17:11:45,399 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 2021-07-10T17:11:45,399 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 2021-07-10T17:11:45,416 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) 2021-07-10T17:11:45,417 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) 2021-07-10T17:11:45,417 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) 2021-07-10T17:11:45,418 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) 2021-07-10T17:11:45,419 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 2021-07-10T17:11:45,419 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) 2021-07-10T17:11:45,420 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) 2021-07-10T17:11:45,420 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) 2021-07-10T17:11:45,421 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 2021-07-10T17:11:45,421 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) 2021-07-10T17:11:45,422 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) 2021-07-10T17:11:45,422 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) 2021-07-10T17:11:45,423 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) 2021-07-10T17:11:45,423 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 2021-07-10T17:11:45,423 Skipping link: not a file: https://pypi.org/simple/whatshap/ 2021-07-10T17:11:45,426 Given no hashes to check 1 links for project 'whatshap': discarding no candidates 2021-07-10T17:11:45,445 Collecting whatshap==0.10 2021-07-10T17:11:45,446 Created temporary directory: /tmp/pip-unpack-a_slee_3 2021-07-10T17:11:45,624 Downloading whatshap-0.10.tar.gz (176 kB) 2021-07-10T17:11:45,855 Added whatshap==0.10 from https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz#sha256=864d4ecfc33eac7265452f5a2f468a830779afc53e723119ecac5ecf73255acc to build tracker '/tmp/pip-req-tracker-qafriutv' 2021-07-10T17:11:45,856 Running setup.py (path:/tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c/setup.py) egg_info for package whatshap 2021-07-10T17:11:45,857 Created temporary directory: /tmp/pip-pip-egg-info-z97lhidv 2021-07-10T17:11:45,858 Running command python setup.py egg_info 2021-07-10T17:11:46,722 running egg_info 2021-07-10T17:11:46,724 creating /tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info 2021-07-10T17:11:46,726 writing /tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/PKG-INFO 2021-07-10T17:11:46,730 writing dependency_links to /tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/dependency_links.txt 2021-07-10T17:11:46,735 writing requirements to /tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/requires.txt 2021-07-10T17:11:46,737 writing top-level names to /tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/top_level.txt 2021-07-10T17:11:46,741 writing manifest file '/tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/SOURCES.txt' 2021-07-10T17:11:46,904 reading manifest file '/tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/SOURCES.txt' 2021-07-10T17:11:46,908 writing manifest file '/tmp/pip-pip-egg-info-z97lhidv/whatshap.egg-info/SOURCES.txt' 2021-07-10T17:11:46,976 Source in /tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c has version 0.10, which satisfies requirement whatshap==0.10 from https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz#sha256=864d4ecfc33eac7265452f5a2f468a830779afc53e723119ecac5ecf73255acc 2021-07-10T17:11:46,977 Removed whatshap==0.10 from https://files.pythonhosted.org/packages/f0/4b/f2b882803ac66b969414d8427ee8b4ca2c29b17cfead0fd85f349dc66983/whatshap-0.10.tar.gz#sha256=864d4ecfc33eac7265452f5a2f468a830779afc53e723119ecac5ecf73255acc from build tracker '/tmp/pip-req-tracker-qafriutv' 2021-07-10T17:11:46,981 Created temporary directory: /tmp/pip-unpack-me7dlp7j 2021-07-10T17:11:46,981 Building wheels for collected packages: whatshap 2021-07-10T17:11:46,987 Created temporary directory: /tmp/pip-wheel-el714_bi 2021-07-10T17:11:46,988 Building wheel for whatshap (setup.py): started 2021-07-10T17:11:46,988 Destination directory: /tmp/pip-wheel-el714_bi 2021-07-10T17:11:46,988 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c/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-el714_bi 2021-07-10T17:11:48,356 running bdist_wheel 2021-07-10T17:11:48,361 running build 2021-07-10T17:11:48,361 running build_py 2021-07-10T17:11:48,500 creating build 2021-07-10T17:11:48,501 creating build/lib.linux-armv7l-3.9 2021-07-10T17:11:48,501 creating build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,503 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,505 copying whatshap/graph.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,506 copying whatshap/args.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,508 copying whatshap/verification.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,510 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,511 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,514 copying whatshap/bam.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,516 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,519 creating build/lib.linux-armv7l-3.9/whatshap/scripts 2021-07-10T17:11:48,520 copying whatshap/scripts/whatshap.py -> build/lib.linux-armv7l-3.9/whatshap/scripts 2021-07-10T17:11:48,524 copying whatshap/scripts/__init__.py -> build/lib.linux-armv7l-3.9/whatshap/scripts 2021-07-10T17:11:48,525 copying whatshap/scripts/phasingstats.py -> build/lib.linux-armv7l-3.9/whatshap/scripts 2021-07-10T17:11:48,529 running build_ext 2021-07-10T17:11:48,536 building 'whatshap.core' extension 2021-07-10T17:11:48,537 creating build/temp.linux-armv7l-3.9 2021-07-10T17:11:48,537 creating build/temp.linux-armv7l-3.9/src 2021-07-10T17:11:48,539 creating build/temp.linux-armv7l-3.9/whatshap 2021-07-10T17:11:48,539 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 -I/usr/include/python3.9 -c src/columncostcomputer.cpp -o build/temp.linux-armv7l-3.9/src/columncostcomputer.o -std=c++11 2021-07-10T17:11:49,979 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 -I/usr/include/python3.9 -c src/columnindexingiterator.cpp -o build/temp.linux-armv7l-3.9/src/columnindexingiterator.o -std=c++11 2021-07-10T17:11:51,114 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::dual_index(unsigned int)’: 2021-07-10T17:11:51,115 src/columnindexingiterator.cpp:101:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:51,115 101 | for(int j=0; j< parent->read_ids.size(); ++j) { // compute the dual of i 2021-07-10T17:11:51,115 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T17:11:51,116 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2021-07-10T17:11:51,116 src/columnindexingiterator.cpp:115:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:51,117 115 | for(int j=0; j< parent->read_ids.size(); ++j) { 2021-07-10T17:11:51,117 | ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T17:11:51,117 src/columnindexingiterator.cpp:117:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-10T17:11:51,117 117 | if(m != -1) { 2021-07-10T17:11:51,117 | ~~^~~~~ 2021-07-10T17:11:51,118 src/columnindexingiterator.cpp:114:16: warning: unused variable ‘s’ [-Wunused-variable] 2021-07-10T17:11:51,118 114 | unsigned int s = 1; 2021-07-10T17:11:51,118 | ^ 2021-07-10T17:11:51,406 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 -I/usr/include/python3.9 -c src/columnindexingscheme.cpp -o build/temp.linux-armv7l-3.9/src/columnindexingscheme.o -std=c++11 2021-07-10T17:11:52,526 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2021-07-10T17:11:52,527 src/columnindexingscheme.cpp:20:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:52,527 20 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:52,527 20 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:52,530 63 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:52,530 63 | while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-10T17:11:54,688 36 | return n < positions->size(); 2021-07-10T17:11:54,688 | ~~^~~~~~~~~~~~~~~~~~~ 2021-07-10T17:11:54,721 src/columniterator.cpp: In member function ‘std::unique_ptr > ColumnIterator::get_next()’: 2021-07-10T17:11:54,722 src/columniterator.cpp:59:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-10T17:11:54,722 59 | while (next_read_index < set.size()) { 2021-07-10T17:11:54,722 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2021-07-10T17:11:55,602 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 -I/usr/include/python3.9 -c src/dptable.cpp -o build/temp.linux-armv7l-3.9/src/dptable.o -std=c++11 2021-07-10T17:11:57,346 src/dptable.cpp: In member function ‘void DPTable::compute_table()’: 2021-07-10T17:11:57,347 src/dptable.cpp:106:10: warning: unused variable ‘pc’ [-Wunused-variable] 2021-07-10T17:11:57,347 106 | double pc = pi; 2021-07-10T17:11:57,347 | ^~ 2021-07-10T17:11:57,347 src/dptable.cpp:107:16: warning: unused variable ‘nc’ [-Wunused-variable] 2021-07-10T17:11:57,347 107 | unsigned int nc = column_iterator.get_column_count(); 2021-07-10T17:11:57,347 | ^~ 2021-07-10T17:11:58,746 src/dptable.cpp:260:23: warning: ‘running_optimal_score_index’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-10T17:11:58,746 260 | optimal_score_index = running_optimal_score_index; 2021-07-10T17:11:58,746 | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T17:11:58,746 src/dptable.cpp:259:17: warning: ‘running_optimal_score’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-10T17:11:58,746 259 | optimal_score = running_optimal_score; 2021-07-10T17:11:58,747 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2021-07-10T17:11:59,441 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 -I/usr/include/python3.9 -c src/entry.cpp -o build/temp.linux-armv7l-3.9/src/entry.o -std=c++11 2021-07-10T17:12:00,266 src/entry.cpp: In function ‘std::ostream& operator<<(std::ostream&, const Entry&)’: 2021-07-10T17:12:00,266 src/entry.cpp:39:1: warning: no return statement in function returning non-void [-Wreturn-type] 2021-07-10T17:12:00,266 39 | } 2021-07-10T17:12:00,266 | ^ 2021-07-10T17:12:00,470 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 -I/usr/include/python3.9 -c src/graycodes.cpp -o build/temp.linux-armv7l-3.9/src/graycodes.o -std=c++11 2021-07-10T17:12:01,626 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 -I/usr/include/python3.9 -c src/indexset.cpp -o build/temp.linux-armv7l-3.9/src/indexset.o -std=c++11 2021-07-10T17:12:03,239 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 -I/usr/include/python3.9 -c src/pedigree.cpp -o build/temp.linux-armv7l-3.9/src/pedigree.o -std=c++11 2021-07-10T17:12:04,371 In file included from src/pedigree.cpp:6: 2021-07-10T17:12:04,371 src/pedigree.h:19:51: error: ‘std::vector’ has not been declared 2021-07-10T17:12:04,372 19 | void addIndividual(unsigned int individual, std::vector genotypes); 2021-07-10T17:12:04,372 | ^~~~~~ 2021-07-10T17:12:04,372 src/pedigree.h:19:57: error: expected ‘,’ or ‘...’ before ‘<’ token 2021-07-10T17:12:04,372 19 | void addIndividual(unsigned int individual, std::vector genotypes); 2021-07-10T17:12:04,373 | ^ 2021-07-10T17:12:04,373 src/pedigree.h:27:7: error: ‘vector’ in namespace ‘std’ does not name a template type 2021-07-10T17:12:04,373 27 | std::vector triples; 2021-07-10T17:12:04,373 | ^~~~~~ 2021-07-10T17:12:04,373 src/pedigree.h:6:1: note: ‘std::vector’ is defined in header ‘’; did you forget to ‘#include ’? 2021-07-10T17:12:04,373 5 | #include 2021-07-10T17:12:04,373 +++ |+#include 2021-07-10T17:12:04,374 6 | 2021-07-10T17:12:04,374 src/pedigree.h:29:7: error: ‘vector’ in namespace ‘std’ does not name a template type 2021-07-10T17:12:04,374 29 | std::vector individuals; 2021-07-10T17:12:04,374 | ^~~~~~ 2021-07-10T17:12:04,374 src/pedigree.h:29:2: note: ‘std::vector’ is defined in header ‘’; did you forget to ‘#include ’? 2021-07-10T17:12:04,374 29 | std::vector individuals; 2021-07-10T17:12:04,374 | ^~~ 2021-07-10T17:12:04,375 src/pedigree.h:30:40: error: ‘vector’ is not a member of ‘std’ 2021-07-10T17:12:04,375 30 | std::unordered_map> genotypes_map; 2021-07-10T17:12:04,375 | ^~~~~~ 2021-07-10T17:12:04,375 src/pedigree.h:30:40: note: ‘std::vector’ is defined in header ‘’; did you forget to ‘#include ’? 2021-07-10T17:12:04,375 src/pedigree.h:30:40: error: ‘vector’ is not a member of ‘std’ 2021-07-10T17:12:04,375 src/pedigree.h:30:40: note: ‘std::vector’ is defined in header ‘’; did you forget to ‘#include ’? 2021-07-10T17:12:04,375 src/pedigree.h:30:59: error: template argument 2 is invalid 2021-07-10T17:12:04,376 30 | std::unordered_map> genotypes_map; 2021-07-10T17:12:04,376 | ^~ 2021-07-10T17:12:04,376 src/pedigree.h:30:59: error: template argument 5 is invalid 2021-07-10T17:12:04,377 src/pedigree.h: In member function ‘size_t Pedigree::size() const’: 2021-07-10T17:12:04,377 src/pedigree.h:25:10: error: ‘individuals’ was not declared in this scope; did you mean ‘addIndividual’? 2021-07-10T17:12:04,377 25 | return individuals.size(); 2021-07-10T17:12:04,377 | ^~~~~~~~~~~ 2021-07-10T17:12:04,377 | addIndividual 2021-07-10T17:12:04,378 src/pedigree.cpp: At global scope: 2021-07-10T17:12:04,379 src/pedigree.cpp:14:52: error: ‘std::vector’ has not been declared 2021-07-10T17:12:04,379 14 | void Pedigree::addIndividual(unsigned int id, std::vector genotypes) { 2021-07-10T17:12:04,379 | ^~~~~~ 2021-07-10T17:12:04,379 src/pedigree.cpp:14:58: error: expected ‘,’ or ‘...’ before ‘<’ token 2021-07-10T17:12:04,379 14 | void Pedigree::addIndividual(unsigned int id, std::vector genotypes) { 2021-07-10T17:12:04,380 | ^ 2021-07-10T17:12:04,380 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, int)’: 2021-07-10T17:12:04,380 src/pedigree.cpp:15:15: error: invalid types ‘int[unsigned int]’ for array subscript 2021-07-10T17:12:04,380 15 | genotypes_map[id] = genotypes; 2021-07-10T17:12:04,380 | ^ 2021-07-10T17:12:04,383 src/pedigree.cpp:15:22: error: ‘genotypes’ was not declared in this scope; did you mean ‘genotypes_map’? 2021-07-10T17:12:04,383 15 | genotypes_map[id] = genotypes; 2021-07-10T17:12:04,383 | ^~~~~~~~~ 2021-07-10T17:12:04,384 | genotypes_map 2021-07-10T17:12:04,387 src/pedigree.cpp:16:2: error: ‘individuals’ was not declared in this scope; did you mean ‘addIndividual’? 2021-07-10T17:12:04,388 16 | individuals.push_back(id); 2021-07-10T17:12:04,388 | ^~~~~~~~~~~ 2021-07-10T17:12:04,388 | addIndividual 2021-07-10T17:12:04,393 src/pedigree.cpp: In member function ‘void Pedigree::addRelationship(unsigned int, unsigned int, unsigned int)’: 2021-07-10T17:12:04,393 src/pedigree.cpp:22:2: error: ‘triples’ was not declared in this scope 2021-07-10T17:12:04,394 22 | triples.push_back(triple_entry); 2021-07-10T17:12:04,394 | ^~~~~~~ 2021-07-10T17:12:04,483 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2021-07-10T17:12:04,555 Building wheel for whatshap (setup.py): finished with status 'error' 2021-07-10T17:12:04,555 ERROR: Failed building wheel for whatshap 2021-07-10T17:12:04,556 Running setup.py clean for whatshap 2021-07-10T17:12:04,556 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-j5npusoh/whatshap_1adda75abf5b4f7fb406a6c272b60f2c/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 2021-07-10T17:12:05,662 running clean 2021-07-10T17:12:05,664 removing 'build/temp.linux-armv7l-3.9' (and everything under it) 2021-07-10T17:12:05,670 removing 'build/lib.linux-armv7l-3.9' (and everything under it) 2021-07-10T17:12:05,675 'build/bdist.linux-armv7l' does not exist -- can't clean it 2021-07-10T17:12:05,675 'build/scripts-3.9' does not exist -- can't clean it 2021-07-10T17:12:05,676 removing 'build' 2021-07-10T17:12:05,732 Failed to build whatshap 2021-07-10T17:12:05,733 ERROR: Failed to build one or more wheels 2021-07-10T17:12:05,734 Exception information: 2021-07-10T17:12:05,734 Traceback (most recent call last): 2021-07-10T17:12:05,734 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/base_command.py", line 180, in _main 2021-07-10T17:12:05,734 status = self.run(options, args) 2021-07-10T17:12:05,734 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/cli/req_command.py", line 205, in wrapper 2021-07-10T17:12:05,734 return func(self, options, args) 2021-07-10T17:12:05,734 File "/usr/local/lib/python3.9/dist-packages/pip/_internal/commands/wheel.py", line 174, in run 2021-07-10T17:12:05,734 raise CommandError( 2021-07-10T17:12:05,734 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2021-07-10T17:12:05,736 Removed build tracker: '/tmp/pip-req-tracker-qafriutv'