2019-07-15T10:17:57 Created temporary directory: /tmp/pip-ephem-wheel-cache-dihxeieb 2019-07-15T10:17:57 Created temporary directory: /tmp/pip-req-tracker-6o_77qe2 2019-07-15T10:17:57 Created requirements tracker '/tmp/pip-req-tracker-6o_77qe2' 2019-07-15T10:17:57 Created temporary directory: /tmp/pip-wheel-he80a_0p 2019-07-15T10:17:57 Collecting whatshap==0.15 2019-07-15T10:17:57 1 location(s) to search for versions of whatshap: 2019-07-15T10:17:57 * https://pypi.org/simple/whatshap/ 2019-07-15T10:17:57 Getting page https://pypi.org/simple/whatshap/ 2019-07-15T10:17:57 Analyzing links from page https://pypi.org/simple/whatshap/ 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 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 2019-07-15T10:17:57 Skipping link 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); it is not compatible with this Python 2019-07-15T10:17:57 Skipping link 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); it is not compatible with this Python 2019-07-15T10:17:57 Skipping link 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); it is not compatible with this Python 2019-07-15T10:17:57 Skipping link 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); it is not compatible with this Python 2019-07-15T10:17:57 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 2019-07-15T10:17:57 Using version 0.15 (newest of versions: 0.15) 2019-07-15T10:17:57 Created temporary directory: /tmp/pip-unpack-3z_ufjcd 2019-07-15T10:17:57 Downloading https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz (443kB) 2019-07-15T10:17:57 Downloading from URL https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 (from https://pypi.org/simple/whatshap/) 2019-07-15T10:17:58 Added whatshap==0.15 from https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 to build tracker '/tmp/pip-req-tracker-6o_77qe2' 2019-07-15T10:17:58 Running setup.py (path:/tmp/pip-wheel-he80a_0p/whatshap/setup.py) egg_info for package whatshap 2019-07-15T10:17:58 Running command python setup.py egg_info 2019-07-15T10:17:59 running egg_info 2019-07-15T10:17:59 creating pip-egg-info/whatshap.egg-info 2019-07-15T10:17:59 writing pip-egg-info/whatshap.egg-info/PKG-INFO 2019-07-15T10:17:59 writing dependency_links to pip-egg-info/whatshap.egg-info/dependency_links.txt 2019-07-15T10:17:59 writing entry points to pip-egg-info/whatshap.egg-info/entry_points.txt 2019-07-15T10:17:59 writing requirements to pip-egg-info/whatshap.egg-info/requires.txt 2019-07-15T10:17:59 writing top-level names to pip-egg-info/whatshap.egg-info/top_level.txt 2019-07-15T10:17:59 writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt' 2019-07-15T10:17:59 reading manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt' 2019-07-15T10:17:59 reading manifest template 'MANIFEST.in' 2019-07-15T10:17:59 warning: no files found matching 'whatshap/readselect.cpp' 2019-07-15T10:17:59 warning: no files found matching 'src/dptable.h' 2019-07-15T10:17:59 warning: no files found matching 'src/columncostcomputer.h' 2019-07-15T10:17:59 writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt' 2019-07-15T10:18:00 Source in /tmp/pip-wheel-he80a_0p/whatshap has version 0.15, which satisfies requirement whatshap==0.15 from https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 2019-07-15T10:18:00 Removed whatshap==0.15 from https://files.pythonhosted.org/packages/ca/13/6454e5e8f6c858a203378b3e22f13518f092ba85aa6d7a9a9796d22c28e0/whatshap-0.15.tar.gz#sha256=2dc9d89d71cf99e10c71b6138edd456bfcf0d7355794bc3491078654df85bc38 from build tracker '/tmp/pip-req-tracker-6o_77qe2' 2019-07-15T10:18:00 Building wheels for collected packages: whatshap 2019-07-15T10:18:00 Created temporary directory: /tmp/pip-wheel-bu45rj36 2019-07-15T10:18:00 Building wheel for whatshap (setup.py): started 2019-07-15T10:18:00 Destination directory: /tmp/pip-wheel-bu45rj36 2019-07-15T10:18:00 Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-he80a_0p/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-bu45rj36 2019-07-15T10:18:01 running bdist_wheel 2019-07-15T10:18:01 running build 2019-07-15T10:18:01 running build_py 2019-07-15T10:18:01 creating build 2019-07-15T10:18:01 creating build/lib.linux-armv7l-3.7 2019-07-15T10:18:01 creating build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/utils.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/timer.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/args.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/hapcut2vcf.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/__main__.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/stats.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/_version.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/bam.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/phase.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/unphase.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/vcf.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/verification.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/haplotag.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/genotype.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:01 copying whatshap/variants.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/coverage.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/compare.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/math.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/__init__.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 copying whatshap/graph.py -> build/lib.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 UPDATING build/lib.linux-armv7l-3.7/whatshap/_version.py 2019-07-15T10:18:02 set build/lib.linux-armv7l-3.7/whatshap/_version.py to '0.15' 2019-07-15T10:18:02 running build_ext 2019-07-15T10:18:02 building 'whatshap.core' extension 2019-07-15T10:18:02 creating build/temp.linux-armv7l-3.7 2019-07-15T10:18:02 creating build/temp.linux-armv7l-3.7/whatshap 2019-07-15T10:18:02 creating build/temp.linux-armv7l-3.7/src 2019-07-15T10:18:02 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 2019-07-15T10:18:06 whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’: 2019-07-15T10:18:06 whatshap/core.cpp:7066:33: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2019-07-15T10:18:06 for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2019-07-15T10:18:06 ~~~~~~~~~~^~~~~~~~~~~ 2019-07-15T10:18:54 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 src/pedigree.cpp -o build/temp.linux-armv7l-3.7/src/pedigree.o -std=c++11 2019-07-15T10:18:56 In file included from /usr/include/c++/8/cassert:44, 2019-07-15T10:18:56 from src/pedigree.cpp:4: 2019-07-15T10:18:56 src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector, std::vector)’: 2019-07-15T10:18:56 src/pedigree.cpp:30:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:18:56 assert(genotypes.size() == variant_count); 2019-07-15T10:18:56 ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2019-07-15T10:18:56 src/pedigree.cpp:31:37: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:18:56 assert(genotype_likelihoods.size() == variant_count); 2019-07-15T10:18:56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2019-07-15T10:18:56 src/pedigree.cpp: In member function ‘unsigned int Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’: 2019-07-15T10:18:56 src/pedigree.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2019-07-15T10:18:56 assert(variant_index < variant_count); 2019-07-15T10:18:56 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2019-07-15T10:18:56 src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’: 2019-07-15T10:18:56 src/pedigree.cpp:79:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 2019-07-15T10:18:56 assert(variant_index < variant_count); 2019-07-15T10:18:56 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2019-07-15T10:18:56 src/pedigree.cpp: In member function ‘std::__cxx11::string Pedigree::toString() const’: 2019-07-15T10:18:56 src/pedigree.cpp:110:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 2019-07-15T10:18:56 for (size_t j=0; j&, size_t, const std::vector&, const Pedigree*, const PedigreePartitions&, bool)’: 2019-07-15T10:19:12 src/pedigreecolumncostcomputer.cpp:24:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2019-07-15T10:19:12 for (unsigned int i = 0; i < (1< PedigreeColumnCostComputer::get_alleles()’: 2019-07-15T10:19:12 src/pedigreecolumncostcomputer.cpp:118:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable] 2019-07-15T10:19:12 unsigned int second_best_cost = numeric_limits < unsigned int >::max(); 2019-07-15T10:19:12 ^~~~~~~~~~~~~~~~ 2019-07-15T10:19:14 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 src/columnindexingiterator.cpp -o build/temp.linux-armv7l-3.7/src/columnindexingiterator.o -std=c++11 2019-07-15T10:19:15 src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’: 2019-07-15T10:19:15 src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:19:15 for(int j=0; j< parent->read_ids.size(); ++j) { 2019-07-15T10:19:15 ~^~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:19:15 src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2019-07-15T10:19:15 if(m != -1) { 2019-07-15T10:19:15 ~~^~~~~ 2019-07-15T10:19:15 src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable] 2019-07-15T10:19:15 unsigned int s = 1; 2019-07-15T10:19:15 ^ 2019-07-15T10:19:16 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 src/columnindexingscheme.cpp -o build/temp.linux-armv7l-3.7/src/columnindexingscheme.o -std=c++11 2019-07-15T10:19:17 src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector&)’: 2019-07-15T10:19:17 src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:19:17 while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:19:17 while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:19:17 while ((iread_ids.size()) && (j::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:19:17 while ((iread_ids.size()) && (j > ColumnIterator::get_next()’: 2019-07-15T10:19:38 src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:19:38 assert(list_it->active_entry < read->getVariantCount()); 2019-07-15T10:19:38 ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:19:38 src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’: 2019-07-15T10:19:38 src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:19:38 assert(active_entry < read->getVariantCount()); 2019-07-15T10:19:38 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:19:41 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 src/indexset.cpp -o build/temp.linux-armv7l-3.7/src/indexset.o -std=c++11 2019-07-15T10:19:43 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 src/pedigreepartitions.cpp -o build/temp.linux-armv7l-3.7/src/pedigreepartitions.o -std=c++11 2019-07-15T10:19:46 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 src/phredgenotypelikelihoods.cpp -o build/temp.linux-armv7l-3.7/src/phredgenotypelikelihoods.o -std=c++11 2019-07-15T10:19:48 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 src/genotyper.cpp -o build/temp.linux-armv7l-3.7/src/genotyper.o -std=c++11 2019-07-15T10:19:52 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 src/genotypedistribution.cpp -o build/temp.linux-armv7l-3.7/src/genotypedistribution.o -std=c++11 2019-07-15T10:19:53 src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’: 2019-07-15T10:19:53 src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:19:53 if (i == best_index) continue; 2019-07-15T10:19:53 ~~^~~~~~~~~~~~~ 2019-07-15T10:19:54 In file included from /usr/include/c++/8/vector:69, 2019-07-15T10:19:54 from src/genotypedistribution.h:4, 2019-07-15T10:19:54 from src/genotypedistribution.cpp:5: 2019-07-15T10:19:54 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2019-07-15T10:19:54 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 2019-07-15T10:19:54 vector<_Tp, _Alloc>:: 2019-07-15T10:19:54 ^~~~~~~~~~~~~~~~~~~ 2019-07-15T10:19:54 In file included from /usr/include/c++/8/vector:64, 2019-07-15T10:19:54 from src/genotypedistribution.h:4, 2019-07-15T10:19:54 from src/genotypedistribution.cpp:5: 2019-07-15T10:19:54 /usr/include/c++/8/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’: 2019-07-15T10:19:54 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2019-07-15T10:19:54 _M_realloc_insert(end(), __x); 2019-07-15T10:19:54 ^~~~~~~~~~~~~~~~~ 2019-07-15T10:19:54 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2019-07-15T10:19:54 _M_realloc_insert(end(), __x); 2019-07-15T10:19:54 ^~~~~~~~~~~~~~~~~ 2019-07-15T10:19:54 /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2019-07-15T10:19:54 _M_realloc_insert(end(), __x); 2019-07-15T10:19:54 ^~~~~~~~~~~~~~~~~ 2019-07-15T10:19:54 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 src/genotypedptable.cpp -o build/temp.linux-armv7l-3.7/src/genotypedptable.o -std=c++11 2019-07-15T10:19:57 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’: 2019-07-15T10:19:57 src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable] 2019-07-15T10:19:57 size_t column_count = input_column_iterator.get_column_count(); 2019-07-15T10:19:57 ^~~~~~~~~~~~ 2019-07-15T10:19:57 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’: 2019-07-15T10:19:57 src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable] 2019-07-15T10:19:57 unsigned int transmission_configurations = std::pow(4, pedigree->triple_count()); 2019-07-15T10:19:57 ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:19:57 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’: 2019-07-15T10:19:57 src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2019-07-15T10:19:57 if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) { 2019-07-15T10:19:57 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ 2019-07-15T10:19:57 src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’: 2019-07-15T10:19:57 src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable] 2019-07-15T10:19:57 size_t k = (size_t)sqrt(input_column_iterator.get_column_count()); 2019-07-15T10:19:57 ^ 2019-07-15T10:20:04 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 src/genotypecolumncostcomputer.cpp -o build/temp.linux-armv7l-3.7/src/genotypecolumncostcomputer.o -std=c++11 2019-07-15T10:20:08 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 src/backwardcolumniterator.cpp -o build/temp.linux-armv7l-3.7/src/backwardcolumniterator.o -std=c++11 2019-07-15T10:20:10 In file included from /usr/include/c++/8/cassert:44, 2019-07-15T10:20:10 from src/backwardcolumniterator.cpp:1: 2019-07-15T10:20:10 src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’: 2019-07-15T10:20:10 src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:20:10 assert(k < positions->size()); 2019-07-15T10:20:10 ~~^~~~~~~~~~~~~~~~~~~ 2019-07-15T10:20:10 src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2019-07-15T10:20:10 assert(active_entry < read->getVariantCount()); 2019-07-15T10:20:10 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:20:13 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 src/transitionprobabilitycomputer.cpp -o build/temp.linux-armv7l-3.7/src/transitionprobabilitycomputer.o -std=c++11 2019-07-15T10:20:16 In file included from /usr/include/c++/8/vector:69, 2019-07-15T10:20:16 from src/vector2d.h:5, 2019-07-15T10:20:16 from src/transitionprobabilitycomputer.h:5, 2019-07-15T10:20:16 from src/transitionprobabilitycomputer.cpp:1: 2019-07-15T10:20:16 /usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: 2019-07-15T10:20:16 /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator > >’} changed in GCC 7.1 2019-07-15T10:20:16 vector<_Tp, _Alloc>:: 2019-07-15T10:20:16 ^~~~~~~~~~~~~~~~~~~ 2019-07-15T10:20:17 /usr/include/c++/8/bits/vector.tcc: In constructor ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector&)’: 2019-07-15T10:20:17 /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 2019-07-15T10:20:17 _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2019-07-15T10:20:17 ^~~~~~~~~~~~~~~~~ 2019-07-15T10:20:18 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/whatshap/core.o build/temp.linux-armv7l-3.7/src/pedigree.o build/temp.linux-armv7l-3.7/src/pedigreedptable.o build/temp.linux-armv7l-3.7/src/pedigreecolumncostcomputer.o build/temp.linux-armv7l-3.7/src/columnindexingiterator.o build/temp.linux-armv7l-3.7/src/columnindexingscheme.o build/temp.linux-armv7l-3.7/src/entry.o build/temp.linux-armv7l-3.7/src/graycodes.o build/temp.linux-armv7l-3.7/src/read.o build/temp.linux-armv7l-3.7/src/readset.o build/temp.linux-armv7l-3.7/src/columniterator.o build/temp.linux-armv7l-3.7/src/indexset.o build/temp.linux-armv7l-3.7/src/pedigreepartitions.o build/temp.linux-armv7l-3.7/src/phredgenotypelikelihoods.o build/temp.linux-armv7l-3.7/src/genotyper.o build/temp.linux-armv7l-3.7/src/genotypedistribution.o build/temp.linux-armv7l-3.7/src/genotypedptable.o build/temp.linux-armv7l-3.7/src/genotypecolumncostcomputer.o build/temp.linux-armv7l-3.7/src/backwardcolumniterator.o build/temp.linux-armv7l-3.7/src/transitionprobabilitycomputer.o -o build/lib.linux-armv7l-3.7/whatshap/core.cpython-37m-arm-linux-gnueabihf.so 2019-07-15T10:20:19 building 'whatshap.priorityqueue' extension 2019-07-15T10:20:19 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/priorityqueue.cpp -o build/temp.linux-armv7l-3.7/whatshap/priorityqueue.o -std=c++11 2019-07-15T10:20:21 whatshap/priorityqueue.cpp: In function ‘void __pyx_f_8whatshap_13priorityqueue_13PriorityQueue__sift_down(__pyx_obj_8whatshap_13priorityqueue_PriorityQueue*, int)’: 2019-07-15T10:20:21 whatshap/priorityqueue.cpp:2482:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector*, int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:20:21 __pyx_t_1 = ((__pyx_v_rchildindex < __pyx_v_self->heap.size()) != 0); 2019-07-15T10:20:21 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:20:21 whatshap/priorityqueue.cpp:2599:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector*, int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2019-07-15T10:20:21 __pyx_t_1 = ((__pyx_v_lchildindex < __pyx_v_self->heap.size()) != 0); 2019-07-15T10:20:21 ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2019-07-15T10:20:27 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/whatshap/priorityqueue.o -o build/lib.linux-armv7l-3.7/whatshap/priorityqueue.cpython-37m-arm-linux-gnueabihf.so 2019-07-15T10:20:28 building 'whatshap.align' extension 2019-07-15T10:20:28 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/align.cpp -o build/temp.linux-armv7l-3.7/whatshap/align.o -std=c++11 2019-07-15T10:20:54 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/whatshap/align.o -o build/lib.linux-armv7l-3.7/whatshap/align.cpython-37m-arm-linux-gnueabihf.so 2019-07-15T10:20:54 building 'whatshap._variants' extension 2019-07-15T10:20:54 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/_variants.cpp -o build/temp.linux-armv7l-3.7/whatshap/_variants.o -std=c++11 2019-07-15T10:21:03 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.7/whatshap/_variants.o -o build/lib.linux-armv7l-3.7/whatshap/_variants.cpython-37m-arm-linux-gnueabihf.so 2019-07-15T10:21:03 installing to build/bdist.linux-armv7l/wheel 2019-07-15T10:21:03 running install 2019-07-15T10:21:03 running install_lib 2019-07-15T10:21:03 creating build/bdist.linux-armv7l 2019-07-15T10:21:03 creating build/bdist.linux-armv7l/wheel 2019-07-15T10:21:03 creating build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/utils.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/align.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/timer.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/args.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/hapcut2vcf.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/__main__.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/stats.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/priorityqueue.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/_version.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/bam.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/_variants.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/phase.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/unphase.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/vcf.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:03 copying build/lib.linux-armv7l-3.7/whatshap/core.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/verification.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/haplotag.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/genotype.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/variants.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/coverage.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/compare.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/pedigree.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/math.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/__init__.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 copying build/lib.linux-armv7l-3.7/whatshap/graph.py -> build/bdist.linux-armv7l/wheel/whatshap 2019-07-15T10:21:04 running install_egg_info 2019-07-15T10:21:04 running egg_info 2019-07-15T10:21:04 writing whatshap.egg-info/PKG-INFO 2019-07-15T10:21:04 writing dependency_links to whatshap.egg-info/dependency_links.txt 2019-07-15T10:21:04 writing entry points to whatshap.egg-info/entry_points.txt 2019-07-15T10:21:04 writing requirements to whatshap.egg-info/requires.txt 2019-07-15T10:21:04 writing top-level names to whatshap.egg-info/top_level.txt 2019-07-15T10:21:04 reading manifest file 'whatshap.egg-info/SOURCES.txt' 2019-07-15T10:21:04 reading manifest template 'MANIFEST.in' 2019-07-15T10:21:04 warning: no files found matching 'whatshap/readselect.cpp' 2019-07-15T10:21:04 warning: no files found matching 'src/dptable.h' 2019-07-15T10:21:04 warning: no files found matching 'src/columncostcomputer.h' 2019-07-15T10:21:04 writing manifest file 'whatshap.egg-info/SOURCES.txt' 2019-07-15T10:21:04 Copying whatshap.egg-info to build/bdist.linux-armv7l/wheel/whatshap-0.15-py3.7.egg-info 2019-07-15T10:21:04 running install_scripts 2019-07-15T10:21:04 creating build/bdist.linux-armv7l/wheel/whatshap-0.15.dist-info/WHEEL 2019-07-15T10:21:04 creating '/tmp/pip-wheel-bu45rj36/whatshap-0.15-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2019-07-15T10:21:04 adding 'whatshap/__init__.py' 2019-07-15T10:21:04 adding 'whatshap/__main__.py' 2019-07-15T10:21:04 adding 'whatshap/_variants.cpython-37m-arm-linux-gnueabihf.so' 2019-07-15T10:21:04 adding 'whatshap/_version.py' 2019-07-15T10:21:05 adding 'whatshap/align.cpython-37m-arm-linux-gnueabihf.so' 2019-07-15T10:21:05 adding 'whatshap/args.py' 2019-07-15T10:21:05 adding 'whatshap/bam.py' 2019-07-15T10:21:05 adding 'whatshap/compare.py' 2019-07-15T10:21:06 adding 'whatshap/core.cpython-37m-arm-linux-gnueabihf.so' 2019-07-15T10:21:06 adding 'whatshap/coverage.py' 2019-07-15T10:21:06 adding 'whatshap/genotype.py' 2019-07-15T10:21:06 adding 'whatshap/graph.py' 2019-07-15T10:21:06 adding 'whatshap/hapcut2vcf.py' 2019-07-15T10:21:06 adding 'whatshap/haplotag.py' 2019-07-15T10:21:06 adding 'whatshap/math.py' 2019-07-15T10:21:06 adding 'whatshap/pedigree.py' 2019-07-15T10:21:06 adding 'whatshap/phase.py' 2019-07-15T10:21:06 adding 'whatshap/priorityqueue.cpython-37m-arm-linux-gnueabihf.so' 2019-07-15T10:21:06 adding 'whatshap/stats.py' 2019-07-15T10:21:06 adding 'whatshap/timer.py' 2019-07-15T10:21:06 adding 'whatshap/unphase.py' 2019-07-15T10:21:06 adding 'whatshap/utils.py' 2019-07-15T10:21:06 adding 'whatshap/variants.py' 2019-07-15T10:21:06 adding 'whatshap/vcf.py' 2019-07-15T10:21:06 adding 'whatshap/verification.py' 2019-07-15T10:21:06 adding 'whatshap-0.15.dist-info/METADATA' 2019-07-15T10:21:06 adding 'whatshap-0.15.dist-info/WHEEL' 2019-07-15T10:21:06 adding 'whatshap-0.15.dist-info/entry_points.txt' 2019-07-15T10:21:06 adding 'whatshap-0.15.dist-info/top_level.txt' 2019-07-15T10:21:06 adding 'whatshap-0.15.dist-info/RECORD' 2019-07-15T10:21:06 removing build/bdist.linux-armv7l/wheel 2019-07-15T10:21:07 Building wheel for whatshap (setup.py): finished with status 'done' 2019-07-15T10:21:07 Stored in directory: /tmp/tmp_914ov__ 2019-07-15T10:21:07 Successfully built whatshap 2019-07-15T10:21:07 Cleaning up... 2019-07-15T10:21:07 Removing source in /tmp/pip-wheel-he80a_0p/whatshap 2019-07-15T10:21:07 Removed build tracker '/tmp/pip-req-tracker-6o_77qe2'