2019-07-16T12:38:27 Created temporary directory: /tmp/pip-ephem-wheel-cache-h72rfi7r
2019-07-16T12:38:27 Created temporary directory: /tmp/pip-req-tracker-bcp5dr0d
2019-07-16T12:38:27 Created requirements tracker '/tmp/pip-req-tracker-bcp5dr0d'
2019-07-16T12:38:27 Created temporary directory: /tmp/pip-wheel-qzjoh7hy
2019-07-16T12:38:27 Collecting whatshap==0.18
2019-07-16T12:38:27   1 location(s) to search for versions of whatshap:
2019-07-16T12:38:27   * https://pypi.org/simple/whatshap/
2019-07-16T12:38:27   Getting page https://pypi.org/simple/whatshap/
2019-07-16T12:38:27   Analyzing links from page https://pypi.org/simple/whatshap/
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27     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
2019-07-16T12:38:27   Using version 0.18 (newest of versions: 0.18)
2019-07-16T12:38:27   Created temporary directory: /tmp/pip-unpack-u5fft5hc
2019-07-16T12:38:28   Downloading https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz (460kB)
2019-07-16T12:38:28   Downloading from URL 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)
2019-07-16T12:38:29   Added whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 to build tracker '/tmp/pip-req-tracker-bcp5dr0d'
2019-07-16T12:38:29     Running setup.py (path:/tmp/pip-wheel-qzjoh7hy/whatshap/setup.py) egg_info for package whatshap
2019-07-16T12:38:29     Running command python setup.py egg_info
2019-07-16T12:38:34     running egg_info
2019-07-16T12:38:34     creating pip-egg-info/whatshap.egg-info
2019-07-16T12:38:34     writing pip-egg-info/whatshap.egg-info/PKG-INFO
2019-07-16T12:38:34     writing dependency_links to pip-egg-info/whatshap.egg-info/dependency_links.txt
2019-07-16T12:38:34     writing entry points to pip-egg-info/whatshap.egg-info/entry_points.txt
2019-07-16T12:38:34     writing requirements to pip-egg-info/whatshap.egg-info/requires.txt
2019-07-16T12:38:34     writing top-level names to pip-egg-info/whatshap.egg-info/top_level.txt
2019-07-16T12:38:34     writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-16T12:38:34     reading manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-16T12:38:34     writing manifest file 'pip-egg-info/whatshap.egg-info/SOURCES.txt'
2019-07-16T12:38:34   Source in /tmp/pip-wheel-qzjoh7hy/whatshap has version 0.18, which satisfies requirement whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695
2019-07-16T12:38:34   Removed whatshap==0.18 from https://files.pythonhosted.org/packages/f0/e4/4392c2f1320ea8d4b79a76e3a6dcb9bd7bf6ed70e11499c9acf2db2d42ef/whatshap-0.18.tar.gz#sha256=c566130eca57fe9e34f5193390856dc44171c397f9708c49fcbf204e575b6695 from build tracker '/tmp/pip-req-tracker-bcp5dr0d'
2019-07-16T12:38:34 Building wheels for collected packages: whatshap
2019-07-16T12:38:34   Created temporary directory: /tmp/pip-wheel-f4kkhh3u
2019-07-16T12:38:34   Building wheel for whatshap (setup.py): started
2019-07-16T12:38:34   Destination directory: /tmp/pip-wheel-f4kkhh3u
2019-07-16T12:38:34   Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-qzjoh7hy/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-f4kkhh3u
2019-07-16T12:38:38   running bdist_wheel
2019-07-16T12:38:38   running build
2019-07-16T12:38:38   running build_py
2019-07-16T12:38:38   creating build
2019-07-16T12:38:38   creating build/lib.linux-armv7l-3.7
2019-07-16T12:38:38   creating build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/graph.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/variants.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/utils.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/compare.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/args.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/__init__.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/__main__.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/verification.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/phase.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/pedigree.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/math.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/coverage.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/testhelpers.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/vcf.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/unphase.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/hapcut2vcf.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/genotype.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/bam.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/haplotag.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/timer.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   copying whatshap/stats.py -> build/lib.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   running build_ext
2019-07-16T12:38:38   building 'whatshap.core' extension
2019-07-16T12:38:38   creating build/temp.linux-armv7l-3.7
2019-07-16T12:38:38   creating build/temp.linux-armv7l-3.7/whatshap
2019-07-16T12:38:38   creating build/temp.linux-armv7l-3.7/src
2019-07-16T12:38:38   creating build/temp.linux-armv7l-3.7/src/hapchat
2019-07-16T12:38:38   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
2019-07-16T12:38:43   In file included from whatshap/core.cpp:653:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2019-07-16T12:38:43      Counter counter_columns;
2019-07-16T12:38:43              ^~~~~~~~~~~~~~~
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43      return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2019-07-16T12:38:43                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   In file included from whatshap/core.cpp:653:
2019-07-16T12:38:43   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)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable]
2019-07-16T12:38:43       int old_k = k_j[input_pointer];
2019-07-16T12:38:43           ^~~~~
2019-07-16T12:38:43   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&)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43             (colJ[j].get_read_id() != -1) &&
2019-07-16T12:38:43              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43             (colQ[i].get_read_id() != -1)) {
2019-07-16T12:38:43              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43      while(cov < column.size() && column[cov].get_read_id() != -1) {
2019-07-16T12:38:43                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43             (colJ[j].get_read_id() != -1) &&
2019-07-16T12:38:43              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43             (colQ[i].get_read_id() != -1)) {
2019-07-16T12:38:43              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:43   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&)’:
2019-07-16T12:38:43   whatshap/../src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:38:43      if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2019-07-16T12:38:43                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:38:44   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_15PedigreeDPTable_4get_super_reads(__pyx_obj_8whatshap_4core_PedigreeDPTable*)’:
2019-07-16T12:38:44   whatshap/core.cpp:7460:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare]
2019-07-16T12:38:44      for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
2019-07-16T12:38:44                          ~~~~~~~~~~^~~~~~~~~~~
2019-07-16T12:38:44   whatshap/core.cpp: In function ‘PyObject* __pyx_pf_8whatshap_4core_11HapChatCore_6get_super_reads(__pyx_obj_8whatshap_4core_HapChatCore*)’:
2019-07-16T12:38:44   whatshap/core.cpp:11086:33: warning: comparison of integer expressions of different signedness: ‘std::vector<ReadSet*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:38:44      for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
2019-07-16T12:38:44                          ~~~~~~~~~~^~~~~~~~~~~
2019-07-16T12:40:07   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 -Werror=return-type
2019-07-16T12:40:10   In file included from /usr/include/c++/8/cassert:44,
2019-07-16T12:40:10                    from src/pedigree.cpp:4:
2019-07-16T12:40:10   src/pedigree.cpp: In member function ‘void Pedigree::addIndividual(unsigned int, std::vector<unsigned int>, std::vector<PhredGenotypeLikelihoods*>)’:
2019-07-16T12:40:10   src/pedigree.cpp:30:26: warning: comparison of integer expressions of different signedness: ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:40:10     assert(genotypes.size() == variant_count);
2019-07-16T12:40:10            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2019-07-16T12:40:10   src/pedigree.cpp:31:37: warning: comparison of integer expressions of different signedness: ‘std::vector<PhredGenotypeLikelihoods*>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:40:10     assert(genotype_likelihoods.size() == variant_count);
2019-07-16T12:40:10            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2019-07-16T12:40:10   src/pedigree.cpp: In member function ‘unsigned int Pedigree::get_genotype_by_id(unsigned int, unsigned int) const’:
2019-07-16T12:40:10   src/pedigree.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2019-07-16T12:40:10     assert(variant_index < variant_count);
2019-07-16T12:40:10            ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2019-07-16T12:40:10   src/pedigree.cpp: In member function ‘const PhredGenotypeLikelihoods* Pedigree::get_genotype_likelihoods_by_id(unsigned int, unsigned int) const’:
2019-07-16T12:40:10   src/pedigree.cpp:79:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
2019-07-16T12:40:10     assert(variant_index < variant_count);
2019-07-16T12:40:10            ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
2019-07-16T12:40:10   src/pedigree.cpp: In member function ‘std::__cxx11::string Pedigree::toString() const’:
2019-07-16T12:40:10   src/pedigree.cpp:110:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
2019-07-16T12:40:10      for (size_t j=0; j<variant_count; ++j) {
2019-07-16T12:40:10                       ~^~~~~~~~~~~~~~
2019-07-16T12:40:14   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/pedigreedptable.cpp -o build/temp.linux-armv7l-3.7/src/pedigreedptable.o -std=c++11 -Werror=return-type
2019-07-16T12:40:25   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/pedigreecolumncostcomputer.cpp -o build/temp.linux-armv7l-3.7/src/pedigreecolumncostcomputer.o -std=c++11 -Werror=return-type
2019-07-16T12:40:28   src/pedigreecolumncostcomputer.cpp: In constructor ‘PedigreeColumnCostComputer::PedigreeColumnCostComputer(const std::vector<const Entry*>&, size_t, const std::vector<unsigned int>&, const Pedigree*, const PedigreePartitions&, bool)’:
2019-07-16T12:40:28   src/pedigreecolumncostcomputer.cpp:24:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:40:28     for (unsigned int i = 0; i < (1<<pedigree_partitions.count()); ++i) {
2019-07-16T12:40:28                              ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:40:28   src/pedigreecolumncostcomputer.cpp:39:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:40:28        if (allele0 + allele1 != genotype) {
2019-07-16T12:40:28            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
2019-07-16T12:40:28   src/pedigreecolumncostcomputer.cpp: In member function ‘std::vector<PedigreeColumnCostComputer::phased_variant_t> PedigreeColumnCostComputer::get_alleles()’:
2019-07-16T12:40:28   src/pedigreecolumncostcomputer.cpp:118:15: warning: unused variable ‘second_best_cost’ [-Wunused-variable]
2019-07-16T12:40:28     unsigned int second_best_cost = numeric_limits < unsigned int >::max();
2019-07-16T12:40:28                  ^~~~~~~~~~~~~~~~
2019-07-16T12:40:30   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 -Werror=return-type
2019-07-16T12:40:32   src/columnindexingiterator.cpp: In member function ‘unsigned int ColumnIndexingIterator::index_forward_projection(unsigned int)’:
2019-07-16T12:40:32   src/columnindexingiterator.cpp:90:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:40:32     for(int j=0; j< parent->read_ids.size(); ++j) {
2019-07-16T12:40:32                  ~^~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:40:32   src/columnindexingiterator.cpp:92:8: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:40:32      if(m != -1) {
2019-07-16T12:40:32         ~~^~~~~
2019-07-16T12:40:32   src/columnindexingiterator.cpp:89:15: warning: unused variable ‘s’ [-Wunused-variable]
2019-07-16T12:40:32     unsigned int s = 1;
2019-07-16T12:40:32                  ^
2019-07-16T12:40:32   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 -Werror=return-type
2019-07-16T12:40:34   src/columnindexingscheme.cpp: In constructor ‘ColumnIndexingScheme::ColumnIndexingScheme(const ColumnIndexingScheme*, const std::vector<unsigned int>&)’:
2019-07-16T12:40:34   src/columnindexingscheme.cpp:22:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:40:34      while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2019-07-16T12:40:34              ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:40:34   src/columnindexingscheme.cpp:22:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:40:34      while ((i<previous_column->read_ids.size()) && (j<read_ids.size())) {
2019-07-16T12:40:34                                                      ~^~~~~~~~~~~~~~~~
2019-07-16T12:40:34   src/columnindexingscheme.cpp: In member function ‘void ColumnIndexingScheme::set_next_column(const ColumnIndexingScheme*)’:
2019-07-16T12:40:34   src/columnindexingscheme.cpp:71:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:40:34     while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2019-07-16T12:40:34             ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:40:34   src/columnindexingscheme.cpp:71:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:40:34     while ((i<next_column->read_ids.size()) && (j<read_ids.size())) {
2019-07-16T12:40:34                                                 ~^~~~~~~~~~~~~~~~
2019-07-16T12:40:35   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/entry.cpp -o build/temp.linux-armv7l-3.7/src/entry.o -std=c++11 -Werror=return-type
2019-07-16T12:40:37   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/graycodes.cpp -o build/temp.linux-armv7l-3.7/src/graycodes.o -std=c++11 -Werror=return-type
2019-07-16T12:40:39   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/read.cpp -o build/temp.linux-armv7l-3.7/src/read.o -std=c++11 -Werror=return-type
2019-07-16T12:40:44   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/readset.cpp -o build/temp.linux-armv7l-3.7/src/readset.o -std=c++11 -Werror=return-type
2019-07-16T12:40:55   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/columniterator.cpp -o build/temp.linux-armv7l-3.7/src/columniterator.o -std=c++11 -Werror=return-type
2019-07-16T12:40:57   In file included from /usr/include/c++/8/cassert:44,
2019-07-16T12:40:57                    from src/columniterator.cpp:1:
2019-07-16T12:40:57   src/columniterator.cpp: In member function ‘std::unique_ptr<std::vector<const Entry*> > ColumnIterator::get_next()’:
2019-07-16T12:40:57   src/columniterator.cpp:105:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:40:57       assert(list_it->active_entry < read->getVariantCount());
2019-07-16T12:40:57              ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:40:57   src/columniterator.cpp: In member function ‘void ColumnIterator::jump_to_column(size_t)’:
2019-07-16T12:40:57   src/columniterator.cpp:161:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:40:57        assert(active_entry < read->getVariantCount());
2019-07-16T12:40:57               ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:01   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 -Werror=return-type
2019-07-16T12:41:04   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/pedigreepartitions.cpp -o build/temp.linux-armv7l-3.7/src/pedigreepartitions.o -std=c++11 -Werror=return-type
2019-07-16T12:41:06   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 -Werror=return-type
2019-07-16T12:41:09   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 -Werror=return-type
2019-07-16T12:41:13   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/genotypedistribution.cpp -o build/temp.linux-armv7l-3.7/src/genotypedistribution.o -std=c++11 -Werror=return-type
2019-07-16T12:41:15   src/genotypedistribution.cpp: In member function ‘double GenotypeDistribution::errorProbability() const’:
2019-07-16T12:41:15   src/genotypedistribution.cpp:55:9: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:41:15      if (i == best_index) continue;
2019-07-16T12:41:15          ~~^~~~~~~~~~~~~
2019-07-16T12:41:16   In file included from /usr/include/c++/8/vector:69,
2019-07-16T12:41:16                    from src/genotypedistribution.h:4,
2019-07-16T12:41:16                    from src/genotypedistribution.cpp:5:
2019-07-16T12:41:16   /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 = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
2019-07-16T12:41:16   /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’} changed in GCC 7.1
2019-07-16T12:41:16          vector<_Tp, _Alloc>::
2019-07-16T12:41:16          ^~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:16   In file included from /usr/include/c++/8/vector:64,
2019-07-16T12:41:16                    from src/genotypedistribution.h:4,
2019-07-16T12:41:16                    from src/genotypedistribution.cpp:5:
2019-07-16T12:41:16   /usr/include/c++/8/bits/stl_vector.h: In constructor ‘GenotypeDistribution::GenotypeDistribution(double, double, double)’:
2019-07-16T12:41:16   /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2019-07-16T12:41:16       _M_realloc_insert(end(), __x);
2019-07-16T12:41:16       ^~~~~~~~~~~~~~~~~
2019-07-16T12:41:16   /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2019-07-16T12:41:16       _M_realloc_insert(end(), __x);
2019-07-16T12:41:16       ^~~~~~~~~~~~~~~~~
2019-07-16T12:41:16   /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2019-07-16T12:41:16       _M_realloc_insert(end(), __x);
2019-07-16T12:41:16       ^~~~~~~~~~~~~~~~~
2019-07-16T12:41:16   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/genotypedptable.cpp -o build/temp.linux-armv7l-3.7/src/genotypedptable.o -std=c++11 -Werror=return-type
2019-07-16T12:41:20   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::clear_forward_table()’:
2019-07-16T12:41:20   src/genotypedptable.cpp:61:12: warning: unused variable ‘column_count’ [-Wunused-variable]
2019-07-16T12:41:20        size_t column_count = input_column_iterator.get_column_count();
2019-07-16T12:41:20               ^~~~~~~~~~~~
2019-07-16T12:41:20   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_index()’:
2019-07-16T12:41:20   src/genotypedptable.cpp:91:18: warning: unused variable ‘transmission_configurations’ [-Wunused-variable]
2019-07-16T12:41:20        unsigned int transmission_configurations = pow(4, pedigree->triple_count());
2019-07-16T12:41:20                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:20   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_backward_prob()’:
2019-07-16T12:41:20   src/genotypedptable.cpp:152:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2019-07-16T12:41:20            if ((k>1) && (column_index < column_count-1) && (((column_index+1)%k) != 0)) {
2019-07-16T12:41:20                          ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
2019-07-16T12:41:20   src/genotypedptable.cpp: In member function ‘void GenotypeDPTable::compute_forward_prob()’:
2019-07-16T12:41:20   src/genotypedptable.cpp:178:12: warning: unused variable ‘k’ [-Wunused-variable]
2019-07-16T12:41:20        size_t k = (size_t)sqrt(input_column_iterator.get_column_count());
2019-07-16T12:41:20               ^
2019-07-16T12:41:27   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 -Werror=return-type
2019-07-16T12:41:32   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 -Werror=return-type
2019-07-16T12:41:34   In file included from /usr/include/c++/8/cassert:44,
2019-07-16T12:41:34                    from src/backwardcolumniterator.cpp:1:
2019-07-16T12:41:34   src/backwardcolumniterator.cpp: In member function ‘void BackwardColumnIterator::jump_to_column(int)’:
2019-07-16T12:41:34   src/backwardcolumniterator.cpp:121:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<unsigned int>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:41:34     assert(k < positions->size());
2019-07-16T12:41:34            ~~^~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:34   src/backwardcolumniterator.cpp:140:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2019-07-16T12:41:34        assert(active_entry < read->getVariantCount());
2019-07-16T12:41:34               ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:37   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 -Werror=return-type
2019-07-16T12:41:41   In file included from /usr/include/c++/8/vector:69,
2019-07-16T12:41:41                    from src/vector2d.h:5,
2019-07-16T12:41:41                    from src/transitionprobabilitycomputer.h:5,
2019-07-16T12:41:41                    from src/transitionprobabilitycomputer.cpp:1:
2019-07-16T12:41:41   /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<long double>]’:
2019-07-16T12:41:41   /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<long double, std::allocator<long double> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double, std::allocator<long double> > >’} changed in GCC 7.1
2019-07-16T12:41:41          vector<_Tp, _Alloc>::
2019-07-16T12:41:41          ^~~~~~~~~~~~~~~~~~~
2019-07-16T12:41:42   /usr/include/c++/8/bits/vector.tcc: In constructor ‘TransitionProbabilityComputer::TransitionProbabilityComputer(size_t, unsigned int, const Pedigree*, const std::vector<PedigreePartitions*>&)’:
2019-07-16T12:41:42   /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double, std::allocator<long double> > >’ changed in GCC 7.1
2019-07-16T12:41:42       _M_realloc_insert(end(), std::forward<_Args>(__args)...);
2019-07-16T12:41:42       ^~~~~~~~~~~~~~~~~
2019-07-16T12:41:44   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/hapchat/basictypes.cpp -o build/temp.linux-armv7l-3.7/src/hapchat/basictypes.o -std=c++11 -Werror=return-type
2019-07-16T12:41:47   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/hapchat/balancedcombinations.cpp -o build/temp.linux-armv7l-3.7/src/hapchat/balancedcombinations.o -std=c++11 -Werror=return-type
2019-07-16T12:41:54   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/hapchat/binomialcoefficient.cpp -o build/temp.linux-armv7l-3.7/src/hapchat/binomialcoefficient.o -std=c++11 -Werror=return-type
2019-07-16T12:41:59   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/hapchat/hapchatcore.cpp -o build/temp.linux-armv7l-3.7/src/hapchat/hapchatcore.o -std=c++11 -Werror=return-type
2019-07-16T12:42:02   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::run_core()’:
2019-07-16T12:42:02   src/hapchat/hapchatcore.cpp:145:11: warning: variable ‘counter_columns’ set but not used [-Wunused-but-set-variable]
2019-07-16T12:42:02      Counter counter_columns;
2019-07-16T12:42:02              ^~~~~~~~~~~~~~~
2019-07-16T12:42:02   src/hapchat/hapchatcore.cpp: In member function ‘bool HapChatCore::check_end(HapChatColumnIterator, const std::vector<std::vector<Entry> >&, const Pointer&, const bool&)’:
2019-07-16T12:42:02   src/hapchat/hapchatcore.cpp:208:74: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:02      return (!re_run && (hap.is_ended() && (input[pointer][0].get_read_id() == -1)));
2019-07-16T12:42:02                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:02   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)’:
2019-07-16T12:42:02   src/hapchat/hapchatcore.cpp:939:8: warning: unused variable ‘old_k’ [-Wunused-variable]
2019-07-16T12:42:02       int old_k = k_j[input_pointer];
2019-07-16T12:42:02           ^~~~~
2019-07-16T12:42:03   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&)’:
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1114:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03             (colJ[j].get_read_id() != -1) &&
2019-07-16T12:42:03              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1115:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03             (colQ[i].get_read_id() != -1)) {
2019-07-16T12:42:03              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp: In member function ‘void HapChatCore::represent_column(const Column&, BitColumn&, Counter&, BitColumn&, Counter&)’:
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1159:58: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03      while(cov < column.size() && column[cov].get_read_id() != -1) {
2019-07-16T12:42:03                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp: In member function ‘int HapChatCore::compute_active_common(const Column&, const Column&, unsigned int&)’:
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1294:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03             (colJ[j].get_read_id() != -1) &&
2019-07-16T12:42:03              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1295:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03             (colQ[i].get_read_id() != -1)) {
2019-07-16T12:42:03              ~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:03   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&)’:
2019-07-16T12:42:03   src/hapchat/hapchatcore.cpp:1350:67: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2019-07-16T12:42:03      if(i < input[pointer].size() && input[pointer][i].get_read_id() != -1)
2019-07-16T12:42:03                                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
2019-07-16T12:42:04   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/hapchat/hapchatcolumniterator.cpp -o build/temp.linux-armv7l-3.7/src/hapchat/hapchatcolumniterator.o -std=c++11 -Werror=return-type
2019-07-16T12:42:08   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 build/temp.linux-armv7l-3.7/src/hapchat/basictypes.o build/temp.linux-armv7l-3.7/src/hapchat/balancedcombinations.o build/temp.linux-armv7l-3.7/src/hapchat/binomialcoefficient.o build/temp.linux-armv7l-3.7/src/hapchat/hapchatcore.o build/temp.linux-armv7l-3.7/src/hapchat/hapchatcolumniterator.o -o build/lib.linux-armv7l-3.7/whatshap/core.cpython-37m-arm-linux-gnueabihf.so
2019-07-16T12:42:10   building 'whatshap.priorityqueue' extension
2019-07-16T12:42:10   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 -Werror=return-type
2019-07-16T12:42:12   whatshap/priorityqueue.cpp: In function ‘void __pyx_f_8whatshap_13priorityqueue_13PriorityQueue__sift_down(__pyx_obj_8whatshap_13priorityqueue_PriorityQueue*, int)’:
2019-07-16T12:42:12   whatshap/priorityqueue.cpp:2483:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::vector<int>*, int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:42:12      __pyx_t_1 = ((__pyx_v_rchildindex < __pyx_v_self->heap.size()) != 0);
2019-07-16T12:42:12                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:42:12   whatshap/priorityqueue.cpp:2600:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<std::vector<int>*, int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
2019-07-16T12:42:12      __pyx_t_1 = ((__pyx_v_lchildindex < __pyx_v_self->heap.size()) != 0);
2019-07-16T12:42:12                    ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
2019-07-16T12:42:19   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
2019-07-16T12:42:20   building 'whatshap.align' extension
2019-07-16T12:42:20   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 -Werror=return-type
2019-07-16T12:42:50   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
2019-07-16T12:42:50   building 'whatshap._variants' extension
2019-07-16T12:42:50   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 -Werror=return-type
2019-07-16T12:43:00   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
2019-07-16T12:43:01   installing to build/bdist.linux-armv7l/wheel
2019-07-16T12:43:01   running install
2019-07-16T12:43:01   running install_lib
2019-07-16T12:43:01   creating build/bdist.linux-armv7l
2019-07-16T12:43:01   creating build/bdist.linux-armv7l/wheel
2019-07-16T12:43:01   creating build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/_variants.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/align.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/graph.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/variants.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/utils.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/compare.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/args.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/__init__.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/priorityqueue.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/__main__.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/verification.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/phase.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/pedigree.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/math.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/coverage.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/testhelpers.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/vcf.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/unphase.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/hapcut2vcf.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/genotype.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/bam.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/haplotag.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/timer.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/stats.py -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:01   copying build/lib.linux-armv7l-3.7/whatshap/core.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/whatshap
2019-07-16T12:43:02   running install_egg_info
2019-07-16T12:43:02   running egg_info
2019-07-16T12:43:02   creating whatshap.egg-info
2019-07-16T12:43:02   writing whatshap.egg-info/PKG-INFO
2019-07-16T12:43:02   writing dependency_links to whatshap.egg-info/dependency_links.txt
2019-07-16T12:43:02   writing entry points to whatshap.egg-info/entry_points.txt
2019-07-16T12:43:02   writing requirements to whatshap.egg-info/requires.txt
2019-07-16T12:43:02   writing top-level names to whatshap.egg-info/top_level.txt
2019-07-16T12:43:02   writing manifest file 'whatshap.egg-info/SOURCES.txt'
2019-07-16T12:43:02   reading manifest file 'whatshap.egg-info/SOURCES.txt'
2019-07-16T12:43:02   writing manifest file 'whatshap.egg-info/SOURCES.txt'
2019-07-16T12:43:02   Copying whatshap.egg-info to build/bdist.linux-armv7l/wheel/whatshap-0.18-py3.7.egg-info
2019-07-16T12:43:02   running install_scripts
2019-07-16T12:43:02   creating build/bdist.linux-armv7l/wheel/whatshap-0.18.dist-info/WHEEL
2019-07-16T12:43:02   creating '/tmp/pip-wheel-f4kkhh3u/whatshap-0.18-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2019-07-16T12:43:02   adding 'whatshap/__init__.py'
2019-07-16T12:43:02   adding 'whatshap/__main__.py'
2019-07-16T12:43:02   adding 'whatshap/_variants.cpython-37m-arm-linux-gnueabihf.so'
2019-07-16T12:43:02   adding 'whatshap/align.cpython-37m-arm-linux-gnueabihf.so'
2019-07-16T12:43:02   adding 'whatshap/args.py'
2019-07-16T12:43:02   adding 'whatshap/bam.py'
2019-07-16T12:43:02   adding 'whatshap/compare.py'
2019-07-16T12:43:04   adding 'whatshap/core.cpython-37m-arm-linux-gnueabihf.so'
2019-07-16T12:43:05   adding 'whatshap/coverage.py'
2019-07-16T12:43:05   adding 'whatshap/genotype.py'
2019-07-16T12:43:05   adding 'whatshap/graph.py'
2019-07-16T12:43:05   adding 'whatshap/hapcut2vcf.py'
2019-07-16T12:43:05   adding 'whatshap/haplotag.py'
2019-07-16T12:43:05   adding 'whatshap/math.py'
2019-07-16T12:43:05   adding 'whatshap/pedigree.py'
2019-07-16T12:43:05   adding 'whatshap/phase.py'
2019-07-16T12:43:05   adding 'whatshap/priorityqueue.cpython-37m-arm-linux-gnueabihf.so'
2019-07-16T12:43:05   adding 'whatshap/stats.py'
2019-07-16T12:43:05   adding 'whatshap/testhelpers.py'
2019-07-16T12:43:05   adding 'whatshap/timer.py'
2019-07-16T12:43:05   adding 'whatshap/unphase.py'
2019-07-16T12:43:05   adding 'whatshap/utils.py'
2019-07-16T12:43:05   adding 'whatshap/variants.py'
2019-07-16T12:43:05   adding 'whatshap/vcf.py'
2019-07-16T12:43:05   adding 'whatshap/verification.py'
2019-07-16T12:43:05   adding 'whatshap-0.18.dist-info/METADATA'
2019-07-16T12:43:05   adding 'whatshap-0.18.dist-info/WHEEL'
2019-07-16T12:43:05   adding 'whatshap-0.18.dist-info/entry_points.txt'
2019-07-16T12:43:05   adding 'whatshap-0.18.dist-info/top_level.txt'
2019-07-16T12:43:05   adding 'whatshap-0.18.dist-info/RECORD'
2019-07-16T12:43:05   removing build/bdist.linux-armv7l/wheel
2019-07-16T12:43:05   Building wheel for whatshap (setup.py): finished with status 'done'
2019-07-16T12:43:05   Stored in directory: /tmp/tmp38424jdd
2019-07-16T12:43:05 Successfully built whatshap
2019-07-16T12:43:05 Cleaning up...
2019-07-16T12:43:05   Removing source in /tmp/pip-wheel-qzjoh7hy/whatshap
2019-07-16T12:43:05 Removed build tracker '/tmp/pip-req-tracker-bcp5dr0d'