2020-02-13T17:33:11,447 Created temporary directory: /tmp/pip-ephem-wheel-cache-h65cmvc9
2020-02-13T17:33:11,451 Created temporary directory: /tmp/pip-req-tracker-2ma75ga0
2020-02-13T17:33:11,452 Initialized build tracking at /tmp/pip-req-tracker-2ma75ga0
2020-02-13T17:33:11,453 Created build tracker: /tmp/pip-req-tracker-2ma75ga0
2020-02-13T17:33:11,453 Entered build tracker: /tmp/pip-req-tracker-2ma75ga0
2020-02-13T17:33:11,454 Created temporary directory: /tmp/pip-wheel-8e_b91e3
2020-02-13T17:33:11,460 1 location(s) to search for versions of ld-estimator:
2020-02-13T17:33:11,460 * https://pypi.org/simple/ld-estimator/
2020-02-13T17:33:11,461 Fetching project page and analyzing links: https://pypi.org/simple/ld-estimator/
2020-02-13T17:33:11,461 Getting page https://pypi.org/simple/ld-estimator/
2020-02-13T17:33:11,464 Found index url https://pypi.org/simple
2020-02-13T17:33:11,467 Getting credentials from keyring for https://pypi.org/simple
2020-02-13T17:33:11,467 Getting credentials from keyring for pypi.org
2020-02-13T17:33:11,805   Found link https://files.pythonhosted.org/packages/ec/08/e7efe451732eb38f0df979b779d57b0f9f2d65ae3a5c54d91b8ef1f00155/ld_estimator-1.0.0.tar.gz#sha256=4bccee9d0ee071c93251c9cf83f49c3fd694a54e614b324e579eaea623544b0f (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.0
2020-02-13T17:33:11,806   Found link https://files.pythonhosted.org/packages/68/de/dd32c64d0155b2adcad94aaea5e9a18a509be7bc0cb2e0b25e143b5b67f0/ld_estimator-1.0.1.tar.gz#sha256=3c4756f950490fe16082a1d6755fe4ff15db7d16e66a397304a51f18f639066c (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.1
2020-02-13T17:33:11,807   Found link https://files.pythonhosted.org/packages/49/b9/a5da72cf83f50a32ae15e2356358d3e454b8095a9d252d9bda83a3e2eb2b/ld_estimator-1.0.2.tar.gz#sha256=a1847a727c7092a7932086a8b4d45cd7440160b4c506f27de3fcd89e4df98c7e (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.2
2020-02-13T17:33:11,808   Found link https://files.pythonhosted.org/packages/29/65/065f3eca02028744bcdd8446abeb88ab1287c738062d25b759259bc5502c/ld_estimator-1.0.3.tar.gz#sha256=4c7ff2b9f8cc628a08f377e72e65db8988db1b7a81f06a3423532046aca3b491 (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.3
2020-02-13T17:33:11,809   Found link https://files.pythonhosted.org/packages/8a/d1/564412c4454fa8127bea8b86a55200d6ba4d6b55839d85a78a8c55828b12/ld_estimator-1.0.4.tar.gz#sha256=de1543ca307e011819237e81ac2d41de49d28cd94ca2e1a896f87de62853cac7 (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.4
2020-02-13T17:33:11,810   Found link https://files.pythonhosted.org/packages/ec/e0/94c5050125b17473f953fe2c922e7fc6693ab3a12e3197ea6487e694f36a/ld_estimator-1.0.5.tar.gz#sha256=8da7cd1c368ed7feb18acb6a41f748db0dd1cba4d126f3848e1bfd12301bd445 (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.5
2020-02-13T17:33:11,811   Found link https://files.pythonhosted.org/packages/66/da/79e2ea9ef3cc62bffa1c104986e2e9ab85443e7d5602b7f300945dd553ae/ld_estimator-1.0.6.tar.gz#sha256=385ae75a757f0bbb38a5e44e384fbc00bca4cd75a60b909305bb5dc2e95e1210 (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.6
2020-02-13T17:33:11,812   Found link https://files.pythonhosted.org/packages/6a/33/e77d7a9197170c9073ea6812aff02b1030a28be9de6ceca09991f0aa4cad/ld_estimator-1.0.7.tar.gz#sha256=af80477ec12d58eb5d0c2ffc59ecd015db1f5c57354cae0a72cb2a073ed932e9 (from https://pypi.org/simple/ld-estimator/) (requires-python:>3.6.0), version: 1.0.7
2020-02-13T17:33:11,821 Given no hashes to check 1 links for project 'ld-estimator': discarding no candidates
2020-02-13T17:33:11,823 Using version 1.0.6 (newest of versions: 1.0.6)
2020-02-13T17:33:11,828 Collecting ld-estimator==1.0.6
2020-02-13T17:33:11,832   Created temporary directory: /tmp/pip-unpack-rws3u2bd
2020-02-13T17:33:11,835   Getting credentials from keyring for files.pythonhosted.org
2020-02-13T17:33:12,069   Downloading ld_estimator-1.0.6.tar.gz (98 kB)
2020-02-13T17:33:12,426   Added ld-estimator==1.0.6 from https://files.pythonhosted.org/packages/66/da/79e2ea9ef3cc62bffa1c104986e2e9ab85443e7d5602b7f300945dd553ae/ld_estimator-1.0.6.tar.gz#sha256=385ae75a757f0bbb38a5e44e384fbc00bca4cd75a60b909305bb5dc2e95e1210 to build tracker '/tmp/pip-req-tracker-2ma75ga0'
2020-02-13T17:33:12,429     Running setup.py (path:/tmp/pip-wheel-8e_b91e3/ld-estimator/setup.py) egg_info for package ld-estimator
2020-02-13T17:33:12,431     Running command python setup.py egg_info
2020-02-13T17:33:15,735     running egg_info
2020-02-13T17:33:15,740     creating /tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info
2020-02-13T17:33:15,742     writing /tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/PKG-INFO
2020-02-13T17:33:15,747     writing dependency_links to /tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/dependency_links.txt
2020-02-13T17:33:15,752     writing requirements to /tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/requires.txt
2020-02-13T17:33:15,754     writing top-level names to /tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/top_level.txt
2020-02-13T17:33:15,758     writing manifest file '/tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/SOURCES.txt'
2020-02-13T17:33:16,056     reading manifest file '/tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/SOURCES.txt'
2020-02-13T17:33:16,059     reading manifest template 'MANIFEST.in'
2020-02-13T17:33:16,078     writing manifest file '/tmp/pip-wheel-8e_b91e3/ld-estimator/pip-egg-info/ld_estimator.egg-info/SOURCES.txt'
2020-02-13T17:33:16,303   Source in /tmp/pip-wheel-8e_b91e3/ld-estimator has version 1.0.6, which satisfies requirement ld-estimator==1.0.6 from https://files.pythonhosted.org/packages/66/da/79e2ea9ef3cc62bffa1c104986e2e9ab85443e7d5602b7f300945dd553ae/ld_estimator-1.0.6.tar.gz#sha256=385ae75a757f0bbb38a5e44e384fbc00bca4cd75a60b909305bb5dc2e95e1210
2020-02-13T17:33:16,305   Removed ld-estimator==1.0.6 from https://files.pythonhosted.org/packages/66/da/79e2ea9ef3cc62bffa1c104986e2e9ab85443e7d5602b7f300945dd553ae/ld_estimator-1.0.6.tar.gz#sha256=385ae75a757f0bbb38a5e44e384fbc00bca4cd75a60b909305bb5dc2e95e1210 from build tracker '/tmp/pip-req-tracker-2ma75ga0'
2020-02-13T17:33:16,309 Building wheels for collected packages: ld-estimator
2020-02-13T17:33:16,319   Created temporary directory: /tmp/pip-wheel-8zi5fl4r
2020-02-13T17:33:16,320   Building wheel for ld-estimator (setup.py): started
2020-02-13T17:33:16,320   Destination directory: /tmp/pip-wheel-8zi5fl4r
2020-02-13T17:33:16,321   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-8e_b91e3/ld-estimator/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-8e_b91e3/ld-estimator/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-8zi5fl4r
2020-02-13T17:33:19,545   running bdist_wheel
2020-02-13T17:33:19,554   running build
2020-02-13T17:33:19,555   running build_py
2020-02-13T17:33:19,831   creating build
2020-02-13T17:33:19,831   creating build/lib.linux-armv7l-3.7
2020-02-13T17:33:19,833   creating build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,836   copying ld_estimator/site.py -> build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,840   copying ld_estimator/utils.py -> build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,845   copying ld_estimator/linkage.py -> build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,849   copying ld_estimator/region.py -> build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,853   copying ld_estimator/__init__.py -> build/lib.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,858   running build_ext
2020-02-13T17:33:19,876   building 'ld_estimator.pairwise' extension
2020-02-13T17:33:19,879   creating build/temp.linux-armv7l-3.7
2020-02-13T17:33:19,880   creating build/temp.linux-armv7l-3.7/ld_estimator
2020-02-13T17:33:19,882   creating build/temp.linux-armv7l-3.7/src
2020-02-13T17:33:19,884   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 -Isrc/ -I/usr/include/python3.7m -c ld_estimator/pairwise.cpp -o build/temp.linux-armv7l-3.7/ld_estimator/pairwise.o -std=c++11
2020-02-13T17:33:37,212   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 -Isrc/ -I/usr/include/python3.7m -c src/ld.cpp -o build/temp.linux-armv7l-3.7/src/ld.o -std=c++11
2020-02-13T17:33:44,001   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 -Isrc/ -I/usr/include/python3.7m -c src/af.cpp -o build/temp.linux-armv7l-3.7/src/af.o -std=c++11
2020-02-13T17:33:44,760   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 -Isrc/ -I/usr/include/python3.7m -c src/confidence.cpp -o build/temp.linux-armv7l-3.7/src/confidence.o -std=c++11
2020-02-13T17:33:45,843   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 -Isrc/ -I/usr/include/python3.7m -c src/dprime.cpp -o build/temp.linux-armv7l-3.7/src/dprime.o -std=c++11
2020-02-13T17:33:46,510   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 -Isrc/ -I/usr/include/python3.7m -c src/flip.cpp -o build/temp.linux-armv7l-3.7/src/flip.o -std=c++11
2020-02-13T17:33:47,206   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 -Isrc/ -I/usr/include/python3.7m -c src/frequencies.cpp -o build/temp.linux-armv7l-3.7/src/frequencies.o -std=c++11
2020-02-13T17:33:47,945   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 -Isrc/ -I/usr/include/python3.7m -c src/likelihoods.cpp -o build/temp.linux-armv7l-3.7/src/likelihoods.o -std=c++11
2020-02-13T17:33:48,943   In file included from /usr/include/c++/8/vector:69,
2020-02-13T17:33:48,943                    from src/likelihoods.h:4,
2020-02-13T17:33:48,944                    from src/likelihoods.cpp:2:
2020-02-13T17:33:48,944   /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>]’:
2020-02-13T17:33:48,944   /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
2020-02-13T17:33:48,944          vector<_Tp, _Alloc>::
2020-02-13T17:33:48,945          ^~~~~~~~~~~~~~~~~~~
2020-02-13T17:33:49,016   In file included from /usr/include/c++/8/vector:64,
2020-02-13T17:33:49,017                    from src/likelihoods.h:4,
2020-02-13T17:33:49,017                    from src/likelihoods.cpp:2:
2020-02-13T17:33:49,017   /usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<double> ld_estimator::get_lsurface(double, double, double, double, ld_estimator::Haps<int>, int)’:
2020-02-13T17:33:49,018   /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
2020-02-13T17:33:49,018       _M_realloc_insert(end(), __x);
2020-02-13T17:33:49,018       ^~~~~~~~~~~~~~~~~
2020-02-13T17:33:49,194   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 -Isrc/ -I/usr/include/python3.7m -c src/optimize.cpp -o build/temp.linux-armv7l-3.7/src/optimize.o -std=c++11
2020-02-13T17:33:50,284   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 -Isrc/ -I/usr/include/python3.7m -c src/tallies.cpp -o build/temp.linux-armv7l-3.7/src/tallies.o -std=c++11
2020-02-13T17:33:59,504   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 -Isrc/ -I/usr/include/python3.7m -c src/utils.cpp -o build/temp.linux-armv7l-3.7/src/utils.o -std=c++11
2020-02-13T17:34:08,060   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/ld_estimator/pairwise.o build/temp.linux-armv7l-3.7/src/ld.o build/temp.linux-armv7l-3.7/src/af.o build/temp.linux-armv7l-3.7/src/confidence.o build/temp.linux-armv7l-3.7/src/dprime.o build/temp.linux-armv7l-3.7/src/flip.o build/temp.linux-armv7l-3.7/src/frequencies.o build/temp.linux-armv7l-3.7/src/likelihoods.o build/temp.linux-armv7l-3.7/src/optimize.o build/temp.linux-armv7l-3.7/src/tallies.o build/temp.linux-armv7l-3.7/src/utils.o -o build/lib.linux-armv7l-3.7/ld_estimator/pairwise.cpython-37m-arm-linux-gnueabihf.so
2020-02-13T17:34:08,911   installing to build/bdist.linux-armv7l/wheel
2020-02-13T17:34:08,912   running install
2020-02-13T17:34:08,917   running install_lib
2020-02-13T17:34:08,930   creating build/bdist.linux-armv7l
2020-02-13T17:34:08,932   creating build/bdist.linux-armv7l/wheel
2020-02-13T17:34:08,937   creating build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:08,940   copying build/lib.linux-armv7l-3.7/ld_estimator/pairwise.cpython-37m-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,132   copying build/lib.linux-armv7l-3.7/ld_estimator/site.py -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,139   copying build/lib.linux-armv7l-3.7/ld_estimator/utils.py -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,146   copying build/lib.linux-armv7l-3.7/ld_estimator/linkage.py -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,152   copying build/lib.linux-armv7l-3.7/ld_estimator/region.py -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,157   copying build/lib.linux-armv7l-3.7/ld_estimator/__init__.py -> build/bdist.linux-armv7l/wheel/ld_estimator
2020-02-13T17:34:09,162   running install_egg_info
2020-02-13T17:34:09,254   running egg_info
2020-02-13T17:34:09,255   writing ld_estimator.egg-info/PKG-INFO
2020-02-13T17:34:09,260   writing dependency_links to ld_estimator.egg-info/dependency_links.txt
2020-02-13T17:34:09,264   writing requirements to ld_estimator.egg-info/requires.txt
2020-02-13T17:34:09,266   writing top-level names to ld_estimator.egg-info/top_level.txt
2020-02-13T17:34:09,282   reading manifest file 'ld_estimator.egg-info/SOURCES.txt'
2020-02-13T17:34:09,293   reading manifest template 'MANIFEST.in'
2020-02-13T17:34:09,324   writing manifest file 'ld_estimator.egg-info/SOURCES.txt'
2020-02-13T17:34:09,328   Copying ld_estimator.egg-info to build/bdist.linux-armv7l/wheel/ld_estimator-1.0.6-py3.7.egg-info
2020-02-13T17:34:09,353   running install_scripts
2020-02-13T17:34:09,452   creating build/bdist.linux-armv7l/wheel/ld_estimator-1.0.6.dist-info/WHEEL
2020-02-13T17:34:09,458   creating '/tmp/pip-wheel-8zi5fl4r/ld_estimator-1.0.6-cp37-cp37m-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2020-02-13T17:34:09,463   adding 'ld_estimator/__init__.py'
2020-02-13T17:34:09,466   adding 'ld_estimator/linkage.py'
2020-02-13T17:34:10,044   adding 'ld_estimator/pairwise.cpython-37m-arm-linux-gnueabihf.so'
2020-02-13T17:34:10,071   adding 'ld_estimator/region.py'
2020-02-13T17:34:10,075   adding 'ld_estimator/site.py'
2020-02-13T17:34:10,078   adding 'ld_estimator/utils.py'
2020-02-13T17:34:10,083   adding 'ld_estimator-1.0.6.dist-info/METADATA'
2020-02-13T17:34:10,085   adding 'ld_estimator-1.0.6.dist-info/WHEEL'
2020-02-13T17:34:10,087   adding 'ld_estimator-1.0.6.dist-info/top_level.txt'
2020-02-13T17:34:10,088   adding 'ld_estimator-1.0.6.dist-info/RECORD'
2020-02-13T17:34:10,146   removing build/bdist.linux-armv7l/wheel
2020-02-13T17:34:10,393   Building wheel for ld-estimator (setup.py): finished with status 'done'
2020-02-13T17:34:10,409   Created wheel for ld-estimator: filename=ld_estimator-1.0.6-cp37-cp37m-linux_armv7l.whl size=637374 sha256=47226ec859cc1275c27590822cf42b78d1006718a7adf1fce692277b692af7d4
2020-02-13T17:34:10,410   Stored in directory: /tmp/pip-ephem-wheel-cache-h65cmvc9/wheels/cb/ca/fe/0673c15d6b87bb65534148cdcf855de35b4798ae688b5442d5
2020-02-13T17:34:10,413 Successfully built ld-estimator
2020-02-13T17:34:10,531 Cleaning up...
2020-02-13T17:34:10,532   Removing source in /tmp/pip-wheel-8e_b91e3/ld-estimator
2020-02-13T17:34:10,624 Removed build tracker: '/tmp/pip-req-tracker-2ma75ga0'