2021-08-24T14:27:41,745 Created temporary directory: /tmp/pip-ephem-wheel-cache-fcyhkhlg 2021-08-24T14:27:41,748 Created temporary directory: /tmp/pip-req-tracker-mq535ye6 2021-08-24T14:27:41,749 Initialized build tracking at /tmp/pip-req-tracker-mq535ye6 2021-08-24T14:27:41,749 Created build tracker: /tmp/pip-req-tracker-mq535ye6 2021-08-24T14:27:41,749 Entered build tracker: /tmp/pip-req-tracker-mq535ye6 2021-08-24T14:27:41,750 Created temporary directory: /tmp/pip-wheel-eadb45la 2021-08-24T14:27:41,785 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2021-08-24T14:27:41,787 2 location(s) to search for versions of pyslow5: 2021-08-24T14:27:41,787 * https://pypi.org/simple/pyslow5/ 2021-08-24T14:27:41,787 * https://www.piwheels.org/simple/pyslow5/ 2021-08-24T14:27:41,788 Fetching project page and analyzing links: https://pypi.org/simple/pyslow5/ 2021-08-24T14:27:41,788 Getting page https://pypi.org/simple/pyslow5/ 2021-08-24T14:27:41,790 Found index url https://pypi.org/simple 2021-08-24T14:27:41,879 Found link https://files.pythonhosted.org/packages/23/0d/38c8cfedd09e7f753347b6ecd717a101c7236daf2ecccb34d44cedc6f125/pyslow5-0.2.0a1.tar.gz#sha256=a72b744ec652ba25eee5060748f8df8a5dc49eee126f48b7682f8d11d6cb434b (from https://pypi.org/simple/pyslow5/), version: 0.2.0a1 2021-08-24T14:27:41,880 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyslow5/ 2021-08-24T14:27:41,880 Getting page https://www.piwheels.org/simple/pyslow5/ 2021-08-24T14:27:41,881 Found index url https://www.piwheels.org/simple 2021-08-24T14:27:41,996 Skipping link: No binaries permitted for pyslow5: https://www.piwheels.org/simple/pyslow5/pyslow5-0.2.0a1-cp35-cp35m-linux_armv6l.whl#sha256=778a99e023f739e757f3a8ac054aaf245b3c3855b3781ba5f9f17403f1f2f323 (from https://www.piwheels.org/simple/pyslow5/) (requires-python:>=3.4.3) 2021-08-24T14:27:41,996 Skipping link: No binaries permitted for pyslow5: https://www.piwheels.org/simple/pyslow5/pyslow5-0.2.0a1-cp35-cp35m-linux_armv7l.whl#sha256=778a99e023f739e757f3a8ac054aaf245b3c3855b3781ba5f9f17403f1f2f323 (from https://www.piwheels.org/simple/pyslow5/) (requires-python:>=3.4.3) 2021-08-24T14:27:41,996 Skipping link: No binaries permitted for pyslow5: https://www.piwheels.org/simple/pyslow5/pyslow5-0.2.0a1-cp37-cp37m-linux_armv6l.whl#sha256=1e44f77d160ed7f970085e6bbd34c072504cd012441dfab74f56f9115217f60a (from https://www.piwheels.org/simple/pyslow5/) (requires-python:>=3.4.3) 2021-08-24T14:27:41,997 Skipping link: No binaries permitted for pyslow5: https://www.piwheels.org/simple/pyslow5/pyslow5-0.2.0a1-cp37-cp37m-linux_armv7l.whl#sha256=1e44f77d160ed7f970085e6bbd34c072504cd012441dfab74f56f9115217f60a (from https://www.piwheels.org/simple/pyslow5/) (requires-python:>=3.4.3) 2021-08-24T14:27:41,997 Skipping link: not a file: https://www.piwheels.org/simple/pyslow5/ 2021-08-24T14:27:41,997 Skipping link: not a file: https://pypi.org/simple/pyslow5/ 2021-08-24T14:27:42,016 Given no hashes to check 1 links for project 'pyslow5': discarding no candidates 2021-08-24T14:27:42,034 Collecting pyslow5==0.2.0a1 2021-08-24T14:27:42,036 Created temporary directory: /tmp/pip-unpack-0qi6r5pc 2021-08-24T14:27:42,077 Downloading pyslow5-0.2.0a1.tar.gz (182 kB) 2021-08-24T14:27:42,250 Added pyslow5==0.2.0a1 from https://files.pythonhosted.org/packages/23/0d/38c8cfedd09e7f753347b6ecd717a101c7236daf2ecccb34d44cedc6f125/pyslow5-0.2.0a1.tar.gz#sha256=a72b744ec652ba25eee5060748f8df8a5dc49eee126f48b7682f8d11d6cb434b to build tracker '/tmp/pip-req-tracker-mq535ye6' 2021-08-24T14:27:42,251 Running setup.py (path:/tmp/pip-wheel-eadb45la/pyslow5_117e3b4628744a449308c39948bd011a/setup.py) egg_info for package pyslow5 2021-08-24T14:27:42,251 Created temporary directory: /tmp/pip-pip-egg-info-41lbh34t 2021-08-24T14:27:42,252 Running command python setup.py egg_info 2021-08-24T14:27:43,622 running egg_info 2021-08-24T14:27:43,624 creating /tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info 2021-08-24T14:27:43,625 writing /tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/PKG-INFO 2021-08-24T14:27:43,627 writing dependency_links to /tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/dependency_links.txt 2021-08-24T14:27:43,629 writing requirements to /tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/requires.txt 2021-08-24T14:27:43,630 writing top-level names to /tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/top_level.txt 2021-08-24T14:27:43,632 writing manifest file '/tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/SOURCES.txt' 2021-08-24T14:27:43,639 reading manifest file '/tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/SOURCES.txt' 2021-08-24T14:27:43,641 reading manifest template 'MANIFEST.in' 2021-08-24T14:27:43,649 writing manifest file '/tmp/pip-pip-egg-info-41lbh34t/pyslow5.egg-info/SOURCES.txt' 2021-08-24T14:27:43,746 Source in /tmp/pip-wheel-eadb45la/pyslow5_117e3b4628744a449308c39948bd011a has version 0.2.0a1, which satisfies requirement pyslow5==0.2.0a1 from https://files.pythonhosted.org/packages/23/0d/38c8cfedd09e7f753347b6ecd717a101c7236daf2ecccb34d44cedc6f125/pyslow5-0.2.0a1.tar.gz#sha256=a72b744ec652ba25eee5060748f8df8a5dc49eee126f48b7682f8d11d6cb434b 2021-08-24T14:27:43,747 Removed pyslow5==0.2.0a1 from https://files.pythonhosted.org/packages/23/0d/38c8cfedd09e7f753347b6ecd717a101c7236daf2ecccb34d44cedc6f125/pyslow5-0.2.0a1.tar.gz#sha256=a72b744ec652ba25eee5060748f8df8a5dc49eee126f48b7682f8d11d6cb434b from build tracker '/tmp/pip-req-tracker-mq535ye6' 2021-08-24T14:27:43,753 Created temporary directory: /tmp/pip-unpack-y3ksnx50 2021-08-24T14:27:43,753 Building wheels for collected packages: pyslow5 2021-08-24T14:27:43,757 Created temporary directory: /tmp/pip-wheel-1n4rvatm 2021-08-24T14:27:43,758 Building wheel for pyslow5 (setup.py): started 2021-08-24T14:27:43,758 Destination directory: /tmp/pip-wheel-1n4rvatm 2021-08-24T14:27:43,758 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-eadb45la/pyslow5_117e3b4628744a449308c39948bd011a/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-eadb45la/pyslow5_117e3b4628744a449308c39948bd011a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-1n4rvatm 2021-08-24T14:27:45,070 running bdist_wheel 2021-08-24T14:27:45,074 running build 2021-08-24T14:27:45,075 running build_ext 2021-08-24T14:27:45,080 cythoning python/pyslow5.pyx to python/pyslow5.c 2021-08-24T14:27:45,727 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-eadb45la/pyslow5_117e3b4628744a449308c39948bd011a/python/pyslow5.pxd 2021-08-24T14:27:45,727 tree = Parsing.p_module(s, pxd, full_module_name) 2021-08-24T14:27:49,518 building 'pyslow5' extension 2021-08-24T14:27:49,519 creating build 2021-08-24T14:27:49,519 creating build/temp.linux-armv7l-3.9 2021-08-24T14:27:49,519 creating build/temp.linux-armv7l-3.9/python 2021-08-24T14:27:49,520 creating build/temp.linux-armv7l-3.9/src 2021-08-24T14:27:49,521 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iinclude/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c python/pyslow5.c -o build/temp.linux-armv7l-3.9/python/pyslow5.o -g -Wall -O2 -std=c99 2021-08-24T14:27:49,977 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-08-24T14:27:49,977 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-08-24T14:27:49,977 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-08-24T14:27:49,977 from python/pyslow5.c:615: 2021-08-24T14:27:49,977 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-08-24T14:27:49,978 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-08-24T14:27:49,978 | ^~~~~~~ 2021-08-24T14:28:18,976 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iinclude/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/slow5.c -o build/temp.linux-armv7l-3.9/src/slow5.o -g -Wall -O2 -std=c99 2021-08-24T14:28:19,192 src/slow5.c: In function ‘slow5_init’: 2021-08-24T14:28:19,193 src/slow5.c:155:51: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-08-24T14:28:19,193 155 | if ((s5p->meta.start_rec_offset = ftello(fp)) == -1) { 2021-08-24T14:28:19,194 | ^~ 2021-08-24T14:28:19,231 src/slow5.c: In function ‘slow5_get_mem’: 2021-08-24T14:28:19,232 src/slow5.c:1712:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-08-24T14:28:19,232 1712 | if (pread(s5p->meta.fd, mem, bytes, offset) != bytes) { 2021-08-24T14:28:19,233 | ^~ 2021-08-24T14:28:19,234 In file included from include/slow5/slow5.h:55, 2021-08-24T14:28:19,234 from src/slow5.c:40: 2021-08-24T14:28:19,234 include/slow5/slow5_error.h:79:28: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘off_t’ {aka ‘long int’} [-Wformat=] 2021-08-24T14:28:19,234 79 | #define SLOW5_ERROR_PREFIX "[%s::ERROR]\033[1;31m " 2021-08-24T14:28:19,234 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,235 include/slow5/slow5_error.h:116:25: note: in expansion of macro ‘SLOW5_ERROR_PREFIX’ 2021-08-24T14:28:19,235 116 | fprintf(stderr, SLOW5_ERROR_PREFIX msg SLOW5_NO_COLOUR \ 2021-08-24T14:28:19,235 | ^~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,235 src/slow5.c:1713:9: note: in expansion of macro ‘SLOW5_ERROR’ 2021-08-24T14:28:19,235 1713 | SLOW5_ERROR("Failed to pread '%zu' bytes at offset '%zu' from slow5 file '%s'.", 2021-08-24T14:28:19,235 | ^~~~~~~~~~~ 2021-08-24T14:28:19,249 src/slow5.c: In function ‘slow5_rec_aux_parse’: 2021-08-24T14:28:19,250 include/slow5/slow5_error.h:79:28: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 2021-08-24T14:28:19,250 79 | #define SLOW5_ERROR_PREFIX "[%s::ERROR]\033[1;31m " 2021-08-24T14:28:19,250 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,251 include/slow5/slow5_error.h:116:25: note: in expansion of macro ‘SLOW5_ERROR_PREFIX’ 2021-08-24T14:28:19,251 116 | fprintf(stderr, SLOW5_ERROR_PREFIX msg SLOW5_NO_COLOUR \ 2021-08-24T14:28:19,251 | ^~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,251 src/slow5.c:2277:17: note: in expansion of macro ‘SLOW5_ERROR’ 2021-08-24T14:28:19,251 2277 | SLOW5_ERROR("Auxiliary field '%s' is missing in record. At offset '%ld' and record size is '%ld'.", aux_meta->attrs[i], offset, read_size); 2021-08-24T14:28:19,251 | ^~~~~~~~~~~ 2021-08-24T14:28:19,252 include/slow5/slow5_error.h:79:28: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 2021-08-24T14:28:19,252 79 | #define SLOW5_ERROR_PREFIX "[%s::ERROR]\033[1;31m " 2021-08-24T14:28:19,252 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,252 include/slow5/slow5_error.h:116:25: note: in expansion of macro ‘SLOW5_ERROR_PREFIX’ 2021-08-24T14:28:19,252 116 | fprintf(stderr, SLOW5_ERROR_PREFIX msg SLOW5_NO_COLOUR \ 2021-08-24T14:28:19,252 | ^~~~~~~~~~~~~~~~~~ 2021-08-24T14:28:19,252 src/slow5.c:2277:17: note: in expansion of macro ‘SLOW5_ERROR’ 2021-08-24T14:28:19,253 2277 | SLOW5_ERROR("Auxiliary field '%s' is missing in record. At offset '%ld' and record size is '%ld'.", aux_meta->attrs[i], offset, read_size); 2021-08-24T14:28:19,253 | ^~~~~~~~~~~ 2021-08-24T14:28:27,431 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iinclude/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/slow5_idx.c -o build/temp.linux-armv7l-3.9/src/slow5_idx.o -g -Wall -O2 -std=c99 2021-08-24T14:28:28,440 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iinclude/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/slow5_misc.c -o build/temp.linux-armv7l-3.9/src/slow5_misc.o -g -Wall -O2 -std=c99 2021-08-24T14:28:28,975 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iinclude/ -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c src/slow5_press.c -o build/temp.linux-armv7l-3.9/src/slow5_press.o -g -Wall -O2 -std=c99 2021-08-24T14:28:29,183 src/slow5_press.c: In function ‘slow5_pread_depress_solo’: 2021-08-24T14:28:29,184 src/slow5_press.c:551:47: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-08-24T14:28:29,184 551 | if ((ret = pread(fd, raw, count, offset)) != count) { 2021-08-24T14:28:29,184 | ^~ 2021-08-24T14:28:29,750 creating build/lib.linux-armv7l-3.9 2021-08-24T14:28:29,751 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/python/pyslow5.o build/temp.linux-armv7l-3.9/src/slow5.o build/temp.linux-armv7l-3.9/src/slow5_idx.o build/temp.linux-armv7l-3.9/src/slow5_misc.o build/temp.linux-armv7l-3.9/src/slow5_press.o -L. -lm -lz -o build/lib.linux-armv7l-3.9/pyslow5.cpython-39-arm-linux-gnueabihf.so 2021-08-24T14:28:30,009 installing to build/bdist.linux-armv7l/wheel 2021-08-24T14:28:30,009 running install 2021-08-24T14:28:30,010 running install_lib 2021-08-24T14:28:30,014 creating build/bdist.linux-armv7l 2021-08-24T14:28:30,014 creating build/bdist.linux-armv7l/wheel 2021-08-24T14:28:30,016 copying build/lib.linux-armv7l-3.9/pyslow5.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2021-08-24T14:28:30,053 running install_egg_info 2021-08-24T14:28:30,079 running egg_info 2021-08-24T14:28:30,080 writing pyslow5.egg-info/PKG-INFO 2021-08-24T14:28:30,082 writing dependency_links to pyslow5.egg-info/dependency_links.txt 2021-08-24T14:28:30,085 writing requirements to pyslow5.egg-info/requires.txt 2021-08-24T14:28:30,087 writing top-level names to pyslow5.egg-info/top_level.txt 2021-08-24T14:28:30,092 reading manifest file 'pyslow5.egg-info/SOURCES.txt' 2021-08-24T14:28:30,096 reading manifest template 'MANIFEST.in' 2021-08-24T14:28:30,104 writing manifest file 'pyslow5.egg-info/SOURCES.txt' 2021-08-24T14:28:30,106 Copying pyslow5.egg-info to build/bdist.linux-armv7l/wheel/pyslow5-0.2.0a1-py3.9.egg-info 2021-08-24T14:28:30,118 running install_scripts 2021-08-24T14:28:30,160 creating build/bdist.linux-armv7l/wheel/pyslow5-0.2.0a1.dist-info/WHEEL 2021-08-24T14:28:30,163 creating '/tmp/pip-wheel-1n4rvatm/pyslow5-0.2.0a1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-08-24T14:28:30,557 adding 'pyslow5.cpython-39-arm-linux-gnueabihf.so' 2021-08-24T14:28:30,575 adding 'pyslow5-0.2.0a1.dist-info/METADATA' 2021-08-24T14:28:30,577 adding 'pyslow5-0.2.0a1.dist-info/WHEEL' 2021-08-24T14:28:30,578 adding 'pyslow5-0.2.0a1.dist-info/top_level.txt' 2021-08-24T14:28:30,579 adding 'pyslow5-0.2.0a1.dist-info/RECORD' 2021-08-24T14:28:30,591 removing build/bdist.linux-armv7l/wheel 2021-08-24T14:28:30,832 Building wheel for pyslow5 (setup.py): finished with status 'done' 2021-08-24T14:28:30,843 Created wheel for pyslow5: filename=pyslow5-0.2.0a1-cp39-cp39-linux_armv7l.whl size=700188 sha256=cde6479a69345d4c2bef55beeb0ab67909d74e8f91a2ec5ef1a0f390aaa3c0dd 2021-08-24T14:28:30,844 Stored in directory: /tmp/pip-ephem-wheel-cache-fcyhkhlg/wheels/c9/d4/29/2ca1c2949fd198eb559d74b174fbdcb71e94fe2a181c81ecc4 2021-08-24T14:28:30,853 Successfully built pyslow5 2021-08-24T14:28:30,884 Removed build tracker: '/tmp/pip-req-tracker-mq535ye6'