2023-09-13T22:49:58,629 Created temporary directory: /tmp/pip-build-tracker-17e2f5gq 2023-09-13T22:49:58,630 Initialized build tracking at /tmp/pip-build-tracker-17e2f5gq 2023-09-13T22:49:58,630 Created build tracker: /tmp/pip-build-tracker-17e2f5gq 2023-09-13T22:49:58,631 Entered build tracker: /tmp/pip-build-tracker-17e2f5gq 2023-09-13T22:49:58,631 Created temporary directory: /tmp/pip-wheel-u4f36ot8 2023-09-13T22:49:58,634 Created temporary directory: /tmp/pip-ephem-wheel-cache-7r76vyrz 2023-09-13T22:49:58,658 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-13T22:49:58,661 2 location(s) to search for versions of strawc: 2023-09-13T22:49:58,661 * https://pypi.org/simple/strawc/ 2023-09-13T22:49:58,661 * https://www.piwheels.org/simple/strawc/ 2023-09-13T22:49:58,662 Fetching project page and analyzing links: https://pypi.org/simple/strawc/ 2023-09-13T22:49:58,663 Getting page https://pypi.org/simple/strawc/ 2023-09-13T22:49:58,665 Found index url https://pypi.org/simple/ 2023-09-13T22:49:58,879 Fetched page https://pypi.org/simple/strawc/ as application/vnd.pypi.simple.v1+json 2023-09-13T22:49:58,881 Found link https://files.pythonhosted.org/packages/14/cd/7e4dbd8964e197806357e1af9cb23374c4b332cfdcc5f5fed56cd6e12f98/strawC-0.0.2.1.tar.gz (from https://pypi.org/simple/strawc/) (requires-python:>3.3), version: 0.0.2.1 2023-09-13T22:49:58,882 Fetching project page and analyzing links: https://www.piwheels.org/simple/strawc/ 2023-09-13T22:49:58,882 Getting page https://www.piwheels.org/simple/strawc/ 2023-09-13T22:49:58,884 Found index url https://www.piwheels.org/simple/ 2023-09-13T22:49:59,138 Fetched page https://www.piwheels.org/simple/strawc/ as text/html 2023-09-13T22:49:59,141 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp35-cp35m-linux_armv6l.whl#sha256=285e873e090a1b25369c6006a59c9753bfc6f5524490dbdb0168cc08224ac41c (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,142 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp35-cp35m-linux_armv7l.whl#sha256=285e873e090a1b25369c6006a59c9753bfc6f5524490dbdb0168cc08224ac41c (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,143 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp37-cp37m-linux_armv6l.whl#sha256=13a50b34db495c160b1502f9a1346a6b35a052a9a4b2d86bc2e0a51644ee87e5 (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,143 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp37-cp37m-linux_armv7l.whl#sha256=13a50b34db495c160b1502f9a1346a6b35a052a9a4b2d86bc2e0a51644ee87e5 (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,144 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp39-cp39-linux_armv6l.whl#sha256=a7b989f38a536293f85601925ff363f61c85819948bfb86ecb2ea2b8c84afd95 (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,144 Skipping link: No binaries permitted for strawc: https://www.piwheels.org/simple/strawc/strawC-0.0.2.1-cp39-cp39-linux_armv7l.whl#sha256=a7b989f38a536293f85601925ff363f61c85819948bfb86ecb2ea2b8c84afd95 (from https://www.piwheels.org/simple/strawc/) (requires-python:>3.3) 2023-09-13T22:49:59,145 Skipping link: not a file: https://www.piwheels.org/simple/strawc/ 2023-09-13T22:49:59,145 Skipping link: not a file: https://pypi.org/simple/strawc/ 2023-09-13T22:49:59,172 Given no hashes to check 1 links for project 'strawc': discarding no candidates 2023-09-13T22:49:59,197 Collecting strawc==0.0.2.1 2023-09-13T22:49:59,200 Created temporary directory: /tmp/pip-unpack-3ttay0ww 2023-09-13T22:49:59,434 Downloading strawC-0.0.2.1.tar.gz (12 kB) 2023-09-13T22:49:59,480 Added strawc==0.0.2.1 from https://files.pythonhosted.org/packages/14/cd/7e4dbd8964e197806357e1af9cb23374c4b332cfdcc5f5fed56cd6e12f98/strawC-0.0.2.1.tar.gz to build tracker '/tmp/pip-build-tracker-17e2f5gq' 2023-09-13T22:49:59,482 Running setup.py (path:/tmp/pip-wheel-u4f36ot8/strawc_64800914414c4ba0ba08de9a2b6ef439/setup.py) egg_info for package strawc 2023-09-13T22:49:59,483 Created temporary directory: /tmp/pip-pip-egg-info-4bgm9yqv 2023-09-13T22:49:59,484 Preparing metadata (setup.py): started 2023-09-13T22:49:59,485 Running command python setup.py egg_info 2023-09-13T22:50:00,358 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-13T22:50:00,358 !! 2023-09-13T22:50:00,359 ******************************************************************************** 2023-09-13T22:50:00,360 Requirements should be satisfied by a PEP 517 installer. 2023-09-13T22:50:00,360 If you are using pip, you can try `pip install --use-pep517`. 2023-09-13T22:50:00,360 ******************************************************************************** 2023-09-13T22:50:00,361 !! 2023-09-13T22:50:00,362 dist.fetch_build_eggs(dist.setup_requires) 2023-09-13T22:50:03,108 running egg_info 2023-09-13T22:50:03,110 creating /tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info 2023-09-13T22:50:03,136 writing /tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/PKG-INFO 2023-09-13T22:50:03,140 writing dependency_links to /tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/dependency_links.txt 2023-09-13T22:50:03,142 writing requirements to /tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/requires.txt 2023-09-13T22:50:03,144 writing top-level names to /tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/top_level.txt 2023-09-13T22:50:03,146 writing manifest file '/tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/SOURCES.txt' 2023-09-13T22:50:03,201 reading manifest file '/tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/SOURCES.txt' 2023-09-13T22:50:03,204 reading manifest template 'MANIFEST.in' 2023-09-13T22:50:03,206 adding license file 'LICENSE' 2023-09-13T22:50:03,208 writing manifest file '/tmp/pip-pip-egg-info-4bgm9yqv/strawC.egg-info/SOURCES.txt' 2023-09-13T22:50:03,318 Preparing metadata (setup.py): finished with status 'done' 2023-09-13T22:50:03,323 Source in /tmp/pip-wheel-u4f36ot8/strawc_64800914414c4ba0ba08de9a2b6ef439 has version 0.0.2.1, which satisfies requirement strawc==0.0.2.1 from https://files.pythonhosted.org/packages/14/cd/7e4dbd8964e197806357e1af9cb23374c4b332cfdcc5f5fed56cd6e12f98/strawC-0.0.2.1.tar.gz 2023-09-13T22:50:03,324 Removed strawc==0.0.2.1 from https://files.pythonhosted.org/packages/14/cd/7e4dbd8964e197806357e1af9cb23374c4b332cfdcc5f5fed56cd6e12f98/strawC-0.0.2.1.tar.gz from build tracker '/tmp/pip-build-tracker-17e2f5gq' 2023-09-13T22:50:03,330 Created temporary directory: /tmp/pip-unpack-vk5iinrs 2023-09-13T22:50:03,331 Created temporary directory: /tmp/pip-unpack-0dctlbjy 2023-09-13T22:50:03,336 Building wheels for collected packages: strawc 2023-09-13T22:50:03,342 Created temporary directory: /tmp/pip-wheel-o9apk5g3 2023-09-13T22:50:03,342 Building wheel for strawc (setup.py): started 2023-09-13T22:50:03,344 Destination directory: /tmp/pip-wheel-o9apk5g3 2023-09-13T22:50:03,344 Running command python setup.py bdist_wheel 2023-09-13T22:50:04,193 /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. 2023-09-13T22:50:04,193 !! 2023-09-13T22:50:04,194 ******************************************************************************** 2023-09-13T22:50:04,195 Requirements should be satisfied by a PEP 517 installer. 2023-09-13T22:50:04,195 If you are using pip, you can try `pip install --use-pep517`. 2023-09-13T22:50:04,196 ******************************************************************************** 2023-09-13T22:50:04,197 !! 2023-09-13T22:50:04,198 dist.fetch_build_eggs(dist.setup_requires) 2023-09-13T22:50:04,533 running bdist_wheel 2023-09-13T22:50:04,610 running build 2023-09-13T22:50:04,611 running build_ext 2023-09-13T22:50:04,618 creating tmp 2023-09-13T22:50:04,618 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c /tmp/tmpg7l8mruz.cpp -o tmp/tmpg7l8mruz.o -std=c++14 2023-09-13T22:50:04,683 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/usr/include/python3.11 -c /tmp/tmph4v6iali.cpp -o tmp/tmph4v6iali.o -fvisibility=hidden 2023-09-13T22:50:05,254 building 'strawC' extension 2023-09-13T22:50:05,263 creating build 2023-09-13T22:50:05,264 creating build/temp.linux-armv7l-cpython-311 2023-09-13T22:50:05,265 creating build/temp.linux-armv7l-cpython-311/src 2023-09-13T22:50:05,266 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-wheel-u4f36ot8/strawc_64800914414c4ba0ba08de9a2b6ef439/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I/tmp/pip-wheel-u4f36ot8/strawc_64800914414c4ba0ba08de9a2b6ef439/.eggs/pybind11-2.11.1-py3.11.egg/pybind11/include -I/usr/include/python3.11 -c src/straw.cpp -o build/temp.linux-armv7l-cpython-311/src/straw.o -DVERSION_INFO=\"0.0.2.1\" -std=c++14 -fvisibility=hidden 2023-09-13T22:50:10,720 src/straw.cpp: In function ‘size_t hdf(char*, size_t, size_t, void*)’: 2023-09-13T22:50:10,721 src/straw.cpp:75:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-13T22:50:10,721 75 | if (found != string::npos) { 2023-09-13T22:50:10,722 | ~~~~~~^~~~~~~~~~~~~~~ 2023-09-13T22:50:10,723 src/straw.cpp:78:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const unsigned int’} [-Wsign-compare] 2023-09-13T22:50:10,723 78 | if (found2 != string::npos) { 2023-09-13T22:50:10,724 | ~~~~~~~^~~~~~~~~~~~~~~ 2023-09-13T22:50:10,763 src/straw.cpp: In function ‘std::map, chromosome> readHeader(std::istream&, long int&)’: 2023-09-13T22:50:10,763 src/straw.cpp:204:14: warning: unused variable ‘nviPosition’ [-Wunused-variable] 2023-09-13T22:50:10,764 204 | long nviPosition = readLongFromFile(fin); 2023-09-13T22:50:10,765 | ^~~~~~~~~~~ 2023-09-13T22:50:10,766 src/straw.cpp:205:14: warning: unused variable ‘nviLength’ [-Wunused-variable] 2023-09-13T22:50:10,767 205 | long nviLength = readLongFromFile(fin); 2023-09-13T22:50:10,767 | ^~~~~~~~~ 2023-09-13T22:50:10,769 src/straw.cpp: In function ‘bool readFooter(std::istream&, long int, int, int, std::string, std::string, int, long int&, indexEntry&, indexEntry&)’: 2023-09-13T22:50:10,769 src/straw.cpp:243:14: warning: unused variable ‘nBytes’ [-Wunused-variable] 2023-09-13T22:50:10,770 243 | long nBytes = readLongFromFile(fin); 2023-09-13T22:50:10,771 | ^~~~~~ 2023-09-13T22:50:10,771 src/straw.cpp:245:13: warning: unused variable ‘nBytes’ [-Wunused-variable] 2023-09-13T22:50:10,772 245 | int nBytes = readIntFromFile(fin); 2023-09-13T22:50:10,773 | ^~~~~~ 2023-09-13T22:50:10,775 src/straw.cpp:258:13: warning: unused variable ‘sizeinbytes’ [-Wunused-variable] 2023-09-13T22:50:10,776 258 | int sizeinbytes = readIntFromFile(fin); 2023-09-13T22:50:10,777 | ^~~~~~~~~~~ 2023-09-13T22:50:10,779 src/straw.cpp:298:17: warning: unused variable ‘chrIdx’ [-Wunused-variable] 2023-09-13T22:50:10,780 298 | int chrIdx = readIntFromFile(fin); 2023-09-13T22:50:10,780 | ^~~~~~ 2023-09-13T22:50:10,781 src/straw.cpp:277:13: warning: unused variable ‘binSize’ [-Wunused-variable] 2023-09-13T22:50:10,782 277 | int binSize = readIntFromFile(fin); 2023-09-13T22:50:10,783 | ^~~~~~~ 2023-09-13T22:50:10,783 src/straw.cpp:333:17: warning: unused variable ‘chrIdx’ [-Wunused-variable] 2023-09-13T22:50:10,784 333 | int chrIdx = readIntFromFile(fin); 2023-09-13T22:50:10,784 | ^~~~~~ 2023-09-13T22:50:10,785 src/straw.cpp:312:13: warning: unused variable ‘binSize’ [-Wunused-variable] 2023-09-13T22:50:10,785 312 | int binSize = readIntFromFile(fin); 2023-09-13T22:50:10,786 | ^~~~~~~ 2023-09-13T22:50:10,831 src/straw.cpp: In function ‘std::map readMatrixHttp(CURL*, long int, std::string, int, int&, int&)’: 2023-09-13T22:50:10,832 src/straw.cpp:484:9: warning: unused variable ‘c1’ [-Wunused-variable] 2023-09-13T22:50:10,833 484 | int c1 = readIntFromFile(bufin); 2023-09-13T22:50:10,834 | ^~ 2023-09-13T22:50:10,834 src/straw.cpp:485:9: warning: unused variable ‘c2’ [-Wunused-variable] 2023-09-13T22:50:10,835 485 | int c2 = readIntFromFile(bufin); 2023-09-13T22:50:10,836 | ^~ 2023-09-13T22:50:10,836 src/straw.cpp: In function ‘std::map readMatrix(std::istream&, long int, std::string, int, int&, int&)’: 2023-09-13T22:50:10,837 src/straw.cpp:511:9: warning: unused variable ‘c1’ [-Wunused-variable] 2023-09-13T22:50:10,838 511 | int c1 = readIntFromFile(fin); 2023-09-13T22:50:10,839 | ^~ 2023-09-13T22:50:10,839 src/straw.cpp:512:9: warning: unused variable ‘c2’ [-Wunused-variable] 2023-09-13T22:50:10,840 512 | int c2 = readIntFromFile(fin); 2023-09-13T22:50:10,841 | ^~ 2023-09-13T22:50:35,629 src/straw.cpp: In function ‘std::vector straw(std::string, std::string, std::string, std::string, std::string, int)’: 2023-09-13T22:50:35,629 src/straw.cpp:993:34: warning: ‘curl’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-13T22:50:35,630 993 | blockMap = readMatrixHttp(curl, myFilePos, unit, binsize, blockBinCount, blockColumnCount); 2023-09-13T22:50:35,630 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-13T22:50:35,631 src/straw.cpp:848:11: note: ‘curl’ was declared here 2023-09-13T22:50:35,632 848 | CURL *curl; 2023-09-13T22:50:35,632 | ^~~~ 2023-09-13T22:50:36,669 src/straw.cpp: In function ‘int getSize(std::string, std::string, std::string, std::string, std::string, int)’: 2023-09-13T22:50:36,669 src/straw.cpp:1142:26: warning: ‘curl’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-13T22:50:36,670 1142 | buffer2 = getData(curl, master, bytes_to_read); 2023-09-13T22:50:36,671 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-13T22:50:36,671 src/straw.cpp:1059:11: note: ‘curl’ was declared here 2023-09-13T22:50:36,672 1059 | CURL *curl; 2023-09-13T22:50:36,673 | ^~~~ 2023-09-13T22:50:42,899 creating build/lib.linux-armv7l-cpython-311 2023-09-13T22:50:42,900 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/src/straw.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/strawC.cpython-311-arm-linux-gnueabihf.so -lcurl -lz 2023-09-13T22:50:43,415 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-13T22:50:43,416 !! 2023-09-13T22:50:43,417 ******************************************************************************** 2023-09-13T22:50:43,418 Please avoid running ``setup.py`` directly. 2023-09-13T22:50:43,419 Instead, use pypa/build, pypa/installer or other 2023-09-13T22:50:43,420 standards-based tools. 2023-09-13T22:50:43,425 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-13T22:50:43,427 ******************************************************************************** 2023-09-13T22:50:43,433 !! 2023-09-13T22:50:43,435 self.initialize_options() 2023-09-13T22:50:43,482 installing to build/bdist.linux-armv7l/wheel 2023-09-13T22:50:43,483 running install 2023-09-13T22:50:43,507 running install_lib 2023-09-13T22:50:43,542 creating build/bdist.linux-armv7l 2023-09-13T22:50:43,543 creating build/bdist.linux-armv7l/wheel 2023-09-13T22:50:43,544 copying build/lib.linux-armv7l-cpython-311/strawC.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2023-09-13T22:50:43,612 running install_egg_info 2023-09-13T22:50:43,677 running egg_info 2023-09-13T22:50:43,702 writing strawC.egg-info/PKG-INFO 2023-09-13T22:50:43,704 writing dependency_links to strawC.egg-info/dependency_links.txt 2023-09-13T22:50:43,706 writing requirements to strawC.egg-info/requires.txt 2023-09-13T22:50:43,708 writing top-level names to strawC.egg-info/top_level.txt 2023-09-13T22:50:43,735 reading manifest file 'strawC.egg-info/SOURCES.txt' 2023-09-13T22:50:43,737 reading manifest template 'MANIFEST.in' 2023-09-13T22:50:43,739 adding license file 'LICENSE' 2023-09-13T22:50:43,741 writing manifest file 'strawC.egg-info/SOURCES.txt' 2023-09-13T22:50:43,742 Copying strawC.egg-info to build/bdist.linux-armv7l/wheel/strawC-0.0.2.1-py3.11.egg-info 2023-09-13T22:50:43,753 running install_scripts 2023-09-13T22:50:43,806 creating build/bdist.linux-armv7l/wheel/strawC-0.0.2.1.dist-info/WHEEL 2023-09-13T22:50:43,809 creating '/tmp/pip-wheel-o9apk5g3/strawC-0.0.2.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-13T22:50:44,366 adding 'strawC.cpython-311-arm-linux-gnueabihf.so' 2023-09-13T22:50:44,397 adding 'strawC-0.0.2.1.dist-info/LICENSE' 2023-09-13T22:50:44,398 adding 'strawC-0.0.2.1.dist-info/METADATA' 2023-09-13T22:50:44,399 adding 'strawC-0.0.2.1.dist-info/WHEEL' 2023-09-13T22:50:44,401 adding 'strawC-0.0.2.1.dist-info/top_level.txt' 2023-09-13T22:50:44,402 adding 'strawC-0.0.2.1.dist-info/RECORD' 2023-09-13T22:50:44,417 removing build/bdist.linux-armv7l/wheel 2023-09-13T22:50:44,563 Building wheel for strawc (setup.py): finished with status 'done' 2023-09-13T22:50:44,580 Created wheel for strawc: filename=strawC-0.0.2.1-cp311-cp311-linux_armv7l.whl size=1171290 sha256=76b70464f58ac3c42f2ec0907850ac187d8d2b6b88e56c89ba70555e1553ec7d 2023-09-13T22:50:44,582 Stored in directory: /tmp/pip-ephem-wheel-cache-7r76vyrz/wheels/c5/75/f6/196817e17d7975788b14930c8f8332def08a40342cee40b3a3 2023-09-13T22:50:44,591 Successfully built strawc 2023-09-13T22:50:44,635 Removed build tracker: '/tmp/pip-build-tracker-17e2f5gq'