2025-09-09T10:00:30,962 Created temporary directory: /tmp/pip-build-tracker-bm6_w8aw 2025-09-09T10:00:30,962 Initialized build tracking at /tmp/pip-build-tracker-bm6_w8aw 2025-09-09T10:00:30,962 Created build tracker: /tmp/pip-build-tracker-bm6_w8aw 2025-09-09T10:00:30,962 Entered build tracker: /tmp/pip-build-tracker-bm6_w8aw 2025-09-09T10:00:30,963 Created temporary directory: /tmp/pip-wheel-bcpi1t63 2025-09-09T10:00:30,966 Created temporary directory: /tmp/pip-ephem-wheel-cache-tdc5m_t5 2025-09-09T10:00:31,024 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T10:00:31,026 2 location(s) to search for versions of py-cortex-api: 2025-09-09T10:00:31,026 * https://pypi.org/simple/py-cortex-api/ 2025-09-09T10:00:31,026 * https://www.piwheels.org/simple/py-cortex-api/ 2025-09-09T10:00:31,026 Fetching project page and analyzing links: https://pypi.org/simple/py-cortex-api/ 2025-09-09T10:00:31,027 Getting page https://pypi.org/simple/py-cortex-api/ 2025-09-09T10:00:31,028 Found index url https://pypi.org/simple/ 2025-09-09T10:00:31,098 Fetched page https://pypi.org/simple/py-cortex-api/ as application/vnd.pypi.simple.v1+json 2025-09-09T10:00:31,099 Found link https://files.pythonhosted.org/packages/10/9a/15dd2926e462ede2596498e7fdaff6177f47a0a3e0e7d55809a295c7c2e0/py-cortex-api-1.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 1.0 2025-09-09T10:00:31,100 Found link https://files.pythonhosted.org/packages/4f/9b/5df6d4526ebcc12ee6d6a932150243ea6d74e7749b813b898504c51e8fd4/py-cortex-api-2.0.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.0.0 2025-09-09T10:00:31,100 Found link https://files.pythonhosted.org/packages/0f/73/39f8d4af8a1819908811755effc9ef16e8a650360e4d9a97aa9f57a24010/py-cortex-api-2.1.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.1.0 2025-09-09T10:00:31,100 Found link https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.2.0 2025-09-09T10:00:31,100 Found link https://files.pythonhosted.org/packages/85/e6/39478462ebcc183ec04acf85dfda6ef3a6cc3b8dd783b50432014170844f/py-cortex-api-2.2.1.tar.gz (from https://pypi.org/simple/py-cortex-api/), version: 2.2.1 2025-09-09T10:00:31,101 Fetching project page and analyzing links: https://www.piwheels.org/simple/py-cortex-api/ 2025-09-09T10:00:31,101 Getting page https://www.piwheels.org/simple/py-cortex-api/ 2025-09-09T10:00:31,102 Found index url https://www.piwheels.org/simple/ 2025-09-09T10:00:31,189 Fetched page https://www.piwheels.org/simple/py-cortex-api/ as text/html 2025-09-09T10:00:31,190 Skipping link: not a file: https://www.piwheels.org/simple/py-cortex-api/ 2025-09-09T10:00:31,190 Skipping link: not a file: https://pypi.org/simple/py-cortex-api/ 2025-09-09T10:00:31,217 Given no hashes to check 1 links for project 'py-cortex-api': discarding no candidates 2025-09-09T10:00:31,218 Collecting py-cortex-api==2.2.0 2025-09-09T10:00:31,219 Created temporary directory: /tmp/pip-unpack-phrquzwr 2025-09-09T10:00:31,356 Downloading py-cortex-api-2.2.0.tar.gz (16 kB) 2025-09-09T10:00:31,388 Added py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-bm6_w8aw' 2025-09-09T10:00:31,390 Running setup.py (path:/tmp/pip-wheel-bcpi1t63/py-cortex-api_d4e3c464cd1f41dca65664a0404566e8/setup.py) egg_info for package py-cortex-api 2025-09-09T10:00:31,391 Created temporary directory: /tmp/pip-pip-egg-info-9ym8pylt 2025-09-09T10:00:31,391 Preparing metadata (setup.py): started 2025-09-09T10:00:31,392 Running command python setup.py egg_info 2025-09-09T10:00:32,184 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-09T10:00:32,185 warnings.warn(msg) 2025-09-09T10:00:32,675 running egg_info 2025-09-09T10:00:32,752 creating /tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info 2025-09-09T10:00:32,752 writing /tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/PKG-INFO 2025-09-09T10:00:32,753 writing dependency_links to /tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/dependency_links.txt 2025-09-09T10:00:32,754 writing requirements to /tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/requires.txt 2025-09-09T10:00:32,754 writing top-level names to /tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/top_level.txt 2025-09-09T10:00:32,755 writing manifest file '/tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/SOURCES.txt' 2025-09-09T10:00:32,908 reading manifest file '/tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/SOURCES.txt' 2025-09-09T10:00:32,908 reading manifest template 'MANIFEST.in' 2025-09-09T10:00:32,909 warning: no files found matching 'cortex/ext/cortex/bin/cortex_var_31_c1' 2025-09-09T10:00:32,910 warning: no files found matching 'cortex/ext/cortex/bin/cortex_var_31_c2' 2025-09-09T10:00:32,910 warning: no previously-included files matching '*~' found anywhere in distribution 2025-09-09T10:00:32,911 warning: no previously-included files matching '*.swp' found anywhere in distribution 2025-09-09T10:00:32,913 writing manifest file '/tmp/pip-pip-egg-info-9ym8pylt/py_cortex_api.egg-info/SOURCES.txt' 2025-09-09T10:00:33,027 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T10:00:33,032 Source in /tmp/pip-wheel-bcpi1t63/py-cortex-api_d4e3c464cd1f41dca65664a0404566e8 has version 2.2.0, which satisfies requirement py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz 2025-09-09T10:00:33,032 Removed py-cortex-api==2.2.0 from https://files.pythonhosted.org/packages/8a/0b/c81cf0f0feeda39cc42e7551864635ac911a3312406d3d68e836b1058a5e/py-cortex-api-2.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-bm6_w8aw' 2025-09-09T10:00:33,035 Created temporary directory: /tmp/pip-unpack-eidf_xys 2025-09-09T10:00:33,035 Created temporary directory: /tmp/pip-unpack-esiqg16k 2025-09-09T10:00:33,036 Building wheels for collected packages: py-cortex-api 2025-09-09T10:00:33,037 Created temporary directory: /tmp/pip-wheel-ag9t4vto 2025-09-09T10:00:33,037 DEPRECATION: Building 'py-cortex-api' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'py-cortex-api'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-09T10:00:33,038 Building wheel for py-cortex-api (setup.py): started 2025-09-09T10:00:33,039 Destination directory: /tmp/pip-wheel-ag9t4vto 2025-09-09T10:00:33,039 Running command python setup.py bdist_wheel 2025-09-09T10:00:33,740 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-09T10:00:33,740 warnings.warn(msg) 2025-09-09T10:00:34,130 running bdist_wheel 2025-09-09T10:00:34,502 running build 2025-09-09T10:00:34,502 running build_py 2025-09-09T10:00:34,503 START: Building backend dependencies 2025-09-09T10:04:29,644 Cloning into 'minimap2'... 2025-09-09T10:04:29,644 fatal: transport 'https' not allowed 2025-09-09T10:04:29,645 ./cortex/ext/install_dependencies.sh: line 15: cd: minimap2_dir: No such file or directory 2025-09-09T10:04:29,645 mv: cannot stat 'minimap2_dir/minimap2': No such file or directory 2025-09-09T10:04:29,645 --2025-09-09 10:00:34-- https://github.com/vcftools/vcftools/releases/download/v0.1.15/vcftools-0.1.15.tar.gz 2025-09-09T10:04:29,645 Resolving github.com (github.com)... 64:ff9b::141a:9cd7, 20.26.156.215 2025-09-09T10:04:29,645 Connecting to github.com (github.com)|64:ff9b::141a:9cd7|:443... connected. 2025-09-09T10:04:29,646 HTTP request sent, awaiting response... 302 Found 2025-09-09T10:04:29,646 Location: https://release-assets.githubusercontent.com/github-production-release-asset/38052058/2e0f4764-22d4-11e7-8512-08df6111866d?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-09-09T10%3A54%3A33Z&rscd=attachment%3B+filename%3Dvcftools-0.1.15.tar.gz&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-09-09T09%3A54%3A01Z&ske=2025-09-09T10%3A54%3A33Z&sks=b&skv=2018-11-09&sig=WoPRPbLRb4IIn7ihnPgf8zOy1LwyYg7KWeLoRktjF4M%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc1NzQxMjMzNCwibmJmIjoxNzU3NDEyMDM0LCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.6Whgmi9Sr6hl4N-lzqldkD9x22Wr0lXeiD1MK_HhzHk&response-content-disposition=attachment%3B%20filename%3Dvcftools-0.1.15.tar.gz&response-content-type=application%2Foctet-stream [following] 2025-09-09T10:04:29,646 --2025-09-09 10:00:34-- https://release-assets.githubusercontent.com/github-production-release-asset/38052058/2e0f4764-22d4-11e7-8512-08df6111866d?sp=r&sv=2018-11-09&sr=b&spr=https&se=2025-09-09T10%3A54%3A33Z&rscd=attachment%3B+filename%3Dvcftools-0.1.15.tar.gz&rsct=application%2Foctet-stream&skoid=96c2d410-5711-43a1-aedd-ab1947aa7ab0&sktid=398a6654-997b-47e9-b12b-9515b896b4de&skt=2025-09-09T09%3A54%3A01Z&ske=2025-09-09T10%3A54%3A33Z&sks=b&skv=2018-11-09&sig=WoPRPbLRb4IIn7ihnPgf8zOy1LwyYg7KWeLoRktjF4M%3D&jwt=eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmVsZWFzZS1hc3NldHMuZ2l0aHVidXNlcmNvbnRlbnQuY29tIiwia2V5Ijoia2V5MSIsImV4cCI6MTc1NzQxMjMzNCwibmJmIjoxNzU3NDEyMDM0LCJwYXRoIjoicmVsZWFzZWFzc2V0cHJvZHVjdGlvbi5ibG9iLmNvcmUud2luZG93cy5uZXQifQ.6Whgmi9Sr6hl4N-lzqldkD9x22Wr0lXeiD1MK_HhzHk&response-content-disposition=attachment%3B%20filename%3Dvcftools-0.1.15.tar.gz&response-content-type=application%2Foctet-stream 2025-09-09T10:04:29,646 Resolving release-assets.githubusercontent.com (release-assets.githubusercontent.com)... 64:ff9b::b9c7:6d85, 64:ff9b::b9c7:6c85, 64:ff9b::b9c7:6f85, ... 2025-09-09T10:04:29,646 Connecting to release-assets.githubusercontent.com (release-assets.githubusercontent.com)|64:ff9b::b9c7:6d85|:443... connected. 2025-09-09T10:04:29,647 HTTP request sent, awaiting response... 200 OK 2025-09-09T10:04:29,647 Length: 481398 (470K) [application/octet-stream] 2025-09-09T10:04:29,647 Saving to: ‘vcftools-0.1.15.tar.gz’ 2025-09-09T10:04:29,647 0K .......... .......... .......... .......... .......... 10% 3.47M 0s 2025-09-09T10:04:29,648 50K .......... .......... .......... .......... .......... 21% 4.18M 0s 2025-09-09T10:04:29,648 100K .......... .......... .......... .......... .......... 31% 11.5M 0s 2025-09-09T10:04:29,648 150K .......... .......... .......... .......... .......... 42% 11.2M 0s 2025-09-09T10:04:29,648 200K .......... .......... .......... .......... .......... 53% 10.6M 0s 2025-09-09T10:04:29,648 250K .......... .......... .......... .......... .......... 63% 10.0M 0s 2025-09-09T10:04:29,649 300K .......... .......... .......... .......... .......... 74% 11.1M 0s 2025-09-09T10:04:29,649 350K .......... .......... .......... .......... .......... 85% 11.2M 0s 2025-09-09T10:04:29,649 400K .......... .......... .......... .......... .......... 95% 11.2M 0s 2025-09-09T10:04:29,649 450K .......... .......... 100% 9.63M=0.06s 2025-09-09T10:04:29,649 2025-09-09 10:00:35 (7.78 MB/s) - ‘vcftools-0.1.15.tar.gz’ saved [481398/481398] 2025-09-09T10:04:29,650 In file included from /usr/include/c++/14/vector:72, 2025-09-09T10:04:29,650 from entry.h:12, 2025-09-09T10:04:29,650 from bcf_entry.h:10, 2025-09-09T10:04:29,651 from bcf_entry_setters.cpp:9: 2025-09-09T10:04:29,651 /usr/include/c++/14/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: 2025-09-09T10:04:29,651 /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2025-09-09T10:04:29,651 700 | vector<_Tp, _Alloc>:: 2025-09-09T10:04:29,651 | ^~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,652 In file included from /usr/include/c++/14/vector:66: 2025-09-09T10:04:29,652 In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2025-09-09T10:04:29,652 inlined from ‘void bcf_entry::set_indv_GQUALITY(unsigned int, const float&)’ at bcf_entry_setters.cpp:333:18: 2025-09-09T10:04:29,652 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T10:04:29,652 1037 | _M_fill_insert(end(), __new_size - size(), __x); 2025-09-09T10:04:29,653 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,653 In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2025-09-09T10:04:29,653 inlined from ‘void bcf_entry::set_indv_GQUALITY(unsigned int, const std::vector&)’ at bcf_entry_setters.cpp:316:18: 2025-09-09T10:04:29,653 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T10:04:29,654 1037 | _M_fill_insert(end(), __new_size - size(), __x); 2025-09-09T10:04:29,654 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,654 variant_file_filters.cpp: In member function ‘void variant_file::filter_individuals_randomly(int)’: 2025-09-09T10:04:29,654 variant_file_filters.cpp:129:23: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 2025-09-09T10:04:29,655 129 | random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order 2025-09-09T10:04:29,655 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,655 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T10:04:29,655 from variant_file.h:15, 2025-09-09T10:04:29,655 from variant_file_filters.cpp:7: 2025-09-09T10:04:29,655 /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 2025-09-09T10:04:29,656 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) 2025-09-09T10:04:29,656 | ^~~~~~~~~~~~~~ 2025-09-09T10:04:29,656 In file included from /usr/include/c++/14/bits/stl_algobase.h:64, 2025-09-09T10:04:29,656 from /usr/include/c++/14/algorithm:60, 2025-09-09T10:04:29,656 from variant_file.h:15, 2025-09-09T10:04:29,656 from variant_file_output.cpp:8: 2025-09-09T10:04:29,656 /usr/include/c++/14/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]’: 2025-09-09T10:04:29,657 variant_file_output.cpp:4424:39: required from here 2025-09-09T10:04:29,657 4424 | p_emission[ui].push_back(make_pair(p_emission_given_auto, p_emission_given_nonauto)); 2025-09-09T10:04:29,657 | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,657 /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 2025-09-09T10:04:29,657 1132 | make_pair(_T1&& __x, _T2&& __y) 2025-09-09T10:04:29,657 | ^~~~~~~~~ 2025-09-09T10:04:29,657 In file included from /usr/include/c++/14/set:62, 2025-09-09T10:04:29,658 from variant_file.h:26: 2025-09-09T10:04:29,658 /usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]’: 2025-09-09T10:04:29,658 /usr/include/c++/14/bits/stl_tree.h:2456:7: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ changed in GCC 7.1 2025-09-09T10:04:29,658 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T10:04:29,658 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,658 In file included from /usr/include/c++/14/map:63, 2025-09-09T10:04:29,658 from variant_file.h:28: 2025-09-09T10:04:29,659 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair; _Compare = std::less; _Alloc = std::allocator > >]’, 2025-09-09T10:04:29,659 inlined from ‘void variant_file::output_TsTv_by_quality(const parameters&)’ at variant_file_output.cpp:3277:21: 2025-09-09T10:04:29,659 /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ changed in GCC 7.1 2025-09-09T10:04:29,659 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T10:04:29,659 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,659 514 | std::tuple(__k), 2025-09-09T10:04:29,659 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,660 515 | std::tuple<>()); 2025-09-09T10:04:29,660 | ~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,660 In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = std::pair; _Compare = std::less; _Alloc = std::allocator > >]’, 2025-09-09T10:04:29,660 inlined from ‘void variant_file::output_TsTv_by_quality(const parameters&)’ at variant_file_output.cpp:3279:21: 2025-09-09T10:04:29,660 /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator’ changed in GCC 7.1 2025-09-09T10:04:29,660 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T10:04:29,661 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,661 514 | std::tuple(__k), 2025-09-09T10:04:29,661 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,661 515 | std::tuple<>()); 2025-09-09T10:04:29,661 | ~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,661 In file included from /usr/include/c++/14/vector:72, 2025-09-09T10:04:29,661 from /usr/include/c++/14/functional:64, 2025-09-09T10:04:29,661 from variant_file.h:24: 2025-09-09T10:04:29,662 /usr/include/c++/14/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’: 2025-09-09T10:04:29,662 /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 2025-09-09T10:04:29,662 700 | vector<_Tp, _Alloc>:: 2025-09-09T10:04:29,662 | ^~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,662 In file included from /usr/include/c++/14/vector:66: 2025-09-09T10:04:29,662 In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]’, 2025-09-09T10:04:29,662 inlined from ‘void variant_file::output_Tajima_D(const parameters&)’ at variant_file_output.cpp:4015:22: 2025-09-09T10:04:29,663 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 2025-09-09T10:04:29,663 1037 | _M_fill_insert(end(), __new_size - size(), __x); 2025-09-09T10:04:29,663 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,663 In file included from /usr/include/c++/14/vector:72, 2025-09-09T10:04:29,663 from entry.h:12, 2025-09-09T10:04:29,663 from vcf_entry.h:12, 2025-09-09T10:04:29,663 from vcf_entry_setters.cpp:9: 2025-09-09T10:04:29,663 /usr/include/c++/14/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: 2025-09-09T10:04:29,664 /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2025-09-09T10:04:29,664 700 | vector<_Tp, _Alloc>:: 2025-09-09T10:04:29,664 | ^~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,664 In file included from /usr/include/c++/14/vector:66: 2025-09-09T10:04:29,664 In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, 2025-09-09T10:04:29,664 inlined from ‘void vcf_entry::set_indv_GQUALITY(unsigned int, double)’ at vcf_entry_setters.cpp:181:18: 2025-09-09T10:04:29,664 /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2025-09-09T10:04:29,665 1037 | _M_fill_insert(end(), __new_size - size(), __x); 2025-09-09T10:04:29,665 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T10:04:29,665 Cloning into 'cortex'... 2025-09-09T10:04:29,665 fatal: transport 'https' not allowed 2025-09-09T10:04:29,665 ERROR: backend compilation failed 128 2025-09-09T10:04:29,764 ERROR: python setup.py bdist_wheel exited with 255 2025-09-09T10:04:29,776 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T10:04:29,776 exec(compile('"'"''"'"''"'"' 2025-09-09T10:04:29,776 # This is -- a caller that pip uses to run setup.py 2025-09-09T10:04:29,776 # 2025-09-09T10:04:29,776 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T10:04:29,776 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T10:04:29,776 # - It provides a clear error message when setuptools is not installed. 2025-09-09T10:04:29,776 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T10:04:29,776 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T10:04:29,776 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T10:04:29,776 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T10:04:29,776 import os, sys, tokenize, traceback 2025-09-09T10:04:29,776 2025-09-09T10:04:29,776 try: 2025-09-09T10:04:29,776 import setuptools 2025-09-09T10:04:29,776 except ImportError: 2025-09-09T10:04:29,776 print( 2025-09-09T10:04:29,776 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T10:04:29,776 "the build environment with exception:", 2025-09-09T10:04:29,776 file=sys.stderr, 2025-09-09T10:04:29,776 ) 2025-09-09T10:04:29,776 traceback.print_exc() 2025-09-09T10:04:29,776 sys.exit(1) 2025-09-09T10:04:29,776 2025-09-09T10:04:29,776 __file__ = %r 2025-09-09T10:04:29,776 sys.argv[0] = __file__ 2025-09-09T10:04:29,776 2025-09-09T10:04:29,776 if os.path.exists(__file__): 2025-09-09T10:04:29,776 filename = __file__ 2025-09-09T10:04:29,776 with tokenize.open(__file__) as f: 2025-09-09T10:04:29,776 setup_py_code = f.read() 2025-09-09T10:04:29,776 else: 2025-09-09T10:04:29,776 filename = "" 2025-09-09T10:04:29,776 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T10:04:29,776 2025-09-09T10:04:29,776 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T10:04:29,776 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-bcpi1t63/py-cortex-api_d4e3c464cd1f41dca65664a0404566e8/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ag9t4vto[/] 2025-09-09T10:04:29,777 [bold magenta]cwd[/]: /tmp/pip-wheel-bcpi1t63/py-cortex-api_d4e3c464cd1f41dca65664a0404566e8/ 2025-09-09T10:04:29,777 Building wheel for py-cortex-api (setup.py): finished with status 'error' 2025-09-09T10:04:29,778 ERROR: Failed building wheel for py-cortex-api 2025-09-09T10:04:29,779 Running setup.py clean for py-cortex-api 2025-09-09T10:04:29,780 Running command python setup.py clean 2025-09-09T10:04:30,621 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-09T10:04:30,621 warnings.warn(msg) 2025-09-09T10:04:31,099 running clean 2025-09-09T10:04:31,249 'build/lib' does not exist -- can't clean it 2025-09-09T10:04:31,249 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-09T10:04:31,249 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T10:04:31,362 Failed to build py-cortex-api 2025-09-09T10:04:31,363 ERROR: Failed to build one or more wheels 2025-09-09T10:04:31,364 Exception information: 2025-09-09T10:04:31,364 Traceback (most recent call last): 2025-09-09T10:04:31,364 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T10:04:31,364 status = _inner_run() 2025-09-09T10:04:31,364 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T10:04:31,364 return self.run(options, args) 2025-09-09T10:04:31,364 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T10:04:31,364 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T10:04:31,364 return func(self, options, args) 2025-09-09T10:04:31,364 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T10:04:31,364 raise CommandError("Failed to build one or more wheels") 2025-09-09T10:04:31,364 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T10:04:31,369 Removed build tracker: '/tmp/pip-build-tracker-bm6_w8aw'