2026-02-09T06:02:27,785 Created temporary directory: /tmp/pip-ephem-wheel-cache-ea9whb9n 2026-02-09T06:02:27,787 Created temporary directory: /tmp/pip-build-tracker-i1s36jtb 2026-02-09T06:02:27,788 Initialized build tracking at /tmp/pip-build-tracker-i1s36jtb 2026-02-09T06:02:27,789 Created build tracker: /tmp/pip-build-tracker-i1s36jtb 2026-02-09T06:02:27,790 Entered build tracker: /tmp/pip-build-tracker-i1s36jtb 2026-02-09T06:02:27,791 Created temporary directory: /tmp/pip-wheel-pohs_afi 2026-02-09T06:02:27,795 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-09T06:02:27,816 Created temporary directory: /tmp/pip-ephem-wheel-cache-t9a5him5 2026-02-09T06:02:27,887 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-09T06:02:27,892 2 location(s) to search for versions of pyinfernal: 2026-02-09T06:02:27,892 * https://pypi.org/simple/pyinfernal/ 2026-02-09T06:02:27,892 * https://www.piwheels.org/simple/pyinfernal/ 2026-02-09T06:02:27,893 Fetching project page and analyzing links: https://pypi.org/simple/pyinfernal/ 2026-02-09T06:02:27,894 Getting page https://pypi.org/simple/pyinfernal/ 2026-02-09T06:02:27,896 Found index url https://pypi.org/simple 2026-02-09T06:02:28,234 Fetched page https://pypi.org/simple/pyinfernal/ as application/vnd.pypi.simple.v1+json 2026-02-09T06:02:28,238 Found link https://files.pythonhosted.org/packages/31/a0/6bf7427ebc462adbc514bb08156bec2aaaafe0fbf0451963395ee90396f8/pyinfernal-0.1.0.dev1.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0.dev1 2026-02-09T06:02:28,239 Found link https://files.pythonhosted.org/packages/0e/3d/a84bbd14073b5c86e0aa953db9d52b695c7174d18bc999d97936bb6185ef/pyinfernal-0.1.0a2.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0a2 2026-02-09T06:02:28,240 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/bf/5f/584cc0ab37ac0b5a84b6d23eb33a4231d689094942cb20f6374ddb7cb201/pyinfernal-0.1.0-cp310-cp310-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,241 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/8c/36/9fd1b69e75631ae2d458c7ab785274b57d85962d069c845188fffb125a2b/pyinfernal-0.1.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,242 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/71/d9/f7c239ee6ace98b14231128c170ac27dc23b10aa0e5610b7c12e402ec848/pyinfernal-0.1.0-cp312-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,243 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/5f/a6/928048d02cd4454ef342a39abf87aae3c8bd85766cae2645a2062538ac63/pyinfernal-0.1.0-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,244 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/c3/e6/ea37886a2a2f02d0749170ea19bc381997b37fdd7b57839719aaeb8e7458/pyinfernal-0.1.0-cp38-cp38-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,245 Skipping link: No binaries permitted for pyinfernal: https://files.pythonhosted.org/packages/51/ae/26ef3e48dfdcc1e25efbbc140e25006c0ae5a9a6772c7132d895e1a400dc/pyinfernal-0.1.0-cp39-cp39-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,246 Found link https://files.pythonhosted.org/packages/8f/76/7f5d68284fdf09776b12ce0a892f55e1204ae576b72f46bba17dd0a7adc1/pyinfernal-0.1.0.tar.gz (from https://pypi.org/simple/pyinfernal/) (requires-python:>=3.7), version: 0.1.0 2026-02-09T06:02:28,248 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyinfernal/ 2026-02-09T06:02:28,249 Getting page https://www.piwheels.org/simple/pyinfernal/ 2026-02-09T06:02:28,250 Found index url https://www.piwheels.org/simple 2026-02-09T06:02:28,467 Fetched page https://www.piwheels.org/simple/pyinfernal/ as text/html 2026-02-09T06:02:28,470 Skipping link: No binaries permitted for pyinfernal: https://www.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp313-cp313-linux_armv6l.whl#sha256=e8f82d698afea0aac958c17ff07114022aa9ae0af8047d941c03f5532198d7bf (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,471 Skipping link: No binaries permitted for pyinfernal: https://www.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp313-cp313-linux_armv7l.whl#sha256=e8f82d698afea0aac958c17ff07114022aa9ae0af8047d941c03f5532198d7bf (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,472 Skipping link: No binaries permitted for pyinfernal: https://www.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp39-cp39-linux_armv6l.whl#sha256=1f14857dce1388dfcb08daec8f93171772e4bf60fb08d64547915376a62c3861 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,472 Skipping link: No binaries permitted for pyinfernal: https://www.piwheels.org/simple/pyinfernal/pyinfernal-0.1.0.dev1-cp39-cp39-linux_armv7l.whl#sha256=1f14857dce1388dfcb08daec8f93171772e4bf60fb08d64547915376a62c3861 (from https://www.piwheels.org/simple/pyinfernal/) (requires-python:>=3.7) 2026-02-09T06:02:28,473 Skipping link: not a file: https://www.piwheels.org/simple/pyinfernal/ 2026-02-09T06:02:28,474 Skipping link: not a file: https://pypi.org/simple/pyinfernal/ 2026-02-09T06:02:28,499 Given no hashes to check 1 links for project 'pyinfernal': discarding no candidates 2026-02-09T06:02:28,523 Collecting pyinfernal==0.1.0a2 2026-02-09T06:02:28,526 Created temporary directory: /tmp/pip-unpack-hs37db3i 2026-02-09T06:02:28,993 Downloading pyinfernal-0.1.0a2.tar.gz (4.6 MB) 2026-02-09T06:02:31,913 Added pyinfernal==0.1.0a2 from https://files.pythonhosted.org/packages/0e/3d/a84bbd14073b5c86e0aa953db9d52b695c7174d18bc999d97936bb6185ef/pyinfernal-0.1.0a2.tar.gz to build tracker '/tmp/pip-build-tracker-i1s36jtb' 2026-02-09T06:02:31,923 Created temporary directory: /tmp/pip-build-env-duavp0gm 2026-02-09T06:02:31,928 Installing build dependencies: started 2026-02-09T06:02:31,930 Running command pip subprocess to install build dependencies 2026-02-09T06:02:33,741 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-02-09T06:02:34,711 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-09T06:02:34,788 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-09T06:02:35,542 Collecting scikit-build-core 2026-02-09T06:02:35,590 Using cached https://www.piwheels.org/simple/scikit-build-core/scikit_build_core-0.11.6-py3-none-any.whl (185 kB) 2026-02-09T06:02:38,859 Collecting cython>=3.0 2026-02-09T06:02:40,557 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-09T06:02:41,922 Collecting pyhmmer~=0.12.0a5 2026-02-09T06:02:42,238 Downloading pyhmmer-0.12.0.tar.gz (4.4 MB) 2026-02-09T06:02:43,037 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 5.6 MB/s eta 0:00:00 2026-02-09T06:02:46,064 Installing build dependencies: started 2026-02-09T06:02:46,065 Running command pip subprocess to install build dependencies 2026-02-09T06:02:49,118 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-02-09T06:02:49,219 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-02-09T06:02:50,040 Collecting scikit-build-core>=0.11 2026-02-09T06:02:50,068 Using cached https://www.piwheels.org/simple/scikit-build-core/scikit_build_core-0.11.6-py3-none-any.whl (185 kB) 2026-02-09T06:02:53,176 Collecting cython>=3.0 2026-02-09T06:02:54,266 Using cached https://www.piwheels.org/simple/cython/cython-3.2.4-cp311-cp311-linux_armv7l.whl (11.1 MB) 2026-02-09T06:02:55,179 Collecting packaging>=23.2 2026-02-09T06:02:55,185 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-09T06:02:55,323 Collecting pathspec>=0.10.1 2026-02-09T06:02:55,329 Using cached pathspec-1.0.4-py3-none-any.whl (55 kB) 2026-02-09T06:02:59,759 Installing collected packages: pathspec, packaging, cython, scikit-build-core 2026-02-09T06:03:06,468 Successfully installed cython-3.2.4 packaging-26.0 pathspec-1.0.4 scikit-build-core-0.11.6 2026-02-09T06:03:07,075 Installing build dependencies: finished with status 'done' 2026-02-09T06:03:07,083 Getting requirements to build wheel: started 2026-02-09T06:03:07,084 Running command Getting requirements to build wheel 2026-02-09T06:03:08,033 Getting requirements to build wheel: finished with status 'done' 2026-02-09T06:03:08,040 Preparing metadata (pyproject.toml): started 2026-02-09T06:03:08,041 Running command Preparing metadata (pyproject.toml) 2026-02-09T06:03:09,156 *** scikit-build-core 0.11.6 using CMake 3.25.1 (metadata_wheel) 2026-02-09T06:03:09,338 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-09T06:03:10,125 Collecting packaging>=23.2 2026-02-09T06:03:10,133 Using cached packaging-26.0-py3-none-any.whl (74 kB) 2026-02-09T06:03:10,290 Collecting pathspec>=0.10.1 2026-02-09T06:03:10,311 Using cached pathspec-1.0.4-py3-none-any.whl (55 kB) 2026-02-09T06:03:11,823 Collecting psutil<8.0,>=5.0 2026-02-09T06:03:12,079 Using cached https://archive1.piwheels.org/simple/psutil/psutil-6.0.0-cp311-abi3-linux_armv7l.whl (285 kB) 2026-02-09T06:03:12,172 Building wheels for collected packages: pyhmmer 2026-02-09T06:03:12,180 Building wheel for pyhmmer (pyproject.toml): started 2026-02-09T06:03:12,181 Running command Building wheel for pyhmmer (pyproject.toml) 2026-02-09T06:03:13,315 *** scikit-build-core 0.11.6 using CMake 3.25.1 (wheel) 2026-02-09T06:03:13,350 *** Configuring CMake... 2026-02-09T06:03:13,486 loading initial cache file build/Release/CMakeInit.txt 2026-02-09T06:03:13,844 -- The C compiler identification is GNU 12.2.0 2026-02-09T06:03:13,990 -- Detecting C compiler ABI info 2026-02-09T06:03:14,516 -- Detecting C compiler ABI info - done 2026-02-09T06:03:14,578 -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc - skipped 2026-02-09T06:03:14,580 -- Detecting C compile features 2026-02-09T06:03:14,583 -- Detecting C compile features - done 2026-02-09T06:03:14,594 -- Try NEON C flag = [ ] 2026-02-09T06:03:14,595 -- Performing Test HAVE_NEON 2026-02-09T06:03:15,370 -- Performing Test HAVE_NEON - Failed 2026-02-09T06:03:15,372 -- Try NEON C flag = [-mfpu=neon] 2026-02-09T06:03:15,373 -- Performing Test HAVE_NEON 2026-02-09T06:03:16,572 -- Performing Test HAVE_NEON - Success 2026-02-09T06:03:16,578 -- Found NEON: -mfpu=neon 2026-02-09T06:03:16,581 -- Try SSE2 C flag = [ ] 2026-02-09T06:03:16,582 -- Performing Test HAVE_SSE2 2026-02-09T06:03:16,992 -- Performing Test HAVE_SSE2 - Failed 2026-02-09T06:03:16,993 -- Try SSE2 C flag = [-msse2] 2026-02-09T06:03:16,994 -- Performing Test HAVE_SSE2 2026-02-09T06:03:17,260 -- Performing Test HAVE_SSE2 - Failed 2026-02-09T06:03:17,261 -- Try SSE2 C flag = [-msse2 -msimd128] 2026-02-09T06:03:17,262 -- Performing Test HAVE_SSE2 2026-02-09T06:03:17,556 -- Performing Test HAVE_SSE2 - Failed 2026-02-09T06:03:17,558 -- Try SSE2 C flag = [-march=core2] 2026-02-09T06:03:17,559 -- Performing Test HAVE_SSE2 2026-02-09T06:03:17,805 -- Performing Test HAVE_SSE2 - Failed 2026-02-09T06:03:17,810 -- Could NOT find SSE2 (missing: SSE2_C_FLAGS) 2026-02-09T06:03:17,813 -- Try SSE4 C flag = [ ] 2026-02-09T06:03:17,814 -- Performing Test HAVE_SSE4 2026-02-09T06:03:18,065 -- Performing Test HAVE_SSE4 - Failed 2026-02-09T06:03:18,067 -- Try SSE4 C flag = [-msse4.1 -msimd128] 2026-02-09T06:03:18,068 -- Performing Test HAVE_SSE4 2026-02-09T06:03:18,230 -- Performing Test HAVE_SSE4 - Failed 2026-02-09T06:03:18,233 -- Try SSE4 C flag = [-msse4.1] 2026-02-09T06:03:18,234 -- Performing Test HAVE_SSE4 2026-02-09T06:03:18,393 -- Performing Test HAVE_SSE4 - Failed 2026-02-09T06:03:18,396 -- Try SSE4 C flag = [-msse4] 2026-02-09T06:03:18,397 -- Performing Test HAVE_SSE4 2026-02-09T06:03:18,550 -- Performing Test HAVE_SSE4 - Failed 2026-02-09T06:03:18,557 -- Could NOT find SSE4 (missing: SSE4_C_FLAGS) 2026-02-09T06:03:18,561 -- Try VMX C flag = [ ] 2026-02-09T06:03:18,563 -- Performing Test HAVE_VMX 2026-02-09T06:03:18,763 -- Performing Test HAVE_VMX - Failed 2026-02-09T06:03:18,770 -- Could NOT find VMX (missing: VMX_C_FLAGS) 2026-02-09T06:03:18,771 -- Installing shared libraries to pyhmmer.libs 2026-02-09T06:03:18,838 -- Looking for stdio.h 2026-02-09T06:03:19,289 -- Looking for stdio.h - found 2026-02-09T06:03:19,291 -- Looking for stdlib.h 2026-02-09T06:03:19,792 -- Looking for stdlib.h - found 2026-02-09T06:03:19,794 -- Looking for string.h 2026-02-09T06:03:20,519 -- Looking for string.h - found 2026-02-09T06:03:20,521 -- Looking for inttypes.h 2026-02-09T06:03:21,222 -- Looking for inttypes.h - found 2026-02-09T06:03:21,225 -- Looking for stdint.h 2026-02-09T06:03:21,913 -- Looking for stdint.h - found 2026-02-09T06:03:21,916 -- Looking for strings.h 2026-02-09T06:03:22,636 -- Looking for strings.h - found 2026-02-09T06:03:22,638 -- Looking for unistd.h 2026-02-09T06:03:23,231 -- Looking for unistd.h - found 2026-02-09T06:03:23,234 -- Looking for endian.h 2026-02-09T06:03:24,004 -- Looking for endian.h - found 2026-02-09T06:03:24,007 -- Looking for netinet/in.h 2026-02-09T06:03:24,465 -- Looking for netinet/in.h - found 2026-02-09T06:03:24,468 -- Looking for sys/mman.h 2026-02-09T06:03:24,994 -- Looking for sys/mman.h - found 2026-02-09T06:03:24,996 -- Looking for sys/param.h 2026-02-09T06:03:25,699 -- Looking for sys/param.h - found 2026-02-09T06:03:25,702 -- Looking for sys/stat.h 2026-02-09T06:03:26,294 -- Looking for sys/stat.h - found 2026-02-09T06:03:26,297 -- Looking for sys/sysctl.h 2026-02-09T06:03:26,659 -- Looking for sys/sysctl.h - not found 2026-02-09T06:03:26,661 -- Looking for sys/types.h 2026-02-09T06:03:27,385 -- Looking for sys/types.h - found 2026-02-09T06:03:27,388 -- Looking for syslog.h 2026-02-09T06:03:27,866 -- Looking for syslog.h - found 2026-02-09T06:03:27,868 -- Looking for aligned_alloc 2026-02-09T06:03:28,348 -- Looking for aligned_alloc - found 2026-02-09T06:03:28,350 -- Looking for erfc 2026-02-09T06:03:28,862 -- Looking for erfc - not found 2026-02-09T06:03:28,864 -- Looking for getpid 2026-02-09T06:03:29,424 -- Looking for getpid - found 2026-02-09T06:03:29,427 -- Looking for _mm_malloc 2026-02-09T06:03:30,112 -- Looking for _mm_malloc - not found 2026-02-09T06:03:30,113 -- Looking for popen 2026-02-09T06:03:30,854 -- Looking for popen - found 2026-02-09T06:03:30,856 -- Looking for posix_memalign 2026-02-09T06:03:31,556 -- Looking for posix_memalign - found 2026-02-09T06:03:31,557 -- Looking for strcasecmp 2026-02-09T06:03:31,915 -- Looking for strcasecmp - found 2026-02-09T06:03:31,916 -- Looking for strsep 2026-02-09T06:03:32,589 -- Looking for strsep - found 2026-02-09T06:03:32,591 -- Looking for sysconf 2026-02-09T06:03:33,271 -- Looking for sysconf - found 2026-02-09T06:03:33,272 -- Looking for sysctl 2026-02-09T06:03:33,960 -- Looking for sysctl - not found 2026-02-09T06:03:33,961 -- Looking for times 2026-02-09T06:03:34,524 -- Looking for times - found 2026-02-09T06:03:34,527 -- Looking for fseeko 2026-02-09T06:03:35,173 -- Looking for fseeko - found 2026-02-09T06:03:36,533 -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter Development.Module 2026-02-09T06:03:36,550 -- Looking for PyInterpreterState_GetID 2026-02-09T06:03:37,640 -- Looking for PyInterpreterState_GetID - not found 2026-02-09T06:03:37,854 -- Building in latest API mode for Python: 3.11 2026-02-09T06:03:37,860 -- Building in latest API mode for Python: 3.11 2026-02-09T06:03:37,864 -- Building in latest API mode for Python: 3.11 2026-02-09T06:03:37,869 -- Building in latest API mode for Python: 3.11 2026-02-09T06:03:37,874 -- Building in latest API mode for Python: 3.11 2026-02-09T06:03:37,880 -- Configuring done 2026-02-09T06:03:38,135 -- Generating done 2026-02-09T06:03:38,253 -- Build files have been written to: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release 2026-02-09T06:03:38,318 *** Building project with Ninja... 2026-02-09T06:03:38,697 [1/427] Copying esl_alloc.c 2026-02-09T06:03:38,735 [2/427] Copying esl_alphabet.c 2026-02-09T06:03:38,756 [3/427] Copying esl_arr2.c 2026-02-09T06:03:38,774 [4/427] Copying esl_arr3.c 2026-02-09T06:03:38,780 [5/427] Copying esl_avx512.c 2026-02-09T06:03:38,841 [6/427] Copying esl_avx.c 2026-02-09T06:03:38,907 [7/427] Copying esl_bitfield.c 2026-02-09T06:03:38,929 [8/427] Patching easel.c 2026-02-09T06:03:38,941 [9/427] Copying esl_cluster.c 2026-02-09T06:03:38,958 [10/427] Copying esl_cpu.c 2026-02-09T06:03:38,989 [11/427] Copying esl_composition.c 2026-02-09T06:03:39,067 [12/427] Copying esl_dirichlet.c 2026-02-09T06:03:39,089 [13/427] Copying esl_distance.c 2026-02-09T06:03:39,118 [14/427] Copying esl_dmatrix.c 2026-02-09T06:03:39,144 [15/427] Copying esl_exponential.c 2026-02-09T06:03:39,159 [16/427] Copying esl_fileparser.c 2026-02-09T06:03:39,233 [17/427] Copying esl_gamma.c 2026-02-09T06:03:39,265 [18/427] Copying esl_gencode.c 2026-02-09T06:03:39,290 [19/427] Patching esl_buffer.c 2026-02-09T06:03:39,307 [20/427] Copying esl_getopts.c 2026-02-09T06:03:39,325 [21/427] Copying esl_gev.c 2026-02-09T06:03:39,332 [22/427] Copying esl_graph.c 2026-02-09T06:03:39,394 [23/427] Copying esl_gumbel.c 2026-02-09T06:03:39,418 [24/427] Copying esl_heap.c 2026-02-09T06:03:39,437 [25/427] Copying esl_hmm.c 2026-02-09T06:03:39,461 [26/427] Copying esl_histogram.c 2026-02-09T06:03:39,504 [27/427] Copying esl_hyperexp.c 2026-02-09T06:03:39,518 [28/427] Copying esl_huffman.c 2026-02-09T06:03:39,552 [29/427] Copying esl_iset.c 2026-02-09T06:03:39,594 [30/427] Copying esl_keyhash.c 2026-02-09T06:03:39,614 [31/427] Copying esl_json.c 2026-02-09T06:03:39,645 [32/427] Copying esl_matrixops.c 2026-02-09T06:03:39,670 [33/427] Copying esl_lognormal.c 2026-02-09T06:03:39,693 [34/427] Copying esl_mem.c 2026-02-09T06:03:39,716 [35/427] Copying esl_minimizer.c 2026-02-09T06:03:39,756 [36/427] Copying esl_mixdchlet.c 2026-02-09T06:03:39,768 [37/427] Copying esl_mixgev.c 2026-02-09T06:03:39,846 [38/427] Copying esl_mpi.c 2026-02-09T06:03:39,869 [39/427] Copying esl_msa.c 2026-02-09T06:03:39,887 [40/427] Copying esl_msacluster.c 2026-02-09T06:03:39,898 [41/427] Copying esl_msafile2.c 2026-02-09T06:03:39,908 [42/427] Copying esl_msafile_a2m.c 2026-02-09T06:03:39,923 [43/427] Copying esl_msafile_afa.c 2026-02-09T06:03:39,992 [44/427] Copying esl_msafile.c 2026-02-09T06:03:40,012 [45/427] Copying esl_msafile_clustal.c 2026-02-09T06:03:40,035 [46/427] Copying esl_msafile_phylip.c 2026-02-09T06:03:40,043 [47/427] Copying esl_msafile_psiblast.c 2026-02-09T06:03:40,076 [48/427] Copying esl_msafile_selex.c 2026-02-09T06:03:40,107 [49/427] Copying esl_msafile_stockholm.c 2026-02-09T06:03:40,127 [50/427] Copying esl_msashuffle.c 2026-02-09T06:03:40,173 [51/427] Copying esl_msaweight.c 2026-02-09T06:03:40,182 [52/427] Copying esl_normal.c 2026-02-09T06:03:40,207 [53/427] Copying esl_neon.c 2026-02-09T06:03:40,237 [54/427] Copying esl_paml.c 2026-02-09T06:03:40,265 [55/427] Copying esl_quicksort.c 2026-02-09T06:03:40,298 [56/427] Copying esl_rand64.c 2026-02-09T06:03:40,317 [57/427] Copying esl_random.c 2026-02-09T06:03:40,337 [58/427] Copying esl_randomseq.c 2026-02-09T06:03:40,374 [59/427] Copying esl_ratematrix.c 2026-02-09T06:03:40,401 [60/427] Copying esl_red_black.c 2026-02-09T06:03:40,441 [61/427] Copying esl_recorder.c 2026-02-09T06:03:40,461 [62/427] Copying esl_regexp.c 2026-02-09T06:03:40,464 [63/427] Copying esl_rootfinder.c 2026-02-09T06:03:40,526 [64/427] Copying esl_scorematrix.c 2026-02-09T06:03:40,564 [65/427] Copying esl_sqio.c 2026-02-09T06:03:40,573 [66/427] Copying esl_sse.c 2026-02-09T06:03:40,609 [67/427] Copying esl_sqio_ncbi.c 2026-02-09T06:03:40,642 [68/427] Copying esl_ssi.c 2026-02-09T06:03:40,697 [69/427] Patching esl_sq.c 2026-02-09T06:03:40,727 [70/427] Copying esl_stack.c 2026-02-09T06:03:40,732 [71/427] Copying esl_stats.c 2026-02-09T06:03:40,776 [72/427] Copying esl_stretchexp.c 2026-02-09T06:03:40,822 [73/427] Copying esl_stopwatch.c 2026-02-09T06:03:40,831 [74/427] Copying esl_subcmd.c 2026-02-09T06:03:40,848 [75/427] Copying esl_threads.c 2026-02-09T06:03:40,872 [76/427] Copying esl_swat.c 2026-02-09T06:03:40,899 [77/427] Copying esl_tree.c 2026-02-09T06:03:40,929 [78/427] Patching esl_sqio_ascii.c 2026-02-09T06:03:40,953 [79/427] Copying esl_vectorops.c 2026-02-09T06:03:40,976 [80/427] Copying esl_varint.c 2026-02-09T06:03:41,002 [81/427] Copying esl_weibull.c 2026-02-09T06:03:41,023 [82/427] Copying esl_vmx.c 2026-02-09T06:03:41,034 [83/427] Copying esl_workqueue.c 2026-02-09T06:03:41,087 [84/427] Copying esl_wuss.c 2026-02-09T06:03:41,132 [85/427] Copying interface_gsl.c 2026-02-09T06:03:41,143 [86/427] Copying interface_lapack.c 2026-02-09T06:03:41,194 [87/427] Copying esl_alphabet.h 2026-02-09T06:03:41,208 [88/427] Copying esl_alloc.h 2026-02-09T06:03:41,227 [89/427] Copying esl_arr2.h 2026-02-09T06:03:41,297 [90/427] Copying esl_arr3.h 2026-02-09T06:03:41,303 [91/427] Copying esl_avx512.h 2026-02-09T06:03:41,323 [92/427] Copying esl_avx.h 2026-02-09T06:03:41,344 [93/427] Copying esl_buffer.h 2026-02-09T06:03:41,362 [94/427] Patching easel.h 2026-02-09T06:03:41,383 [95/427] Copying esl_bitfield.h 2026-02-09T06:03:41,440 [96/427] Copying esl_composition.h 2026-02-09T06:03:41,460 [97/427] Copying esl_cluster.h 2026-02-09T06:03:41,488 [98/427] Copying esl_cpu.h 2026-02-09T06:03:41,498 [99/427] Copying esl_dirichlet.h 2026-02-09T06:03:41,517 [100/427] Copying esl_distance.h 2026-02-09T06:03:41,535 [101/427] Copying esl_dmatrix.h 2026-02-09T06:03:41,544 [102/427] Copying esl_dsqdata.h 2026-02-09T06:03:41,603 [103/427] Copying esl_fileparser.h 2026-02-09T06:03:41,624 [104/427] Copying esl_gamma.h 2026-02-09T06:03:41,649 [105/427] Copying esl_gencode.h 2026-02-09T06:03:41,658 [106/427] Copying esl_exponential.h 2026-02-09T06:03:41,685 [107/427] Copying esl_getopts.h 2026-02-09T06:03:41,707 [108/427] Copying esl_gev.h 2026-02-09T06:03:41,741 [109/427] Copying esl_histogram.h 2026-02-09T06:03:41,746 [110/427] Copying esl_graph.h 2026-02-09T06:03:41,804 [111/427] Copying esl_heap.h 2026-02-09T06:03:41,824 [112/427] Copying esl_gumbel.h 2026-02-09T06:03:41,845 [113/427] Copying esl_huffman.h 2026-02-09T06:03:41,849 [114/427] Copying esl_hmm.h 2026-02-09T06:03:41,880 [115/427] Copying esl_hyperexp.h 2026-02-09T06:03:41,915 [116/427] Copying esl_iset.h 2026-02-09T06:03:41,928 [117/427] Copying esl_json.h 2026-02-09T06:03:41,976 [118/427] Copying esl_keyhash.h 2026-02-09T06:03:41,982 [119/427] Copying esl_lognormal.h 2026-02-09T06:03:42,005 [120/427] Copying esl_matrixops.h 2026-02-09T06:03:42,055 [121/427] Copying esl_mem.h 2026-02-09T06:03:42,064 [122/427] Copying esl_mixdchlet.h 2026-02-09T06:03:42,075 [123/427] Copying esl_minimizer.h 2026-02-09T06:03:42,095 [124/427] Copying esl_mixgev.h 2026-02-09T06:03:42,117 [125/427] Copying esl_mpi.h 2026-02-09T06:03:42,141 [126/427] Copying esl_msacluster.h 2026-02-09T06:03:42,207 [127/427] Copying esl_msafile2.h 2026-02-09T06:03:42,225 [128/427] Copying esl_msafile_a2m.h 2026-02-09T06:03:42,237 [129/427] Copying esl_msafile_afa.h 2026-02-09T06:03:42,251 [130/427] Copying esl_msafile_clustal.h 2026-02-09T06:03:42,257 [131/427] Copying esl_msafile.h 2026-02-09T06:03:42,285 [132/427] Copying esl_msafile_phylip.h 2026-02-09T06:03:42,319 [133/427] Copying esl_msafile_selex.h 2026-02-09T06:03:42,346 [134/427] Copying esl_msafile_psiblast.h 2026-02-09T06:03:42,376 [135/427] Copying esl_msashuffle.h 2026-02-09T06:03:42,385 [136/427] Copying esl_msafile_stockholm.h 2026-02-09T06:03:42,404 [137/427] Copying esl_msaweight.h 2026-02-09T06:03:42,406 [138/427] Copying esl_msa.h 2026-02-09T06:03:42,456 [139/427] Copying esl_neon.h 2026-02-09T06:03:42,513 [140/427] Copying esl_quicksort.h 2026-02-09T06:03:42,538 [141/427] Copying esl_normal.h 2026-02-09T06:03:42,551 [142/427] Copying esl_paml.h 2026-02-09T06:03:42,562 [143/427] Copying esl_rand64.h 2026-02-09T06:03:42,572 [144/427] Copying 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[162/427] Copying esl_subcmd.h 2026-02-09T06:03:43,252 [163/427] Copying esl_varint.h 2026-02-09T06:03:43,283 [164/427] Copying esl_tree.h 2026-02-09T06:03:43,293 [165/427] Copying esl_vectorops.h 2026-02-09T06:03:43,308 [166/427] Copying esl_vmx.h 2026-02-09T06:03:43,317 [167/427] Copying esl_weibull.h 2026-02-09T06:03:43,373 [168/427] Patching esl_threads.h 2026-02-09T06:03:43,404 [169/427] Copying esl_wuss.h 2026-02-09T06:03:43,405 [170/427] Copying esl_workqueue.h 2026-02-09T06:03:43,420 [171/427] Copying interface_gsl.h 2026-02-09T06:03:43,425 [172/427] Copying interface_lapack.h 2026-02-09T06:03:43,850 [173/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_avx512.c.o 2026-02-09T06:03:43,980 [174/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_alloc.c.o 2026-02-09T06:03:44,058 [175/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_arr2.c.o 2026-02-09T06:03:44,188 [176/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_avx.c.o 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Building C object src/easel/CMakeFiles/libeasel.dir/esl_huffman.c.o 2026-02-09T06:03:53,208 [197/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_getopts.c.o 2026-02-09T06:03:53,751 [198/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_hmm.c.o 2026-02-09T06:03:54,272 [199/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_histogram.c.o 2026-02-09T06:03:54,583 [200/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_lognormal.c.o 2026-02-09T06:03:54,923 [201/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_hyperexp.c.o 2026-02-09T06:03:55,007 [202/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_keyhash.c.o 2026-02-09T06:03:56,091 [203/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_iset.c.o 2026-02-09T06:03:57,051 [204/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_minimizer.c.o 2026-02-09T06:03:57,242 [205/427] Building C object src/easel/CMakeFiles/libeasel.dir/esl_matrixops.c.o 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2026-02-09T06:05:27,101 [408/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/optacc.c.o 2026-02-09T06:05:27,850 [409/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/stotrace.c.o 2026-02-09T06:05:29,842 [410/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/p7_omx.c.o 2026-02-09T06:05:30,626 [411/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/vitfilter.c.o 2026-02-09T06:05:38,906 [412/427] Cythonizing easel.pyx to easel.c 2026-02-09T06:05:38,912 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/exceptions.pxi:45:0: Exception check on '_py_handler' will always require the GIL to be acquired. 2026-02-09T06:05:38,913 Possible solutions: 2026-02-09T06:05:38,914 1. Declare '_py_handler' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:05:38,914 2. Use an 'int' return type on '_py_handler' to allow an error code to be returned. 2026-02-09T06:05:38,915 warning: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/easel.pyx:9172:8: Unreachable code 2026-02-09T06:05:39,725 [413/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/p7_oprofile.c.o 2026-02-09T06:05:45,550 [414/427] Building C object src/pyhmmer/platform/CMakeFiles/pyhmmer.platform.linux.dir/linux.c.o 2026-02-09T06:05:45,923 [415/427] Linking C shared module src/pyhmmer/platform/linux.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:06:00,519 [416/427] Building C object src/pyhmmer/CMakeFiles/pyhmmer.errors.dir/errors.c.o 2026-02-09T06:06:00,873 [417/427] Linking C shared module src/pyhmmer/errors.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:06:32,455 [418/427] Building C object src/hmmer/CMakeFiles/libhmmer.dir/impl_neon/ssvfilter.c.o 2026-02-09T06:06:33,002 [419/427] Linking C shared library src/hmmer/liblibhmmer.so 2026-02-09T06:06:57,788 [420/427] Cythonizing daemon.pyx to daemon.c 2026-02-09T06:07:24,355 [421/427] Cythonizing plan7.pyx to plan7.c 2026-02-09T06:07:24,365 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/exceptions.pxi:45:0: Exception check on '_py_handler' will always require the GIL to be acquired. 2026-02-09T06:07:24,366 Possible solutions: 2026-02-09T06:07:24,367 1. Declare '_py_handler' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,368 2. Use an 'int' return type on '_py_handler' to allow an error code to be returned. 2026-02-09T06:07:24,369 warning: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:5793:12: Unreachable code 2026-02-09T06:07:24,370 warning: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:5766:8: Unreachable code 2026-02-09T06:07:24,371 warning: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:6920:8: Unreachable code 2026-02-09T06:07:24,372 warning: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:6906:8: Unreachable code 2026-02-09T06:07:24,373 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3429:71: Exception check after calling 'p7_hmmfile_WriteBinary' will always require the GIL to be acquired. Declare 'p7_hmmfile_WriteBinary' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,374 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3433:70: Exception check after calling 'p7_hmmfile_WriteASCII' will always require the GIL to be acquired. Declare 'p7_hmmfile_WriteASCII' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,375 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3549:69: Exception check after calling 'esl_fileparser_Create' will always require the GIL to be acquired. Declare 'esl_fileparser_Create' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,377 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3561:64: Exception check after calling 'esl_fileparser_NextLine' will always require the GIL to be acquired. Declare 'esl_fileparser_NextLine' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,387 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3569:64: Exception check after calling 'esl_fileparser_GetToken' will always require the GIL to be acquired. Declare 'esl_fileparser_GetToken' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,389 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:3753:56: Exception check after calling 'p7_hmmfile_Read' will always require the GIL to be acquired. Declare 'p7_hmmfile_Read' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,391 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:4712:59: Exception check after calling 'p7_oprofile_Write' will always require the GIL to be acquired. Declare 'p7_oprofile_Write' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,392 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:8824:74: Exception check after calling 'p7_tophits_TabularTargets' will always require the GIL to be acquired. Declare 'p7_tophits_TabularTargets' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:24,394 performance hint: /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/src/pyhmmer/plan7.pyx:8835:74: Exception check after calling 'p7_tophits_TabularDomains' will always require the GIL to be acquired. Declare 'p7_tophits_TabularDomains' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2026-02-09T06:07:58,846 [422/427] Building C object src/pyhmmer/CMakeFiles/pyhmmer.daemon.dir/daemon.c.o 2026-02-09T06:07:58,846 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4208:153: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,848 4208 | P7_OPROFILE *(*__pyx_fuse_0_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_HMM *, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args); 2026-02-09T06:07:58,849 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,850 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4209:157: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,851 4209 | P7_OPROFILE *(*__pyx_fuse_1_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_Profile *, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args); 2026-02-09T06:07:58,852 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,857 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4210:166: warning: ‘struct __pyx_fuse_2__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,859 4210 | P7_OPROFILE *(*__pyx_fuse_2_get_om_from_query)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5plan7_OptimizedProfile *, struct __pyx_fuse_2__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline__get_om_from_query *__pyx_optional_args); 2026-02-09T06:07:58,861 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,863 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4217:255: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,867 4217 | struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_0search_msa)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalMSA *, struct __pyx_obj_7pyhmmer_5easel_SequenceFile *, int __pyx_skip_dispatch, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa *__pyx_optional_args); 2026-02-09T06:07:58,878 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,887 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4218:263: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,888 4218 | struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_1search_msa)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalMSA *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequenceBlock *, int __pyx_skip_dispatch, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_msa *__pyx_optional_args); 2026-02-09T06:07:58,891 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,907 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4219:260: warning: ‘struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,917 4219 | struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_0search_seq)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequence *, struct __pyx_obj_7pyhmmer_5easel_SequenceFile *, int __pyx_skip_dispatch, struct __pyx_fuse_0__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq *__pyx_optional_args); 2026-02-09T06:07:58,920 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:58,922 /tmp/pip-install-bbieapha/pyhmmer_323b859318e34a129cde69e243917aa2/build/Release/src/pyhmmer/daemon.c:4220:268: warning: ‘struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq’ declared inside parameter list will not be visible outside of this definition or declaration 2026-02-09T06:07:58,924 4220 | struct __pyx_obj_7pyhmmer_5plan7_TopHits *(*__pyx_fuse_1search_seq)(struct __pyx_obj_7pyhmmer_5plan7_LongTargetsPipeline *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequence *, struct __pyx_obj_7pyhmmer_5easel_DigitalSequenceBlock *, int __pyx_skip_dispatch, struct __pyx_fuse_1__pyx_opt_args_7pyhmmer_5plan7_19LongTargetsPipeline_search_seq *__pyx_optional_args); 2026-02-09T06:07:58,938 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2026-02-09T06:07:59,261 [423/427] Linking C shared module src/pyhmmer/daemon.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:10:46,921 [424/427] Building C object src/pyhmmer/CMakeFiles/pyhmmer.easel.dir/easel.c.o 2026-02-09T06:10:47,488 [425/427] Linking C shared module src/pyhmmer/easel.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:45,767 [426/427] Building C object src/pyhmmer/CMakeFiles/pyhmmer.plan7.dir/plan7.c.o 2026-02-09T06:11:46,057 [427/427] Linking C shared module src/pyhmmer/plan7.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:46,063 *** Installing project into wheel... 2026-02-09T06:11:46,122 -- Install configuration: "Release" 2026-02-09T06:11:46,125 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include 2026-02-09T06:11:46,131 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/capacity.pxd 2026-02-09T06:11:46,136 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/pthread_mutex.pxd 2026-02-09T06:11:46,140 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer 2026-02-09T06:11:46,145 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/modelconfig.pxd 2026-02-09T06:11:46,150 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_profile.pxd 2026-02-09T06:11:46,154 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_alidisplay.pxd 2026-02-09T06:11:46,159 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/generic.pxd 2026-02-09T06:11:46,164 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_spensemble.pxd 2026-02-09T06:11:46,168 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/tracealign.pxd 2026-02-09T06:11:46,173 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/fm.pxd 2026-02-09T06:11:46,178 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_vmx 2026-02-09T06:11:46,183 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_vmx/p7_omx.pxd 2026-02-09T06:11:46,187 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_vmx/p7_oprofile.pxd 2026-02-09T06:11:46,192 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_vmx/io.pxd 2026-02-09T06:11:46,196 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_vmx/__init__.pxd 2026-02-09T06:11:46,201 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/hmmpgmd.pxd 2026-02-09T06:11:46,206 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_trace.pxd 2026-02-09T06:11:46,210 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/h2_io.pxd 2026-02-09T06:11:46,215 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl 2026-02-09T06:11:46,220 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl/p7_omx.pxd 2026-02-09T06:11:46,225 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl/p7_oprofile.pxd 2026-02-09T06:11:46,230 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl/io.pxd 2026-02-09T06:11:46,235 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl/__init__.pxd 2026-02-09T06:11:46,239 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_scoredata.pxd 2026-02-09T06:11:46,244 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_sse 2026-02-09T06:11:46,249 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_sse/p7_omx.pxd 2026-02-09T06:11:46,254 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_sse/p7_oprofile.pxd 2026-02-09T06:11:46,259 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_sse/io.pxd 2026-02-09T06:11:46,263 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_sse/__init__.pxd 2026-02-09T06:11:46,267 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/nhmmer.pxd 2026-02-09T06:11:46,272 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_domaindef.pxd 2026-02-09T06:11:46,276 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_hmm.pxd 2026-02-09T06:11:46,280 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_prior.pxd 2026-02-09T06:11:46,285 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_hit.pxd 2026-02-09T06:11:46,289 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/logsum.pxd 2026-02-09T06:11:46,294 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_neon 2026-02-09T06:11:46,299 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_neon/p7_omx.pxd 2026-02-09T06:11:46,303 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_neon/p7_oprofile.pxd 2026-02-09T06:11:46,308 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_neon/io.pxd 2026-02-09T06:11:46,313 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/impl_neon/__init__.pxd 2026-02-09T06:11:46,318 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/modelstats.pxd 2026-02-09T06:11:46,323 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_gmx.pxd 2026-02-09T06:11:46,327 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/cython/include/libhmmer/p7_builder.pxd 2026-02-09T06:11:46,332 -- Installing: 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/tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_neon.h 2026-02-09T06:11:47,051 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_normal.h 2026-02-09T06:11:47,056 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_paml.h 2026-02-09T06:11:47,061 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_quicksort.h 2026-02-09T06:11:47,066 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_rand64.h 2026-02-09T06:11:47,071 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_random.h 2026-02-09T06:11:47,076 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_randomseq.h 2026-02-09T06:11:47,082 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_ratematrix.h 2026-02-09T06:11:47,087 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_recorder.h 2026-02-09T06:11:47,092 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_red_black.h 2026-02-09T06:11:47,097 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_regexp.h 2026-02-09T06:11:47,102 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_rootfinder.h 2026-02-09T06:11:47,107 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_scorematrix.h 2026-02-09T06:11:47,113 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_sq.h 2026-02-09T06:11:47,119 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_sqio_ascii.h 2026-02-09T06:11:47,125 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_sqio.h 2026-02-09T06:11:47,130 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_sqio_ncbi.h 2026-02-09T06:11:47,136 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_sse.h 2026-02-09T06:11:47,142 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_ssi.h 2026-02-09T06:11:47,148 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_stack.h 2026-02-09T06:11:47,153 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_stats.h 2026-02-09T06:11:47,159 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_stopwatch.h 2026-02-09T06:11:47,164 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_stretchexp.h 2026-02-09T06:11:47,169 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_subcmd.h 2026-02-09T06:11:47,174 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_threads.h 2026-02-09T06:11:47,179 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_tree.h 2026-02-09T06:11:47,185 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_varint.h 2026-02-09T06:11:47,190 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_vectorops.h 2026-02-09T06:11:47,196 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_vmx.h 2026-02-09T06:11:47,201 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_weibull.h 2026-02-09T06:11:47,206 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_workqueue.h 2026-02-09T06:11:47,212 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/esl_wuss.h 2026-02-09T06:11:47,217 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/interface_gsl.h 2026-02-09T06:11:47,223 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libeasel/interface_lapack.h 2026-02-09T06:11:47,231 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/liblibhmmer.so 2026-02-09T06:11:47,256 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/liblibhmmer.so" to "$ORIGIN/" 2026-02-09T06:11:47,331 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/p7_config.h 2026-02-09T06:11:47,337 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/cachedb.h 2026-02-09T06:11:47,342 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/cachedb_shard.h 2026-02-09T06:11:47,347 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/hmmer.h 2026-02-09T06:11:47,355 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/hmmpgmd.h 2026-02-09T06:11:47,361 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/hmmpgmd_shard.h 2026-02-09T06:11:47,366 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/p7_gbands.h 2026-02-09T06:11:47,372 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/p7_gmxb.h 2026-02-09T06:11:47,377 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/p7_gmxchk.h 2026-02-09T06:11:47,383 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/p7_hmmcache.h 2026-02-09T06:11:47,390 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/libhmmer/impl_neon/impl_neon.h 2026-02-09T06:11:47,403 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer/platform/linux.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:47,413 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer/platform/linux.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../../pyhmmer.libs" 2026-02-09T06:11:47,437 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/pyhmmer/platform/linux.h 2026-02-09T06:11:47,442 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/pyhmmer/platform/bsd.h 2026-02-09T06:11:47,447 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer.libs/include/pyhmmer/platform/util.h 2026-02-09T06:11:47,452 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer/errors.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:47,464 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer/errors.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../pyhmmer.libs" 2026-02-09T06:11:47,489 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer/easel.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:47,543 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer/easel.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../pyhmmer.libs" 2026-02-09T06:11:47,666 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer/plan7.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:47,717 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer/plan7.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../pyhmmer.libs" 2026-02-09T06:11:47,832 -- Installing: /tmp/tmp1hlg392b/wheel/platlib/pyhmmer/daemon.cpython-311-arm-linux-gnueabihf.so 2026-02-09T06:11:47,848 -- Set runtime path of "/tmp/tmp1hlg392b/wheel/platlib/pyhmmer/daemon.cpython-311-arm-linux-gnueabihf.so" to "$ORIGIN/../pyhmmer.libs" 2026-02-09T06:11:47,913 *** Making wheel... 2026-02-09T06:11:52,613 *** Created pyhmmer-0.12.0-cp311-cp311-linux_armv7l.whl 2026-02-09T06:11:52,706 Building wheel for pyhmmer (pyproject.toml): finished with status 'done' 2026-02-09T06:11:52,850 Created wheel for pyhmmer: filename=pyhmmer-0.12.0-cp311-cp311-linux_armv7l.whl size=4052217 sha256=d4fd6601db2a7f3e66cbc2e686defc47ccaac96ae91f4736d07b0c83c9855e2c 2026-02-09T06:11:52,851 Stored in directory: /home/piwheels/.cache/pip/wheels/8c/a5/ac/ba50095780848b877bde3b144429dea4baabb8a8d71b243031 2026-02-09T06:11:52,880 Successfully built pyhmmer 2026-02-09T06:11:57,375 Installing collected packages: psutil, pathspec, packaging, cython, scikit-build-core, pyhmmer 2026-02-09T06:12:03,751 Creating /tmp/pip-build-env-duavp0gm/overlay/local/bin 2026-02-09T06:12:03,753 changing mode of /tmp/pip-build-env-duavp0gm/overlay/local/bin/cygdb to 755 2026-02-09T06:12:03,756 changing mode of /tmp/pip-build-env-duavp0gm/overlay/local/bin/cython to 755 2026-02-09T06:12:03,759 changing mode of /tmp/pip-build-env-duavp0gm/overlay/local/bin/cythonize to 755 2026-02-09T06:12:06,457 Successfully installed cython-3.2.4 packaging-26.0 pathspec-1.0.4 psutil-6.0.0 pyhmmer-0.12.0 scikit-build-core-0.11.6 2026-02-09T06:12:08,054 Installing build dependencies: finished with status 'done' 2026-02-09T06:12:08,064 Getting requirements to build wheel: started 2026-02-09T06:12:08,065 Running command Getting requirements to build wheel 2026-02-09T06:12:09,113 Getting requirements to build wheel: finished with status 'done' 2026-02-09T06:12:09,117 Created temporary directory: /tmp/pip-modern-metadata-87zod76z 2026-02-09T06:12:09,121 Preparing metadata (pyproject.toml): started 2026-02-09T06:12:09,122 Running command Preparing metadata (pyproject.toml) 2026-02-09T06:12:10,150 2026-02-09 06:12:10,150 - scikit_build_core - WARNING - Unknown keys in top-level of pyproject.toml: tool.mypy-pyinfernal.tests.* 2026-02-09T06:12:10,217 *** scikit-build-core 0.11.6 using CMake 3.25.1 (metadata_wheel) 2026-02-09T06:12:10,346 Preparing metadata (pyproject.toml): finished with status 'done' 2026-02-09T06:12:10,353 Source in /tmp/pip-wheel-pohs_afi/pyinfernal_07a163401e064802bab58d4f19731bfa has version 0.1.0a2, which satisfies requirement pyinfernal==0.1.0a2 from https://files.pythonhosted.org/packages/0e/3d/a84bbd14073b5c86e0aa953db9d52b695c7174d18bc999d97936bb6185ef/pyinfernal-0.1.0a2.tar.gz 2026-02-09T06:12:10,355 Removed pyinfernal==0.1.0a2 from https://files.pythonhosted.org/packages/0e/3d/a84bbd14073b5c86e0aa953db9d52b695c7174d18bc999d97936bb6185ef/pyinfernal-0.1.0a2.tar.gz from build tracker '/tmp/pip-build-tracker-i1s36jtb' 2026-02-09T06:12:10,362 Created temporary directory: /tmp/pip-unpack-2ctq4k00 2026-02-09T06:12:10,363 Building wheels for collected packages: pyinfernal 2026-02-09T06:12:10,381 Created temporary directory: /tmp/pip-wheel-sa_c4myi 2026-02-09T06:12:10,381 Destination directory: /tmp/pip-wheel-sa_c4myi 2026-02-09T06:12:10,385 Building wheel for pyinfernal (pyproject.toml): started 2026-02-09T06:12:10,386 Running command Building wheel for pyinfernal (pyproject.toml) 2026-02-09T06:12:11,455 2026-02-09 06:12:11,455 - scikit_build_core - WARNING - Unknown keys in top-level of pyproject.toml: tool.mypy-pyinfernal.tests.* 2026-02-09T06:12:11,583 *** scikit-build-core 0.11.6 using CMake 3.25.1 (wheel) 2026-02-09T06:12:11,629 *** Configuring CMake... 2026-02-09T06:12:12,026 loading initial cache file build/Release/CMakeInit.txt 2026-02-09T06:12:12,477 -- The C compiler identification is GNU 12.2.0 2026-02-09T06:12:12,609 -- Detecting C compiler ABI info 2026-02-09T06:12:13,264 -- Detecting C compiler ABI info - done 2026-02-09T06:12:13,347 -- Check for working C compiler: /usr/bin/arm-linux-gnueabihf-gcc - skipped 2026-02-09T06:12:13,350 -- Detecting C compile features 2026-02-09T06:12:13,352 -- Detecting C compile features - done 2026-02-09T06:12:13,377 -- Installing shared libraries to pyinfernal.libs 2026-02-09T06:12:13,394 -- Looking for alloca.h 2026-02-09T06:12:13,974 -- Looking for alloca.h - found 2026-02-09T06:12:14,998 -- Found Python: /usr/bin/python3 (found version "3.11.2") found components: Interpreter Development.Module 2026-02-09T06:12:15,001 -- Looking for PyInterpreterState_GetID 2026-02-09T06:12:16,098 -- Looking for PyInterpreterState_GetID - not found 2026-02-09T06:12:16,101 -- Linking to libinfernal 2026-02-09T06:12:16,117 -- Configuring done 2026-02-09T06:12:16,274 -- Generating done 2026-02-09T06:12:16,334 -- Build files have been written to: /tmp/pip-wheel-pohs_afi/pyinfernal_07a163401e064802bab58d4f19731bfa/build/Release 2026-02-09T06:12:16,383 *** Building project with Ninja... 2026-02-09T06:12:16,562 ninja: error: 'src/infernal/DEPENDS_EXPLICIT_ONLY', needed by '/tmp/pip-wheel-pohs_afi/pyinfernal_07a163401e064802bab58d4f19731bfa/build/Release/src/infernal/cm.c', missing and no known rule to make it 2026-02-09T06:12:16,583 *** CMake build failed 2026-02-09T06:12:16,785 ERROR: [present-rich] Building wheel for pyinfernal (pyproject.toml) exited with 1 2026-02-09T06:12:16,810 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/lib/python3/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmpfcyiz5yq[/] 2026-02-09T06:12:16,811 [bold magenta]cwd[/]: /tmp/pip-wheel-pohs_afi/pyinfernal_07a163401e064802bab58d4f19731bfa 2026-02-09T06:12:16,812 Building wheel for pyinfernal (pyproject.toml): finished with status 'error' 2026-02-09T06:12:16,815 ERROR: Failed building wheel for pyinfernal 2026-02-09T06:12:16,827 Failed to build pyinfernal 2026-02-09T06:12:16,828 ERROR: Failed to build one or more wheels 2026-02-09T06:12:16,830 Exception information: 2026-02-09T06:12:16,830 Traceback (most recent call last): 2026-02-09T06:12:16,830 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 160, in exc_logging_wrapper 2026-02-09T06:12:16,830 status = run_func(*args) 2026-02-09T06:12:16,830 ^^^^^^^^^^^^^^^ 2026-02-09T06:12:16,830 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper 2026-02-09T06:12:16,830 return func(self, options, args) 2026-02-09T06:12:16,830 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2026-02-09T06:12:16,830 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 201, in run 2026-02-09T06:12:16,830 raise CommandError("Failed to build one or more wheels") 2026-02-09T06:12:16,830 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2026-02-09T06:12:16,836 Removed build tracker: '/tmp/pip-build-tracker-i1s36jtb'