2025-09-08T12:31:55,287 Created temporary directory: /tmp/pip-build-tracker-yfw17bt3 2025-09-08T12:31:55,288 Initialized build tracking at /tmp/pip-build-tracker-yfw17bt3 2025-09-08T12:31:55,288 Created build tracker: /tmp/pip-build-tracker-yfw17bt3 2025-09-08T12:31:55,288 Entered build tracker: /tmp/pip-build-tracker-yfw17bt3 2025-09-08T12:31:55,289 Created temporary directory: /tmp/pip-wheel-p2j7jyav 2025-09-08T12:31:55,292 Created temporary directory: /tmp/pip-ephem-wheel-cache-ct_s1hst 2025-09-08T12:31:55,346 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T12:31:55,349 2 location(s) to search for versions of rnatools: 2025-09-08T12:31:55,349 * https://pypi.org/simple/rnatools/ 2025-09-08T12:31:55,349 * https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:31:55,349 Fetching project page and analyzing links: https://pypi.org/simple/rnatools/ 2025-09-08T12:31:55,349 Getting page https://pypi.org/simple/rnatools/ 2025-09-08T12:31:55,350 Found index url https://pypi.org/simple/ 2025-09-08T12:31:55,495 Fetched page https://pypi.org/simple/rnatools/ as application/vnd.pypi.simple.v1+json 2025-09-08T12:31:55,497 Found link https://files.pythonhosted.org/packages/1e/ab/9d2e7f5b59b995b07b28c62d3aa903efd10e1e5bd597be89605afa6dc748/RNAtools-0.8.3.tar.gz (from https://pypi.org/simple/rnatools/), version: 0.8.3 2025-09-08T12:31:55,498 Found link https://files.pythonhosted.org/packages/3e/5c/ad715fb57216877e8269dd63b6ccd11e7ba38f809cdab4f7a204c3e3fe28/RNAtools-0.8.4.tar.gz (from https://pypi.org/simple/rnatools/), version: 0.8.4 2025-09-08T12:31:55,499 Found link https://files.pythonhosted.org/packages/86/a9/5d78b7e0c804cff750b772986af2a91fc42e8034438970220b06b2395351/RNAtools-0.8.5.tar.gz (from https://pypi.org/simple/rnatools/), version: 0.8.5 2025-09-08T12:31:55,499 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:31:55,500 Getting page https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:31:55,502 Found index url https://www.piwheels.org/simple/ 2025-09-08T12:31:55,597 Fetched page https://www.piwheels.org/simple/rnatools/ as text/html 2025-09-08T12:31:55,603 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp34-cp34m-linux_armv6l.whl#sha256=5615a6824f6f823c85eba01d4558f981948a1e6fa4a64deb978d21027e999788 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp34-cp34m-linux_armv7l.whl#sha256=5615a6824f6f823c85eba01d4558f981948a1e6fa4a64deb978d21027e999788 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp35-cp35m-linux_armv6l.whl#sha256=251d013a1d28538fe1cc413a2dd126138f3f19b2a076656f28819844aa8ad40c (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp35-cp35m-linux_armv7l.whl#sha256=251d013a1d28538fe1cc413a2dd126138f3f19b2a076656f28819844aa8ad40c (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp37-cp37m-linux_armv7l.whl#sha256=d21defac36eb74ed6c6d345c9431ef5326995e3bde02cee8eae7642c08b6699e (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp37-cp37m-linux_armv6l.whl#sha256=d21defac36eb74ed6c6d345c9431ef5326995e3bde02cee8eae7642c08b6699e (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,604 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp39-cp39-linux_armv6l.whl#sha256=cf8667ddc1c0407e69e54cb9df68b885340cb8891c176c4217fae9cff0ded320 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.5-cp39-cp39-linux_armv7l.whl#sha256=cf8667ddc1c0407e69e54cb9df68b885340cb8891c176c4217fae9cff0ded320 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp35-cp35m-linux_armv7l.whl#sha256=c1b2c1379d76d9a8ffce84b1bb073bd970fbe71e27c57b3ceba26645dd05c06f (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp35-cp35m-linux_armv6l.whl#sha256=c1b2c1379d76d9a8ffce84b1bb073bd970fbe71e27c57b3ceba26645dd05c06f (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp34-cp34m-linux_armv6l.whl#sha256=bbbd7cd84b80eef632d03789cd3a7e3f9569bf22cb3d8efb8d1033e6eb3855b9 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp34-cp34m-linux_armv7l.whl#sha256=bbbd7cd84b80eef632d03789cd3a7e3f9569bf22cb3d8efb8d1033e6eb3855b9 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp37-cp37m-linux_armv7l.whl#sha256=18377cdf66f64c8433f5f95d1aa36b409cfe6675cdf2ebd38d026ab7e2cae8d3 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,605 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp37-cp37m-linux_armv6l.whl#sha256=18377cdf66f64c8433f5f95d1aa36b409cfe6675cdf2ebd38d026ab7e2cae8d3 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp39-cp39-linux_armv6l.whl#sha256=9c2f48be38b47abcdb6de616e48164d229821822eb7f160e7b868faf990290bf (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.4-cp39-cp39-linux_armv7l.whl#sha256=9c2f48be38b47abcdb6de616e48164d229821822eb7f160e7b868faf990290bf (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp35-cp35m-linux_armv7l.whl#sha256=f09a0981e9206680a9918cb1e131007391479a5ef04765e20657326af824221f (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp35-cp35m-linux_armv6l.whl#sha256=f09a0981e9206680a9918cb1e131007391479a5ef04765e20657326af824221f (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp34-cp34m-linux_armv6l.whl#sha256=abe8347ca022be8b53730c88f66419df75b69115a82f0a8ab444cd8482f2bacd (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp34-cp34m-linux_armv7l.whl#sha256=abe8347ca022be8b53730c88f66419df75b69115a82f0a8ab444cd8482f2bacd (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,606 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp37-cp37m-linux_armv7l.whl#sha256=ab75769b5da02893476a572dc1790bdfea78f43656a5a87996cd7bd184e5ed54 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,607 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp37-cp37m-linux_armv6l.whl#sha256=ab75769b5da02893476a572dc1790bdfea78f43656a5a87996cd7bd184e5ed54 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,607 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp39-cp39-linux_armv6l.whl#sha256=3ac96edd4f697748723d60e968919f23681f4918098ed2b19e7f8c476e325904 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,607 Skipping link: No binaries permitted for rnatools: https://archive1.piwheels.org/simple/rnatools/RNAtools-0.8.3-cp39-cp39-linux_armv7l.whl#sha256=3ac96edd4f697748723d60e968919f23681f4918098ed2b19e7f8c476e325904 (from https://www.piwheels.org/simple/rnatools/) 2025-09-08T12:31:55,607 Skipping link: not a file: https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:31:55,607 Skipping link: not a file: https://pypi.org/simple/rnatools/ 2025-09-08T12:31:55,632 Given no hashes to check 1 links for project 'rnatools': discarding no candidates 2025-09-08T12:31:55,633 Collecting rnatools==0.8.3 2025-09-08T12:31:55,634 Created temporary directory: /tmp/pip-unpack-po0huujc 2025-09-08T12:31:55,773 Downloading RNAtools-0.8.3.tar.gz (78 kB) 2025-09-08T12:31:55,832 Added rnatools==0.8.3 from https://files.pythonhosted.org/packages/1e/ab/9d2e7f5b59b995b07b28c62d3aa903efd10e1e5bd597be89605afa6dc748/RNAtools-0.8.3.tar.gz to build tracker '/tmp/pip-build-tracker-yfw17bt3' 2025-09-08T12:31:55,833 Running setup.py (path:/tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44/setup.py) egg_info for package rnatools 2025-09-08T12:31:55,833 Created temporary directory: /tmp/pip-pip-egg-info-3ivsotcc 2025-09-08T12:31:55,833 Preparing metadata (setup.py): started 2025-09-08T12:31:55,834 Running command python setup.py egg_info 2025-09-08T12:31:57,179 running egg_info 2025-09-08T12:31:57,256 creating /tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info 2025-09-08T12:31:57,256 writing /tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/PKG-INFO 2025-09-08T12:31:57,258 writing dependency_links to /tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/dependency_links.txt 2025-09-08T12:31:57,258 writing entry points to /tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/entry_points.txt 2025-09-08T12:31:57,259 writing top-level names to /tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/top_level.txt 2025-09-08T12:31:57,259 writing manifest file '/tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:31:57,482 reading manifest file '/tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:31:57,483 reading manifest template 'MANIFEST.in' 2025-09-08T12:31:57,487 writing manifest file '/tmp/pip-pip-egg-info-3ivsotcc/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:31:57,624 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T12:31:57,628 Source in /tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44 has version 0.8.3, which satisfies requirement rnatools==0.8.3 from https://files.pythonhosted.org/packages/1e/ab/9d2e7f5b59b995b07b28c62d3aa903efd10e1e5bd597be89605afa6dc748/RNAtools-0.8.3.tar.gz 2025-09-08T12:31:57,629 Removed rnatools==0.8.3 from https://files.pythonhosted.org/packages/1e/ab/9d2e7f5b59b995b07b28c62d3aa903efd10e1e5bd597be89605afa6dc748/RNAtools-0.8.3.tar.gz from build tracker '/tmp/pip-build-tracker-yfw17bt3' 2025-09-08T12:31:57,631 Created temporary directory: /tmp/pip-unpack-4wvk_58w 2025-09-08T12:31:57,632 Created temporary directory: /tmp/pip-unpack-9_etg9of 2025-09-08T12:31:57,632 Building wheels for collected packages: rnatools 2025-09-08T12:31:57,633 Created temporary directory: /tmp/pip-wheel-ja26bzhk 2025-09-08T12:31:57,634 DEPRECATION: Building 'rnatools' 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 'rnatools'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T12:31:57,635 Building wheel for rnatools (setup.py): started 2025-09-08T12:31:57,635 Destination directory: /tmp/pip-wheel-ja26bzhk 2025-09-08T12:31:57,635 Running command python setup.py bdist_wheel 2025-09-08T12:31:58,909 running bdist_wheel 2025-09-08T12:31:59,204 running build 2025-09-08T12:31:59,205 running build_py 2025-09-08T12:31:59,282 creating build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:31:59,282 copying RNAtools/__init__.py -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:31:59,283 copying RNAtools/graph.py -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:31:59,284 running egg_info 2025-09-08T12:31:59,359 writing RNAtools.egg-info/PKG-INFO 2025-09-08T12:31:59,361 writing dependency_links to RNAtools.egg-info/dependency_links.txt 2025-09-08T12:31:59,361 writing entry points to RNAtools.egg-info/entry_points.txt 2025-09-08T12:31:59,362 writing top-level names to RNAtools.egg-info/top_level.txt 2025-09-08T12:31:59,438 reading manifest file 'RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:31:59,440 reading manifest template 'MANIFEST.in' 2025-09-08T12:31:59,445 writing manifest file 'RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:31:59,446 copying RNAtools/partAlign.pyx -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:31:59,447 running build_ext 2025-09-08T12:31:59,797 Compiling RNAtools/partAlign.pyx because it changed. 2025-09-08T12:31:59,798 [1/1] Cythonizing RNAtools/partAlign.pyx 2025-09-08T12:32:00,680 Error compiling Cython file: 2025-09-08T12:32:00,681 ------------------------------------------------------------ 2025-09-08T12:32:00,681 ... 2025-09-08T12:32:00,681 print("#"*30) 2025-09-08T12:32:00,681 print("backtrace") 2025-09-08T12:32:00,681 tmp1, tmp2, scoreMax = align_RNA_partition_backtrace(x,y) 2025-09-08T12:32:00,681 print(list(tmp1)) 2025-09-08T12:32:00,681 print(list(tmp2)) 2025-09-08T12:32:00,681 print scoreMax 2025-09-08T12:32:00,681 ^ 2025-09-08T12:32:00,681 ------------------------------------------------------------ 2025-09-08T12:32:00,682 RNAtools/partAlign.pyx:437:10: Syntax error in simple statement list 2025-09-08T12:32:00,691 Traceback (most recent call last): 2025-09-08T12:32:00,698 File "", line 2, in 2025-09-08T12:32:00,699 exec(compile(''' 2025-09-08T12:32:00,699 ~~~~^^^^^^^^^^^^ 2025-09-08T12:32:00,699 # This is -- a caller that pip uses to run setup.py 2025-09-08T12:32:00,699 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,699 ...<32 lines>... 2025-09-08T12:32:00,699 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T12:32:00,699 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,699 ''' % ('/tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44/setup.py',), "", "exec")) 2025-09-08T12:32:00,699 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,700 File "", line 35, in 2025-09-08T12:32:00,700 File "/tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44/setup.py", line 12, in 2025-09-08T12:32:00,700 setup(name='RNAtools', 2025-09-08T12:32:00,700 ~~~~~^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,700 version='0.8.3', 2025-09-08T12:32:00,700 ^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,700 ...<13 lines>... 2025-09-08T12:32:00,700 'cleanCT=RNAtools.scripts.cleanCT:main'] 2025-09-08T12:32:00,701 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,701 }) 2025-09-08T12:32:00,701 ^^ 2025-09-08T12:32:00,701 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T12:32:00,701 return distutils.core.setup(**attrs) 2025-09-08T12:32:00,701 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,701 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T12:32:00,701 return run_commands(dist) 2025-09-08T12:32:00,702 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T12:32:00,702 dist.run_commands() 2025-09-08T12:32:00,702 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:32:00,702 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T12:32:00,702 self.run_command(cmd) 2025-09-08T12:32:00,702 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T12:32:00,702 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:32:00,702 super().run_command(command) 2025-09-08T12:32:00,703 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,703 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:32:00,703 cmd_obj.run() 2025-09-08T12:32:00,703 ~~~~~~~~~~~^^ 2025-09-08T12:32:00,703 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T12:32:00,703 self.run_command("build") 2025-09-08T12:32:00,703 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,703 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T12:32:00,703 self.distribution.run_command(command) 2025-09-08T12:32:00,704 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,704 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:32:00,704 super().run_command(command) 2025-09-08T12:32:00,704 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,704 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:32:00,704 cmd_obj.run() 2025-09-08T12:32:00,704 ~~~~~~~~~~~^^ 2025-09-08T12:32:00,704 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T12:32:00,704 self.run_command(cmd_name) 2025-09-08T12:32:00,705 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T12:32:00,705 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T12:32:00,705 self.distribution.run_command(command) 2025-09-08T12:32:00,705 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,705 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:32:00,705 super().run_command(command) 2025-09-08T12:32:00,705 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:32:00,705 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:32:00,706 cmd_obj.run() 2025-09-08T12:32:00,706 ~~~~~~~~~~~^^ 2025-09-08T12:32:00,706 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T12:32:00,706 self.build_extensions() 2025-09-08T12:32:00,706 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:32:00,706 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T12:32:00,706 self._build_extensions_serial() 2025-09-08T12:32:00,706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:32:00,707 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T12:32:00,707 self.build_extension(ext) 2025-09-08T12:32:00,707 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T12:32:00,707 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T12:32:00,707 new_ext = cythonize( 2025-09-08T12:32:00,707 ~~~~~~~~~^ 2025-09-08T12:32:00,707 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T12:32:00,707 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:32:00,708 )[0] 2025-09-08T12:32:00,708 ^ 2025-09-08T12:32:00,708 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T12:32:00,708 cythonize_one(*args) 2025-09-08T12:32:00,708 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T12:32:00,708 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T12:32:00,708 raise CompileError(None, pyx_file) 2025-09-08T12:32:00,709 Cython.Compiler.Errors.CompileError: RNAtools/partAlign.pyx 2025-09-08T12:32:00,984 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T12:32:00,997 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T12:32:00,997 exec(compile('"'"''"'"''"'"' 2025-09-08T12:32:00,997 # This is -- a caller that pip uses to run setup.py 2025-09-08T12:32:00,997 # 2025-09-08T12:32:00,997 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T12:32:00,997 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T12:32:00,997 # - It provides a clear error message when setuptools is not installed. 2025-09-08T12:32:00,997 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T12:32:00,997 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T12:32:00,997 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T12:32:00,997 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T12:32:00,997 import os, sys, tokenize, traceback 2025-09-08T12:32:00,997 2025-09-08T12:32:00,997 try: 2025-09-08T12:32:00,997 import setuptools 2025-09-08T12:32:00,997 except ImportError: 2025-09-08T12:32:00,997 print( 2025-09-08T12:32:00,997 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T12:32:00,997 "the build environment with exception:", 2025-09-08T12:32:00,997 file=sys.stderr, 2025-09-08T12:32:00,997 ) 2025-09-08T12:32:00,997 traceback.print_exc() 2025-09-08T12:32:00,997 sys.exit(1) 2025-09-08T12:32:00,997 2025-09-08T12:32:00,997 __file__ = %r 2025-09-08T12:32:00,997 sys.argv[0] = __file__ 2025-09-08T12:32:00,997 2025-09-08T12:32:00,997 if os.path.exists(__file__): 2025-09-08T12:32:00,997 filename = __file__ 2025-09-08T12:32:00,997 with tokenize.open(__file__) as f: 2025-09-08T12:32:00,997 setup_py_code = f.read() 2025-09-08T12:32:00,997 else: 2025-09-08T12:32:00,997 filename = "" 2025-09-08T12:32:00,997 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T12:32:00,997 2025-09-08T12:32:00,997 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T12:32:00,997 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ja26bzhk[/] 2025-09-08T12:32:00,997 [bold magenta]cwd[/]: /tmp/pip-wheel-p2j7jyav/rnatools_ee4245e6296347d5a6fbfce22a7b8d44/ 2025-09-08T12:32:00,997 Building wheel for rnatools (setup.py): finished with status 'error' 2025-09-08T12:32:00,998 ERROR: Failed building wheel for rnatools 2025-09-08T12:32:00,999 Running setup.py clean for rnatools 2025-09-08T12:32:00,999 Running command python setup.py clean 2025-09-08T12:32:02,357 running clean 2025-09-08T12:32:02,505 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T12:32:02,505 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T12:32:02,506 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T12:32:02,506 removing 'build' 2025-09-08T12:32:02,641 Failed to build rnatools 2025-09-08T12:32:02,642 ERROR: Failed to build one or more wheels 2025-09-08T12:32:02,643 Exception information: 2025-09-08T12:32:02,643 Traceback (most recent call last): 2025-09-08T12:32:02,643 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T12:32:02,643 status = _inner_run() 2025-09-08T12:32:02,643 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T12:32:02,643 return self.run(options, args) 2025-09-08T12:32:02,643 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T12:32:02,643 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T12:32:02,643 return func(self, options, args) 2025-09-08T12:32:02,643 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T12:32:02,643 raise CommandError("Failed to build one or more wheels") 2025-09-08T12:32:02,643 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T12:32:02,647 Removed build tracker: '/tmp/pip-build-tracker-yfw17bt3'