2025-09-08T12:33:37,406 Created temporary directory: /tmp/pip-build-tracker-bnrq_9nv 2025-09-08T12:33:37,406 Initialized build tracking at /tmp/pip-build-tracker-bnrq_9nv 2025-09-08T12:33:37,407 Created build tracker: /tmp/pip-build-tracker-bnrq_9nv 2025-09-08T12:33:37,407 Entered build tracker: /tmp/pip-build-tracker-bnrq_9nv 2025-09-08T12:33:37,407 Created temporary directory: /tmp/pip-wheel-d237yqq1 2025-09-08T12:33:37,410 Created temporary directory: /tmp/pip-ephem-wheel-cache-yal32dwh 2025-09-08T12:33:37,469 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T12:33:37,471 2 location(s) to search for versions of rnatools: 2025-09-08T12:33:37,471 * https://pypi.org/simple/rnatools/ 2025-09-08T12:33:37,471 * https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:33:37,472 Fetching project page and analyzing links: https://pypi.org/simple/rnatools/ 2025-09-08T12:33:37,472 Getting page https://pypi.org/simple/rnatools/ 2025-09-08T12:33:37,473 Found index url https://pypi.org/simple/ 2025-09-08T12:33:37,543 Fetched page https://pypi.org/simple/rnatools/ as application/vnd.pypi.simple.v1+json 2025-09-08T12:33:37,544 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 2025-09-08T12:33:37,544 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 2025-09-08T12:33:37,544 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 2025-09-08T12:33:37,545 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:33:37,545 Getting page https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:33:37,546 Found index url https://www.piwheels.org/simple/ 2025-09-08T12:33:37,646 Fetched page https://www.piwheels.org/simple/rnatools/ as text/html 2025-09-08T12:33:37,650 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/) 2025-09-08T12:33:37,650 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/) 2025-09-08T12:33:37,650 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,651 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,652 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/) 2025-09-08T12:33:37,653 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/) 2025-09-08T12:33:37,653 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/) 2025-09-08T12:33:37,653 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/) 2025-09-08T12:33:37,653 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/) 2025-09-08T12:33:37,653 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/) 2025-09-08T12:33:37,653 Skipping link: not a file: https://www.piwheels.org/simple/rnatools/ 2025-09-08T12:33:37,653 Skipping link: not a file: https://pypi.org/simple/rnatools/ 2025-09-08T12:33:37,676 Given no hashes to check 1 links for project 'rnatools': discarding no candidates 2025-09-08T12:33:37,677 Collecting rnatools==0.8.5 2025-09-08T12:33:37,679 Created temporary directory: /tmp/pip-unpack-6ajal0r0 2025-09-08T12:33:37,817 Downloading RNAtools-0.8.5.tar.gz (79 kB) 2025-09-08T12:33:37,874 Added rnatools==0.8.5 from https://files.pythonhosted.org/packages/86/a9/5d78b7e0c804cff750b772986af2a91fc42e8034438970220b06b2395351/RNAtools-0.8.5.tar.gz to build tracker '/tmp/pip-build-tracker-bnrq_9nv' 2025-09-08T12:33:37,875 Running setup.py (path:/tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b/setup.py) egg_info for package rnatools 2025-09-08T12:33:37,876 Created temporary directory: /tmp/pip-pip-egg-info-_5vbqmwp 2025-09-08T12:33:37,876 Preparing metadata (setup.py): started 2025-09-08T12:33:37,877 Running command python setup.py egg_info 2025-09-08T12:33:39,279 running egg_info 2025-09-08T12:33:39,355 creating /tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info 2025-09-08T12:33:39,355 writing /tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/PKG-INFO 2025-09-08T12:33:39,356 writing dependency_links to /tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/dependency_links.txt 2025-09-08T12:33:39,357 writing entry points to /tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/entry_points.txt 2025-09-08T12:33:39,357 writing top-level names to /tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/top_level.txt 2025-09-08T12:33:39,358 writing manifest file '/tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:33:39,581 reading manifest file '/tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:33:39,582 reading manifest template 'MANIFEST.in' 2025-09-08T12:33:39,584 adding license file 'LICENSE' 2025-09-08T12:33:39,587 writing manifest file '/tmp/pip-pip-egg-info-_5vbqmwp/RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:33:39,722 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T12:33:39,727 Source in /tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b has version 0.8.5, which satisfies requirement rnatools==0.8.5 from https://files.pythonhosted.org/packages/86/a9/5d78b7e0c804cff750b772986af2a91fc42e8034438970220b06b2395351/RNAtools-0.8.5.tar.gz 2025-09-08T12:33:39,727 Removed rnatools==0.8.5 from https://files.pythonhosted.org/packages/86/a9/5d78b7e0c804cff750b772986af2a91fc42e8034438970220b06b2395351/RNAtools-0.8.5.tar.gz from build tracker '/tmp/pip-build-tracker-bnrq_9nv' 2025-09-08T12:33:39,730 Created temporary directory: /tmp/pip-unpack-xmsgmjka 2025-09-08T12:33:39,730 Created temporary directory: /tmp/pip-unpack-eac9otbj 2025-09-08T12:33:39,730 Building wheels for collected packages: rnatools 2025-09-08T12:33:39,731 Created temporary directory: /tmp/pip-wheel-ebfwsfbb 2025-09-08T12:33:39,732 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 2025-09-08T12:33:39,733 Building wheel for rnatools (setup.py): started 2025-09-08T12:33:39,734 Destination directory: /tmp/pip-wheel-ebfwsfbb 2025-09-08T12:33:39,734 Running command python setup.py bdist_wheel 2025-09-08T12:33:41,003 running bdist_wheel 2025-09-08T12:33:41,297 running build 2025-09-08T12:33:41,297 running build_py 2025-09-08T12:33:41,373 creating build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:33:41,373 copying RNAtools/__init__.py -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:33:41,374 copying RNAtools/graph.py -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:33:41,374 running egg_info 2025-09-08T12:33:41,449 writing RNAtools.egg-info/PKG-INFO 2025-09-08T12:33:41,450 writing dependency_links to RNAtools.egg-info/dependency_links.txt 2025-09-08T12:33:41,450 writing entry points to RNAtools.egg-info/entry_points.txt 2025-09-08T12:33:41,451 writing top-level names to RNAtools.egg-info/top_level.txt 2025-09-08T12:33:41,526 reading manifest file 'RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:33:41,529 reading manifest template 'MANIFEST.in' 2025-09-08T12:33:41,531 adding license file 'LICENSE' 2025-09-08T12:33:41,534 writing manifest file 'RNAtools.egg-info/SOURCES.txt' 2025-09-08T12:33:41,535 copying RNAtools/partAlign.pyx -> build/lib.linux-armv7l-cpython-313/RNAtools 2025-09-08T12:33:41,536 running build_ext 2025-09-08T12:33:41,866 Compiling RNAtools/partAlign.pyx because it changed. 2025-09-08T12:33:41,866 [1/1] Cythonizing RNAtools/partAlign.pyx 2025-09-08T12:33:42,735 Error compiling Cython file: 2025-09-08T12:33:42,736 ------------------------------------------------------------ 2025-09-08T12:33:42,736 ... 2025-09-08T12:33:42,736 print("#"*30) 2025-09-08T12:33:42,736 print("backtrace") 2025-09-08T12:33:42,736 tmp1, tmp2, scoreMax = align_RNA_partition_backtrace(x,y) 2025-09-08T12:33:42,736 print(list(tmp1)) 2025-09-08T12:33:42,736 print(list(tmp2)) 2025-09-08T12:33:42,736 print scoreMax 2025-09-08T12:33:42,736 ^ 2025-09-08T12:33:42,736 ------------------------------------------------------------ 2025-09-08T12:33:42,737 RNAtools/partAlign.pyx:437:10: Syntax error in simple statement list 2025-09-08T12:33:42,747 Traceback (most recent call last): 2025-09-08T12:33:42,754 File "", line 2, in 2025-09-08T12:33:42,755 exec(compile(''' 2025-09-08T12:33:42,755 ~~~~^^^^^^^^^^^^ 2025-09-08T12:33:42,755 # This is -- a caller that pip uses to run setup.py 2025-09-08T12:33:42,755 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,755 ...<32 lines>... 2025-09-08T12:33:42,755 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T12:33:42,755 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,755 ''' % ('/tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b/setup.py',), "", "exec")) 2025-09-08T12:33:42,755 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,756 File "", line 35, in 2025-09-08T12:33:42,756 File "/tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b/setup.py", line 12, in 2025-09-08T12:33:42,756 setup(name='RNAtools', 2025-09-08T12:33:42,756 ~~~~~^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,756 version='0.8.5', 2025-09-08T12:33:42,756 ^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,756 ...<13 lines>... 2025-09-08T12:33:42,756 'cleanCT=RNAtools.scripts.cleanCT:main'] 2025-09-08T12:33:42,757 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,757 }) 2025-09-08T12:33:42,757 ^^ 2025-09-08T12:33:42,757 File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup 2025-09-08T12:33:42,757 return distutils.core.setup(**attrs) 2025-09-08T12:33:42,757 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,757 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup 2025-09-08T12:33:42,757 return run_commands(dist) 2025-09-08T12:33:42,758 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands 2025-09-08T12:33:42,758 dist.run_commands() 2025-09-08T12:33:42,758 ~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:33:42,758 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands 2025-09-08T12:33:42,758 self.run_command(cmd) 2025-09-08T12:33:42,758 ~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T12:33:42,758 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:33:42,758 super().run_command(command) 2025-09-08T12:33:42,758 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,759 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:33:42,759 cmd_obj.run() 2025-09-08T12:33:42,759 ~~~~~~~~~~~^^ 2025-09-08T12:33:42,759 File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run 2025-09-08T12:33:42,759 self.run_command("build") 2025-09-08T12:33:42,759 ~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,759 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T12:33:42,760 self.distribution.run_command(command) 2025-09-08T12:33:42,760 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,760 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:33:42,760 super().run_command(command) 2025-09-08T12:33:42,760 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,760 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:33:42,760 cmd_obj.run() 2025-09-08T12:33:42,760 ~~~~~~~~~~~^^ 2025-09-08T12:33:42,761 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run 2025-09-08T12:33:42,761 self.run_command(cmd_name) 2025-09-08T12:33:42,761 ~~~~~~~~~~~~~~~~^^^^^^^^^^ 2025-09-08T12:33:42,761 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command 2025-09-08T12:33:42,761 self.distribution.run_command(command) 2025-09-08T12:33:42,761 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,761 File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command 2025-09-08T12:33:42,761 super().run_command(command) 2025-09-08T12:33:42,761 ~~~~~~~~~~~~~~~~~~~^^^^^^^^^ 2025-09-08T12:33:42,762 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command 2025-09-08T12:33:42,762 cmd_obj.run() 2025-09-08T12:33:42,762 ~~~~~~~~~~~^^ 2025-09-08T12:33:42,762 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 368, in run 2025-09-08T12:33:42,762 self.build_extensions() 2025-09-08T12:33:42,762 ~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:33:42,762 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 484, in build_extensions 2025-09-08T12:33:42,762 self._build_extensions_serial() 2025-09-08T12:33:42,763 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T12:33:42,763 File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build_ext.py", line 510, in _build_extensions_serial 2025-09-08T12:33:42,763 self.build_extension(ext) 2025-09-08T12:33:42,763 ~~~~~~~~~~~~~~~~~~~~^^^^^ 2025-09-08T12:33:42,763 File "/usr/local/lib/python3.13/dist-packages/Cython/Distutils/build_ext.py", line 131, in build_extension 2025-09-08T12:33:42,763 new_ext = cythonize( 2025-09-08T12:33:42,763 ~~~~~~~~~^ 2025-09-08T12:33:42,764 ext,force=self.force, quiet=self.verbose == 0, **options 2025-09-08T12:33:42,764 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T12:33:42,764 )[0] 2025-09-08T12:33:42,764 ^ 2025-09-08T12:33:42,764 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize 2025-09-08T12:33:42,764 cythonize_one(*args) 2025-09-08T12:33:42,764 ~~~~~~~~~~~~~^^^^^^^ 2025-09-08T12:33:42,764 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one 2025-09-08T12:33:42,765 raise CompileError(None, pyx_file) 2025-09-08T12:33:42,765 Cython.Compiler.Errors.CompileError: RNAtools/partAlign.pyx 2025-09-08T12:33:43,033 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T12:33:43,044 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T12:33:43,044 exec(compile('"'"''"'"''"'"' 2025-09-08T12:33:43,044 # This is -- a caller that pip uses to run setup.py 2025-09-08T12:33:43,044 # 2025-09-08T12:33:43,044 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T12:33:43,044 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T12:33:43,044 # - It provides a clear error message when setuptools is not installed. 2025-09-08T12:33:43,044 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T12:33:43,044 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T12:33:43,044 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T12:33:43,044 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T12:33:43,044 import os, sys, tokenize, traceback 2025-09-08T12:33:43,044 2025-09-08T12:33:43,044 try: 2025-09-08T12:33:43,044 import setuptools 2025-09-08T12:33:43,044 except ImportError: 2025-09-08T12:33:43,044 print( 2025-09-08T12:33:43,044 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T12:33:43,044 "the build environment with exception:", 2025-09-08T12:33:43,044 file=sys.stderr, 2025-09-08T12:33:43,044 ) 2025-09-08T12:33:43,044 traceback.print_exc() 2025-09-08T12:33:43,044 sys.exit(1) 2025-09-08T12:33:43,044 2025-09-08T12:33:43,044 __file__ = %r 2025-09-08T12:33:43,044 sys.argv[0] = __file__ 2025-09-08T12:33:43,044 2025-09-08T12:33:43,044 if os.path.exists(__file__): 2025-09-08T12:33:43,044 filename = __file__ 2025-09-08T12:33:43,044 with tokenize.open(__file__) as f: 2025-09-08T12:33:43,044 setup_py_code = f.read() 2025-09-08T12:33:43,044 else: 2025-09-08T12:33:43,044 filename = "" 2025-09-08T12:33:43,044 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T12:33:43,044 2025-09-08T12:33:43,044 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T12:33:43,044 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ebfwsfbb[/] 2025-09-08T12:33:43,045 [bold magenta]cwd[/]: /tmp/pip-wheel-d237yqq1/rnatools_1874b9b3964546b6a81030e4969c1d5b/ 2025-09-08T12:33:43,045 Building wheel for rnatools (setup.py): finished with status 'error' 2025-09-08T12:33:43,045 ERROR: Failed building wheel for rnatools 2025-09-08T12:33:43,046 Running setup.py clean for rnatools 2025-09-08T12:33:43,047 Running command python setup.py clean 2025-09-08T12:33:44,385 running clean 2025-09-08T12:33:44,531 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T12:33:44,532 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T12:33:44,532 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T12:33:44,532 removing 'build' 2025-09-08T12:33:44,666 Failed to build rnatools 2025-09-08T12:33:44,667 ERROR: Failed to build one or more wheels 2025-09-08T12:33:44,668 Exception information: 2025-09-08T12:33:44,668 Traceback (most recent call last): 2025-09-08T12:33:44,668 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T12:33:44,668 status = _inner_run() 2025-09-08T12:33:44,668 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T12:33:44,668 return self.run(options, args) 2025-09-08T12:33:44,668 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T12:33:44,668 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T12:33:44,668 return func(self, options, args) 2025-09-08T12:33:44,668 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T12:33:44,668 raise CommandError("Failed to build one or more wheels") 2025-09-08T12:33:44,668 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T12:33:44,673 Removed build tracker: '/tmp/pip-build-tracker-bnrq_9nv'