2025-09-10T14:45:17,116 Created temporary directory: /tmp/pip-build-tracker-e00tcy1c 2025-09-10T14:45:17,116 Initialized build tracking at /tmp/pip-build-tracker-e00tcy1c 2025-09-10T14:45:17,117 Created build tracker: /tmp/pip-build-tracker-e00tcy1c 2025-09-10T14:45:17,117 Entered build tracker: /tmp/pip-build-tracker-e00tcy1c 2025-09-10T14:45:17,117 Created temporary directory: /tmp/pip-wheel-z8x0cli8 2025-09-10T14:45:17,120 Created temporary directory: /tmp/pip-ephem-wheel-cache-5zii55nw 2025-09-10T14:45:17,180 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-10T14:45:17,182 2 location(s) to search for versions of hotknots: 2025-09-10T14:45:17,182 * https://pypi.org/simple/hotknots/ 2025-09-10T14:45:17,182 * https://www.piwheels.org/simple/hotknots/ 2025-09-10T14:45:17,183 Fetching project page and analyzing links: https://pypi.org/simple/hotknots/ 2025-09-10T14:45:17,183 Getting page https://pypi.org/simple/hotknots/ 2025-09-10T14:45:17,184 Found index url https://pypi.org/simple/ 2025-09-10T14:45:17,331 Fetched page https://pypi.org/simple/hotknots/ as application/vnd.pypi.simple.v1+json 2025-09-10T14:45:17,333 Skipping link: No binaries permitted for hotknots: https://files.pythonhosted.org/packages/48/e3/1068c7ff2648921adfa12727976509ddb9044e3c73c776f237ed3d93f279/hotknots-2.4-cp38-cp38-macosx_10_14_x86_64.whl (from https://pypi.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,334 Found link https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz (from https://pypi.org/simple/hotknots/) (requires-python:>3.5.2), version: 2.4 2025-09-10T14:45:17,335 Fetching project page and analyzing links: https://www.piwheels.org/simple/hotknots/ 2025-09-10T14:45:17,336 Getting page https://www.piwheels.org/simple/hotknots/ 2025-09-10T14:45:17,337 Found index url https://www.piwheels.org/simple/ 2025-09-10T14:45:17,442 Fetched page https://www.piwheels.org/simple/hotknots/ as text/html 2025-09-10T14:45:17,444 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp37-cp37m-linux_armv6l.whl#sha256=8fdfa32985674cf83beb88e9f83a7688cba37815db50709fbc0f11bd3a5a60e3 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp37-cp37m-linux_armv7l.whl#sha256=8fdfa32985674cf83beb88e9f83a7688cba37815db50709fbc0f11bd3a5a60e3 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp39-cp39-linux_armv6l.whl#sha256=c1e9c91c02634a50036bdada1cefe6c3fa08e3917ca4617f81b58564137af013 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp39-cp39-linux_armv7l.whl#sha256=c1e9c91c02634a50036bdada1cefe6c3fa08e3917ca4617f81b58564137af013 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp311-cp311-linux_armv6l.whl#sha256=c0cb646f635ea8be9f2fefe0eb261e1e4653f94570838c8c75ea48ed37289244 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: No binaries permitted for hotknots: https://archive1.piwheels.org/simple/hotknots/hotknots-2.4-cp311-cp311-linux_armv7l.whl#sha256=c0cb646f635ea8be9f2fefe0eb261e1e4653f94570838c8c75ea48ed37289244 (from https://www.piwheels.org/simple/hotknots/) (requires-python:>3.5.2) 2025-09-10T14:45:17,445 Skipping link: not a file: https://www.piwheels.org/simple/hotknots/ 2025-09-10T14:45:17,446 Skipping link: not a file: https://pypi.org/simple/hotknots/ 2025-09-10T14:45:17,474 Given no hashes to check 1 links for project 'hotknots': discarding no candidates 2025-09-10T14:45:17,475 Collecting hotknots==2.4 2025-09-10T14:45:17,477 Created temporary directory: /tmp/pip-unpack-1y14o_q6 2025-09-10T14:45:17,617 Downloading hotknots-2.4.tar.gz (435 kB) 2025-09-10T14:45:17,865 Added hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz to build tracker '/tmp/pip-build-tracker-e00tcy1c' 2025-09-10T14:45:17,866 Running setup.py (path:/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/setup.py) egg_info for package hotknots 2025-09-10T14:45:17,866 Created temporary directory: /tmp/pip-pip-egg-info-l56jmlex 2025-09-10T14:45:17,866 Preparing metadata (setup.py): started 2025-09-10T14:45:17,867 Running command python setup.py egg_info 2025-09-10T14:45:18,963 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-10T14:45:18,963 !! 2025-09-10T14:45:18,963 ******************************************************************************** 2025-09-10T14:45:18,964 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-10T14:45:18,964 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-10T14:45:18,964 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-10T14:45:18,964 ******************************************************************************** 2025-09-10T14:45:18,964 !! 2025-09-10T14:45:18,964 self._finalize_license_expression() 2025-09-10T14:45:19,038 running egg_info 2025-09-10T14:45:19,115 creating /tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info 2025-09-10T14:45:19,115 writing /tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/PKG-INFO 2025-09-10T14:45:19,116 writing dependency_links to /tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/dependency_links.txt 2025-09-10T14:45:19,117 writing top-level names to /tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/top_level.txt 2025-09-10T14:45:19,117 writing manifest file '/tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/SOURCES.txt' 2025-09-10T14:45:19,501 reading manifest file '/tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/SOURCES.txt' 2025-09-10T14:45:19,502 reading manifest template 'MANIFEST.in' 2025-09-10T14:45:19,509 warning: no files found matching '*.c' under directory 'src' 2025-09-10T14:45:19,509 adding license file 'LICENSE' 2025-09-10T14:45:19,516 writing manifest file '/tmp/pip-pip-egg-info-l56jmlex/hotknots.egg-info/SOURCES.txt' 2025-09-10T14:45:19,630 Preparing metadata (setup.py): finished with status 'done' 2025-09-10T14:45:19,635 Source in /tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb has version 2.4, which satisfies requirement hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz 2025-09-10T14:45:19,635 Removed hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz from build tracker '/tmp/pip-build-tracker-e00tcy1c' 2025-09-10T14:45:19,639 Created temporary directory: /tmp/pip-unpack-4qhijzcg 2025-09-10T14:45:19,639 Created temporary directory: /tmp/pip-unpack-yuiozmd6 2025-09-10T14:45:19,640 Building wheels for collected packages: hotknots 2025-09-10T14:45:19,641 Created temporary directory: /tmp/pip-wheel-7dauto_8 2025-09-10T14:45:19,641 DEPRECATION: Building 'hotknots' 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 'hotknots'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-10T14:45:19,643 Building wheel for hotknots (setup.py): started 2025-09-10T14:45:19,643 Destination directory: /tmp/pip-wheel-7dauto_8 2025-09-10T14:45:19,644 Running command python setup.py bdist_wheel 2025-09-10T14:45:20,744 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-10T14:45:20,744 !! 2025-09-10T14:45:20,744 ******************************************************************************** 2025-09-10T14:45:20,744 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-10T14:45:20,744 License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+) 2025-09-10T14:45:20,745 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-10T14:45:20,745 ******************************************************************************** 2025-09-10T14:45:20,745 !! 2025-09-10T14:45:20,745 self._finalize_license_expression() 2025-09-10T14:45:20,745 running bdist_wheel 2025-09-10T14:45:21,115 running build 2025-09-10T14:45:21,115 running build_py 2025-09-10T14:45:21,195 creating build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,195 copying hotknots/__init__.py -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,202 copying hotknots/walter-coaxstack-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,203 copying hotknots/turner-tstacki-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,203 copying hotknots/turner-tstackh-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,204 copying hotknots/turner-triloop-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,204 copying hotknots/turner-tloop-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,205 copying hotknots/turner-stack-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,205 copying hotknots/turner-sint4-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,206 copying hotknots/turner-sint2-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,207 copying hotknots/turner-miscloop-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,208 copying hotknots/turner-loop-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,208 copying hotknots/turner-dangle-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,209 copying hotknots/turner-asint1x2-rna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,209 copying hotknots/tstackcoax.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,210 copying hotknots/pkmodelRE.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,210 copying hotknots/pkmodelDP.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,211 copying hotknots/pkmodelCC2006.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,211 copying hotknots/mathews-tstacki-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,212 copying hotknots/mathews-tstackh-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,213 copying hotknots/mathews-triloop-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,213 copying hotknots/mathews-tloop-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,214 copying hotknots/mathews-stack-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,214 copying hotknots/mathews-sint4-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,215 copying hotknots/mathews-sint2-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,215 copying hotknots/mathews-miscloop-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,216 copying hotknots/mathews-loop-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,216 copying hotknots/mathews-dangle-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,217 copying hotknots/mathews-asint1x2-dna.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,218 copying hotknots/coaxstack.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,218 copying hotknots/coaxial.dat -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,219 copying hotknots/turner-tstacki-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,219 copying hotknots/turner-tstackh-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,220 copying hotknots/turner-triloop-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,220 copying hotknots/turner-tloop-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,221 copying hotknots/turner-stack-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,221 copying hotknots/turner-sint4-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,222 copying hotknots/turner-sint2-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,223 copying hotknots/turner-miscloop-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,223 copying hotknots/turner-loop-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,224 copying hotknots/turner-dangle-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,224 copying hotknots/turner-asint1x2-rna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,225 copying hotknots/mathews-tstacki-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,226 copying hotknots/mathews-tstackh-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,226 copying hotknots/mathews-triloop-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,227 copying hotknots/mathews-tloop-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,227 copying hotknots/mathews-stack-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,228 copying hotknots/mathews-sint4-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,228 copying hotknots/mathews-sint2-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,229 copying hotknots/mathews-miscloop-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,229 copying hotknots/mathews-loop-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,230 copying hotknots/mathews-dangle-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,231 copying hotknots/mathews-asint1x2-dna.dh -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,231 copying hotknots/pkenergy.conf -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,232 copying hotknots/multirnafold.conf -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,232 copying hotknots/turner-tstacki-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,233 copying hotknots/turner-tstackh-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,233 copying hotknots/turner-triloop-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,234 copying hotknots/turner-tloop-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,234 copying hotknots/turner-stack-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,235 copying hotknots/turner-sint4-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,236 copying hotknots/turner-sint2-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,236 copying hotknots/turner-miscloop-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,237 copying hotknots/turner-loop-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,237 copying hotknots/turner-dangle-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,238 copying hotknots/turner-asint1x2-rna.dg -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,239 copying hotknots/turner_partypes_fm363.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,239 copying hotknots/turner_parameters_fm363_constrdangles.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,240 copying hotknots/parameters_DP09.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,240 copying hotknots/parameters_DP03.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,241 copying hotknots/parameters_CC09.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,241 copying hotknots/parameters_CC06.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,242 copying hotknots/CG_best_parameters_ISMB2007.txt -> build/lib.linux-armv7l-cpython-313/hotknots 2025-09-10T14:45:21,243 running build_ext 2025-09-10T14:45:21,606 building 'hotknots.hotknots' extension 2025-09-10T14:45:21,611 creating build/temp.linux-armv7l-cpython-313/src 2025-09-10T14:45:21,614 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/Bands.cpp -o build/temp.linux-armv7l-cpython-313/src/Bands.o -g 2025-09-10T14:45:22,540 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/Input.cpp -o build/temp.linux-armv7l-cpython-313/src/Input.o -g 2025-09-10T14:45:23,651 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/Loop.cpp -o build/temp.linux-armv7l-cpython-313/src/Loop.o -g 2025-09-10T14:45:25,218 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyDP()’: 2025-09-10T14:45:25,218 ./src/Loop.cpp:3084:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,218 3084 | int special; 2025-09-10T14:45:25,218 | ^~~~~~~ 2025-09-10T14:45:25,228 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyDP(double**, double*, double&, int, int)’: 2025-09-10T14:45:25,229 ./src/Loop.cpp:3286:14: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,229 3286 | char c_structure[MaxN]; 2025-09-10T14:45:25,229 | ^~~~~~~~~~~ 2025-09-10T14:45:25,233 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyDP()’: 2025-09-10T14:45:25,233 ./src/Loop.cpp:3498:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:25,233 3498 | if (DEBUG) 2025-09-10T14:45:25,233 | ^~ 2025-09-10T14:45:25,233 ./src/Loop.cpp:3499:121: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-10T14:45:25,233 3499 | printf("[ILoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2025-09-10T14:45:25,233 | ^~~~~~ 2025-09-10T14:45:25,233 ./src/Loop.cpp:3508:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:25,234 3508 | if (DEBUG) 2025-09-10T14:45:25,234 | ^~ 2025-09-10T14:45:25,234 ./src/Loop.cpp:3509:121: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-10T14:45:25,234 3509 | printf("[MLoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2025-09-10T14:45:25,234 | ^~~~~~ 2025-09-10T14:45:25,236 ./src/Loop.cpp: In member function ‘int Loop::startsMultiSpanningBand(int)’: 2025-09-10T14:45:25,237 ./src/Loop.cpp:3618:13: warning: variable ‘startsMulti’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,237 3618 | int startsMulti = 0; 2025-09-10T14:45:25,237 | ^~~~~~~~~~~ 2025-09-10T14:45:25,257 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyRE()’: 2025-09-10T14:45:25,257 ./src/Loop.cpp:4072:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,257 4072 | int special; 2025-09-10T14:45:25,257 | ^~~~~~~ 2025-09-10T14:45:25,259 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyRE()’: 2025-09-10T14:45:25,260 ./src/Loop.cpp:4198:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:25,260 4198 | if (DEBUG) 2025-09-10T14:45:25,260 | ^~ 2025-09-10T14:45:25,260 ./src/Loop.cpp:4199:113: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-10T14:45:25,260 4199 | printf("[ILoops RE]: (%d, %d) Energy: %.2f \n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2025-09-10T14:45:25,260 | ^~~~~~ 2025-09-10T14:45:25,260 ./src/Loop.cpp:4209:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:25,260 4209 | if (DEBUG) 2025-09-10T14:45:25,260 | ^~ 2025-09-10T14:45:25,261 ./src/Loop.cpp:4210:111: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-10T14:45:25,261 4210 | printf("[MLoopsRE]: (%d, %d) Energy: %.2f\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2025-09-10T14:45:25,261 | ^~~~~~ 2025-09-10T14:45:25,276 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2025-09-10T14:45:25,276 ./src/Loop.cpp:4671:14: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,276 4671 | char c_structure[MaxN]; 2025-09-10T14:45:25,276 | ^~~~~~~~~~~ 2025-09-10T14:45:25,281 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyCC2006a()’: 2025-09-10T14:45:25,282 ./src/Loop.cpp:4800:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:25,282 4800 | int special; 2025-09-10T14:45:25,282 | ^~~~~~~ 2025-09-10T14:45:25,311 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2025-09-10T14:45:25,311 ./src/Loop.cpp:5157:13: warning: unused variable ‘num_params_pkfree’ [-Wunused-variable] 2025-09-10T14:45:25,311 5157 | int num_params_pkfree = get_num_params(); 2025-09-10T14:45:25,311 | ^~~~~~~~~~~~~~~~~ 2025-09-10T14:45:29,341 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyDP(double**, double*, double&, int, int)’: 2025-09-10T14:45:29,341 ./src/Loop.cpp:3802:72: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 2025-09-10T14:45:29,342 3802 | if (c != NUL) { delete c_temp; } 2025-09-10T14:45:29,342 | ^~~~~~ 2025-09-10T14:45:29,342 ./src/Loop.cpp:3770:87: note: returned from ‘void* operator new [](std::size_t)’ 2025-09-10T14:45:29,342 3770 | c_temp = new double[num_params]; 2025-09-10T14:45:29,342 | ^ 2025-09-10T14:45:29,342 ./src/Loop.cpp:3913:49: warning: ‘void operator delete(void*, std::size_t)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 2025-09-10T14:45:29,342 3913 | if (c != NUL) { delete c_temp; } 2025-09-10T14:45:29,342 | ^~~~~~ 2025-09-10T14:45:29,343 ./src/Loop.cpp:3871:63: note: returned from ‘void* operator new [](std::size_t)’ 2025-09-10T14:45:29,343 3871 | c_temp = new double[num_params]; 2025-09-10T14:45:29,343 | ^ 2025-09-10T14:45:32,107 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/LoopList.cpp -o build/temp.linux-armv7l-cpython-313/src/LoopList.o -g 2025-09-10T14:45:32,740 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP()’: 2025-09-10T14:45:32,741 ./src/LoopList.cpp:165:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:32,741 165 | int special; 2025-09-10T14:45:32,741 | ^~~~~~~ 2025-09-10T14:45:32,751 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP(double*, double&, int, int)’: 2025-09-10T14:45:32,751 ./src/LoopList.cpp:349:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:32,751 349 | int special; 2025-09-10T14:45:32,751 | ^~~~~~~ 2025-09-10T14:45:32,758 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyRE()’: 2025-09-10T14:45:32,758 ./src/LoopList.cpp:598:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:32,759 598 | int special; 2025-09-10T14:45:32,759 | ^~~~~~~ 2025-09-10T14:45:34,079 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/Stack.cpp -o build/temp.linux-armv7l-cpython-313/src/Stack.o -g 2025-09-10T14:45:34,975 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/common.cpp -o build/temp.linux-armv7l-cpython-313/src/common.o -g 2025-09-10T14:45:36,651 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/commonPK.cpp -o build/temp.linux-armv7l-cpython-313/src/commonPK.o -g 2025-09-10T14:45:37,341 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:37,341 ./src/commonPK.cpp:2066:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,341 2066 | PARAMTYPE energy; 2025-09-10T14:45:37,341 | ^~~~~~ 2025-09-10T14:45:37,342 ./src/commonPK.cpp:2070:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,342 2070 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:37,342 | ^~~~~~~~~~~ 2025-09-10T14:45:37,344 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:37,344 ./src/commonPK.cpp:2180:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,344 2180 | PARAMTYPE energy; 2025-09-10T14:45:37,344 | ^~~~~~ 2025-09-10T14:45:37,344 ./src/commonPK.cpp:2186:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,344 2186 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:37,344 | ^~~~~~~~~~~ 2025-09-10T14:45:37,346 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:37,347 ./src/commonPK.cpp:2275:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,347 2275 | PARAMTYPE energy; 2025-09-10T14:45:37,347 | ^~~~~~ 2025-09-10T14:45:37,347 ./src/commonPK.cpp:2279:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:37,347 2279 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:37,347 | ^~~~~~~~~~~ 2025-09-10T14:45:39,200 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:39,200 ./src/commonPK.cpp:2108:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,200 2108 | counter[index_top]++; 2025-09-10T14:45:39,201 | ^~~~~~~~~ 2025-09-10T14:45:39,201 ./src/commonPK.cpp:2069:9: note: ‘index_top’ was declared here 2025-09-10T14:45:39,201 2069 | int index_top, index_bot; 2025-09-10T14:45:39,201 | ^~~~~~~~~ 2025-09-10T14:45:39,201 ./src/commonPK.cpp:2098:21: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,201 2098 | counter[index_bot]++; 2025-09-10T14:45:39,201 | ^~~~~~~~~ 2025-09-10T14:45:39,201 ./src/commonPK.cpp:2069:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:39,201 2069 | int index_top, index_bot; 2025-09-10T14:45:39,202 | ^~~~~~~~~ 2025-09-10T14:45:39,266 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:39,267 ./src/commonPK.cpp:2225:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,267 2225 | counter[index_top]++; 2025-09-10T14:45:39,267 | ^~~~~~~~~ 2025-09-10T14:45:39,267 ./src/commonPK.cpp:2183:9: note: ‘index_top’ was declared here 2025-09-10T14:45:39,267 2183 | int index_top, index_bot; 2025-09-10T14:45:39,267 | ^~~~~~~~~ 2025-09-10T14:45:39,267 ./src/commonPK.cpp:2258:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,267 2258 | counter[index_bot]++; 2025-09-10T14:45:39,267 | ^~~~~~~~~ 2025-09-10T14:45:39,267 ./src/commonPK.cpp:2183:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:39,268 2183 | int index_top, index_bot; 2025-09-10T14:45:39,268 | ^~~~~~~~~ 2025-09-10T14:45:39,325 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:39,325 ./src/commonPK.cpp:2318:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,325 2318 | counter[index_top]++; 2025-09-10T14:45:39,325 | ^~~~~~~~~ 2025-09-10T14:45:39,326 ./src/commonPK.cpp:2278:9: note: ‘index_top’ was declared here 2025-09-10T14:45:39,326 2278 | int index_top, index_bot; 2025-09-10T14:45:39,326 | ^~~~~~~~~ 2025-09-10T14:45:39,326 ./src/commonPK.cpp:2351:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:39,326 2351 | counter[index_bot]++; 2025-09-10T14:45:39,326 | ^~~~~~~~~ 2025-09-10T14:45:39,326 ./src/commonPK.cpp:2278:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:39,326 2278 | int index_top, index_bot; 2025-09-10T14:45:39,326 | ^~~~~~~~~ 2025-09-10T14:45:39,458 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/goodStem.cpp -o build/temp.linux-armv7l-cpython-313/src/goodStem.o -g 2025-09-10T14:45:40,321 ./src/goodStem.cpp: In function ‘void trace(int, char*, int, int, int**, int**, int**, int**, int**, int**, short int)’: 2025-09-10T14:45:40,321 ./src/goodStem.cpp:296:23: warning: ‘ti’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:40,321 296 | if (V[ti][tj] == 0) break; 2025-09-10T14:45:40,321 | ^~ 2025-09-10T14:45:40,321 ./src/goodStem.cpp:248:13: note: ‘ti’ was declared here 2025-09-10T14:45:40,321 248 | int ti, tj, startbase,mm,hl; 2025-09-10T14:45:40,321 | ^~ 2025-09-10T14:45:40,322 ./src/goodStem.cpp:296:27: warning: ‘tj’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:40,322 296 | if (V[ti][tj] == 0) break; 2025-09-10T14:45:40,322 | ^~ 2025-09-10T14:45:40,322 ./src/goodStem.cpp:248:17: note: ‘tj’ was declared here 2025-09-10T14:45:40,322 248 | int ti, tj, startbase,mm,hl; 2025-09-10T14:45:40,322 | ^~ 2025-09-10T14:45:40,620 ./src/goodStem.cpp: In function ‘void GenerateStemList(int, char*, char*)’: 2025-09-10T14:45:40,620 ./src/goodStem.cpp:176:47: warning: ‘delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:40,620 176 | G[i][j] = V[i-1][j-1] + delta; //s[i] matched with T[j] 2025-09-10T14:45:40,620 | ~~~~~~~~~~~~^~~~~~~ 2025-09-10T14:45:40,620 ./src/goodStem.cpp:79:20: note: ‘delta’ was declared here 2025-09-10T14:45:40,621 79 | int i,j,jo,delta; 2025-09-10T14:45:40,621 | ^~~~~ 2025-09-10T14:45:40,797 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/hotspot.cpp -o build/temp.linux-armv7l-cpython-313/src/hotspot.o -g 2025-09-10T14:45:41,769 ./src/hotspot.cpp: In function ‘int FindHotspots(char*, char*, int)’: 2025-09-10T14:45:41,769 ./src/hotspot.cpp:206:61: warning: ‘replace’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:41,769 206 | hotspots->substruct[nh].pairTable[mm] = startbase + mm; 2025-09-10T14:45:41,769 | ^~ 2025-09-10T14:45:41,769 ./src/hotspot.cpp:105:13: note: ‘replace’ was declared here 2025-09-10T14:45:41,769 105 | int replace; 2025-09-10T14:45:41,769 | ^~~~~~~ 2025-09-10T14:45:42,344 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/init.cpp -o build/temp.linux-armv7l-cpython-313/src/init.o -g 2025-09-10T14:45:45,242 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/initPK.cpp -o build/temp.linux-armv7l-cpython-313/src/initPK.o -g 2025-09-10T14:45:45,844 ./src/initPK.cpp: In function ‘void read_pkmodelCC2006_file(char*, float, float (*)[12], float (*)[12], float (*)[11], float (*)[11])’: 2025-09-10T14:45:45,844 ./src/initPK.cpp:253:16: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:45,844 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2025-09-10T14:45:45,845 | ^ 2025-09-10T14:45:45,845 ./src/initPK.cpp:253:23: warning: variable ‘jj’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:45,845 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2025-09-10T14:45:45,845 | ^~ 2025-09-10T14:45:45,854 ./src/initPK.cpp: In function ‘void init_dataPK(char*, char*, int, double)’: 2025-09-10T14:45:45,854 ./src/initPK.cpp:472:14: warning: unused variable ‘conf’ [-Wunused-variable] 2025-09-10T14:45:45,854 472 | char conf[200]; 2025-09-10T14:45:45,854 | ^~~~ 2025-09-10T14:45:45,854 ./src/initPK.cpp:485:13: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-10T14:45:45,854 485 | int i; 2025-09-10T14:45:45,854 | ^ 2025-09-10T14:45:46,783 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/params.cpp -o build/temp.linux-armv7l-cpython-313/src/params.o -g 2025-09-10T14:45:47,423 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:47,423 ./src/params.cpp:518:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,423 518 | PARAMTYPE energy; 2025-09-10T14:45:47,423 | ^~~~~~ 2025-09-10T14:45:47,423 ./src/params.cpp:522:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,423 522 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:47,424 | ^~~~~~~~~~~ 2025-09-10T14:45:47,426 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:47,426 ./src/params.cpp:632:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,426 632 | PARAMTYPE energy; 2025-09-10T14:45:47,426 | ^~~~~~ 2025-09-10T14:45:47,426 ./src/params.cpp:638:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,426 638 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:47,426 | ^~~~~~~~~~~ 2025-09-10T14:45:47,428 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:47,428 ./src/params.cpp:727:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,428 727 | PARAMTYPE energy; 2025-09-10T14:45:47,428 | ^~~~~~ 2025-09-10T14:45:47,429 ./src/params.cpp:731:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,429 731 | int first_index; // first index should be dangle_top[0][3][0] 2025-09-10T14:45:47,429 | ^~~~~~~~~~~ 2025-09-10T14:45:47,431 ./src/params.cpp: In function ‘void count_penalty_by_size(int, char, double*)’: 2025-09-10T14:45:47,431 ./src/params.cpp:851:27: warning: variable ‘penalty’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,431 851 | PARAMTYPE penaltyMAX, penalty; 2025-09-10T14:45:47,431 | ^~~~~~~ 2025-09-10T14:45:47,459 ./src/params.cpp: In function ‘void print_counter(double*, double)’: 2025-09-10T14:45:47,460 ./src/params.cpp:1479:33: warning: ' ' flag used with ‘%s’ gnu_printf format [-Wformat=] 2025-09-10T14:45:47,460 1479 | printf ("%4d\t%30s\t% 10s\t%4.2lf\n", num_params, "FREE PARAMETER", "", (double)free_value); 2025-09-10T14:45:47,460 | ^ 2025-09-10T14:45:47,522 ./src/params.cpp: In function ‘void fill_data_structures_with_new_parameters(char*)’: 2025-09-10T14:45:47,522 ./src/params.cpp:4206:9: warning: variable ‘index’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,523 4206 | int index; 2025-09-10T14:45:47,523 | ^~~~~ 2025-09-10T14:45:47,532 ./src/params.cpp: In function ‘double simfold_restricted_logZ_gradient(char*, char*, char*, double*)’: 2025-09-10T14:45:47,532 ./src/params.cpp:5021:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,533 5021 | double min_energy, max_energy; 2025-09-10T14:45:47,533 | ^~~~~~~~~~ 2025-09-10T14:45:47,538 ./src/params.cpp: In function ‘double compute_f(char*)’: 2025-09-10T14:45:47,538 ./src/params.cpp:5212:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,538 5212 | int k; 2025-09-10T14:45:47,538 | ^ 2025-09-10T14:45:47,539 ./src/params.cpp: In function ‘double compute_likelihood_exactly(char*)’: 2025-09-10T14:45:47,540 ./src/params.cpp:5262:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,540 5262 | int k; 2025-09-10T14:45:47,540 | ^ 2025-09-10T14:45:47,541 ./src/params.cpp: In function ‘double compute_log_likelihood_smart(char*)’: 2025-09-10T14:45:47,541 ./src/params.cpp:5314:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,541 5314 | int k; 2025-09-10T14:45:47,541 | ^ 2025-09-10T14:45:47,542 ./src/params.cpp: In function ‘void compute_gradient_f(char*, double*)’: 2025-09-10T14:45:47,543 ./src/params.cpp:5366:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,543 5366 | int k; 2025-09-10T14:45:47,543 | ^ 2025-09-10T14:45:47,544 ./src/params.cpp: In function ‘void compute_gradient_f_smart(char*, double*)’: 2025-09-10T14:45:47,544 ./src/params.cpp:5416:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,545 5416 | int k; 2025-09-10T14:45:47,545 | ^ 2025-09-10T14:45:47,546 ./src/params.cpp: In function ‘double compute_f_and_gradient_f_smart(char*, double*)’: 2025-09-10T14:45:47,546 ./src/params.cpp:5470:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,547 5470 | int k; 2025-09-10T14:45:47,547 | ^ 2025-09-10T14:45:47,550 ./src/params.cpp: In function ‘double compute_f_and_gradient_f(char*, double*)’: 2025-09-10T14:45:47,550 ./src/params.cpp:5511:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,551 5511 | double min_energy, max_energy; 2025-09-10T14:45:47,551 | ^~~~~~~~~~ 2025-09-10T14:45:47,553 ./src/params.cpp: In function ‘void compute_counts_vector_LP(char*, double*)’: 2025-09-10T14:45:47,553 ./src/params.cpp:5627:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,553 5627 | double R, temp, beta; 2025-09-10T14:45:47,553 | ^~~~ 2025-09-10T14:45:47,553 ./src/params.cpp:5639:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,553 5639 | int k; 2025-09-10T14:45:47,553 | ^ 2025-09-10T14:45:47,555 ./src/params.cpp: In function ‘void compute_counts_matrix_LP(char*, int)’: 2025-09-10T14:45:47,556 ./src/params.cpp:5699:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,556 5699 | double R, temp, beta; 2025-09-10T14:45:47,556 | ^~~~ 2025-09-10T14:45:47,556 ./src/params.cpp:5711:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,556 5711 | int k; 2025-09-10T14:45:47,556 | ^ 2025-09-10T14:45:47,558 ./src/params.cpp: In function ‘int generate_structure_withbb(char*, char*, char*, char*, char (*)[1000], double*, int)’: 2025-09-10T14:45:47,558 ./src/params.cpp:5844:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:47,559 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,559 | ^~~ 2025-09-10T14:45:47,559 ./src/params.cpp:5844:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2025-09-10T14:45:47,559 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,559 | ^~~~~~~~~~ 2025-09-10T14:45:47,562 ./src/params.cpp:5865:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,562 5865 | int tried = 0; 2025-09-10T14:45:47,562 | ^~~~~ 2025-09-10T14:45:47,567 ./src/params.cpp: In function ‘int generate_structure_withbb_many_thresholds(char*, char (*)[1000], double*, double*, int*, double, int)’: 2025-09-10T14:45:47,567 ./src/params.cpp:6284:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:47,568 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,568 | ^~~ 2025-09-10T14:45:47,568 ./src/params.cpp:6284:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2025-09-10T14:45:47,568 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,568 | ^~~~~~~~~~ 2025-09-10T14:45:47,571 ./src/params.cpp:6305:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,571 6305 | int tried = 0; 2025-09-10T14:45:47,571 | ^~~~~ 2025-09-10T14:45:47,574 ./src/params.cpp: In function ‘void search_bb(char*, double*, int, int)’: 2025-09-10T14:45:47,574 ./src/params.cpp:6437:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2025-09-10T14:45:47,574 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,574 | ^~~ 2025-09-10T14:45:47,575 ./src/params.cpp:6437:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2025-09-10T14:45:47,575 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2025-09-10T14:45:47,575 | ^~~~~~~~~~ 2025-09-10T14:45:47,578 ./src/params.cpp:6458:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,578 6458 | int tried = 0; 2025-09-10T14:45:47,578 | ^~~~~ 2025-09-10T14:45:47,578 ./src/params.cpp:6410:20: warning: variable ‘numstr’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,578 6410 | int seqlen, i, numstr; 2025-09-10T14:45:47,578 | ^~~~~~ 2025-09-10T14:45:47,610 ./src/params.cpp: In function ‘void fill_similarity_rule_with_optical_melting_reference(char*)’: 2025-09-10T14:45:47,610 ./src/params.cpp:7832:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:45:47,610 7832 | int k; 2025-09-10T14:45:47,610 | ^ 2025-09-10T14:45:49,468 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:49,468 ./src/params.cpp:560:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,468 560 | counter[index_top]++; 2025-09-10T14:45:49,468 | ^~~~~~~~~ 2025-09-10T14:45:49,468 ./src/params.cpp:521:9: note: ‘index_top’ was declared here 2025-09-10T14:45:49,469 521 | int index_top, index_bot; 2025-09-10T14:45:49,469 | ^~~~~~~~~ 2025-09-10T14:45:49,469 ./src/params.cpp:550:21: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,469 550 | counter[index_bot]++; 2025-09-10T14:45:49,469 | ^~~~~~~~~ 2025-09-10T14:45:49,469 ./src/params.cpp:521:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:49,469 521 | int index_top, index_bot; 2025-09-10T14:45:49,469 | ^~~~~~~~~ 2025-09-10T14:45:49,533 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:49,534 ./src/params.cpp:677:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,534 677 | counter[index_top]++; 2025-09-10T14:45:49,534 | ^~~~~~~~~ 2025-09-10T14:45:49,534 ./src/params.cpp:635:9: note: ‘index_top’ was declared here 2025-09-10T14:45:49,534 635 | int index_top, index_bot; 2025-09-10T14:45:49,534 | ^~~~~~~~~ 2025-09-10T14:45:49,534 ./src/params.cpp:710:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,534 710 | counter[index_bot]++; 2025-09-10T14:45:49,534 | ^~~~~~~~~ 2025-09-10T14:45:49,535 ./src/params.cpp:635:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:49,535 635 | int index_top, index_bot; 2025-09-10T14:45:49,535 | ^~~~~~~~~ 2025-09-10T14:45:49,592 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2025-09-10T14:45:49,592 ./src/params.cpp:770:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,592 770 | counter[index_top]++; 2025-09-10T14:45:49,592 | ^~~~~~~~~ 2025-09-10T14:45:49,592 ./src/params.cpp:730:9: note: ‘index_top’ was declared here 2025-09-10T14:45:49,593 730 | int index_top, index_bot; 2025-09-10T14:45:49,593 | ^~~~~~~~~ 2025-09-10T14:45:49,593 ./src/params.cpp:803:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:49,593 803 | counter[index_bot]++; 2025-09-10T14:45:49,593 | ^~~~~~~~~ 2025-09-10T14:45:49,593 ./src/params.cpp:730:20: note: ‘index_bot’ was declared here 2025-09-10T14:45:49,593 730 | int index_top, index_bot; 2025-09-10T14:45:49,593 | ^~~~~~~~~ 2025-09-10T14:45:51,002 ./src/params.cpp: In function ‘void similarity_bulge_type(int, char*)’: 2025-09-10T14:45:51,002 ./src/params.cpp:2261:33: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2025-09-10T14:45:51,002 2261 | sprintf (similarity, "%s%.4lf bulge1[5'-%c%c%c/%c%c-3'] - %.4lf stack[5'-%c%c/%c%c-3']", similarity, 1.0/num, 2025-09-10T14:45:51,002 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:45:51,003 2262 | int_to_nuc(i), int_to_nuc(bulged_base), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j), 2025-09-10T14:45:51,003 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:45:51,003 2263 | 1.0/num, int_to_nuc(i), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j)); 2025-09-10T14:45:51,003 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:45:51,003 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2025-09-10T14:45:51,003 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2025-09-10T14:45:51,003 | ~~~~~~^~~~~~~~~~ 2025-09-10T14:45:51,003 ./src/params.cpp:2265:53: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2025-09-10T14:45:51,003 2265 | if (num2 < num) sprintf (similarity, "%s + ", similarity); 2025-09-10T14:45:51,003 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:45:51,004 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2025-09-10T14:45:51,004 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2025-09-10T14:45:51,004 | ~~~~~~^~~~~~~~~~ 2025-09-10T14:45:51,519 ./src/params.cpp: In function ‘int traverse_features_and_do_work(char*, int*, char*)’: 2025-09-10T14:45:51,519 ./src/params.cpp:4111:16: warning: ‘file’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:45:51,519 4111 | fclose (file); 2025-09-10T14:45:51,519 | ~~~~~~~^~~~~~ 2025-09-10T14:45:51,519 ./src/params.cpp:2287:11: note: ‘file’ was declared here 2025-09-10T14:45:51,520 2287 | FILE *file; 2025-09-10T14:45:51,520 | ^~~~ 2025-09-10T14:45:58,608 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/paramsPK.cpp -o build/temp.linux-armv7l-cpython-313/src/paramsPK.o -g 2025-09-10T14:46:01,588 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/python.cpp -o build/temp.linux-armv7l-cpython-313/src/python.o -g 2025-09-10T14:46:02,687 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_energy_matrix.cpp -o build/temp.linux-armv7l-cpython-313/src/s_energy_matrix.o -g 2025-09-10T14:46:03,150 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_hairpin_loop.cpp -o build/temp.linux-armv7l-cpython-313/src/s_hairpin_loop.o -g 2025-09-10T14:46:03,278 ./src/s_hairpin_loop.cpp: In constructor ‘s_hairpin_loop::s_hairpin_loop(char*, int*, int)’: 2025-09-10T14:46:03,278 ./src/s_hairpin_loop.cpp:42:16: warning: statement has no effect [-Wunused-value] 2025-09-10T14:46:03,278 42 | toupper(csequence[i]); 2025-09-10T14:46:03,278 | ~~~~~~~^~~~~~~~~~~~~~ 2025-09-10T14:46:03,293 ./src/s_hairpin_loop.cpp: In static member function ‘static void s_hairpin_loop::count_get_energy(int, int, int*, char*, double*)’: 2025-09-10T14:46:03,293 ./src/s_hairpin_loop.cpp:487:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:03,293 487 | PARAMTYPE energy=0; 2025-09-10T14:46:03,293 | ^~~~~~ 2025-09-10T14:46:03,927 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_internal_loop.cpp -o build/temp.linux-armv7l-cpython-313/src/s_internal_loop.o -g 2025-09-10T14:46:04,145 ./src/s_internal_loop.cpp: In static member function ‘static void s_internal_loop::count_get_energy(int, int, int, int, int*, double*)’: 2025-09-10T14:46:04,145 ./src/s_internal_loop.cpp:646:19: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:04,145 646 | PARAMTYPE energy; 2025-09-10T14:46:04,146 | ^~~~~~ 2025-09-10T14:46:06,055 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_min_folding.cpp -o build/temp.linux-armv7l-cpython-313/src/s_min_folding.o -g 2025-09-10T14:46:06,259 ./src/s_min_folding.cpp: In member function ‘int s_min_folding::compute_W_br2_restricted(int, str_features*, int&)’: 2025-09-10T14:46:06,260 ./src/s_min_folding.cpp:1066:13: warning: variable ‘chosen’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:06,260 1066 | int chosen = 0; 2025-09-10T14:46:06,260 | ^~~~~~ 2025-09-10T14:46:06,260 ./src/s_min_folding.cpp:1067:13: warning: variable ‘best_i’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:06,260 1067 | int best_i = 0; 2025-09-10T14:46:06,260 | ^~~~~~ 2025-09-10T14:46:06,909 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack(seq_interval*)’: 2025-09-10T14:46:06,909 ./src/s_min_folding.cpp:557:51: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,909 557 | if (best_k-i > TURN) 2025-09-10T14:46:06,909 | ~~~~~~^~ 2025-09-10T14:46:06,909 ./src/s_min_folding.cpp:462:21: note: ‘best_k’ was declared here 2025-09-10T14:46:06,909 462 | int best_k, best_row; 2025-09-10T14:46:06,909 | ^~~~~~ 2025-09-10T14:46:06,910 ./src/s_min_folding.cpp:452:51: warning: ‘best_i’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,910 452 | if (best_i-1 > TURN) 2025-09-10T14:46:06,910 | ~~~~~~^~ 2025-09-10T14:46:06,910 ./src/s_min_folding.cpp:367:34: note: ‘best_i’ was declared here 2025-09-10T14:46:06,910 367 | int best_row, i, best_i; 2025-09-10T14:46:06,910 | ^~~~~~ 2025-09-10T14:46:06,910 ./src/s_min_folding.cpp:352:53: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,910 352 | insert_node (best_k+1, j-1, M_WM); break; 2025-09-10T14:46:06,910 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:46:06,910 ./src/s_min_folding.cpp:314:32: note: ‘best_k’ was declared here 2025-09-10T14:46:06,911 314 | int k, best_k, best_row; 2025-09-10T14:46:06,911 | ^~~~~~ 2025-09-10T14:46:06,911 ./src/s_min_folding.cpp:349:25: warning: ‘best_row’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,911 349 | switch (best_row){ 2025-09-10T14:46:06,911 | ^~~~~~ 2025-09-10T14:46:06,911 ./src/s_min_folding.cpp:314:40: note: ‘best_row’ was declared here 2025-09-10T14:46:06,911 314 | int k, best_k, best_row; 2025-09-10T14:46:06,911 | ^~~~~~~~ 2025-09-10T14:46:06,911 ./src/s_min_folding.cpp:305:25: warning: ‘best_ip’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,912 305 | if (best_ip < best_jp){ 2025-09-10T14:46:06,912 | ^~ 2025-09-10T14:46:06,912 ./src/s_min_folding.cpp:292:37: note: ‘best_ip’ was declared here 2025-09-10T14:46:06,912 292 | int ip, jp, best_ip, best_jp, minq; 2025-09-10T14:46:06,912 | ^~~~~~~ 2025-09-10T14:46:06,912 ./src/s_min_folding.cpp:305:25: warning: ‘best_jp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:06,912 305 | if (best_ip < best_jp){ 2025-09-10T14:46:06,912 | ^~ 2025-09-10T14:46:06,912 ./src/s_min_folding.cpp:292:46: note: ‘best_jp’ was declared here 2025-09-10T14:46:06,912 292 | int ip, jp, best_ip, best_jp, minq; 2025-09-10T14:46:06,913 | ^~~~~~~ 2025-09-10T14:46:07,526 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack_restricted(seq_interval*, str_features*)’: 2025-09-10T14:46:07,526 ./src/s_min_folding.cpp:958:51: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,526 958 | if (best_k-i > 0) 2025-09-10T14:46:07,526 | ~~~~~~^~ 2025-09-10T14:46:07,526 ./src/s_min_folding.cpp:853:21: note: ‘best_k’ was declared here 2025-09-10T14:46:07,527 853 | int best_k, best_row; 2025-09-10T14:46:07,527 | ^~~~~~ 2025-09-10T14:46:07,527 ./src/s_min_folding.cpp:843:51: warning: ‘best_i’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,527 843 | if (best_i-1 > 0) 2025-09-10T14:46:07,527 | ~~~~~~^~ 2025-09-10T14:46:07,528 ./src/s_min_folding.cpp:710:34: note: ‘best_i’ was declared here 2025-09-10T14:46:07,528 710 | int best_row, i, best_i; 2025-09-10T14:46:07,528 | ^~~~~~ 2025-09-10T14:46:07,528 ./src/s_min_folding.cpp:692:61: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,528 692 | insert_node (best_k+1, j-1, M_WM); break; 2025-09-10T14:46:07,528 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-10T14:46:07,528 ./src/s_min_folding.cpp:640:32: note: ‘best_k’ was declared here 2025-09-10T14:46:07,528 640 | int k, best_k, best_row; 2025-09-10T14:46:07,528 | ^~~~~~ 2025-09-10T14:46:07,528 ./src/s_min_folding.cpp:689:25: warning: ‘best_row’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,529 689 | switch (best_row) 2025-09-10T14:46:07,529 | ^~~~~~ 2025-09-10T14:46:07,529 ./src/s_min_folding.cpp:640:40: note: ‘best_row’ was declared here 2025-09-10T14:46:07,529 640 | int k, best_k, best_row; 2025-09-10T14:46:07,529 | ^~~~~~~~ 2025-09-10T14:46:07,529 ./src/s_min_folding.cpp:628:25: warning: ‘best_ip’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,529 628 | if (best_ip < best_jp) 2025-09-10T14:46:07,529 | ^~ 2025-09-10T14:46:07,529 ./src/s_min_folding.cpp:610:37: note: ‘best_ip’ was declared here 2025-09-10T14:46:07,530 610 | int ip, jp, best_ip, best_jp, minq; 2025-09-10T14:46:07,530 | ^~~~~~~ 2025-09-10T14:46:07,530 ./src/s_min_folding.cpp:628:25: warning: ‘best_jp’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:07,530 628 | if (best_ip < best_jp) 2025-09-10T14:46:07,530 | ^~ 2025-09-10T14:46:07,530 ./src/s_min_folding.cpp:610:46: note: ‘best_jp’ was declared here 2025-09-10T14:46:07,530 610 | int ip, jp, best_ip, best_jp, minq; 2025-09-10T14:46:07,530 | ^~~~~~~ 2025-09-10T14:46:08,559 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_multi_loop.cpp -o build/temp.linux-armv7l-cpython-313/src/s_multi_loop.o -g 2025-09-10T14:46:09,351 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_multi_loop_sub.cpp -o build/temp.linux-armv7l-cpython-313/src/s_multi_loop_sub.o -g 2025-09-10T14:46:09,463 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1(int)’: 2025-09-10T14:46:09,463 ./src/s_multi_loop_sub.cpp:64:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:09,463 64 | int i, tmp_k, ij, k; 2025-09-10T14:46:09,464 | ^~~~~ 2025-09-10T14:46:09,465 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM(int)’: 2025-09-10T14:46:09,465 ./src/s_multi_loop_sub.cpp:110:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:09,466 110 | int i, tmp_k, k, ij; 2025-09-10T14:46:09,466 | ^~~~~ 2025-09-10T14:46:09,469 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1_restricted(int, str_features*)’: 2025-09-10T14:46:09,469 ./src/s_multi_loop_sub.cpp:173:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:09,469 173 | int i, tmp_k, ij, k; 2025-09-10T14:46:09,469 | ^~~~~ 2025-09-10T14:46:09,471 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM_restricted(int, str_features*)’: 2025-09-10T14:46:09,471 ./src/s_multi_loop_sub.cpp:220:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:09,471 220 | int i, tmp_k, k, ij; 2025-09-10T14:46:09,471 | ^~~~~ 2025-09-10T14:46:09,965 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_partition_function.cpp -o build/temp.linux-armv7l-cpython-313/src/s_partition_function.o -g 2025-09-10T14:46:10,575 ./src/s_partition_function.cpp: In constructor ‘s_partition_function::s_partition_function(char*, int, int, char*)’: 2025-09-10T14:46:10,575 ./src/s_partition_function.cpp:78:16: warning: statement has no effect [-Wunused-value] 2025-09-10T14:46:10,575 78 | toupper(csequence[i]); 2025-09-10T14:46:10,575 | ~~~~~~~^~~~~~~~~~~~~~ 2025-09-10T14:46:10,599 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function()’: 2025-09-10T14:46:10,600 ./src/s_partition_function.cpp:415:15: warning: variable ‘ij’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,600 415 | int i, j, ij; 2025-09-10T14:46:10,600 | ^~ 2025-09-10T14:46:10,611 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm_nodangles(int, int)’: 2025-09-10T14:46:10,612 ./src/s_partition_function.cpp:692:12: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,612 692 | int h, hj; 2025-09-10T14:46:10,612 | ^~ 2025-09-10T14:46:10,629 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm(int, int)’: 2025-09-10T14:46:10,629 ./src/s_partition_function.cpp:1028:37: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,630 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2025-09-10T14:46:10,630 | ^~~~~~ 2025-09-10T14:46:10,630 ./src/s_partition_function.cpp:1028:45: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,630 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2025-09-10T14:46:10,630 | ^~~~~~ 2025-09-10T14:46:10,630 ./src/s_partition_function.cpp:1028:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,630 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2025-09-10T14:46:10,630 | ^~~~~~ 2025-09-10T14:46:10,630 ./src/s_partition_function.cpp:1028:61: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,630 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2025-09-10T14:46:10,631 | ^~~~~~ 2025-09-10T14:46:10,631 ./src/s_partition_function.cpp:1028:69: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,631 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2025-09-10T14:46:10,631 | ^~ 2025-09-10T14:46:10,670 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_needmidd3(int, int)’: 2025-09-10T14:46:10,670 ./src/s_partition_function.cpp:1717:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,670 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,670 | ^~~~~~ 2025-09-10T14:46:10,670 ./src/s_partition_function.cpp:1717:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,670 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,670 | ^~~~~~ 2025-09-10T14:46:10,672 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_noneedmidd3(int, int)’: 2025-09-10T14:46:10,672 ./src/s_partition_function.cpp:1747:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,672 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,672 | ^~~~~~ 2025-09-10T14:46:10,672 ./src/s_partition_function.cpp:1747:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,673 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,673 | ^~~~~~ 2025-09-10T14:46:10,673 ./src/s_partition_function.cpp:1747:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,673 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,673 | ^~~~~~ 2025-09-10T14:46:10,673 ./src/s_partition_function.cpp:1747:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,673 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,673 | ^~~~~~ 2025-09-10T14:46:10,673 ./src/s_partition_function.cpp:1747:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,673 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,674 | ^~~~~~ 2025-09-10T14:46:10,674 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_needmidd3(int, int)’: 2025-09-10T14:46:10,675 ./src/s_partition_function.cpp:1779:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,675 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,675 | ^~~~~~ 2025-09-10T14:46:10,675 ./src/s_partition_function.cpp:1779:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,675 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,675 | ^~~~~~ 2025-09-10T14:46:10,677 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_noneedmidd3(int, int)’: 2025-09-10T14:46:10,677 ./src/s_partition_function.cpp:1808:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,677 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,677 | ^~~~~~ 2025-09-10T14:46:10,677 ./src/s_partition_function.cpp:1808:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,678 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,678 | ^~~~~~ 2025-09-10T14:46:10,678 ./src/s_partition_function.cpp:1808:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,678 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,678 | ^~~~~~ 2025-09-10T14:46:10,678 ./src/s_partition_function.cpp:1808:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,678 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,678 | ^~~~~~ 2025-09-10T14:46:10,678 ./src/s_partition_function.cpp:1808:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,678 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2025-09-10T14:46:10,679 | ^~~~~~ 2025-09-10T14:46:10,705 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function_exhaustively()’: 2025-09-10T14:46:10,705 ./src/s_partition_function.cpp:2288:12: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,706 2288 | double min_energy, max_energy; 2025-09-10T14:46:10,706 | ^~~~~~~~~~ 2025-09-10T14:46:10,706 ./src/s_partition_function.cpp:2288:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,706 2288 | double min_energy, max_energy; 2025-09-10T14:46:10,706 | ^~~~~~~~~~ 2025-09-10T14:46:10,724 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::verify_recurrences()’: 2025-09-10T14:46:10,724 ./src/s_partition_function.cpp:2667:9: warning: variable ‘error’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,724 2667 | int error = 0; 2025-09-10T14:46:10,724 | ^~~~~ 2025-09-10T14:46:10,728 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient_exhaustively()’: 2025-09-10T14:46:10,729 ./src/s_partition_function.cpp:2868:9: warning: variable ‘real_str_found’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,729 2868 | int real_str_found, actual_num_str; 2025-09-10T14:46:10,729 | ^~~~~~~~~~~~~~ 2025-09-10T14:46:10,812 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient()’: 2025-09-10T14:46:10,812 ./src/s_partition_function.cpp:3000:15: warning: variable ‘AUpen’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,812 3000 | PARAMTYPE AUpen; //, dangle, dangle5, dangle3; 2025-09-10T14:46:10,812 | ^~~~~ 2025-09-10T14:46:10,834 ./src/s_partition_function.cpp: In member function ‘int s_partition_function::correct_gradient()’: 2025-09-10T14:46:10,834 ./src/s_partition_function.cpp:4925:9: warning: variable ‘index_param’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:10,834 4925 | int index_param; 2025-09-10T14:46:10,834 | ^~~~~~~~~~~ 2025-09-10T14:46:22,779 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_specific_functions.cpp -o build/temp.linux-armv7l-cpython-313/src/s_specific_functions.o -g 2025-09-10T14:46:23,402 ./src/s_specific_functions.cpp: In function ‘int s_calculate_energy(int*, char*, char*, str_features*, str_features*)’: 2025-09-10T14:46:23,403 ./src/s_specific_functions.cpp:483:29: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:23,403 483 | int special; 2025-09-10T14:46:23,403 | ^~~~~~~ 2025-09-10T14:46:23,415 ./src/s_specific_functions.cpp: In function ‘int s_calculate_enthalpy(int*, char*, str_features*)’: 2025-09-10T14:46:23,415 ./src/s_specific_functions.cpp:662:29: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:23,415 662 | int special; 2025-09-10T14:46:23,416 | ^~~~~~~ 2025-09-10T14:46:23,431 ./src/s_specific_functions.cpp: In function ‘void simfold_gradient_smart(char*, double*, int, int)’: 2025-09-10T14:46:23,431 ./src/s_specific_functions.cpp:1089:16: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:23,431 1089 | PFTYPE pf; 2025-09-10T14:46:23,432 | ^~ 2025-09-10T14:46:23,435 ./src/s_specific_functions.cpp: In function ‘double simfold_partition_function_approximately(char*)’: 2025-09-10T14:46:23,435 ./src/s_specific_functions.cpp:1147:16: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:23,435 1147 | double min_energy, max_energy; 2025-09-10T14:46:23,435 | ^~~~~~~~~~ 2025-09-10T14:46:23,435 ./src/s_specific_functions.cpp:1147:28: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:23,435 1147 | double min_energy, max_energy; 2025-09-10T14:46:23,436 | ^~~~~~~~~~ 2025-09-10T14:46:25,437 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_stacked_pair.cpp -o build/temp.linux-armv7l-cpython-313/src/s_stacked_pair.o -g 2025-09-10T14:46:25,674 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/s_sub_folding.cpp -o build/temp.linux-armv7l-cpython-313/src/s_sub_folding.o -g 2025-09-10T14:46:27,857 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/sc.cpp -o build/temp.linux-armv7l-cpython-313/src/sc.o -g 2025-09-10T14:46:28,771 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/score.cpp -o build/temp.linux-armv7l-cpython-313/src/score.o -g 2025-09-10T14:46:29,708 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/temp.cpp -o build/temp.linux-armv7l-cpython-313/src/temp.o -g 2025-09-10T14:46:31,146 ./src/temp.cpp: In function ‘Fold* best(char*, char*)’: 2025-09-10T14:46:31,146 ./src/temp.cpp:80:16: warning: variable ‘min_en’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:31,146 80 | double min_en; 2025-09-10T14:46:31,146 | ^~~~~~ 2025-09-10T14:46:31,577 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/timer.cpp -o build/temp.linux-armv7l-cpython-313/src/timer.o -g 2025-09-10T14:46:32,141 ./src/timer.cpp: In member function ‘void timer::start()’: 2025-09-10T14:46:32,142 ./src/timer.cpp:23:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:32,142 23 | clock_t t; 2025-09-10T14:46:32,142 | ^ 2025-09-10T14:46:32,142 ./src/timer.cpp: In member function ‘void timer::stop()’: 2025-09-10T14:46:32,142 ./src/timer.cpp:32:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:32,142 32 | clock_t t; 2025-09-10T14:46:32,142 | ^ 2025-09-10T14:46:32,143 ./src/timer.cpp: In member function ‘void timer::reset()’: 2025-09-10T14:46:32,143 ./src/timer.cpp:41:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:32,143 41 | clock_t t; 2025-09-10T14:46:32,143 | ^ 2025-09-10T14:46:32,143 ./src/timer.cpp: In member function ‘float timer::elapsed()’: 2025-09-10T14:46:32,143 ./src/timer.cpp:52:13: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2025-09-10T14:46:32,143 52 | clock_t t; 2025-09-10T14:46:32,143 | ^ 2025-09-10T14:46:32,368 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I. -I... -I/tmp/pip-wheel-z8x0cli8/hotknots_00f2d9ce17e4490da994cf5e7eda40cb/include -I/usr/include/python3.13 -c ./src/utils.cpp -o build/temp.linux-armv7l-cpython-313/src/utils.o -g 2025-09-10T14:46:32,696 ./src/utils.cpp: In function ‘void bpseq2dp(int, short int*, char*)’: 2025-09-10T14:46:32,697 ./src/utils.cpp:146:13: warning: ‘stackindex_push’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-10T14:46:32,697 146 | int stackindex_push; 2025-09-10T14:46:32,697 | ^~~~~~~~~~~~~~~ 2025-09-10T14:46:32,771 arm-linux-gnueabihf-g++ -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-313/src/Bands.o build/temp.linux-armv7l-cpython-313/src/Input.o build/temp.linux-armv7l-cpython-313/src/Loop.o build/temp.linux-armv7l-cpython-313/src/LoopList.o build/temp.linux-armv7l-cpython-313/src/Stack.o build/temp.linux-armv7l-cpython-313/src/common.o build/temp.linux-armv7l-cpython-313/src/commonPK.o build/temp.linux-armv7l-cpython-313/src/goodStem.o build/temp.linux-armv7l-cpython-313/src/hotspot.o build/temp.linux-armv7l-cpython-313/src/init.o build/temp.linux-armv7l-cpython-313/src/initPK.o build/temp.linux-armv7l-cpython-313/src/params.o build/temp.linux-armv7l-cpython-313/src/paramsPK.o build/temp.linux-armv7l-cpython-313/src/python.o build/temp.linux-armv7l-cpython-313/src/s_energy_matrix.o build/temp.linux-armv7l-cpython-313/src/s_hairpin_loop.o build/temp.linux-armv7l-cpython-313/src/s_internal_loop.o build/temp.linux-armv7l-cpython-313/src/s_min_folding.o build/temp.linux-armv7l-cpython-313/src/s_multi_loop.o build/temp.linux-armv7l-cpython-313/src/s_multi_loop_sub.o build/temp.linux-armv7l-cpython-313/src/s_partition_function.o build/temp.linux-armv7l-cpython-313/src/s_specific_functions.o build/temp.linux-armv7l-cpython-313/src/s_stacked_pair.o build/temp.linux-armv7l-cpython-313/src/s_sub_folding.o build/temp.linux-armv7l-cpython-313/src/sc.o build/temp.linux-armv7l-cpython-313/src/score.o build/temp.linux-armv7l-cpython-313/src/temp.o build/temp.linux-armv7l-cpython-313/src/timer.o build/temp.linux-armv7l-cpython-313/src/utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-313/hotknots/hotknots.cpython-313-arm-linux-gnueabihf.so -lm 2025-09-10T14:46:33,174 running build_scripts 2025-09-10T14:46:33,175 creating build/scripts-3.13 2025-09-10T14:46:33,175 copying and adjusting hotknots.py -> build/scripts-3.13 2025-09-10T14:46:33,175 changing mode of build/scripts-3.13/hotknots.py from 644 to 755 2025-09-10T14:46:33,314 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-10T14:46:33,314 !! 2025-09-10T14:46:33,315 ******************************************************************************** 2025-09-10T14:46:33,315 Please avoid running ``setup.py`` directly. 2025-09-10T14:46:33,315 Instead, use pypa/build, pypa/installer or other 2025-09-10T14:46:33,315 standards-based tools. 2025-09-10T14:46:33,315 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-10T14:46:33,315 or your builds will no longer be supported. 2025-09-10T14:46:33,315 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-10T14:46:33,316 ******************************************************************************** 2025-09-10T14:46:33,316 !! 2025-09-10T14:46:33,316 self.initialize_options() 2025-09-10T14:46:33,392 installing to build/bdist.linux-armv7l/wheel 2025-09-10T14:46:33,392 running install 2025-09-10T14:46:33,415 running install_lib 2025-09-10T14:46:33,489 creating build/bdist.linux-armv7l/wheel 2025-09-10T14:46:33,490 creating build/bdist.linux-armv7l/wheel/hotknots 2025-09-10T14:46:33,490 copying build/lib.linux-armv7l-cpython-313/hotknots/hotknots.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,497 copying build/lib.linux-armv7l-cpython-313/hotknots/CG_best_parameters_ISMB2007.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,498 copying build/lib.linux-armv7l-cpython-313/hotknots/parameters_CC06.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,498 copying build/lib.linux-armv7l-cpython-313/hotknots/parameters_CC09.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,499 copying build/lib.linux-armv7l-cpython-313/hotknots/parameters_DP03.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,499 copying build/lib.linux-armv7l-cpython-313/hotknots/parameters_DP09.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,500 copying build/lib.linux-armv7l-cpython-313/hotknots/turner_parameters_fm363_constrdangles.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,500 copying build/lib.linux-armv7l-cpython-313/hotknots/turner_partypes_fm363.txt -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,501 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-asint1x2-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,502 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-dangle-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,502 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-loop-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,503 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-miscloop-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,504 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint2-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,504 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint4-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,505 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-stack-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,506 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tloop-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,506 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-triloop-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,507 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstackh-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,507 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstacki-rna.dg -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,508 copying build/lib.linux-armv7l-cpython-313/hotknots/multirnafold.conf -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,508 copying build/lib.linux-armv7l-cpython-313/hotknots/pkenergy.conf -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,509 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-asint1x2-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,510 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-dangle-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,510 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-loop-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,511 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-miscloop-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,511 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-sint2-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,512 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-sint4-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,513 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-stack-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,513 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tloop-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,514 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-triloop-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,514 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tstackh-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,515 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tstacki-dna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,516 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-asint1x2-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,516 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-dangle-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,517 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-loop-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,517 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-miscloop-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,518 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint2-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,519 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint4-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,519 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-stack-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,520 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tloop-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,521 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-triloop-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,521 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstackh-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,522 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstacki-rna.dh -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,522 copying build/lib.linux-armv7l-cpython-313/hotknots/coaxial.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,523 copying build/lib.linux-armv7l-cpython-313/hotknots/coaxstack.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,523 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-asint1x2-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,524 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-dangle-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,525 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-loop-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,525 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-miscloop-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,526 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-sint2-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,526 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-sint4-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,527 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-stack-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,528 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tloop-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,528 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-triloop-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,529 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tstackh-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,530 copying build/lib.linux-armv7l-cpython-313/hotknots/mathews-tstacki-dna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,530 copying build/lib.linux-armv7l-cpython-313/hotknots/pkmodelCC2006.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,531 copying build/lib.linux-armv7l-cpython-313/hotknots/pkmodelDP.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,531 copying build/lib.linux-armv7l-cpython-313/hotknots/pkmodelRE.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,531 copying build/lib.linux-armv7l-cpython-313/hotknots/tstackcoax.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,532 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-asint1x2-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,532 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-dangle-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,533 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-loop-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,533 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-miscloop-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,534 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint2-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,534 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-sint4-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,535 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-stack-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,535 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tloop-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,535 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-triloop-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,536 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstackh-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,536 copying build/lib.linux-armv7l-cpython-313/hotknots/turner-tstacki-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,536 copying build/lib.linux-armv7l-cpython-313/hotknots/walter-coaxstack-rna.dat -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,537 copying build/lib.linux-armv7l-cpython-313/hotknots/__init__.py -> build/bdist.linux-armv7l/wheel/./hotknots 2025-09-10T14:46:33,537 running install_egg_info 2025-09-10T14:46:33,619 running egg_info 2025-09-10T14:46:33,694 writing hotknots.egg-info/PKG-INFO 2025-09-10T14:46:33,695 writing dependency_links to hotknots.egg-info/dependency_links.txt 2025-09-10T14:46:33,696 writing top-level names to hotknots.egg-info/top_level.txt 2025-09-10T14:46:33,778 reading manifest file 'hotknots.egg-info/SOURCES.txt' 2025-09-10T14:46:33,790 reading manifest template 'MANIFEST.in' 2025-09-10T14:46:33,797 warning: no files found matching '*.c' under directory 'src' 2025-09-10T14:46:33,797 adding license file 'LICENSE' 2025-09-10T14:46:33,807 writing manifest file 'hotknots.egg-info/SOURCES.txt' 2025-09-10T14:46:33,808 Copying hotknots.egg-info to build/bdist.linux-armv7l/wheel/./hotknots-2.4-py3.13.egg-info 2025-09-10T14:46:33,809 running install_scripts 2025-09-10T14:46:33,810 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2025-09-10T14:46:33,810 copying build/scripts-3.13/hotknots.py -> build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2025-09-10T14:46:33,811 changing mode of build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts/hotknots.py to 755 2025-09-10T14:46:33,860 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.dist-info/WHEEL 2025-09-10T14:46:33,861 creating '/tmp/pip-wheel-7dauto_8/hotknots-2.4-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-10T14:46:33,862 adding 'hotknots/CG_best_parameters_ISMB2007.txt' 2025-09-10T14:46:33,863 adding 'hotknots/__init__.py' 2025-09-10T14:46:33,864 adding 'hotknots/coaxial.dat' 2025-09-10T14:46:33,865 adding 'hotknots/coaxstack.dat' 2025-09-10T14:46:34,194 adding 'hotknots/hotknots.cpython-313-arm-linux-gnueabihf.so' 2025-09-10T14:46:34,206 adding 'hotknots/mathews-asint1x2-dna.dat' 2025-09-10T14:46:34,208 adding 'hotknots/mathews-asint1x2-dna.dh' 2025-09-10T14:46:34,209 adding 'hotknots/mathews-dangle-dna.dat' 2025-09-10T14:46:34,210 adding 'hotknots/mathews-dangle-dna.dh' 2025-09-10T14:46:34,210 adding 'hotknots/mathews-loop-dna.dat' 2025-09-10T14:46:34,211 adding 'hotknots/mathews-loop-dna.dh' 2025-09-10T14:46:34,212 adding 'hotknots/mathews-miscloop-dna.dat' 2025-09-10T14:46:34,212 adding 'hotknots/mathews-miscloop-dna.dh' 2025-09-10T14:46:34,213 adding 'hotknots/mathews-sint2-dna.dat' 2025-09-10T14:46:34,214 adding 'hotknots/mathews-sint2-dna.dh' 2025-09-10T14:46:34,217 adding 'hotknots/mathews-sint4-dna.dat' 2025-09-10T14:46:34,220 adding 'hotknots/mathews-sint4-dna.dh' 2025-09-10T14:46:34,221 adding 'hotknots/mathews-stack-dna.dat' 2025-09-10T14:46:34,222 adding 'hotknots/mathews-stack-dna.dh' 2025-09-10T14:46:34,222 adding 'hotknots/mathews-tloop-dna.dat' 2025-09-10T14:46:34,223 adding 'hotknots/mathews-tloop-dna.dh' 2025-09-10T14:46:34,223 adding 'hotknots/mathews-triloop-dna.dat' 2025-09-10T14:46:34,224 adding 'hotknots/mathews-triloop-dna.dh' 2025-09-10T14:46:34,225 adding 'hotknots/mathews-tstackh-dna.dat' 2025-09-10T14:46:34,225 adding 'hotknots/mathews-tstackh-dna.dh' 2025-09-10T14:46:34,226 adding 'hotknots/mathews-tstacki-dna.dat' 2025-09-10T14:46:34,227 adding 'hotknots/mathews-tstacki-dna.dh' 2025-09-10T14:46:34,227 adding 'hotknots/multirnafold.conf' 2025-09-10T14:46:34,228 adding 'hotknots/parameters_CC06.txt' 2025-09-10T14:46:34,230 adding 'hotknots/parameters_CC09.txt' 2025-09-10T14:46:34,230 adding 'hotknots/parameters_DP03.txt' 2025-09-10T14:46:34,231 adding 'hotknots/parameters_DP09.txt' 2025-09-10T14:46:34,232 adding 'hotknots/pkenergy.conf' 2025-09-10T14:46:34,232 adding 'hotknots/pkmodelCC2006.dat' 2025-09-10T14:46:34,233 adding 'hotknots/pkmodelDP.dat' 2025-09-10T14:46:34,234 adding 'hotknots/pkmodelRE.dat' 2025-09-10T14:46:34,234 adding 'hotknots/tstackcoax.dat' 2025-09-10T14:46:34,236 adding 'hotknots/turner-asint1x2-rna.dat' 2025-09-10T14:46:34,239 adding 'hotknots/turner-asint1x2-rna.dg' 2025-09-10T14:46:34,242 adding 'hotknots/turner-asint1x2-rna.dh' 2025-09-10T14:46:34,243 adding 'hotknots/turner-dangle-rna.dat' 2025-09-10T14:46:34,244 adding 'hotknots/turner-dangle-rna.dg' 2025-09-10T14:46:34,245 adding 'hotknots/turner-dangle-rna.dh' 2025-09-10T14:46:34,246 adding 'hotknots/turner-loop-rna.dat' 2025-09-10T14:46:34,246 adding 'hotknots/turner-loop-rna.dg' 2025-09-10T14:46:34,247 adding 'hotknots/turner-loop-rna.dh' 2025-09-10T14:46:34,247 adding 'hotknots/turner-miscloop-rna.dat' 2025-09-10T14:46:34,248 adding 'hotknots/turner-miscloop-rna.dg' 2025-09-10T14:46:34,249 adding 'hotknots/turner-miscloop-rna.dh' 2025-09-10T14:46:34,250 adding 'hotknots/turner-sint2-rna.dat' 2025-09-10T14:46:34,250 adding 'hotknots/turner-sint2-rna.dg' 2025-09-10T14:46:34,251 adding 'hotknots/turner-sint2-rna.dh' 2025-09-10T14:46:34,257 adding 'hotknots/turner-sint4-rna.dat' 2025-09-10T14:46:34,261 adding 'hotknots/turner-sint4-rna.dg' 2025-09-10T14:46:34,271 adding 'hotknots/turner-sint4-rna.dh' 2025-09-10T14:46:34,272 adding 'hotknots/turner-stack-rna.dat' 2025-09-10T14:46:34,273 adding 'hotknots/turner-stack-rna.dg' 2025-09-10T14:46:34,274 adding 'hotknots/turner-stack-rna.dh' 2025-09-10T14:46:34,274 adding 'hotknots/turner-tloop-rna.dat' 2025-09-10T14:46:34,275 adding 'hotknots/turner-tloop-rna.dg' 2025-09-10T14:46:34,275 adding 'hotknots/turner-tloop-rna.dh' 2025-09-10T14:46:34,276 adding 'hotknots/turner-triloop-rna.dat' 2025-09-10T14:46:34,276 adding 'hotknots/turner-triloop-rna.dg' 2025-09-10T14:46:34,277 adding 'hotknots/turner-triloop-rna.dh' 2025-09-10T14:46:34,278 adding 'hotknots/turner-tstackh-rna.dat' 2025-09-10T14:46:34,278 adding 'hotknots/turner-tstackh-rna.dg' 2025-09-10T14:46:34,279 adding 'hotknots/turner-tstackh-rna.dh' 2025-09-10T14:46:34,280 adding 'hotknots/turner-tstacki-rna.dat' 2025-09-10T14:46:34,281 adding 'hotknots/turner-tstacki-rna.dg' 2025-09-10T14:46:34,282 adding 'hotknots/turner-tstacki-rna.dh' 2025-09-10T14:46:34,282 adding 'hotknots/turner_parameters_fm363_constrdangles.txt' 2025-09-10T14:46:34,284 adding 'hotknots/turner_partypes_fm363.txt' 2025-09-10T14:46:34,284 adding 'hotknots/walter-coaxstack-rna.dat' 2025-09-10T14:46:34,285 adding 'hotknots-2.4.data/scripts/hotknots.py' 2025-09-10T14:46:34,291 adding 'hotknots-2.4.dist-info/licenses/LICENSE' 2025-09-10T14:46:34,292 adding 'hotknots-2.4.dist-info/METADATA' 2025-09-10T14:46:34,292 adding 'hotknots-2.4.dist-info/WHEEL' 2025-09-10T14:46:34,293 adding 'hotknots-2.4.dist-info/top_level.txt' 2025-09-10T14:46:34,294 adding 'hotknots-2.4.dist-info/RECORD' 2025-09-10T14:46:34,295 removing build/bdist.linux-armv7l/wheel 2025-09-10T14:46:34,446 Building wheel for hotknots (setup.py): finished with status 'done' 2025-09-10T14:46:34,456 Created wheel for hotknots: filename=hotknots-2.4-cp313-cp313-linux_armv7l.whl size=778354 sha256=f91ccd800eab8f8f0d64610e2d730ece7a9a02af583841ead3b05c8f78df555c 2025-09-10T14:46:34,457 Stored in directory: /tmp/pip-ephem-wheel-cache-5zii55nw/wheels/c9/10/78/3d7d7bc389a6ef08aa2cb44ab904953206cb41fcd137c4b2ef 2025-09-10T14:46:34,468 Successfully built hotknots 2025-09-10T14:46:34,471 Removed build tracker: '/tmp/pip-build-tracker-e00tcy1c'