2023-09-17T17:09:05,245 Created temporary directory: /tmp/pip-build-tracker-rlti101h 2023-09-17T17:09:05,246 Initialized build tracking at /tmp/pip-build-tracker-rlti101h 2023-09-17T17:09:05,247 Created build tracker: /tmp/pip-build-tracker-rlti101h 2023-09-17T17:09:05,247 Entered build tracker: /tmp/pip-build-tracker-rlti101h 2023-09-17T17:09:05,248 Created temporary directory: /tmp/pip-wheel-zcstj02e 2023-09-17T17:09:05,251 Created temporary directory: /tmp/pip-ephem-wheel-cache-2rnbkxwz 2023-09-17T17:09:05,275 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-17T17:09:05,291 2 location(s) to search for versions of hotknots: 2023-09-17T17:09:05,291 * https://pypi.org/simple/hotknots/ 2023-09-17T17:09:05,291 * https://www.piwheels.org/simple/hotknots/ 2023-09-17T17:09:05,292 Fetching project page and analyzing links: https://pypi.org/simple/hotknots/ 2023-09-17T17:09:05,293 Getting page https://pypi.org/simple/hotknots/ 2023-09-17T17:09:05,294 Found index url https://pypi.org/simple/ 2023-09-17T17:09:05,583 Fetched page https://pypi.org/simple/hotknots/ as application/vnd.pypi.simple.v1+json 2023-09-17T17:09:05,584 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) 2023-09-17T17:09:05,585 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 2023-09-17T17:09:05,586 Fetching project page and analyzing links: https://www.piwheels.org/simple/hotknots/ 2023-09-17T17:09:05,586 Getting page https://www.piwheels.org/simple/hotknots/ 2023-09-17T17:09:05,587 Found index url https://www.piwheels.org/simple/ 2023-09-17T17:09:05,889 Fetched page https://www.piwheels.org/simple/hotknots/ as text/html 2023-09-17T17:09:05,891 Skipping link: No binaries permitted for hotknots: https://www.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) 2023-09-17T17:09:05,892 Skipping link: No binaries permitted for hotknots: https://www.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) 2023-09-17T17:09:05,893 Skipping link: No binaries permitted for hotknots: https://www.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) 2023-09-17T17:09:05,893 Skipping link: No binaries permitted for hotknots: https://www.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) 2023-09-17T17:09:05,894 Skipping link: not a file: https://www.piwheels.org/simple/hotknots/ 2023-09-17T17:09:05,894 Skipping link: not a file: https://pypi.org/simple/hotknots/ 2023-09-17T17:09:05,913 Given no hashes to check 1 links for project 'hotknots': discarding no candidates 2023-09-17T17:09:05,931 Collecting hotknots==2.4 2023-09-17T17:09:05,933 Created temporary directory: /tmp/pip-unpack-sqr1njxy 2023-09-17T17:09:06,155 Downloading hotknots-2.4.tar.gz (435 kB) 2023-09-17T17:09:06,781 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-rlti101h' 2023-09-17T17:09:06,783 Running setup.py (path:/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/setup.py) egg_info for package hotknots 2023-09-17T17:09:06,784 Created temporary directory: /tmp/pip-pip-egg-info-3_ivwadh 2023-09-17T17:09:06,785 Preparing metadata (setup.py): started 2023-09-17T17:09:06,786 Running command python setup.py egg_info 2023-09-17T17:09:07,842 running egg_info 2023-09-17T17:09:07,843 creating /tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info 2023-09-17T17:09:07,867 writing /tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/PKG-INFO 2023-09-17T17:09:07,870 writing dependency_links to /tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/dependency_links.txt 2023-09-17T17:09:07,872 writing top-level names to /tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/top_level.txt 2023-09-17T17:09:07,874 writing manifest file '/tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/SOURCES.txt' 2023-09-17T17:09:08,005 reading manifest file '/tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/SOURCES.txt' 2023-09-17T17:09:08,006 reading manifest template 'MANIFEST.in' 2023-09-17T17:09:08,035 warning: no files found matching '*.c' under directory 'src' 2023-09-17T17:09:08,036 adding license file 'LICENSE' 2023-09-17T17:09:08,043 writing manifest file '/tmp/pip-pip-egg-info-3_ivwadh/hotknots.egg-info/SOURCES.txt' 2023-09-17T17:09:08,156 Preparing metadata (setup.py): finished with status 'done' 2023-09-17T17:09:08,159 Source in /tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907 has version 2.4, which satisfies requirement hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz 2023-09-17T17:09:08,160 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-rlti101h' 2023-09-17T17:09:08,166 Created temporary directory: /tmp/pip-unpack-zg0qefzr 2023-09-17T17:09:08,167 Created temporary directory: /tmp/pip-unpack-k1x7r95i 2023-09-17T17:09:08,170 Building wheels for collected packages: hotknots 2023-09-17T17:09:08,174 Created temporary directory: /tmp/pip-wheel-b10m74u7 2023-09-17T17:09:08,175 Building wheel for hotknots (setup.py): started 2023-09-17T17:09:08,176 Destination directory: /tmp/pip-wheel-b10m74u7 2023-09-17T17:09:08,177 Running command python setup.py bdist_wheel 2023-09-17T17:09:09,155 running bdist_wheel 2023-09-17T17:09:09,249 running build 2023-09-17T17:09:09,249 running build_py 2023-09-17T17:09:09,276 creating build 2023-09-17T17:09:09,276 creating build/lib.linux-armv7l-cpython-311 2023-09-17T17:09:09,277 creating build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,279 copying hotknots/__init__.py -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,288 copying hotknots/coaxial.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,291 copying hotknots/mathews-tstackh-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,293 copying hotknots/pkmodelCC2006.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,296 copying hotknots/mathews-asint1x2-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,299 copying hotknots/pkmodelRE.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,301 copying hotknots/turner-triloop-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,303 copying hotknots/turner-tstackh-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,305 copying hotknots/mathews-miscloop-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,307 copying hotknots/tstackcoax.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,311 copying hotknots/turner-sint4-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,315 copying hotknots/turner-tloop-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,317 copying hotknots/turner-stack-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,319 copying hotknots/turner-loop-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,322 copying hotknots/mathews-loop-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,324 copying hotknots/mathews-stack-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,326 copying hotknots/turner-tstacki-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,329 copying hotknots/mathews-dangle-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,331 copying hotknots/mathews-tstacki-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,333 copying hotknots/pkmodelDP.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,335 copying hotknots/turner-miscloop-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,337 copying hotknots/mathews-triloop-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,339 copying hotknots/turner-dangle-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,342 copying hotknots/mathews-tloop-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,344 copying hotknots/mathews-sint4-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,347 copying hotknots/turner-sint2-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,349 copying hotknots/walter-coaxstack-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,352 copying hotknots/mathews-sint2-dna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,354 copying hotknots/turner-asint1x2-rna.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,357 copying hotknots/coaxstack.dat -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,360 copying hotknots/turner-sint2-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,362 copying hotknots/mathews-dangle-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,365 copying hotknots/mathews-stack-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,367 copying hotknots/turner-sint4-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,371 copying hotknots/mathews-sint4-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,374 copying hotknots/mathews-tstackh-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,377 copying hotknots/turner-dangle-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,379 copying hotknots/mathews-asint1x2-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,383 copying hotknots/turner-stack-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,385 copying hotknots/mathews-tloop-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,388 copying hotknots/turner-loop-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,390 copying hotknots/turner-tstacki-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,393 copying hotknots/turner-tstackh-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,395 copying hotknots/mathews-loop-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,397 copying hotknots/mathews-triloop-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,400 copying hotknots/mathews-miscloop-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,402 copying hotknots/turner-miscloop-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,403 copying hotknots/turner-asint1x2-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,406 copying hotknots/turner-triloop-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,408 copying hotknots/mathews-tstacki-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,411 copying hotknots/turner-tloop-rna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,413 copying hotknots/mathews-sint2-dna.dh -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,415 copying hotknots/multirnafold.conf -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,417 copying hotknots/pkenergy.conf -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,419 copying hotknots/turner-tstackh-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,421 copying hotknots/turner-triloop-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,423 copying hotknots/turner-tstacki-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,425 copying hotknots/turner-stack-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,428 copying hotknots/turner-tloop-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,430 copying hotknots/turner-sint4-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,433 copying hotknots/turner-miscloop-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,435 copying hotknots/turner-asint1x2-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,438 copying hotknots/turner-loop-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,440 copying hotknots/turner-sint2-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,442 copying hotknots/turner-dangle-rna.dg -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,444 copying hotknots/parameters_DP03.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,446 copying hotknots/turner_partypes_fm363.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,449 copying hotknots/parameters_DP09.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,451 copying hotknots/parameters_CC06.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,453 copying hotknots/parameters_CC09.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,455 copying hotknots/CG_best_parameters_ISMB2007.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,457 copying hotknots/turner_parameters_fm363_constrdangles.txt -> build/lib.linux-armv7l-cpython-311/hotknots 2023-09-17T17:09:09,460 running build_ext 2023-09-17T17:09:09,967 building 'hotknots.hotknots' extension 2023-09-17T17:09:09,968 creating build/temp.linux-armv7l-cpython-311 2023-09-17T17:09:09,969 creating build/temp.linux-armv7l-cpython-311/src 2023-09-17T17:09:09,971 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/Bands.cpp -o build/temp.linux-armv7l-cpython-311/./src/Bands.o -g 2023-09-17T17:09:10,998 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/Input.cpp -o build/temp.linux-armv7l-cpython-311/./src/Input.o -g 2023-09-17T17:09:12,178 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/Loop.cpp -o build/temp.linux-armv7l-cpython-311/./src/Loop.o -g 2023-09-17T17:09:13,799 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyDP()’: 2023-09-17T17:09:13,799 ./src/Loop.cpp:3084:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,800 3084 | int special; 2023-09-17T17:09:13,801 | ^~~~~~~ 2023-09-17T17:09:13,812 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyDP(double**, double*, double&, int, int)’: 2023-09-17T17:09:13,812 ./src/Loop.cpp:3286:14: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,813 3286 | char c_structure[MaxN]; 2023-09-17T17:09:13,813 | ^~~~~~~~~~~ 2023-09-17T17:09:13,817 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyDP()’: 2023-09-17T17:09:13,817 ./src/Loop.cpp:3498:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:13,818 3498 | if (DEBUG) 2023-09-17T17:09:13,819 | ^~ 2023-09-17T17:09:13,819 ./src/Loop.cpp:3499:121: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-17T17:09:13,820 3499 | printf("[ILoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2023-09-17T17:09:13,820 | ^~~~~~ 2023-09-17T17:09:13,821 ./src/Loop.cpp:3508:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:13,821 3508 | if (DEBUG) 2023-09-17T17:09:13,822 | ^~ 2023-09-17T17:09:13,823 ./src/Loop.cpp:3509:121: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-17T17:09:13,823 3509 | printf("[MLoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2023-09-17T17:09:13,824 | ^~~~~~ 2023-09-17T17:09:13,825 ./src/Loop.cpp: In member function ‘int Loop::startsMultiSpanningBand(int)’: 2023-09-17T17:09:13,825 ./src/Loop.cpp:3618:13: warning: variable ‘startsMulti’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,826 3618 | int startsMulti = 0; 2023-09-17T17:09:13,827 | ^~~~~~~~~~~ 2023-09-17T17:09:13,849 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyRE()’: 2023-09-17T17:09:13,850 ./src/Loop.cpp:4072:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,850 4072 | int special; 2023-09-17T17:09:13,851 | ^~~~~~~ 2023-09-17T17:09:13,852 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyRE()’: 2023-09-17T17:09:13,853 ./src/Loop.cpp:4198:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:13,854 4198 | if (DEBUG) 2023-09-17T17:09:13,854 | ^~ 2023-09-17T17:09:13,855 ./src/Loop.cpp:4199:113: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-17T17:09:13,856 4199 | printf("[ILoops RE]: (%d, %d) Energy: %.2f \n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2023-09-17T17:09:13,856 | ^~~~~~ 2023-09-17T17:09:13,857 ./src/Loop.cpp:4209:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:13,858 4209 | if (DEBUG) 2023-09-17T17:09:13,858 | ^~ 2023-09-17T17:09:13,859 ./src/Loop.cpp:4210:111: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2023-09-17T17:09:13,860 4210 | printf("[MLoopsRE]: (%d, %d) Energy: %.2f\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2023-09-17T17:09:13,861 | ^~~~~~ 2023-09-17T17:09:13,873 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2023-09-17T17:09:13,874 ./src/Loop.cpp:4671:14: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,874 4671 | char c_structure[MaxN]; 2023-09-17T17:09:13,875 | ^~~~~~~~~~~ 2023-09-17T17:09:13,880 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyCC2006a()’: 2023-09-17T17:09:13,881 ./src/Loop.cpp:4800:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:13,881 4800 | int special; 2023-09-17T17:09:13,882 | ^~~~~~~ 2023-09-17T17:09:13,917 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2023-09-17T17:09:13,917 ./src/Loop.cpp:5157:13: warning: unused variable ‘num_params_pkfree’ [-Wunused-variable] 2023-09-17T17:09:13,918 5157 | int num_params_pkfree = get_num_params(); 2023-09-17T17:09:13,918 | ^~~~~~~~~~~~~~~~~ 2023-09-17T17:09:17,813 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyDP(double**, double*, double&, int, int)’: 2023-09-17T17:09:17,814 ./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] 2023-09-17T17:09:17,814 3802 | if (c != NUL) { delete c_temp; } 2023-09-17T17:09:17,815 | ^~~~~~ 2023-09-17T17:09:17,816 ./src/Loop.cpp:3770:87: note: returned from ‘void* operator new [](std::size_t)’ 2023-09-17T17:09:17,817 3770 | c_temp = new double[num_params]; 2023-09-17T17:09:17,817 | ^ 2023-09-17T17:09:17,818 ./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] 2023-09-17T17:09:17,819 3913 | if (c != NUL) { delete c_temp; } 2023-09-17T17:09:17,820 | ^~~~~~ 2023-09-17T17:09:17,820 ./src/Loop.cpp:3871:63: note: returned from ‘void* operator new [](std::size_t)’ 2023-09-17T17:09:17,821 3871 | c_temp = new double[num_params]; 2023-09-17T17:09:17,822 | ^ 2023-09-17T17:09:20,501 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/LoopList.cpp -o build/temp.linux-armv7l-cpython-311/./src/LoopList.o -g 2023-09-17T17:09:21,182 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP()’: 2023-09-17T17:09:21,182 ./src/LoopList.cpp:165:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:21,183 165 | int special; 2023-09-17T17:09:21,183 | ^~~~~~~ 2023-09-17T17:09:21,196 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP(double*, double&, int, int)’: 2023-09-17T17:09:21,197 ./src/LoopList.cpp:349:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:21,198 349 | int special; 2023-09-17T17:09:21,199 | ^~~~~~~ 2023-09-17T17:09:21,206 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyRE()’: 2023-09-17T17:09:21,207 ./src/LoopList.cpp:598:13: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:21,208 598 | int special; 2023-09-17T17:09:21,208 | ^~~~~~~ 2023-09-17T17:09:22,510 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/Stack.cpp -o build/temp.linux-armv7l-cpython-311/./src/Stack.o -g 2023-09-17T17:09:23,483 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/common.cpp -o build/temp.linux-armv7l-cpython-311/./src/common.o -g 2023-09-17T17:09:25,210 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/commonPK.cpp -o build/temp.linux-armv7l-cpython-311/./src/commonPK.o -g 2023-09-17T17:09:25,969 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:25,969 ./src/commonPK.cpp:2066:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,970 2066 | PARAMTYPE energy; 2023-09-17T17:09:25,970 | ^~~~~~ 2023-09-17T17:09:25,971 ./src/commonPK.cpp:2070:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,972 2070 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:25,972 | ^~~~~~~~~~~ 2023-09-17T17:09:25,975 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:25,976 ./src/commonPK.cpp:2180:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,976 2180 | PARAMTYPE energy; 2023-09-17T17:09:25,977 | ^~~~~~ 2023-09-17T17:09:25,978 ./src/commonPK.cpp:2186:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,978 2186 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:25,979 | ^~~~~~~~~~~ 2023-09-17T17:09:25,981 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:25,982 ./src/commonPK.cpp:2275:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,982 2275 | PARAMTYPE energy; 2023-09-17T17:09:25,983 | ^~~~~~ 2023-09-17T17:09:25,984 ./src/commonPK.cpp:2279:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:25,984 2279 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:25,985 | ^~~~~~~~~~~ 2023-09-17T17:09:27,671 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:27,672 ./src/commonPK.cpp:2118:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,673 2118 | counter[index_bot]++; 2023-09-17T17:09:27,673 | ^~~~~~~~~ 2023-09-17T17:09:27,674 ./src/commonPK.cpp:2069:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:27,675 2069 | int index_top, index_bot; 2023-09-17T17:09:27,675 | ^~~~~~~~~ 2023-09-17T17:09:27,676 ./src/commonPK.cpp:2123:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,677 2123 | counter[index_top]++; 2023-09-17T17:09:27,678 | ^~~~~~~~~ 2023-09-17T17:09:27,678 ./src/commonPK.cpp:2069:9: note: ‘index_top’ was declared here 2023-09-17T17:09:27,679 2069 | int index_top, index_bot; 2023-09-17T17:09:27,679 | ^~~~~~~~~ 2023-09-17T17:09:27,740 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:27,740 ./src/commonPK.cpp:2258:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,741 2258 | counter[index_bot]++; 2023-09-17T17:09:27,742 | ^~~~~~~~~ 2023-09-17T17:09:27,742 ./src/commonPK.cpp:2183:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:27,743 2183 | int index_top, index_bot; 2023-09-17T17:09:27,743 | ^~~~~~~~~ 2023-09-17T17:09:27,744 ./src/commonPK.cpp:2214:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,744 2214 | counter[index_top]++; 2023-09-17T17:09:27,745 | ^~~~~~~~~ 2023-09-17T17:09:27,745 ./src/commonPK.cpp:2183:9: note: ‘index_top’ was declared here 2023-09-17T17:09:27,746 2183 | int index_top, index_bot; 2023-09-17T17:09:27,746 | ^~~~~~~~~ 2023-09-17T17:09:27,799 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:27,800 ./src/commonPK.cpp:2307:21: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,800 2307 | counter[index_bot]++; 2023-09-17T17:09:27,801 | ^~~~~~~~~ 2023-09-17T17:09:27,801 ./src/commonPK.cpp:2278:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:27,802 2278 | int index_top, index_bot; 2023-09-17T17:09:27,803 | ^~~~~~~~~ 2023-09-17T17:09:27,804 ./src/commonPK.cpp:2331:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:27,804 2331 | counter[index_top]++; 2023-09-17T17:09:27,805 | ^~~~~~~~~ 2023-09-17T17:09:27,805 ./src/commonPK.cpp:2278:9: note: ‘index_top’ was declared here 2023-09-17T17:09:27,806 2278 | int index_top, index_bot; 2023-09-17T17:09:27,807 | ^~~~~~~~~ 2023-09-17T17:09:27,929 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/goodStem.cpp -o build/temp.linux-armv7l-cpython-311/./src/goodStem.o -g 2023-09-17T17:09:28,857 ./src/goodStem.cpp: In function ‘void trace(int, char*, int, int, int**, int**, int**, int**, int**, int**, short int)’: 2023-09-17T17:09:28,858 ./src/goodStem.cpp:296:27: warning: ‘tj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:28,859 296 | if (V[ti][tj] == 0) break; 2023-09-17T17:09:28,859 | ^~ 2023-09-17T17:09:28,860 ./src/goodStem.cpp:248:17: note: ‘tj’ was declared here 2023-09-17T17:09:28,861 248 | int ti, tj, startbase,mm,hl; 2023-09-17T17:09:28,861 | ^~ 2023-09-17T17:09:28,862 ./src/goodStem.cpp:296:23: warning: ‘ti’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:28,862 296 | if (V[ti][tj] == 0) break; 2023-09-17T17:09:28,863 | ^~ 2023-09-17T17:09:28,864 ./src/goodStem.cpp:248:13: note: ‘ti’ was declared here 2023-09-17T17:09:28,864 248 | int ti, tj, startbase,mm,hl; 2023-09-17T17:09:28,865 | ^~ 2023-09-17T17:09:28,966 ./src/goodStem.cpp: In function ‘void traceback(int, char*, int**, int**, int**, int**, int**, int**)’: 2023-09-17T17:09:28,967 ./src/goodStem.cpp:234:30: warning: ‘cBj’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:28,968 234 | trace(length, seq, cBi, cBj, V, G, F, E, R, flag,1); //start tracing from si, sj and recording 2023-09-17T17:09:28,968 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:28,969 ./src/goodStem.cpp:214:59: note: ‘cBj’ was declared here 2023-09-17T17:09:28,969 214 | int currentBest = -1, previousBest = 999999, cBi, cBj; 2023-09-17T17:09:28,969 | ^~~ 2023-09-17T17:09:28,970 ./src/goodStem.cpp:234:30: warning: ‘cBi’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:28,970 234 | trace(length, seq, cBi, cBj, V, G, F, E, R, flag,1); //start tracing from si, sj and recording 2023-09-17T17:09:28,971 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:28,971 ./src/goodStem.cpp:214:54: note: ‘cBi’ was declared here 2023-09-17T17:09:28,972 214 | int currentBest = -1, previousBest = 999999, cBi, cBj; 2023-09-17T17:09:28,972 | ^~~ 2023-09-17T17:09:29,145 ./src/goodStem.cpp: In function ‘void GenerateStemList(int, char*, char*)’: 2023-09-17T17:09:29,146 ./src/goodStem.cpp:176:47: warning: ‘delta’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:29,146 176 | G[i][j] = V[i-1][j-1] + delta; //s[i] matched with T[j] 2023-09-17T17:09:29,147 | ~~~~~~~~~~~~^~~~~~~ 2023-09-17T17:09:29,147 ./src/goodStem.cpp:79:20: note: ‘delta’ was declared here 2023-09-17T17:09:29,148 79 | int i,j,jo,delta; 2023-09-17T17:09:29,149 | ^~~~~ 2023-09-17T17:09:29,323 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/hotspot.cpp -o build/temp.linux-armv7l-cpython-311/./src/hotspot.o -g 2023-09-17T17:09:30,335 ./src/hotspot.cpp: In function ‘int FindHotspots(char*, char*, int)’: 2023-09-17T17:09:30,335 ./src/hotspot.cpp:206:61: warning: ‘replace’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:30,336 206 | hotspots->substruct[nh].pairTable[mm] = startbase + mm; 2023-09-17T17:09:30,337 | ^~ 2023-09-17T17:09:30,338 ./src/hotspot.cpp:105:13: note: ‘replace’ was declared here 2023-09-17T17:09:30,339 105 | int replace; 2023-09-17T17:09:30,340 | ^~~~~~~ 2023-09-17T17:09:30,873 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/init.cpp -o build/temp.linux-armv7l-cpython-311/./src/init.o -g 2023-09-17T17:09:33,713 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/initPK.cpp -o build/temp.linux-armv7l-cpython-311/./src/initPK.o -g 2023-09-17T17:09:34,368 ./src/initPK.cpp: In function ‘void read_pkmodelCC2006_file(char*, float, float (*)[12], float (*)[12], float (*)[11], float (*)[11])’: 2023-09-17T17:09:34,369 ./src/initPK.cpp:253:16: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:34,370 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2023-09-17T17:09:34,370 | ^ 2023-09-17T17:09:34,371 ./src/initPK.cpp:253:23: warning: variable ‘jj’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:34,372 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2023-09-17T17:09:34,372 | ^~ 2023-09-17T17:09:34,383 ./src/initPK.cpp: In function ‘void init_dataPK(char*, char*, int, double)’: 2023-09-17T17:09:34,383 ./src/initPK.cpp:472:14: warning: unused variable ‘conf’ [-Wunused-variable] 2023-09-17T17:09:34,384 472 | char conf[200]; 2023-09-17T17:09:34,384 | ^~~~ 2023-09-17T17:09:34,385 ./src/initPK.cpp:485:13: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T17:09:34,385 485 | int i; 2023-09-17T17:09:34,386 | ^ 2023-09-17T17:09:35,293 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/params.cpp -o build/temp.linux-armv7l-cpython-311/./src/params.o -g 2023-09-17T17:09:35,991 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:35,991 ./src/params.cpp:518:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:35,992 518 | PARAMTYPE energy; 2023-09-17T17:09:35,992 | ^~~~~~ 2023-09-17T17:09:35,993 ./src/params.cpp:522:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:35,994 522 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:35,994 | ^~~~~~~~~~~ 2023-09-17T17:09:35,995 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:35,996 ./src/params.cpp:632:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:35,996 632 | PARAMTYPE energy; 2023-09-17T17:09:35,997 | ^~~~~~ 2023-09-17T17:09:35,997 ./src/params.cpp:638:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:35,998 638 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:35,999 | ^~~~~~~~~~~ 2023-09-17T17:09:36,000 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:36,000 ./src/params.cpp:727:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,001 727 | PARAMTYPE energy; 2023-09-17T17:09:36,002 | ^~~~~~ 2023-09-17T17:09:36,002 ./src/params.cpp:731:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,003 731 | int first_index; // first index should be dangle_top[0][3][0] 2023-09-17T17:09:36,004 | ^~~~~~~~~~~ 2023-09-17T17:09:36,004 ./src/params.cpp: In function ‘void count_penalty_by_size(int, char, double*)’: 2023-09-17T17:09:36,005 ./src/params.cpp:851:27: warning: variable ‘penalty’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,006 851 | PARAMTYPE penaltyMAX, penalty; 2023-09-17T17:09:36,006 | ^~~~~~~ 2023-09-17T17:09:36,035 ./src/params.cpp: In function ‘void print_counter(double*, double)’: 2023-09-17T17:09:36,036 ./src/params.cpp:1479:33: warning: ' ' flag used with ‘%s’ gnu_printf format [-Wformat=] 2023-09-17T17:09:36,036 1479 | printf ("%4d\t%30s\t% 10s\t%4.2lf\n", num_params, "FREE PARAMETER", "", (double)free_value); 2023-09-17T17:09:36,037 | ^ 2023-09-17T17:09:36,110 ./src/params.cpp: In function ‘void fill_data_structures_with_new_parameters(char*)’: 2023-09-17T17:09:36,111 ./src/params.cpp:4206:9: warning: variable ‘index’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,111 4206 | int index; 2023-09-17T17:09:36,112 | ^~~~~ 2023-09-17T17:09:36,121 ./src/params.cpp: In function ‘double simfold_restricted_logZ_gradient(char*, char*, char*, double*)’: 2023-09-17T17:09:36,121 ./src/params.cpp:5021:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,122 5021 | double min_energy, max_energy; 2023-09-17T17:09:36,122 | ^~~~~~~~~~ 2023-09-17T17:09:36,128 ./src/params.cpp: In function ‘double compute_f(char*)’: 2023-09-17T17:09:36,128 ./src/params.cpp:5212:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,129 5212 | int k; 2023-09-17T17:09:36,129 | ^ 2023-09-17T17:09:36,130 ./src/params.cpp: In function ‘double compute_likelihood_exactly(char*)’: 2023-09-17T17:09:36,131 ./src/params.cpp:5262:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,131 5262 | int k; 2023-09-17T17:09:36,132 | ^ 2023-09-17T17:09:36,132 ./src/params.cpp: In function ‘double compute_log_likelihood_smart(char*)’: 2023-09-17T17:09:36,133 ./src/params.cpp:5314:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,133 5314 | int k; 2023-09-17T17:09:36,134 | ^ 2023-09-17T17:09:36,134 ./src/params.cpp: In function ‘void compute_gradient_f(char*, double*)’: 2023-09-17T17:09:36,135 ./src/params.cpp:5366:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,135 5366 | int k; 2023-09-17T17:09:36,136 | ^ 2023-09-17T17:09:36,137 ./src/params.cpp: In function ‘void compute_gradient_f_smart(char*, double*)’: 2023-09-17T17:09:36,137 ./src/params.cpp:5416:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,138 5416 | int k; 2023-09-17T17:09:36,139 | ^ 2023-09-17T17:09:36,140 ./src/params.cpp: In function ‘double compute_f_and_gradient_f_smart(char*, double*)’: 2023-09-17T17:09:36,140 ./src/params.cpp:5470:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,141 5470 | int k; 2023-09-17T17:09:36,142 | ^ 2023-09-17T17:09:36,145 ./src/params.cpp: In function ‘double compute_f_and_gradient_f(char*, double*)’: 2023-09-17T17:09:36,146 ./src/params.cpp:5511:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,146 5511 | double min_energy, max_energy; 2023-09-17T17:09:36,147 | ^~~~~~~~~~ 2023-09-17T17:09:36,148 ./src/params.cpp: In function ‘void compute_counts_vector_LP(char*, double*)’: 2023-09-17T17:09:36,148 ./src/params.cpp:5627:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,149 5627 | double R, temp, beta; 2023-09-17T17:09:36,150 | ^~~~ 2023-09-17T17:09:36,150 ./src/params.cpp:5639:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,151 5639 | int k; 2023-09-17T17:09:36,152 | ^ 2023-09-17T17:09:36,152 ./src/params.cpp: In function ‘void compute_counts_matrix_LP(char*, int)’: 2023-09-17T17:09:36,153 ./src/params.cpp:5699:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,154 5699 | double R, temp, beta; 2023-09-17T17:09:36,155 | ^~~~ 2023-09-17T17:09:36,155 ./src/params.cpp:5711:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,156 5711 | int k; 2023-09-17T17:09:36,157 | ^ 2023-09-17T17:09:36,158 ./src/params.cpp: In function ‘int generate_structure_withbb(char*, char*, char*, char*, char (*)[1000], double*, int)’: 2023-09-17T17:09:36,158 ./src/params.cpp:5844:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:36,159 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,160 | ^~~ 2023-09-17T17:09:36,160 ./src/params.cpp:5844:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2023-09-17T17:09:36,161 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,161 | ^~~~~~~~~~ 2023-09-17T17:09:36,162 ./src/params.cpp:5865:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,163 5865 | int tried = 0; 2023-09-17T17:09:36,163 | ^~~~~ 2023-09-17T17:09:36,168 ./src/params.cpp: In function ‘int generate_structure_withbb_many_thresholds(char*, char (*)[1000], double*, double*, int*, double, int)’: 2023-09-17T17:09:36,168 ./src/params.cpp:6284:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:36,169 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,169 | ^~~ 2023-09-17T17:09:36,170 ./src/params.cpp:6284:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2023-09-17T17:09:36,170 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,171 | ^~~~~~~~~~ 2023-09-17T17:09:36,173 ./src/params.cpp:6305:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,173 6305 | int tried = 0; 2023-09-17T17:09:36,174 | ^~~~~ 2023-09-17T17:09:36,176 ./src/params.cpp: In function ‘void search_bb(char*, double*, int, int)’: 2023-09-17T17:09:36,177 ./src/params.cpp:6437:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2023-09-17T17:09:36,177 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,178 | ^~~ 2023-09-17T17:09:36,179 ./src/params.cpp:6437:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2023-09-17T17:09:36,180 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2023-09-17T17:09:36,180 | ^~~~~~~~~~ 2023-09-17T17:09:36,181 ./src/params.cpp:6458:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,182 6458 | int tried = 0; 2023-09-17T17:09:36,182 | ^~~~~ 2023-09-17T17:09:36,183 ./src/params.cpp:6410:20: warning: variable ‘numstr’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,184 6410 | int seqlen, i, numstr; 2023-09-17T17:09:36,184 | ^~~~~~ 2023-09-17T17:09:36,221 ./src/params.cpp: In function ‘void fill_similarity_rule_with_optical_melting_reference(char*)’: 2023-09-17T17:09:36,222 ./src/params.cpp:7832:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:36,222 7832 | int k; 2023-09-17T17:09:36,223 | ^ 2023-09-17T17:09:37,915 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:37,915 ./src/params.cpp:570:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:37,916 570 | counter[index_bot]++; 2023-09-17T17:09:37,917 | ^~~~~~~~~ 2023-09-17T17:09:37,918 ./src/params.cpp:521:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:37,918 521 | int index_top, index_bot; 2023-09-17T17:09:37,919 | ^~~~~~~~~ 2023-09-17T17:09:37,919 ./src/params.cpp:575:17: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:37,920 575 | counter[index_top]++; 2023-09-17T17:09:37,920 | ^~~~~~~~~ 2023-09-17T17:09:37,921 ./src/params.cpp:521:9: note: ‘index_top’ was declared here 2023-09-17T17:09:37,921 521 | int index_top, index_bot; 2023-09-17T17:09:37,922 | ^~~~~~~~~ 2023-09-17T17:09:37,979 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:37,980 ./src/params.cpp:710:17: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:37,980 710 | counter[index_bot]++; 2023-09-17T17:09:37,981 | ^~~~~~~~~ 2023-09-17T17:09:37,981 ./src/params.cpp:635:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:37,982 635 | int index_top, index_bot; 2023-09-17T17:09:37,982 | ^~~~~~~~~ 2023-09-17T17:09:37,983 ./src/params.cpp:666:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:37,983 666 | counter[index_top]++; 2023-09-17T17:09:37,984 | ^~~~~~~~~ 2023-09-17T17:09:37,984 ./src/params.cpp:635:9: note: ‘index_top’ was declared here 2023-09-17T17:09:37,985 635 | int index_top, index_bot; 2023-09-17T17:09:37,986 | ^~~~~~~~~ 2023-09-17T17:09:38,034 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2023-09-17T17:09:38,035 ./src/params.cpp:759:21: warning: ‘index_bot’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:38,035 759 | counter[index_bot]++; 2023-09-17T17:09:38,036 | ^~~~~~~~~ 2023-09-17T17:09:38,037 ./src/params.cpp:730:20: note: ‘index_bot’ was declared here 2023-09-17T17:09:38,038 730 | int index_top, index_bot; 2023-09-17T17:09:38,038 | ^~~~~~~~~ 2023-09-17T17:09:38,039 ./src/params.cpp:783:21: warning: ‘index_top’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:38,040 783 | counter[index_top]++; 2023-09-17T17:09:38,040 | ^~~~~~~~~ 2023-09-17T17:09:38,041 ./src/params.cpp:730:9: note: ‘index_top’ was declared here 2023-09-17T17:09:38,042 730 | int index_top, index_bot; 2023-09-17T17:09:38,042 | ^~~~~~~~~ 2023-09-17T17:09:39,243 ./src/params.cpp: In function ‘void similarity_bulge_type(int, char*)’: 2023-09-17T17:09:39,244 ./src/params.cpp:2261:33: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2023-09-17T17:09:39,244 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, 2023-09-17T17:09:39,245 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:39,246 2262 | int_to_nuc(i), int_to_nuc(bulged_base), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j), 2023-09-17T17:09:39,246 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:39,247 2263 | 1.0/num, int_to_nuc(i), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j)); 2023-09-17T17:09:39,247 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:39,248 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2023-09-17T17:09:39,249 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2023-09-17T17:09:39,250 | ~~~~~~^~~~~~~~~~ 2023-09-17T17:09:39,250 ./src/params.cpp:2265:53: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2023-09-17T17:09:39,251 2265 | if (num2 < num) sprintf (similarity, "%s + ", similarity); 2023-09-17T17:09:39,251 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:39,252 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2023-09-17T17:09:39,252 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2023-09-17T17:09:39,253 | ~~~~~~^~~~~~~~~~ 2023-09-17T17:09:39,658 ./src/params.cpp: In function ‘int traverse_features_and_do_work(char*, int*, char*)’: 2023-09-17T17:09:39,659 ./src/params.cpp:2328:45: warning: ‘file’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:39,660 2328 | fprintf (file, "%.2lf\n", stack[i][j][k][l]/100.0); 2023-09-17T17:09:39,660 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:39,661 ./src/params.cpp:2287:11: note: ‘file’ was declared here 2023-09-17T17:09:39,661 2287 | FILE *file; 2023-09-17T17:09:39,662 | ^~~~ 2023-09-17T17:09:46,176 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/paramsPK.cpp -o build/temp.linux-armv7l-cpython-311/./src/paramsPK.o -g 2023-09-17T17:09:49,253 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/python.cpp -o build/temp.linux-armv7l-cpython-311/./src/python.o -g 2023-09-17T17:09:50,421 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_energy_matrix.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_energy_matrix.o -g 2023-09-17T17:09:50,904 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_hairpin_loop.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_hairpin_loop.o -g 2023-09-17T17:09:51,043 ./src/s_hairpin_loop.cpp: In constructor ‘s_hairpin_loop::s_hairpin_loop(char*, int*, int)’: 2023-09-17T17:09:51,043 ./src/s_hairpin_loop.cpp:42:16: warning: statement has no effect [-Wunused-value] 2023-09-17T17:09:51,044 42 | toupper(csequence[i]); 2023-09-17T17:09:51,045 | ~~~~~~~^~~~~~~~~~~~~~ 2023-09-17T17:09:51,062 ./src/s_hairpin_loop.cpp: In static member function ‘static void s_hairpin_loop::count_get_energy(int, int, int*, char*, double*)’: 2023-09-17T17:09:51,062 ./src/s_hairpin_loop.cpp:487:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:51,063 487 | PARAMTYPE energy=0; 2023-09-17T17:09:51,064 | ^~~~~~ 2023-09-17T17:09:51,665 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_internal_loop.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_internal_loop.o -g 2023-09-17T17:09:51,902 ./src/s_internal_loop.cpp: In static member function ‘static void s_internal_loop::count_get_energy(int, int, int, int, int*, double*)’: 2023-09-17T17:09:51,903 ./src/s_internal_loop.cpp:646:19: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:51,904 646 | PARAMTYPE energy; 2023-09-17T17:09:51,905 | ^~~~~~ 2023-09-17T17:09:53,598 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_min_folding.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_min_folding.o -g 2023-09-17T17:09:53,831 ./src/s_min_folding.cpp: In member function ‘int s_min_folding::compute_W_br2_restricted(int, str_features*, int&)’: 2023-09-17T17:09:53,832 ./src/s_min_folding.cpp:1066:13: warning: variable ‘chosen’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:53,832 1066 | int chosen = 0; 2023-09-17T17:09:53,833 | ^~~~~~ 2023-09-17T17:09:53,834 ./src/s_min_folding.cpp:1067:13: warning: variable ‘best_i’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:53,834 1067 | int best_i = 0; 2023-09-17T17:09:53,835 | ^~~~~~ 2023-09-17T17:09:54,366 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack(seq_interval*)’: 2023-09-17T17:09:54,366 ./src/s_min_folding.cpp:560:61: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,367 560 | insert_node (best_k+1, j, M_WM); 2023-09-17T17:09:54,368 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,369 ./src/s_min_folding.cpp:462:21: note: ‘best_k’ was declared here 2023-09-17T17:09:54,369 462 | int best_k, best_row; 2023-09-17T17:09:54,370 | ^~~~~~ 2023-09-17T17:09:54,371 ./src/s_min_folding.cpp:349:25: warning: ‘best_row’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,372 349 | switch (best_row){ 2023-09-17T17:09:54,372 | ^~~~~~ 2023-09-17T17:09:54,373 ./src/s_min_folding.cpp:314:40: note: ‘best_row’ was declared here 2023-09-17T17:09:54,374 314 | int k, best_k, best_row; 2023-09-17T17:09:54,375 | ^~~~~~~~ 2023-09-17T17:09:54,375 ./src/s_min_folding.cpp:352:53: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,376 352 | insert_node (best_k+1, j-1, M_WM); break; 2023-09-17T17:09:54,377 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,377 ./src/s_min_folding.cpp:314:32: note: ‘best_k’ was declared here 2023-09-17T17:09:54,378 314 | int k, best_k, best_row; 2023-09-17T17:09:54,379 | ^~~~~~ 2023-09-17T17:09:54,379 ./src/s_min_folding.cpp:306:45: warning: ‘best_jp’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,380 306 | insert_node (best_ip, best_jp, LOOP); 2023-09-17T17:09:54,381 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,381 ./src/s_min_folding.cpp:292:46: note: ‘best_jp’ was declared here 2023-09-17T17:09:54,382 292 | int ip, jp, best_ip, best_jp, minq; 2023-09-17T17:09:54,383 | ^~~~~~~ 2023-09-17T17:09:54,384 ./src/s_min_folding.cpp:306:45: warning: ‘best_ip’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,384 306 | insert_node (best_ip, best_jp, LOOP); 2023-09-17T17:09:54,385 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,385 ./src/s_min_folding.cpp:292:37: note: ‘best_ip’ was declared here 2023-09-17T17:09:54,386 292 | int ip, jp, best_ip, best_jp, minq; 2023-09-17T17:09:54,386 | ^~~~~~~ 2023-09-17T17:09:54,875 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack_restricted(seq_interval*, str_features*)’: 2023-09-17T17:09:54,876 ./src/s_min_folding.cpp:961:61: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,876 961 | insert_node (best_k+1, j, M_WM); 2023-09-17T17:09:54,878 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,878 ./src/s_min_folding.cpp:853:21: note: ‘best_k’ was declared here 2023-09-17T17:09:54,879 853 | int best_k, best_row; 2023-09-17T17:09:54,880 | ^~~~~~ 2023-09-17T17:09:54,880 ./src/s_min_folding.cpp:689:25: warning: ‘best_row’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,881 689 | switch (best_row) 2023-09-17T17:09:54,881 | ^~~~~~ 2023-09-17T17:09:54,882 ./src/s_min_folding.cpp:640:40: note: ‘best_row’ was declared here 2023-09-17T17:09:54,883 640 | int k, best_k, best_row; 2023-09-17T17:09:54,884 | ^~~~~~~~ 2023-09-17T17:09:54,884 ./src/s_min_folding.cpp:692:61: warning: ‘best_k’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,885 692 | insert_node (best_k+1, j-1, M_WM); break; 2023-09-17T17:09:54,886 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,886 ./src/s_min_folding.cpp:640:32: note: ‘best_k’ was declared here 2023-09-17T17:09:54,887 640 | int k, best_k, best_row; 2023-09-17T17:09:54,888 | ^~~~~~ 2023-09-17T17:09:54,889 ./src/s_min_folding.cpp:629:45: warning: ‘best_jp’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,889 629 | insert_node (best_ip, best_jp, LOOP); 2023-09-17T17:09:54,890 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,891 ./src/s_min_folding.cpp:610:46: note: ‘best_jp’ was declared here 2023-09-17T17:09:54,891 610 | int ip, jp, best_ip, best_jp, minq; 2023-09-17T17:09:54,892 | ^~~~~~~ 2023-09-17T17:09:54,893 ./src/s_min_folding.cpp:629:45: warning: ‘best_ip’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:09:54,893 629 | insert_node (best_ip, best_jp, LOOP); 2023-09-17T17:09:54,894 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T17:09:54,895 ./src/s_min_folding.cpp:610:37: note: ‘best_ip’ was declared here 2023-09-17T17:09:54,895 610 | int ip, jp, best_ip, best_jp, minq; 2023-09-17T17:09:54,896 | ^~~~~~~ 2023-09-17T17:09:55,820 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_multi_loop.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_multi_loop.o -g 2023-09-17T17:09:56,573 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_multi_loop_sub.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_multi_loop_sub.o -g 2023-09-17T17:09:56,689 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1(int)’: 2023-09-17T17:09:56,690 ./src/s_multi_loop_sub.cpp:64:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:56,691 64 | int i, tmp_k, ij, k; 2023-09-17T17:09:56,691 | ^~~~~ 2023-09-17T17:09:56,692 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM(int)’: 2023-09-17T17:09:56,692 ./src/s_multi_loop_sub.cpp:110:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:56,693 110 | int i, tmp_k, k, ij; 2023-09-17T17:09:56,693 | ^~~~~ 2023-09-17T17:09:56,696 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1_restricted(int, str_features*)’: 2023-09-17T17:09:56,697 ./src/s_multi_loop_sub.cpp:173:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:56,697 173 | int i, tmp_k, ij, k; 2023-09-17T17:09:56,698 | ^~~~~ 2023-09-17T17:09:56,699 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM_restricted(int, str_features*)’: 2023-09-17T17:09:56,700 ./src/s_multi_loop_sub.cpp:220:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:56,700 220 | int i, tmp_k, k, ij; 2023-09-17T17:09:56,701 | ^~~~~ 2023-09-17T17:09:57,157 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_partition_function.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_partition_function.o -g 2023-09-17T17:09:57,825 ./src/s_partition_function.cpp: In constructor ‘s_partition_function::s_partition_function(char*, int, int, char*)’: 2023-09-17T17:09:57,826 ./src/s_partition_function.cpp:78:16: warning: statement has no effect [-Wunused-value] 2023-09-17T17:09:57,827 78 | toupper(csequence[i]); 2023-09-17T17:09:57,827 | ~~~~~~~^~~~~~~~~~~~~~ 2023-09-17T17:09:57,854 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function()’: 2023-09-17T17:09:57,855 ./src/s_partition_function.cpp:415:15: warning: variable ‘ij’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,856 415 | int i, j, ij; 2023-09-17T17:09:57,856 | ^~ 2023-09-17T17:09:57,866 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm_nodangles(int, int)’: 2023-09-17T17:09:57,867 ./src/s_partition_function.cpp:692:12: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,868 692 | int h, hj; 2023-09-17T17:09:57,868 | ^~ 2023-09-17T17:09:57,886 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm(int, int)’: 2023-09-17T17:09:57,887 ./src/s_partition_function.cpp:1028:37: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,888 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2023-09-17T17:09:57,888 | ^~~~~~ 2023-09-17T17:09:57,889 ./src/s_partition_function.cpp:1028:45: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,890 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2023-09-17T17:09:57,891 | ^~~~~~ 2023-09-17T17:09:57,891 ./src/s_partition_function.cpp:1028:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,892 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2023-09-17T17:09:57,893 | ^~~~~~ 2023-09-17T17:09:57,893 ./src/s_partition_function.cpp:1028:61: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,894 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2023-09-17T17:09:57,894 | ^~~~~~ 2023-09-17T17:09:57,895 ./src/s_partition_function.cpp:1028:69: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,895 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2023-09-17T17:09:57,896 | ^~ 2023-09-17T17:09:57,931 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_needmidd3(int, int)’: 2023-09-17T17:09:57,932 ./src/s_partition_function.cpp:1717:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,932 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,933 | ^~~~~~ 2023-09-17T17:09:57,934 ./src/s_partition_function.cpp:1717:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,935 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,935 | ^~~~~~ 2023-09-17T17:09:57,936 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_noneedmidd3(int, int)’: 2023-09-17T17:09:57,937 ./src/s_partition_function.cpp:1747:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,937 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,938 | ^~~~~~ 2023-09-17T17:09:57,939 ./src/s_partition_function.cpp:1747:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,939 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,940 | ^~~~~~ 2023-09-17T17:09:57,940 ./src/s_partition_function.cpp:1747:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,941 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,942 | ^~~~~~ 2023-09-17T17:09:57,943 ./src/s_partition_function.cpp:1747:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,943 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,944 | ^~~~~~ 2023-09-17T17:09:57,944 ./src/s_partition_function.cpp:1747:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,945 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,946 | ^~~~~~ 2023-09-17T17:09:57,947 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_needmidd3(int, int)’: 2023-09-17T17:09:57,947 ./src/s_partition_function.cpp:1779:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,948 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,949 | ^~~~~~ 2023-09-17T17:09:57,950 ./src/s_partition_function.cpp:1779:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,950 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,951 | ^~~~~~ 2023-09-17T17:09:57,951 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_noneedmidd3(int, int)’: 2023-09-17T17:09:57,952 ./src/s_partition_function.cpp:1808:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,952 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,953 | ^~~~~~ 2023-09-17T17:09:57,954 ./src/s_partition_function.cpp:1808:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,954 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,955 | ^~~~~~ 2023-09-17T17:09:57,955 ./src/s_partition_function.cpp:1808:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,956 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,956 | ^~~~~~ 2023-09-17T17:09:57,957 ./src/s_partition_function.cpp:1808:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,958 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,958 | ^~~~~~ 2023-09-17T17:09:57,959 ./src/s_partition_function.cpp:1808:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,960 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2023-09-17T17:09:57,960 | ^~~~~~ 2023-09-17T17:09:57,976 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function_exhaustively()’: 2023-09-17T17:09:57,977 ./src/s_partition_function.cpp:2288:12: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,978 2288 | double min_energy, max_energy; 2023-09-17T17:09:57,978 | ^~~~~~~~~~ 2023-09-17T17:09:57,979 ./src/s_partition_function.cpp:2288:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,980 2288 | double min_energy, max_energy; 2023-09-17T17:09:57,981 | ^~~~~~~~~~ 2023-09-17T17:09:57,997 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::verify_recurrences()’: 2023-09-17T17:09:57,998 ./src/s_partition_function.cpp:2667:9: warning: variable ‘error’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:57,999 2667 | int error = 0; 2023-09-17T17:09:57,999 | ^~~~~ 2023-09-17T17:09:58,003 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient_exhaustively()’: 2023-09-17T17:09:58,004 ./src/s_partition_function.cpp:2868:9: warning: variable ‘real_str_found’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:58,004 2868 | int real_str_found, actual_num_str; 2023-09-17T17:09:58,005 | ^~~~~~~~~~~~~~ 2023-09-17T17:09:58,104 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient()’: 2023-09-17T17:09:58,105 ./src/s_partition_function.cpp:3000:15: warning: variable ‘AUpen’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:58,105 3000 | PARAMTYPE AUpen; //, dangle, dangle5, dangle3; 2023-09-17T17:09:58,106 | ^~~~~ 2023-09-17T17:09:58,126 ./src/s_partition_function.cpp: In member function ‘int s_partition_function::correct_gradient()’: 2023-09-17T17:09:58,127 ./src/s_partition_function.cpp:4925:9: warning: variable ‘index_param’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:09:58,128 4925 | int index_param; 2023-09-17T17:09:58,129 | ^~~~~~~~~~~ 2023-09-17T17:10:09,357 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_specific_functions.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_specific_functions.o -g 2023-09-17T17:10:10,065 ./src/s_specific_functions.cpp: In function ‘int s_calculate_energy(int*, char*, char*, str_features*, str_features*)’: 2023-09-17T17:10:10,065 ./src/s_specific_functions.cpp:483:29: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:10,066 483 | int special; 2023-09-17T17:10:10,066 | ^~~~~~~ 2023-09-17T17:10:10,079 ./src/s_specific_functions.cpp: In function ‘int s_calculate_enthalpy(int*, char*, str_features*)’: 2023-09-17T17:10:10,080 ./src/s_specific_functions.cpp:662:29: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:10,080 662 | int special; 2023-09-17T17:10:10,081 | ^~~~~~~ 2023-09-17T17:10:10,098 ./src/s_specific_functions.cpp: In function ‘void simfold_gradient_smart(char*, double*, int, int)’: 2023-09-17T17:10:10,098 ./src/s_specific_functions.cpp:1089:16: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:10,099 1089 | PFTYPE pf; 2023-09-17T17:10:10,100 | ^~ 2023-09-17T17:10:10,103 ./src/s_specific_functions.cpp: In function ‘double simfold_partition_function_approximately(char*)’: 2023-09-17T17:10:10,104 ./src/s_specific_functions.cpp:1147:16: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:10,104 1147 | double min_energy, max_energy; 2023-09-17T17:10:10,105 | ^~~~~~~~~~ 2023-09-17T17:10:10,106 ./src/s_specific_functions.cpp:1147:28: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:10,106 1147 | double min_energy, max_energy; 2023-09-17T17:10:10,107 | ^~~~~~~~~~ 2023-09-17T17:10:11,985 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_stacked_pair.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_stacked_pair.o -g 2023-09-17T17:10:12,238 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/s_sub_folding.cpp -o build/temp.linux-armv7l-cpython-311/./src/s_sub_folding.o -g 2023-09-17T17:10:14,382 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/sc.cpp -o build/temp.linux-armv7l-cpython-311/./src/sc.o -g 2023-09-17T17:10:15,400 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/score.cpp -o build/temp.linux-armv7l-cpython-311/./src/score.o -g 2023-09-17T17:10:16,419 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/temp.cpp -o build/temp.linux-armv7l-cpython-311/./src/temp.o -g 2023-09-17T17:10:17,850 ./src/temp.cpp: In function ‘Fold* best(char*, char*)’: 2023-09-17T17:10:17,850 ./src/temp.cpp:80:16: warning: variable ‘min_en’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:17,851 80 | double min_en; 2023-09-17T17:10:17,851 | ^~~~~~ 2023-09-17T17:10:18,343 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/timer.cpp -o build/temp.linux-armv7l-cpython-311/./src/timer.o -g 2023-09-17T17:10:18,943 ./src/timer.cpp: In member function ‘void timer::start()’: 2023-09-17T17:10:18,943 ./src/timer.cpp:23:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:18,944 23 | clock_t t; 2023-09-17T17:10:18,945 | ^ 2023-09-17T17:10:18,945 ./src/timer.cpp: In member function ‘void timer::stop()’: 2023-09-17T17:10:18,946 ./src/timer.cpp:32:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:18,946 32 | clock_t t; 2023-09-17T17:10:18,947 | ^ 2023-09-17T17:10:18,947 ./src/timer.cpp: In member function ‘void timer::reset()’: 2023-09-17T17:10:18,948 ./src/timer.cpp:41:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:18,949 41 | clock_t t; 2023-09-17T17:10:18,949 | ^ 2023-09-17T17:10:18,950 ./src/timer.cpp: In member function ‘float timer::elapsed()’: 2023-09-17T17:10:18,951 ./src/timer.cpp:52:13: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2023-09-17T17:10:18,952 52 | clock_t t; 2023-09-17T17:10:18,952 | ^ 2023-09-17T17:10:19,219 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-zcstj02e/hotknots_cc9a532ad0f94fbc926356eea4afe907/include -I/usr/include/python3.11 -c ./src/utils.cpp -o build/temp.linux-armv7l-cpython-311/./src/utils.o -g 2023-09-17T17:10:19,566 ./src/utils.cpp: In function ‘void bpseq2dp(int, short int*, char*)’: 2023-09-17T17:10:19,566 ./src/utils.cpp:146:13: warning: ‘stackindex_push’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T17:10:19,567 146 | int stackindex_push; 2023-09-17T17:10:19,568 | ^~~~~~~~~~~~~~~ 2023-09-17T17:10:19,642 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/./src/Bands.o build/temp.linux-armv7l-cpython-311/./src/Input.o build/temp.linux-armv7l-cpython-311/./src/Loop.o build/temp.linux-armv7l-cpython-311/./src/LoopList.o build/temp.linux-armv7l-cpython-311/./src/Stack.o build/temp.linux-armv7l-cpython-311/./src/common.o build/temp.linux-armv7l-cpython-311/./src/commonPK.o build/temp.linux-armv7l-cpython-311/./src/goodStem.o build/temp.linux-armv7l-cpython-311/./src/hotspot.o build/temp.linux-armv7l-cpython-311/./src/init.o build/temp.linux-armv7l-cpython-311/./src/initPK.o build/temp.linux-armv7l-cpython-311/./src/params.o build/temp.linux-armv7l-cpython-311/./src/paramsPK.o build/temp.linux-armv7l-cpython-311/./src/python.o build/temp.linux-armv7l-cpython-311/./src/s_energy_matrix.o build/temp.linux-armv7l-cpython-311/./src/s_hairpin_loop.o build/temp.linux-armv7l-cpython-311/./src/s_internal_loop.o build/temp.linux-armv7l-cpython-311/./src/s_min_folding.o build/temp.linux-armv7l-cpython-311/./src/s_multi_loop.o build/temp.linux-armv7l-cpython-311/./src/s_multi_loop_sub.o build/temp.linux-armv7l-cpython-311/./src/s_partition_function.o build/temp.linux-armv7l-cpython-311/./src/s_specific_functions.o build/temp.linux-armv7l-cpython-311/./src/s_stacked_pair.o build/temp.linux-armv7l-cpython-311/./src/s_sub_folding.o build/temp.linux-armv7l-cpython-311/./src/sc.o build/temp.linux-armv7l-cpython-311/./src/score.o build/temp.linux-armv7l-cpython-311/./src/temp.o build/temp.linux-armv7l-cpython-311/./src/timer.o build/temp.linux-armv7l-cpython-311/./src/utils.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/hotknots/hotknots.cpython-311-arm-linux-gnueabihf.so -lm 2023-09-17T17:10:20,047 running build_scripts 2023-09-17T17:10:20,048 creating build/scripts-3.11 2023-09-17T17:10:20,049 copying and adjusting hotknots.py -> build/scripts-3.11 2023-09-17T17:10:20,051 changing mode of build/scripts-3.11/hotknots.py from 644 to 755 2023-09-17T17:10:20,095 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-09-17T17:10:20,095 !! 2023-09-17T17:10:20,096 ******************************************************************************** 2023-09-17T17:10:20,097 Please avoid running ``setup.py`` directly. 2023-09-17T17:10:20,097 Instead, use pypa/build, pypa/installer or other 2023-09-17T17:10:20,098 standards-based tools. 2023-09-17T17:10:20,099 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-09-17T17:10:20,099 ******************************************************************************** 2023-09-17T17:10:20,100 !! 2023-09-17T17:10:20,101 self.initialize_options() 2023-09-17T17:10:20,123 installing to build/bdist.linux-armv7l/wheel 2023-09-17T17:10:20,123 running install 2023-09-17T17:10:20,148 running install_lib 2023-09-17T17:10:20,173 creating build/bdist.linux-armv7l 2023-09-17T17:10:20,173 creating build/bdist.linux-armv7l/wheel 2023-09-17T17:10:20,176 creating build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,178 copying build/lib.linux-armv7l-cpython-311/hotknots/coaxial.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,180 copying build/lib.linux-armv7l-cpython-311/hotknots/parameters_DP03.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,182 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tstackh-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,185 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint2-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,188 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-dangle-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,190 copying build/lib.linux-armv7l-cpython-311/hotknots/pkmodelCC2006.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,192 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-stack-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,195 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-asint1x2-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,198 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint4-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,202 copying build/lib.linux-armv7l-cpython-311/hotknots/pkmodelRE.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,204 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-triloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,206 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstackh-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,208 copying build/lib.linux-armv7l-cpython-311/hotknots/turner_partypes_fm363.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,211 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-miscloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,213 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-sint4-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,217 copying build/lib.linux-armv7l-cpython-311/hotknots/tstackcoax.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,219 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstackh-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,222 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-triloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,224 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint4-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,227 copying build/lib.linux-armv7l-cpython-311/hotknots/parameters_DP09.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,229 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,231 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tstackh-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,233 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-stack-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,236 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstacki-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,238 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-dangle-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,240 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-loop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,242 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-asint1x2-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,246 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-loop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,248 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-stack-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,250 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-stack-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,253 copying build/lib.linux-armv7l-cpython-311/hotknots/multirnafold.conf -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,255 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,257 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-loop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,259 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstacki-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,261 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,263 copying build/lib.linux-armv7l-cpython-311/hotknots/parameters_CC06.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,266 copying build/lib.linux-armv7l-cpython-311/hotknots/parameters_CC09.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,268 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-stack-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,271 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstacki-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,273 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-dangle-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,275 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tstackh-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,278 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-loop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,280 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tstacki-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,282 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-triloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,284 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-miscloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,286 copying build/lib.linux-armv7l-cpython-311/hotknots/pkenergy.conf -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,288 copying build/lib.linux-armv7l-cpython-311/hotknots/pkmodelDP.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,290 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-miscloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,292 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint4-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,296 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-triloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,298 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-miscloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,300 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-miscloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,302 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-dangle-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,304 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-asint1x2-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,307 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-asint1x2-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,311 copying build/lib.linux-armv7l-cpython-311/hotknots/CG_best_parameters_ISMB2007.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,313 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,315 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-triloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,316 copying build/lib.linux-armv7l-cpython-311/hotknots/__init__.py -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,318 copying build/lib.linux-armv7l-cpython-311/hotknots/hotknots.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,404 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-sint4-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,414 copying build/lib.linux-armv7l-cpython-311/hotknots/turner_parameters_fm363_constrdangles.txt -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,416 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-tstacki-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,418 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-tloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,420 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint2-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,423 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-loop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,425 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-sint2-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,428 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-dangle-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,431 copying build/lib.linux-armv7l-cpython-311/hotknots/walter-coaxstack-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,435 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-sint2-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,438 copying build/lib.linux-armv7l-cpython-311/hotknots/mathews-sint2-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,441 copying build/lib.linux-armv7l-cpython-311/hotknots/turner-asint1x2-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,445 copying build/lib.linux-armv7l-cpython-311/hotknots/coaxstack.dat -> build/bdist.linux-armv7l/wheel/hotknots 2023-09-17T17:10:20,449 running install_egg_info 2023-09-17T17:10:20,763 running egg_info 2023-09-17T17:10:20,814 writing hotknots.egg-info/PKG-INFO 2023-09-17T17:10:20,817 writing dependency_links to hotknots.egg-info/dependency_links.txt 2023-09-17T17:10:20,819 writing top-level names to hotknots.egg-info/top_level.txt 2023-09-17T17:10:20,867 reading manifest file 'hotknots.egg-info/SOURCES.txt' 2023-09-17T17:10:20,883 reading manifest template 'MANIFEST.in' 2023-09-17T17:10:20,910 warning: no files found matching '*.c' under directory 'src' 2023-09-17T17:10:20,911 adding license file 'LICENSE' 2023-09-17T17:10:20,921 writing manifest file 'hotknots.egg-info/SOURCES.txt' 2023-09-17T17:10:20,923 Copying hotknots.egg-info to build/bdist.linux-armv7l/wheel/hotknots-2.4-py3.11.egg-info 2023-09-17T17:10:20,931 running install_scripts 2023-09-17T17:10:20,932 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.data 2023-09-17T17:10:20,933 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2023-09-17T17:10:20,935 copying build/scripts-3.11/hotknots.py -> build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2023-09-17T17:10:20,936 changing mode of build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts/hotknots.py to 755 2023-09-17T17:10:20,990 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.dist-info/WHEEL 2023-09-17T17:10:20,993 creating '/tmp/pip-wheel-b10m74u7/hotknots-2.4-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-17T17:10:20,997 adding 'hotknots/CG_best_parameters_ISMB2007.txt' 2023-09-17T17:10:20,998 adding 'hotknots/__init__.py' 2023-09-17T17:10:21,000 adding 'hotknots/coaxial.dat' 2023-09-17T17:10:21,002 adding 'hotknots/coaxstack.dat' 2023-09-17T17:10:21,336 adding 'hotknots/hotknots.cpython-311-arm-linux-gnueabihf.so' 2023-09-17T17:10:21,351 adding 'hotknots/mathews-asint1x2-dna.dat' 2023-09-17T17:10:21,355 adding 'hotknots/mathews-asint1x2-dna.dh' 2023-09-17T17:10:21,357 adding 'hotknots/mathews-dangle-dna.dat' 2023-09-17T17:10:21,358 adding 'hotknots/mathews-dangle-dna.dh' 2023-09-17T17:10:21,360 adding 'hotknots/mathews-loop-dna.dat' 2023-09-17T17:10:21,362 adding 'hotknots/mathews-loop-dna.dh' 2023-09-17T17:10:21,363 adding 'hotknots/mathews-miscloop-dna.dat' 2023-09-17T17:10:21,365 adding 'hotknots/mathews-miscloop-dna.dh' 2023-09-17T17:10:21,367 adding 'hotknots/mathews-sint2-dna.dat' 2023-09-17T17:10:21,368 adding 'hotknots/mathews-sint2-dna.dh' 2023-09-17T17:10:21,372 adding 'hotknots/mathews-sint4-dna.dat' 2023-09-17T17:10:21,376 adding 'hotknots/mathews-sint4-dna.dh' 2023-09-17T17:10:21,378 adding 'hotknots/mathews-stack-dna.dat' 2023-09-17T17:10:21,379 adding 'hotknots/mathews-stack-dna.dh' 2023-09-17T17:10:21,381 adding 'hotknots/mathews-tloop-dna.dat' 2023-09-17T17:10:21,382 adding 'hotknots/mathews-tloop-dna.dh' 2023-09-17T17:10:21,384 adding 'hotknots/mathews-triloop-dna.dat' 2023-09-17T17:10:21,385 adding 'hotknots/mathews-triloop-dna.dh' 2023-09-17T17:10:21,386 adding 'hotknots/mathews-tstackh-dna.dat' 2023-09-17T17:10:21,388 adding 'hotknots/mathews-tstackh-dna.dh' 2023-09-17T17:10:21,389 adding 'hotknots/mathews-tstacki-dna.dat' 2023-09-17T17:10:21,391 adding 'hotknots/mathews-tstacki-dna.dh' 2023-09-17T17:10:21,393 adding 'hotknots/multirnafold.conf' 2023-09-17T17:10:21,395 adding 'hotknots/parameters_CC06.txt' 2023-09-17T17:10:21,397 adding 'hotknots/parameters_CC09.txt' 2023-09-17T17:10:21,399 adding 'hotknots/parameters_DP03.txt' 2023-09-17T17:10:21,400 adding 'hotknots/parameters_DP09.txt' 2023-09-17T17:10:21,402 adding 'hotknots/pkenergy.conf' 2023-09-17T17:10:21,403 adding 'hotknots/pkmodelCC2006.dat' 2023-09-17T17:10:21,405 adding 'hotknots/pkmodelDP.dat' 2023-09-17T17:10:21,407 adding 'hotknots/pkmodelRE.dat' 2023-09-17T17:10:21,408 adding 'hotknots/tstackcoax.dat' 2023-09-17T17:10:21,412 adding 'hotknots/turner-asint1x2-rna.dat' 2023-09-17T17:10:21,415 adding 'hotknots/turner-asint1x2-rna.dg' 2023-09-17T17:10:21,420 adding 'hotknots/turner-asint1x2-rna.dh' 2023-09-17T17:10:21,422 adding 'hotknots/turner-dangle-rna.dat' 2023-09-17T17:10:21,424 adding 'hotknots/turner-dangle-rna.dg' 2023-09-17T17:10:21,426 adding 'hotknots/turner-dangle-rna.dh' 2023-09-17T17:10:21,427 adding 'hotknots/turner-loop-rna.dat' 2023-09-17T17:10:21,429 adding 'hotknots/turner-loop-rna.dg' 2023-09-17T17:10:21,430 adding 'hotknots/turner-loop-rna.dh' 2023-09-17T17:10:21,432 adding 'hotknots/turner-miscloop-rna.dat' 2023-09-17T17:10:21,433 adding 'hotknots/turner-miscloop-rna.dg' 2023-09-17T17:10:21,435 adding 'hotknots/turner-miscloop-rna.dh' 2023-09-17T17:10:21,437 adding 'hotknots/turner-sint2-rna.dat' 2023-09-17T17:10:21,439 adding 'hotknots/turner-sint2-rna.dg' 2023-09-17T17:10:21,441 adding 'hotknots/turner-sint2-rna.dh' 2023-09-17T17:10:21,447 adding 'hotknots/turner-sint4-rna.dat' 2023-09-17T17:10:21,452 adding 'hotknots/turner-sint4-rna.dg' 2023-09-17T17:10:21,463 adding 'hotknots/turner-sint4-rna.dh' 2023-09-17T17:10:21,465 adding 'hotknots/turner-stack-rna.dat' 2023-09-17T17:10:21,467 adding 'hotknots/turner-stack-rna.dg' 2023-09-17T17:10:21,469 adding 'hotknots/turner-stack-rna.dh' 2023-09-17T17:10:21,471 adding 'hotknots/turner-tloop-rna.dat' 2023-09-17T17:10:21,473 adding 'hotknots/turner-tloop-rna.dg' 2023-09-17T17:10:21,474 adding 'hotknots/turner-tloop-rna.dh' 2023-09-17T17:10:21,476 adding 'hotknots/turner-triloop-rna.dat' 2023-09-17T17:10:21,477 adding 'hotknots/turner-triloop-rna.dg' 2023-09-17T17:10:21,479 adding 'hotknots/turner-triloop-rna.dh' 2023-09-17T17:10:21,480 adding 'hotknots/turner-tstackh-rna.dat' 2023-09-17T17:10:21,482 adding 'hotknots/turner-tstackh-rna.dg' 2023-09-17T17:10:21,484 adding 'hotknots/turner-tstackh-rna.dh' 2023-09-17T17:10:21,486 adding 'hotknots/turner-tstacki-rna.dat' 2023-09-17T17:10:21,488 adding 'hotknots/turner-tstacki-rna.dg' 2023-09-17T17:10:21,489 adding 'hotknots/turner-tstacki-rna.dh' 2023-09-17T17:10:21,491 adding 'hotknots/turner_parameters_fm363_constrdangles.txt' 2023-09-17T17:10:21,493 adding 'hotknots/turner_partypes_fm363.txt' 2023-09-17T17:10:21,495 adding 'hotknots/walter-coaxstack-rna.dat' 2023-09-17T17:10:21,498 adding 'hotknots-2.4.data/scripts/hotknots.py' 2023-09-17T17:10:21,505 adding 'hotknots-2.4.dist-info/LICENSE' 2023-09-17T17:10:21,507 adding 'hotknots-2.4.dist-info/METADATA' 2023-09-17T17:10:21,508 adding 'hotknots-2.4.dist-info/WHEEL' 2023-09-17T17:10:21,509 adding 'hotknots-2.4.dist-info/top_level.txt' 2023-09-17T17:10:21,512 adding 'hotknots-2.4.dist-info/RECORD' 2023-09-17T17:10:21,562 removing build/bdist.linux-armv7l/wheel 2023-09-17T17:10:21,736 Building wheel for hotknots (setup.py): finished with status 'done' 2023-09-17T17:10:21,749 Created wheel for hotknots: filename=hotknots-2.4-cp311-cp311-linux_armv7l.whl size=780368 sha256=c0cb646f635ea8be9f2fefe0eb261e1e4653f94570838c8c75ea48ed37289244 2023-09-17T17:10:21,750 Stored in directory: /tmp/pip-ephem-wheel-cache-2rnbkxwz/wheels/f5/d3/17/b5b767b2bc1c77c0e4a50c166658fccad277631452c8004413 2023-09-17T17:10:21,763 Successfully built hotknots 2023-09-17T17:10:21,787 Removed build tracker: '/tmp/pip-build-tracker-rlti101h'