2022-05-20T18:09:27,083 Created temporary directory: /tmp/pip-ephem-wheel-cache-d0ae0dbp 2022-05-20T18:09:27,088 Created temporary directory: /tmp/pip-build-tracker-x0gs6kbx 2022-05-20T18:09:27,089 Initialized build tracking at /tmp/pip-build-tracker-x0gs6kbx 2022-05-20T18:09:27,090 Created build tracker: /tmp/pip-build-tracker-x0gs6kbx 2022-05-20T18:09:27,090 Entered build tracker: /tmp/pip-build-tracker-x0gs6kbx 2022-05-20T18:09:27,091 Created temporary directory: /tmp/pip-wheel-vu6ibjd9 2022-05-20T18:09:27,161 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-05-20T18:09:27,170 2 location(s) to search for versions of hotknots: 2022-05-20T18:09:27,170 * https://pypi.org/simple/hotknots/ 2022-05-20T18:09:27,170 * https://www.piwheels.org/simple/hotknots/ 2022-05-20T18:09:27,171 Fetching project page and analyzing links: https://pypi.org/simple/hotknots/ 2022-05-20T18:09:27,172 Getting page https://pypi.org/simple/hotknots/ 2022-05-20T18:09:27,175 Found index url https://pypi.org/simple 2022-05-20T18:09:27,287 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#sha256=cc55e00447864849c539a3acb1cdba6c34d9cb38f9cf1ea99cbfe8e875de7f5a (from https://pypi.org/simple/hotknots/) (requires-python:>3.5.2) 2022-05-20T18:09:27,288 Found link https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz#sha256=f9e8b14dc77c250735117452ea57f09c550d2cd56f5403ef0175a1c75cccc5a3 (from https://pypi.org/simple/hotknots/) (requires-python:>3.5.2), version: 2.4 2022-05-20T18:09:27,289 Fetching project page and analyzing links: https://www.piwheels.org/simple/hotknots/ 2022-05-20T18:09:27,290 Getting page https://www.piwheels.org/simple/hotknots/ 2022-05-20T18:09:27,292 Found index url https://www.piwheels.org/simple 2022-05-20T18:09:27,520 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) 2022-05-20T18:09:27,520 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) 2022-05-20T18:09:27,521 Skipping link: not a file: https://www.piwheels.org/simple/hotknots/ 2022-05-20T18:09:27,521 Skipping link: not a file: https://pypi.org/simple/hotknots/ 2022-05-20T18:09:27,562 Given no hashes to check 1 links for project 'hotknots': discarding no candidates 2022-05-20T18:09:27,600 Collecting hotknots==2.4 2022-05-20T18:09:27,605 Created temporary directory: /tmp/pip-unpack-ou2qurf8 2022-05-20T18:09:27,703 Downloading hotknots-2.4.tar.gz (435 kB) 2022-05-20T18:09:29,032 Added hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz#sha256=f9e8b14dc77c250735117452ea57f09c550d2cd56f5403ef0175a1c75cccc5a3 to build tracker '/tmp/pip-build-tracker-x0gs6kbx' 2022-05-20T18:09:29,036 Running setup.py (path:/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/setup.py) egg_info for package hotknots 2022-05-20T18:09:29,037 Created temporary directory: /tmp/pip-pip-egg-info-_h5iwx32 2022-05-20T18:09:29,038 Preparing metadata (setup.py): started 2022-05-20T18:09:29,040 Running command python setup.py egg_info 2022-05-20T18:09:35,135 running egg_info 2022-05-20T18:09:35,140 creating /tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info 2022-05-20T18:09:35,744 writing /tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/PKG-INFO 2022-05-20T18:09:36,317 writing dependency_links to /tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/dependency_links.txt 2022-05-20T18:09:39,690 writing top-level names to /tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/top_level.txt 2022-05-20T18:09:39,693 writing manifest file '/tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/SOURCES.txt' 2022-05-20T18:09:41,117 reading manifest file '/tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/SOURCES.txt' 2022-05-20T18:09:41,119 reading manifest template 'MANIFEST.in' 2022-05-20T18:09:41,189 warning: no files found matching '*.c' under directory 'src' 2022-05-20T18:09:41,189 adding license file 'LICENSE' 2022-05-20T18:09:41,210 writing manifest file '/tmp/pip-pip-egg-info-_h5iwx32/hotknots.egg-info/SOURCES.txt' 2022-05-20T18:09:41,431 Preparing metadata (setup.py): finished with status 'done' 2022-05-20T18:09:41,442 Source in /tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa has version 2.4, which satisfies requirement hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz#sha256=f9e8b14dc77c250735117452ea57f09c550d2cd56f5403ef0175a1c75cccc5a3 2022-05-20T18:09:41,444 Removed hotknots==2.4 from https://files.pythonhosted.org/packages/66/13/8e7f5a2afeb2fa51c9e8b81a4bbc5d75c0b5e35f403f09ab76e4495c6140/hotknots-2.4.tar.gz#sha256=f9e8b14dc77c250735117452ea57f09c550d2cd56f5403ef0175a1c75cccc5a3 from build tracker '/tmp/pip-build-tracker-x0gs6kbx' 2022-05-20T18:09:41,456 Created temporary directory: /tmp/pip-unpack-mij16tm8 2022-05-20T18:09:41,457 Building wheels for collected packages: hotknots 2022-05-20T18:09:41,466 Created temporary directory: /tmp/pip-wheel-yvvz1o90 2022-05-20T18:09:41,467 Building wheel for hotknots (setup.py): started 2022-05-20T18:09:41,469 Destination directory: /tmp/pip-wheel-yvvz1o90 2022-05-20T18:09:41,469 Running command python setup.py bdist_wheel 2022-05-20T18:09:46,991 running bdist_wheel 2022-05-20T18:09:47,734 running build 2022-05-20T18:09:47,735 running build_py 2022-05-20T18:09:48,352 creating build 2022-05-20T18:09:48,354 creating build/lib.linux-armv7l-cpython-39 2022-05-20T18:09:48,355 creating build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,358 copying hotknots/__init__.py -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,386 copying hotknots/turner-tstackh-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,391 copying hotknots/pkmodelCC2006.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,396 copying hotknots/coaxial.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,401 copying hotknots/turner-tstacki-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,406 copying hotknots/turner-loop-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,411 copying hotknots/coaxstack.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,417 copying hotknots/mathews-loop-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,421 copying hotknots/walter-coaxstack-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,427 copying hotknots/mathews-dangle-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,432 copying hotknots/mathews-tstacki-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,437 copying hotknots/mathews-tstackh-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,441 copying hotknots/mathews-sint2-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,447 copying hotknots/turner-asint1x2-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,455 copying hotknots/turner-sint2-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,460 copying hotknots/pkmodelDP.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,464 copying hotknots/pkmodelRE.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,469 copying hotknots/turner-miscloop-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,473 copying hotknots/turner-stack-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,477 copying hotknots/mathews-triloop-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,481 copying hotknots/mathews-sint4-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,490 copying hotknots/mathews-stack-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,494 copying hotknots/mathews-tloop-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,498 copying hotknots/turner-tloop-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,502 copying hotknots/mathews-asint1x2-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,509 copying hotknots/mathews-miscloop-dna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,513 copying hotknots/turner-triloop-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,517 copying hotknots/turner-dangle-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,521 copying hotknots/turner-sint4-rna.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,530 copying hotknots/tstackcoax.dat -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,534 copying hotknots/turner-loop-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,538 copying hotknots/turner-sint4-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,546 copying hotknots/turner-tstacki-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,551 copying hotknots/mathews-tstackh-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,555 copying hotknots/turner-stack-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,559 copying hotknots/mathews-miscloop-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,563 copying hotknots/mathews-triloop-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,566 copying hotknots/turner-sint2-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,572 copying hotknots/mathews-sint2-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,577 copying hotknots/turner-dangle-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,582 copying hotknots/mathews-tloop-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,585 copying hotknots/turner-tstackh-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,590 copying hotknots/mathews-asint1x2-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,596 copying hotknots/turner-tloop-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,600 copying hotknots/turner-asint1x2-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,607 copying hotknots/turner-triloop-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,610 copying hotknots/turner-miscloop-rna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,614 copying hotknots/mathews-tstacki-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,618 copying hotknots/mathews-dangle-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,622 copying hotknots/mathews-stack-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,627 copying hotknots/mathews-loop-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,631 copying hotknots/mathews-sint4-dna.dh -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,638 copying hotknots/multirnafold.conf -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,642 copying hotknots/pkenergy.conf -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,646 copying hotknots/turner-sint4-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,654 copying hotknots/turner-tstacki-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,659 copying hotknots/turner-miscloop-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,663 copying hotknots/turner-dangle-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,667 copying hotknots/turner-triloop-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,671 copying hotknots/turner-asint1x2-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,679 copying hotknots/turner-stack-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,683 copying hotknots/turner-sint2-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,688 copying hotknots/turner-tloop-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,692 copying hotknots/turner-tstackh-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,696 copying hotknots/turner-loop-rna.dg -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,700 copying hotknots/parameters_DP03.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,704 copying hotknots/parameters_CC09.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,708 copying hotknots/CG_best_parameters_ISMB2007.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,712 copying hotknots/turner_parameters_fm363_constrdangles.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,716 copying hotknots/turner_partypes_fm363.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,720 copying hotknots/parameters_CC06.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,724 copying hotknots/parameters_DP09.txt -> build/lib.linux-armv7l-cpython-39/hotknots 2022-05-20T18:09:48,730 running build_ext 2022-05-20T18:09:48,746 building 'hotknots.hotknots' extension 2022-05-20T18:09:48,748 creating build/temp.linux-armv7l-cpython-39 2022-05-20T18:09:48,749 creating build/temp.linux-armv7l-cpython-39/src 2022-05-20T18:09:48,754 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/Bands.cpp -o build/temp.linux-armv7l-cpython-39/./src/Bands.o -g 2022-05-20T18:09:49,826 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/Input.cpp -o build/temp.linux-armv7l-cpython-39/./src/Input.o -g 2022-05-20T18:09:51,220 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/Loop.cpp -o build/temp.linux-armv7l-cpython-39/./src/Loop.o -g 2022-05-20T18:09:53,760 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyDP()’: 2022-05-20T18:09:53,761 ./src/Loop.cpp:3084:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,761 3084 | int special; 2022-05-20T18:09:53,762 | ^~~~~~~ 2022-05-20T18:09:53,786 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyDP(double**, double*, double&, int, int)’: 2022-05-20T18:09:53,786 ./src/Loop.cpp:3286:7: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,786 3286 | char c_structure[MaxN]; 2022-05-20T18:09:53,787 | ^~~~~~~~~~~ 2022-05-20T18:09:53,796 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyDP()’: 2022-05-20T18:09:53,797 ./src/Loop.cpp:3498:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:09:53,797 3498 | if (DEBUG) 2022-05-20T18:09:53,797 | ^~ 2022-05-20T18:09:53,798 ./src/Loop.cpp:3499:100: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-05-20T18:09:53,798 3499 | printf("[ILoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2022-05-20T18:09:53,799 | ^~~~~~ 2022-05-20T18:09:53,800 ./src/Loop.cpp:3508:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:09:53,801 3508 | if (DEBUG) 2022-05-20T18:09:53,801 | ^~ 2022-05-20T18:09:53,802 ./src/Loop.cpp:3509:100: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-05-20T18:09:53,802 3509 | printf("[MLoopsDP]: (%d, %d) Energy: %.2f 10cal/mol\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2022-05-20T18:09:53,802 | ^~~~~~ 2022-05-20T18:09:53,807 ./src/Loop.cpp: In member function ‘int Loop::startsMultiSpanningBand(int)’: 2022-05-20T18:09:53,808 ./src/Loop.cpp:3618:6: warning: variable ‘startsMulti’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,808 3618 | int startsMulti = 0; 2022-05-20T18:09:53,808 | ^~~~~~~~~~~ 2022-05-20T18:09:53,851 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyRE()’: 2022-05-20T18:09:53,852 ./src/Loop.cpp:4072:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,852 4072 | int special; 2022-05-20T18:09:53,852 | ^~~~~~~ 2022-05-20T18:09:53,856 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyRE()’: 2022-05-20T18:09:53,856 ./src/Loop.cpp:4198:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:09:53,857 4198 | if (DEBUG) 2022-05-20T18:09:53,857 | ^~ 2022-05-20T18:09:53,857 ./src/Loop.cpp:4199:92: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-05-20T18:09:53,858 4199 | printf("[ILoops RE]: (%d, %d) Energy: %.2f \n", L1->Num, Input->BasePair(L1->Num), en); fflush(stdout); 2022-05-20T18:09:53,858 | ^~~~~~ 2022-05-20T18:09:53,858 ./src/Loop.cpp:4209:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:09:53,859 4209 | if (DEBUG) 2022-05-20T18:09:53,859 | ^~ 2022-05-20T18:09:53,859 ./src/Loop.cpp:4210:90: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2022-05-20T18:09:53,860 4210 | printf("[MLoopsRE]: (%d, %d) Energy: %.2f\n", L2->Num, Input->BasePair(L2->Num), en); fflush(stdout); 2022-05-20T18:09:53,860 | ^~~~~~ 2022-05-20T18:09:53,891 ./src/Loop.cpp: In member function ‘double Loop::nestedPseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2022-05-20T18:09:53,892 ./src/Loop.cpp:4671:7: warning: variable ‘c_structure’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,892 4671 | char c_structure[MaxN]; 2022-05-20T18:09:53,892 | ^~~~~~~~~~~ 2022-05-20T18:09:53,903 ./src/Loop.cpp: In member function ‘double Loop::multiEnergyCC2006a()’: 2022-05-20T18:09:53,904 ./src/Loop.cpp:4800:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:09:53,904 4800 | int special; 2022-05-20T18:09:53,904 | ^~~~~~~ 2022-05-20T18:09:53,973 ./src/Loop.cpp: In member function ‘float Loop::pseudoEnergyCC2006b(double**, double*, double&, int, int)’: 2022-05-20T18:09:53,974 ./src/Loop.cpp:5157:6: warning: unused variable ‘num_params_pkfree’ [-Wunused-variable] 2022-05-20T18:09:53,974 5157 | int num_params_pkfree = get_num_params(); 2022-05-20T18:09:53,975 | ^~~~~~~~~~~~~~~~~ 2022-05-20T18:10:07,074 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/LoopList.cpp -o build/temp.linux-armv7l-cpython-39/./src/LoopList.o -g 2022-05-20T18:10:07,749 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP()’: 2022-05-20T18:10:07,750 ./src/LoopList.cpp:165:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:07,750 165 | int special; 2022-05-20T18:10:07,751 | ^~~~~~~ 2022-05-20T18:10:07,772 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyDP(double*, double&, int, int)’: 2022-05-20T18:10:07,772 ./src/LoopList.cpp:349:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:07,773 349 | int special; 2022-05-20T18:10:07,773 | ^~~~~~~ 2022-05-20T18:10:07,786 ./src/LoopList.cpp: In member function ‘float LoopList::multiPseudoEnergyRE()’: 2022-05-20T18:10:07,787 ./src/LoopList.cpp:598:6: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:07,787 598 | int special; 2022-05-20T18:10:07,788 | ^~~~~~~ 2022-05-20T18:10:10,160 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/Stack.cpp -o build/temp.linux-armv7l-cpython-39/./src/Stack.o -g 2022-05-20T18:10:11,116 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/common.cpp -o build/temp.linux-armv7l-cpython-39/./src/common.o -g 2022-05-20T18:10:13,547 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/commonPK.cpp -o build/temp.linux-armv7l-cpython-39/./src/commonPK.o -g 2022-05-20T18:10:14,363 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:14,364 ./src/commonPK.cpp:2066:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,364 2066 | PARAMTYPE energy; 2022-05-20T18:10:14,364 | ^~~~~~ 2022-05-20T18:10:14,365 ./src/commonPK.cpp:2070:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,365 2070 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:14,366 | ^~~~~~~~~~~ 2022-05-20T18:10:14,372 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:14,372 ./src/commonPK.cpp:2180:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,373 2180 | PARAMTYPE energy; 2022-05-20T18:10:14,373 | ^~~~~~ 2022-05-20T18:10:14,374 ./src/commonPK.cpp:2186:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,374 2186 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:14,374 | ^~~~~~~~~~~ 2022-05-20T18:10:14,380 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:14,381 ./src/commonPK.cpp:2275:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,381 2275 | PARAMTYPE energy; 2022-05-20T18:10:14,381 | ^~~~~~ 2022-05-20T18:10:14,382 ./src/commonPK.cpp:2279:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:14,382 2279 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:14,383 | ^~~~~~~~~~~ 2022-05-20T18:10:17,483 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:17,483 ./src/commonPK.cpp:2118:17: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,483 2118 | counter[index_bot]++; 2022-05-20T18:10:17,484 | ^~~~~~~~~ 2022-05-20T18:10:17,484 ./src/commonPK.cpp:2123:17: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,485 2123 | counter[index_top]++; 2022-05-20T18:10:17,485 | ^~~~~~~~~ 2022-05-20T18:10:17,615 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:17,616 ./src/commonPK.cpp:2258:17: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,616 2258 | counter[index_bot]++; 2022-05-20T18:10:17,616 | ^~~~~~~~~ 2022-05-20T18:10:17,617 ./src/commonPK.cpp:2214:21: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,618 2214 | counter[index_top]++; 2022-05-20T18:10:17,618 | ^~~~~~~~~ 2022-05-20T18:10:17,729 ./src/commonPK.cpp: In function ‘void count_LEdangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:17,729 ./src/commonPK.cpp:2307:21: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,730 2307 | counter[index_bot]++; 2022-05-20T18:10:17,730 | ^~~~~~~~~ 2022-05-20T18:10:17,730 ./src/commonPK.cpp:2331:21: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:17,731 2331 | counter[index_top]++; 2022-05-20T18:10:17,731 | ^~~~~~~~~ 2022-05-20T18:10:18,068 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/goodStem.cpp -o build/temp.linux-armv7l-cpython-39/./src/goodStem.o -g 2022-05-20T18:10:18,865 ./src/goodStem.cpp: In function ‘void trace(int, char*, int, int, int**, int**, int**, int**, int**, int**, short int)’: 2022-05-20T18:10:18,866 ./src/goodStem.cpp:296:13: warning: ‘tj’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:18,866 296 | if (V[ti][tj] == 0) break; 2022-05-20T18:10:18,867 | ^~ 2022-05-20T18:10:18,867 ./src/goodStem.cpp:296:9: warning: ‘ti’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:18,867 296 | if (V[ti][tj] == 0) break; 2022-05-20T18:10:18,868 | ^~ 2022-05-20T18:10:19,103 ./src/goodStem.cpp: In function ‘void traceback(int, char*, int**, int**, int**, int**, int**, int**)’: 2022-05-20T18:10:19,103 ./src/goodStem.cpp:234:9: warning: ‘cBj’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:19,104 234 | trace(length, seq, cBi, cBj, V, G, F, E, R, flag,1); //start tracing from si, sj and recording 2022-05-20T18:10:19,104 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:19,105 ./src/goodStem.cpp:234:9: warning: ‘cBi’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:19,448 ./src/goodStem.cpp: In function ‘void GenerateStemList(int, char*, char*)’: 2022-05-20T18:10:19,449 ./src/goodStem.cpp:176:26: warning: ‘delta’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:19,449 176 | G[i][j] = V[i-1][j-1] + delta; //s[i] matched with T[j] 2022-05-20T18:10:19,450 | ~~~~~~~~~~~~^~~~~~~ 2022-05-20T18:10:19,897 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/hotspot.cpp -o build/temp.linux-armv7l-cpython-39/./src/hotspot.o -g 2022-05-20T18:10:20,849 ./src/hotspot.cpp: In function ‘int FindHotspots(char*, char*, int)’: 2022-05-20T18:10:20,850 ./src/hotspot.cpp:206:26: warning: ‘replace’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:20,850 206 | hotspots->substruct[nh].pairTable[mm] = startbase + mm; 2022-05-20T18:10:20,850 | ^~ 2022-05-20T18:10:21,985 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/init.cpp -o build/temp.linux-armv7l-cpython-39/./src/init.o -g 2022-05-20T18:10:26,649 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/initPK.cpp -o build/temp.linux-armv7l-cpython-39/./src/initPK.o -g 2022-05-20T18:10:27,267 ./src/initPK.cpp: In function ‘void read_pkmodelCC2006_file(char*, float, float (*)[12], float (*)[12], float (*)[11], float (*)[11])’: 2022-05-20T18:10:27,268 ./src/initPK.cpp:253:9: warning: variable ‘j’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:27,268 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2022-05-20T18:10:27,269 | ^ 2022-05-20T18:10:27,269 ./src/initPK.cpp:253:16: warning: variable ‘jj’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:27,270 253 | int i, j, ii, jj; // ii = i+1; jj = j-1 2022-05-20T18:10:27,270 | ^~ 2022-05-20T18:10:27,291 ./src/initPK.cpp: In function ‘void init_dataPK(char*, char*, int, double)’: 2022-05-20T18:10:27,292 ./src/initPK.cpp:472:7: warning: unused variable ‘conf’ [-Wunused-variable] 2022-05-20T18:10:27,292 472 | char conf[200]; 2022-05-20T18:10:27,293 | ^~~~ 2022-05-20T18:10:27,293 ./src/initPK.cpp:485:6: warning: unused variable ‘i’ [-Wunused-variable] 2022-05-20T18:10:27,293 485 | int i; 2022-05-20T18:10:27,294 | ^ 2022-05-20T18:10:28,854 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/params.cpp -o build/temp.linux-armv7l-cpython-39/./src/params.o -g 2022-05-20T18:10:29,562 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:29,562 ./src/params.cpp:518:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,562 518 | PARAMTYPE energy; 2022-05-20T18:10:29,563 | ^~~~~~ 2022-05-20T18:10:29,563 ./src/params.cpp:522:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,564 522 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:29,564 | ^~~~~~~~~~~ 2022-05-20T18:10:29,570 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:29,570 ./src/params.cpp:632:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,571 632 | PARAMTYPE energy; 2022-05-20T18:10:29,571 | ^~~~~~ 2022-05-20T18:10:29,572 ./src/params.cpp:638:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,572 638 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:29,572 | ^~~~~~~~~~~ 2022-05-20T18:10:29,578 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:29,579 ./src/params.cpp:727:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,579 727 | PARAMTYPE energy; 2022-05-20T18:10:29,579 | ^~~~~~ 2022-05-20T18:10:29,580 ./src/params.cpp:731:9: warning: variable ‘first_index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,580 731 | int first_index; // first index should be dangle_top[0][3][0] 2022-05-20T18:10:29,580 | ^~~~~~~~~~~ 2022-05-20T18:10:29,586 ./src/params.cpp: In function ‘void count_penalty_by_size(int, char, double*)’: 2022-05-20T18:10:29,587 ./src/params.cpp:851:27: warning: variable ‘penalty’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,587 851 | PARAMTYPE penaltyMAX, penalty; 2022-05-20T18:10:29,587 | ^~~~~~~ 2022-05-20T18:10:29,644 ./src/params.cpp: In function ‘void print_counter(double*, double)’: 2022-05-20T18:10:29,645 ./src/params.cpp:1479:33: warning: ' ' flag used with ‘%s’ gnu_printf format [-Wformat=] 2022-05-20T18:10:29,645 1479 | printf ("%4d\t%30s\t% 10s\t%4.2lf\n", num_params, "FREE PARAMETER", "", (double)free_value); 2022-05-20T18:10:29,645 | ^ 2022-05-20T18:10:29,780 ./src/params.cpp: In function ‘void fill_data_structures_with_new_parameters(char*)’: 2022-05-20T18:10:29,780 ./src/params.cpp:4206:9: warning: variable ‘index’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,781 4206 | int index; 2022-05-20T18:10:29,781 | ^~~~~ 2022-05-20T18:10:29,800 ./src/params.cpp: In function ‘double simfold_restricted_logZ_gradient(char*, char*, char*, double*)’: 2022-05-20T18:10:29,800 ./src/params.cpp:5021:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,801 5021 | double min_energy, max_energy; 2022-05-20T18:10:29,801 | ^~~~~~~~~~ 2022-05-20T18:10:29,812 ./src/params.cpp: In function ‘double compute_f(char*)’: 2022-05-20T18:10:29,812 ./src/params.cpp:5212:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,813 5212 | int k; 2022-05-20T18:10:29,813 | ^ 2022-05-20T18:10:29,815 ./src/params.cpp: In function ‘double compute_likelihood_exactly(char*)’: 2022-05-20T18:10:29,815 ./src/params.cpp:5262:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,816 5262 | int k; 2022-05-20T18:10:29,816 | ^ 2022-05-20T18:10:29,818 ./src/params.cpp: In function ‘double compute_log_likelihood_smart(char*)’: 2022-05-20T18:10:29,818 ./src/params.cpp:5314:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,819 5314 | int k; 2022-05-20T18:10:29,819 | ^ 2022-05-20T18:10:29,821 ./src/params.cpp: In function ‘void compute_gradient_f(char*, double*)’: 2022-05-20T18:10:29,822 ./src/params.cpp:5366:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,822 5366 | int k; 2022-05-20T18:10:29,822 | ^ 2022-05-20T18:10:29,825 ./src/params.cpp: In function ‘void compute_gradient_f_smart(char*, double*)’: 2022-05-20T18:10:29,826 ./src/params.cpp:5416:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,826 5416 | int k; 2022-05-20T18:10:29,826 | ^ 2022-05-20T18:10:29,830 ./src/params.cpp: In function ‘double compute_f_and_gradient_f_smart(char*, double*)’: 2022-05-20T18:10:29,830 ./src/params.cpp:5470:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,830 5470 | int k; 2022-05-20T18:10:29,831 | ^ 2022-05-20T18:10:29,838 ./src/params.cpp: In function ‘double compute_f_and_gradient_f(char*, double*)’: 2022-05-20T18:10:29,839 ./src/params.cpp:5511:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,839 5511 | double min_energy, max_energy; 2022-05-20T18:10:29,839 | ^~~~~~~~~~ 2022-05-20T18:10:29,843 ./src/params.cpp: In function ‘void compute_counts_vector_LP(char*, double*)’: 2022-05-20T18:10:29,843 ./src/params.cpp:5627:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,844 5627 | double R, temp, beta; 2022-05-20T18:10:29,844 | ^~~~ 2022-05-20T18:10:29,844 ./src/params.cpp:5639:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,845 5639 | int k; 2022-05-20T18:10:29,845 | ^ 2022-05-20T18:10:29,849 ./src/params.cpp: In function ‘void compute_counts_matrix_LP(char*, int)’: 2022-05-20T18:10:29,849 ./src/params.cpp:5699:21: warning: variable ‘beta’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,849 5699 | double R, temp, beta; 2022-05-20T18:10:29,850 | ^~~~ 2022-05-20T18:10:29,850 ./src/params.cpp:5711:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,851 5711 | int k; 2022-05-20T18:10:29,851 | ^ 2022-05-20T18:10:29,855 ./src/params.cpp: In function ‘int generate_structure_withbb(char*, char*, char*, char*, char (*)[1000], double*, int)’: 2022-05-20T18:10:29,855 ./src/params.cpp:5844:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:10:29,855 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,856 | ^~~ 2022-05-20T18:10:29,856 ./src/params.cpp:5844:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2022-05-20T18:10:29,857 5844 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,857 | ^~~~~~~~~~ 2022-05-20T18:10:29,862 ./src/params.cpp:5865:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,863 5865 | int tried = 0; 2022-05-20T18:10:29,863 | ^~~~~ 2022-05-20T18:10:29,873 ./src/params.cpp: In function ‘int generate_structure_withbb_many_thresholds(char*, char (*)[1000], double*, double*, int*, double, int)’: 2022-05-20T18:10:29,874 ./src/params.cpp:6284:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:10:29,874 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,875 | ^~~ 2022-05-20T18:10:29,875 ./src/params.cpp:6284:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2022-05-20T18:10:29,875 6284 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,876 | ^~~~~~~~~~ 2022-05-20T18:10:29,881 ./src/params.cpp:6305:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,882 6305 | int tried = 0; 2022-05-20T18:10:29,882 | ^~~~~ 2022-05-20T18:10:29,887 ./src/params.cpp: In function ‘void search_bb(char*, double*, int, int)’: 2022-05-20T18:10:29,888 ./src/params.cpp:6437:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2022-05-20T18:10:29,888 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,888 | ^~~ 2022-05-20T18:10:29,889 ./src/params.cpp:6437:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2022-05-20T18:10:29,889 6437 | for (i=0; i < seqlen; i++) restricted[i] = '_'; restricted [seqlen] = '\0'; 2022-05-20T18:10:29,889 | ^~~~~~~~~~ 2022-05-20T18:10:29,895 ./src/params.cpp:6458:25: warning: variable ‘tried’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,895 6458 | int tried = 0; 2022-05-20T18:10:29,896 | ^~~~~ 2022-05-20T18:10:29,896 ./src/params.cpp:6410:20: warning: variable ‘numstr’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,896 6410 | int seqlen, i, numstr; 2022-05-20T18:10:29,897 | ^~~~~~ 2022-05-20T18:10:29,965 ./src/params.cpp: In function ‘void fill_similarity_rule_with_optical_melting_reference(char*)’: 2022-05-20T18:10:29,965 ./src/params.cpp:7832:9: warning: variable ‘k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:29,965 7832 | int k; 2022-05-20T18:10:29,966 | ^ 2022-05-20T18:10:32,741 ./src/params.cpp: In function ‘void count_dangling_energy(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:32,741 ./src/params.cpp:570:17: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,742 570 | counter[index_bot]++; 2022-05-20T18:10:32,742 | ^~~~~~~~~ 2022-05-20T18:10:32,742 ./src/params.cpp:575:17: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,743 575 | counter[index_top]++; 2022-05-20T18:10:32,743 | ^~~~~~~~~ 2022-05-20T18:10:32,872 ./src/params.cpp: In function ‘void count_dangling_energy_left(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:32,872 ./src/params.cpp:710:17: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,873 710 | counter[index_bot]++; 2022-05-20T18:10:32,873 | ^~~~~~~~~ 2022-05-20T18:10:32,873 ./src/params.cpp:666:21: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,874 666 | counter[index_top]++; 2022-05-20T18:10:32,874 | ^~~~~~~~~ 2022-05-20T18:10:32,982 ./src/params.cpp: In function ‘void count_dangling_energy_right(int*, char*, int, int, int, int, int, double*)’: 2022-05-20T18:10:32,982 ./src/params.cpp:759:21: warning: ‘index_bot’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,983 759 | counter[index_bot]++; 2022-05-20T18:10:32,983 | ^~~~~~~~~ 2022-05-20T18:10:32,983 ./src/params.cpp:783:21: warning: ‘index_top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:32,984 783 | counter[index_top]++; 2022-05-20T18:10:32,984 | ^~~~~~~~~ 2022-05-20T18:10:35,241 ./src/params.cpp: In function ‘void similarity_bulge_type(int, char*)’: 2022-05-20T18:10:35,242 ./src/params.cpp:2261:33: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2022-05-20T18:10:35,242 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, 2022-05-20T18:10:35,242 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:35,243 2262 | int_to_nuc(i), int_to_nuc(bulged_base), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j), 2022-05-20T18:10:35,243 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:35,243 2263 | 1.0/num, int_to_nuc(i), int_to_nuc(ip), int_to_nuc(jp), int_to_nuc(j)); 2022-05-20T18:10:35,244 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:35,244 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2022-05-20T18:10:35,244 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2022-05-20T18:10:35,245 | ~~~~~~^~~~~~~~~~ 2022-05-20T18:10:35,245 ./src/params.cpp:2265:53: warning: ‘sprintf’ argument 3 overlaps destination object ‘similarity’ [-Wrestrict] 2022-05-20T18:10:35,245 2265 | if (num2 < num) sprintf (similarity, "%s + ", similarity); 2022-05-20T18:10:35,246 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:35,246 ./src/params.cpp:2222:52: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 2022-05-20T18:10:35,246 2222 | void similarity_bulge_type (int bulged_base, char *similarity) 2022-05-20T18:10:35,247 | ~~~~~~^~~~~~~~~~ 2022-05-20T18:10:35,939 ./src/params.cpp: In function ‘int traverse_features_and_do_work(char*, int*, char*)’: 2022-05-20T18:10:35,940 ./src/params.cpp:3934:21: warning: ‘file’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:10:35,940 3934 | fprintf (file, "%.2lf\n", misc.hairpin_GGG/100.0); 2022-05-20T18:10:35,941 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:10:48,870 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/paramsPK.cpp -o build/temp.linux-armv7l-cpython-39/./src/paramsPK.o -g 2022-05-20T18:10:54,243 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/python.cpp -o build/temp.linux-armv7l-cpython-39/./src/python.o -g 2022-05-20T18:10:55,581 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_energy_matrix.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_energy_matrix.o -g 2022-05-20T18:10:56,643 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_hairpin_loop.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_hairpin_loop.o -g 2022-05-20T18:10:56,939 ./src/s_hairpin_loop.cpp: In constructor ‘s_hairpin_loop::s_hairpin_loop(char*, int*, int)’: 2022-05-20T18:10:56,939 ./src/s_hairpin_loop.cpp:42:16: warning: statement has no effect [-Wunused-value] 2022-05-20T18:10:56,940 42 | toupper(csequence[i]); 2022-05-20T18:10:56,940 | ~~~~~~~^~~~~~~~~~~~~~ 2022-05-20T18:10:56,971 ./src/s_hairpin_loop.cpp: In static member function ‘static void s_hairpin_loop::count_get_energy(int, int, int*, char*, double*)’: 2022-05-20T18:10:56,972 ./src/s_hairpin_loop.cpp:487:15: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:56,972 487 | PARAMTYPE energy=0; 2022-05-20T18:10:56,972 | ^~~~~~ 2022-05-20T18:10:58,093 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_internal_loop.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_internal_loop.o -g 2022-05-20T18:10:58,578 ./src/s_internal_loop.cpp: In static member function ‘static void s_internal_loop::count_get_energy(int, int, int, int, int*, double*)’: 2022-05-20T18:10:58,578 ./src/s_internal_loop.cpp:646:12: warning: variable ‘energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:10:58,578 646 | PARAMTYPE energy; 2022-05-20T18:10:58,579 | ^~~~~~ 2022-05-20T18:11:01,960 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_min_folding.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_min_folding.o -g 2022-05-20T18:11:02,446 ./src/s_min_folding.cpp: In member function ‘int s_min_folding::compute_W_br2_restricted(int, str_features*, int&)’: 2022-05-20T18:11:02,447 ./src/s_min_folding.cpp:1066:6: warning: variable ‘chosen’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:02,447 1066 | int chosen = 0; 2022-05-20T18:11:02,448 | ^~~~~~ 2022-05-20T18:11:02,448 ./src/s_min_folding.cpp:1067:6: warning: variable ‘best_i’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:02,448 1067 | int best_i = 0; 2022-05-20T18:11:02,449 | ^~~~~~ 2022-05-20T18:11:03,388 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack(seq_interval*)’: 2022-05-20T18:11:03,388 ./src/s_min_folding.cpp:560:19: warning: ‘best_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:03,389 560 | insert_node (best_k+1, j, M_WM); 2022-05-20T18:11:03,389 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:03,390 ./src/s_min_folding.cpp:349:4: warning: ‘best_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:03,390 349 | switch (best_row){ 2022-05-20T18:11:03,391 | ^~~~~~ 2022-05-20T18:11:03,391 ./src/s_min_folding.cpp:352:18: warning: ‘best_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:03,391 352 | insert_node (best_k+1, j-1, M_WM); break; 2022-05-20T18:11:03,392 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:03,392 ./src/s_min_folding.cpp:308:12: warning: ‘best_jp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:03,392 308 | printf ("NOT GOOD INTER, i=%d, j=%d, best_ip=%d, best_jp=%d\n", i, j, best_ip, best_jp); 2022-05-20T18:11:03,393 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:03,393 ./src/s_min_folding.cpp:308:12: warning: ‘best_ip’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:04,396 ./src/s_min_folding.cpp: In member function ‘void s_min_folding::backtrack_restricted(seq_interval*, str_features*)’: 2022-05-20T18:11:04,396 ./src/s_min_folding.cpp:961:19: warning: ‘best_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:04,397 961 | insert_node (best_k+1, j, M_WM); 2022-05-20T18:11:04,397 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:04,397 ./src/s_min_folding.cpp:689:4: warning: ‘best_row’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:04,398 689 | switch (best_row) 2022-05-20T18:11:04,398 | ^~~~~~ 2022-05-20T18:11:04,399 ./src/s_min_folding.cpp:692:19: warning: ‘best_k’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:04,399 692 | insert_node (best_k+1, j-1, M_WM); break; 2022-05-20T18:11:04,399 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:04,400 ./src/s_min_folding.cpp:632:12: warning: ‘best_jp’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:04,400 632 | printf ("NOT GOOD RESTR INTER, i=%d, j=%d, best_ip=%d, best_jp=%d\n", i, j, best_ip, best_jp); 2022-05-20T18:11:04,400 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-05-20T18:11:04,401 ./src/s_min_folding.cpp:632:12: warning: ‘best_ip’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:06,303 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_multi_loop.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_multi_loop.o -g 2022-05-20T18:11:07,864 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_multi_loop_sub.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_multi_loop_sub.o -g 2022-05-20T18:11:08,114 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1(int)’: 2022-05-20T18:11:08,115 ./src/s_multi_loop_sub.cpp:64:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:08,115 64 | int i, tmp_k, ij, k; 2022-05-20T18:11:08,116 | ^~~~~ 2022-05-20T18:11:08,119 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM(int)’: 2022-05-20T18:11:08,119 ./src/s_multi_loop_sub.cpp:110:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:08,120 110 | int i, tmp_k, k, ij; 2022-05-20T18:11:08,120 | ^~~~~ 2022-05-20T18:11:08,127 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM1_restricted(int, str_features*)’: 2022-05-20T18:11:08,127 ./src/s_multi_loop_sub.cpp:173:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:08,128 173 | int i, tmp_k, ij, k; 2022-05-20T18:11:08,128 | ^~~~~ 2022-05-20T18:11:08,132 ./src/s_multi_loop_sub.cpp: In member function ‘void s_multi_loop_sub::compute_energy_FM_restricted(int, str_features*)’: 2022-05-20T18:11:08,132 ./src/s_multi_loop_sub.cpp:220:12: warning: variable ‘tmp_k’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:08,132 220 | int i, tmp_k, k, ij; 2022-05-20T18:11:08,133 | ^~~~~ 2022-05-20T18:11:09,061 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_partition_function.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_partition_function.o -g 2022-05-20T18:11:09,716 ./src/s_partition_function.cpp: In constructor ‘s_partition_function::s_partition_function(char*, int, int, char*)’: 2022-05-20T18:11:09,716 ./src/s_partition_function.cpp:78:16: warning: statement has no effect [-Wunused-value] 2022-05-20T18:11:09,717 78 | toupper(csequence[i]); 2022-05-20T18:11:09,717 | ~~~~~~~^~~~~~~~~~~~~~ 2022-05-20T18:11:09,771 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function()’: 2022-05-20T18:11:09,772 ./src/s_partition_function.cpp:415:15: warning: variable ‘ij’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,772 415 | int i, j, ij; 2022-05-20T18:11:09,772 | ^~ 2022-05-20T18:11:09,791 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm_nodangles(int, int)’: 2022-05-20T18:11:09,792 ./src/s_partition_function.cpp:692:12: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,792 692 | int h, hj; 2022-05-20T18:11:09,792 | ^~ 2022-05-20T18:11:09,826 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_upm(int, int)’: 2022-05-20T18:11:09,827 ./src/s_partition_function.cpp:1028:37: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,827 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2022-05-20T18:11:09,827 | ^~~~~~ 2022-05-20T18:11:09,828 ./src/s_partition_function.cpp:1028:45: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,828 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2022-05-20T18:11:09,828 | ^~~~~~ 2022-05-20T18:11:09,829 ./src/s_partition_function.cpp:1028:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,829 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2022-05-20T18:11:09,829 | ^~~~~~ 2022-05-20T18:11:09,830 ./src/s_partition_function.cpp:1028:61: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,830 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2022-05-20T18:11:09,830 | ^~~~~~ 2022-05-20T18:11:09,831 ./src/s_partition_function.cpp:1028:69: warning: variable ‘hj’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,831 1028 | int ip1l, ip2l, lp2jm1, lp1jm1, lp2jm2, lp1jm2, lp2jm3, lp1jm3, hj; 2022-05-20T18:11:09,831 | ^~ 2022-05-20T18:11:09,905 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_needmidd3(int, int)’: 2022-05-20T18:11:09,905 ./src/s_partition_function.cpp:1717:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,906 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,906 | ^~~~~~ 2022-05-20T18:11:09,907 ./src/s_partition_function.cpp:1717:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,907 1717 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,907 | ^~~~~~ 2022-05-20T18:11:09,910 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmd3_noneedmidd3(int, int)’: 2022-05-20T18:11:09,910 ./src/s_partition_function.cpp:1747:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,910 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,911 | ^~~~~~ 2022-05-20T18:11:09,911 ./src/s_partition_function.cpp:1747:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,911 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,912 | ^~~~~~ 2022-05-20T18:11:09,912 ./src/s_partition_function.cpp:1747:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,912 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,913 | ^~~~~~ 2022-05-20T18:11:09,913 ./src/s_partition_function.cpp:1747:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,913 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,914 | ^~~~~~ 2022-05-20T18:11:09,914 ./src/s_partition_function.cpp:1747:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,914 1747 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,915 | ^~~~~~ 2022-05-20T18:11:09,915 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_needmidd3(int, int)’: 2022-05-20T18:11:09,915 ./src/s_partition_function.cpp:1779:21: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,916 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,916 | ^~~~~~ 2022-05-20T18:11:09,916 ./src/s_partition_function.cpp:1779:29: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,917 1779 | int ij, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,917 | ^~~~~~ 2022-05-20T18:11:09,919 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_pmnod3_noneedmidd3(int, int)’: 2022-05-20T18:11:09,919 ./src/s_partition_function.cpp:1808:21: warning: variable ‘lp1jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,920 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,920 | ^~~~~~ 2022-05-20T18:11:09,920 ./src/s_partition_function.cpp:1808:29: warning: variable ‘lp1jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,921 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,921 | ^~~~~~ 2022-05-20T18:11:09,921 ./src/s_partition_function.cpp:1808:37: warning: variable ‘lp2jm1’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,922 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,922 | ^~~~~~ 2022-05-20T18:11:09,922 ./src/s_partition_function.cpp:1808:45: warning: variable ‘lp2jm2’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,923 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,923 | ^~~~~~ 2022-05-20T18:11:09,923 ./src/s_partition_function.cpp:1808:53: warning: variable ‘lp2jm3’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,924 1808 | int ij, lp1jm1, lp1jm2, lp1jm3, lp2jm1, lp2jm2, lp2jm3, il; 2022-05-20T18:11:09,924 | ^~~~~~ 2022-05-20T18:11:09,978 ./src/s_partition_function.cpp: In member function ‘double s_partition_function::compute_partition_function_exhaustively()’: 2022-05-20T18:11:09,978 ./src/s_partition_function.cpp:2288:12: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,979 2288 | double min_energy, max_energy; 2022-05-20T18:11:09,979 | ^~~~~~~~~~ 2022-05-20T18:11:09,979 ./src/s_partition_function.cpp:2288:24: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:09,980 2288 | double min_energy, max_energy; 2022-05-20T18:11:09,980 | ^~~~~~~~~~ 2022-05-20T18:11:10,016 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::verify_recurrences()’: 2022-05-20T18:11:10,016 ./src/s_partition_function.cpp:2667:9: warning: variable ‘error’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:10,017 2667 | int error = 0; 2022-05-20T18:11:10,017 | ^~~~~ 2022-05-20T18:11:10,026 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient_exhaustively()’: 2022-05-20T18:11:10,026 ./src/s_partition_function.cpp:2868:9: warning: variable ‘real_str_found’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:10,026 2868 | int real_str_found, actual_num_str; 2022-05-20T18:11:10,027 | ^~~~~~~~~~~~~~ 2022-05-20T18:11:10,209 ./src/s_partition_function.cpp: In member function ‘void s_partition_function::compute_logZ_gradient()’: 2022-05-20T18:11:10,210 ./src/s_partition_function.cpp:3000:15: warning: variable ‘AUpen’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:10,210 3000 | PARAMTYPE AUpen; //, dangle, dangle5, dangle3; 2022-05-20T18:11:10,210 | ^~~~~ 2022-05-20T18:11:10,255 ./src/s_partition_function.cpp: In member function ‘int s_partition_function::correct_gradient()’: 2022-05-20T18:11:10,256 ./src/s_partition_function.cpp:4925:9: warning: variable ‘index_param’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:10,256 4925 | int index_param; 2022-05-20T18:11:10,256 | ^~~~~~~~~~~ 2022-05-20T18:11:31,813 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_specific_functions.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_specific_functions.o -g 2022-05-20T18:11:32,478 ./src/s_specific_functions.cpp: In function ‘int s_calculate_energy(int*, char*, char*, str_features*, str_features*)’: 2022-05-20T18:11:32,479 ./src/s_specific_functions.cpp:483:8: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:32,479 483 | int special; 2022-05-20T18:11:32,480 | ^~~~~~~ 2022-05-20T18:11:32,506 ./src/s_specific_functions.cpp: In function ‘int s_calculate_enthalpy(int*, char*, str_features*)’: 2022-05-20T18:11:32,506 ./src/s_specific_functions.cpp:662:8: warning: variable ‘special’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:32,507 662 | int special; 2022-05-20T18:11:32,507 | ^~~~~~~ 2022-05-20T18:11:32,538 ./src/s_specific_functions.cpp: In function ‘void simfold_gradient_smart(char*, double*, int, int)’: 2022-05-20T18:11:32,539 ./src/s_specific_functions.cpp:1089:9: warning: variable ‘pf’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:32,539 1089 | PFTYPE pf; 2022-05-20T18:11:32,540 | ^~ 2022-05-20T18:11:32,546 ./src/s_specific_functions.cpp: In function ‘double simfold_partition_function_approximately(char*)’: 2022-05-20T18:11:32,547 ./src/s_specific_functions.cpp:1147:9: warning: variable ‘min_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:32,547 1147 | double min_energy, max_energy; 2022-05-20T18:11:32,547 | ^~~~~~~~~~ 2022-05-20T18:11:32,548 ./src/s_specific_functions.cpp:1147:21: warning: variable ‘max_energy’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:32,548 1147 | double min_energy, max_energy; 2022-05-20T18:11:32,549 | ^~~~~~~~~~ 2022-05-20T18:11:36,101 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_stacked_pair.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_stacked_pair.o -g 2022-05-20T18:11:36,650 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/s_sub_folding.cpp -o build/temp.linux-armv7l-cpython-39/./src/s_sub_folding.o -g 2022-05-20T18:11:41,020 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/sc.cpp -o build/temp.linux-armv7l-cpython-39/./src/sc.o -g 2022-05-20T18:11:42,013 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/score.cpp -o build/temp.linux-armv7l-cpython-39/./src/score.o -g 2022-05-20T18:11:43,094 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/temp.cpp -o build/temp.linux-armv7l-cpython-39/./src/temp.o -g 2022-05-20T18:11:45,259 ./src/temp.cpp: In function ‘Fold* best(char*, char*)’: 2022-05-20T18:11:45,260 ./src/temp.cpp:80:9: warning: variable ‘min_en’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:45,260 80 | double min_en; 2022-05-20T18:11:45,261 | ^~~~~~ 2022-05-20T18:11:45,929 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/timer.cpp -o build/temp.linux-armv7l-cpython-39/./src/timer.o -g 2022-05-20T18:11:46,447 ./src/timer.cpp: In member function ‘void timer::start()’: 2022-05-20T18:11:46,447 ./src/timer.cpp:23:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:46,448 23 | clock_t t; 2022-05-20T18:11:46,448 | ^ 2022-05-20T18:11:46,448 ./src/timer.cpp: In member function ‘void timer::stop()’: 2022-05-20T18:11:46,449 ./src/timer.cpp:32:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:46,449 32 | clock_t t; 2022-05-20T18:11:46,450 | ^ 2022-05-20T18:11:46,450 ./src/timer.cpp: In member function ‘void timer::reset()’: 2022-05-20T18:11:46,451 ./src/timer.cpp:41:11: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:46,451 41 | clock_t t; 2022-05-20T18:11:46,451 | ^ 2022-05-20T18:11:46,452 ./src/timer.cpp: In member function ‘float timer::elapsed()’: 2022-05-20T18:11:46,452 ./src/timer.cpp:52:13: warning: variable ‘t’ set but not used [-Wunused-but-set-variable] 2022-05-20T18:11:46,452 52 | clock_t t; 2022-05-20T18:11:46,453 | ^ 2022-05-20T18:11:46,660 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I. -I... -I/tmp/pip-wheel-vu6ibjd9/hotknots_a863665fbf204665b04c45b8fbc123aa/include -I/usr/include/python3.9 -c ./src/utils.cpp -o build/temp.linux-armv7l-cpython-39/./src/utils.o -g 2022-05-20T18:11:47,300 ./src/utils.cpp: In function ‘void bpseq2dp(int, short int*, char*)’: 2022-05-20T18:11:47,301 ./src/utils.cpp:146:6: warning: ‘stackindex_push’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2022-05-20T18:11:47,301 146 | int stackindex_push; 2022-05-20T18:11:47,301 | ^~~~~~~~~~~~~~~ 2022-05-20T18:11:47,507 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/./src/Bands.o build/temp.linux-armv7l-cpython-39/./src/Input.o build/temp.linux-armv7l-cpython-39/./src/Loop.o build/temp.linux-armv7l-cpython-39/./src/LoopList.o build/temp.linux-armv7l-cpython-39/./src/Stack.o build/temp.linux-armv7l-cpython-39/./src/common.o build/temp.linux-armv7l-cpython-39/./src/commonPK.o build/temp.linux-armv7l-cpython-39/./src/goodStem.o build/temp.linux-armv7l-cpython-39/./src/hotspot.o build/temp.linux-armv7l-cpython-39/./src/init.o build/temp.linux-armv7l-cpython-39/./src/initPK.o build/temp.linux-armv7l-cpython-39/./src/params.o build/temp.linux-armv7l-cpython-39/./src/paramsPK.o build/temp.linux-armv7l-cpython-39/./src/python.o build/temp.linux-armv7l-cpython-39/./src/s_energy_matrix.o build/temp.linux-armv7l-cpython-39/./src/s_hairpin_loop.o build/temp.linux-armv7l-cpython-39/./src/s_internal_loop.o build/temp.linux-armv7l-cpython-39/./src/s_min_folding.o build/temp.linux-armv7l-cpython-39/./src/s_multi_loop.o build/temp.linux-armv7l-cpython-39/./src/s_multi_loop_sub.o build/temp.linux-armv7l-cpython-39/./src/s_partition_function.o build/temp.linux-armv7l-cpython-39/./src/s_specific_functions.o build/temp.linux-armv7l-cpython-39/./src/s_stacked_pair.o build/temp.linux-armv7l-cpython-39/./src/s_sub_folding.o build/temp.linux-armv7l-cpython-39/./src/sc.o build/temp.linux-armv7l-cpython-39/./src/score.o build/temp.linux-armv7l-cpython-39/./src/temp.o build/temp.linux-armv7l-cpython-39/./src/timer.o build/temp.linux-armv7l-cpython-39/./src/utils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/hotknots/hotknots.cpython-39-arm-linux-gnueabihf.so -lm 2022-05-20T18:11:48,576 running build_scripts 2022-05-20T18:11:48,577 creating build/scripts-3.9 2022-05-20T18:11:48,580 copying and adjusting hotknots.py -> build/scripts-3.9 2022-05-20T18:11:48,582 changing mode of build/scripts-3.9/hotknots.py from 644 to 755 2022-05-20T18:11:49,247 /usr/local/lib/python3.9/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2022-05-20T18:11:49,248 warnings.warn( 2022-05-20T18:11:49,866 installing to build/bdist.linux-armv7l/wheel 2022-05-20T18:11:49,866 running install 2022-05-20T18:11:49,929 running install_lib 2022-05-20T18:11:50,551 creating build/bdist.linux-armv7l 2022-05-20T18:11:50,551 creating build/bdist.linux-armv7l/wheel 2022-05-20T18:11:50,557 creating build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,559 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstackh-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,564 copying build/lib.linux-armv7l-cpython-39/hotknots/pkmodelCC2006.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,567 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-loop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,571 copying build/lib.linux-armv7l-cpython-39/hotknots/coaxial.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,575 copying build/lib.linux-armv7l-cpython-39/hotknots/parameters_DP03.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,578 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstacki-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,582 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint4-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,590 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint4-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,600 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-loop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,603 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstacki-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,607 copying build/lib.linux-armv7l-cpython-39/hotknots/coaxstack.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,611 copying build/lib.linux-armv7l-cpython-39/hotknots/parameters_CC09.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,614 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tstackh-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,618 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-loop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,621 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-stack-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,625 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-miscloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,629 copying build/lib.linux-armv7l-cpython-39/hotknots/CG_best_parameters_ISMB2007.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,632 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-triloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,635 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstacki-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,639 copying build/lib.linux-armv7l-cpython-39/hotknots/turner_parameters_fm363_constrdangles.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,642 copying build/lib.linux-armv7l-cpython-39/hotknots/multirnafold.conf -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,645 copying build/lib.linux-armv7l-cpython-39/hotknots/walter-coaxstack-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,649 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-dangle-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,653 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tstacki-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,657 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint2-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,662 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tstackh-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,666 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-miscloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,669 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-sint2-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,673 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-asint1x2-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,682 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint2-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,686 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-sint2-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,691 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-dangle-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,695 copying build/lib.linux-armv7l-cpython-39/hotknots/pkmodelDP.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,698 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-dangle-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,703 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tloop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,706 copying build/lib.linux-armv7l-cpython-39/hotknots/hotknots.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,794 copying build/lib.linux-armv7l-cpython-39/hotknots/pkmodelRE.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,798 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-miscloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,801 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-triloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,804 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstackh-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,808 copying build/lib.linux-armv7l-cpython-39/hotknots/__init__.py -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,811 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-stack-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,815 copying build/lib.linux-armv7l-cpython-39/hotknots/turner_partypes_fm363.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,819 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-triloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,822 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-asint1x2-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,828 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-sint4-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,836 copying build/lib.linux-armv7l-cpython-39/hotknots/pkenergy.conf -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,839 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,842 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-stack-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,846 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,850 copying build/lib.linux-armv7l-cpython-39/hotknots/parameters_CC06.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,853 copying build/lib.linux-armv7l-cpython-39/hotknots/parameters_DP09.txt -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,856 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-asint1x2-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,862 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-asint1x2-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,868 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,871 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-triloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,874 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-miscloop-rna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,877 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-asint1x2-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,883 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-miscloop-dna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,886 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-tstacki-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,890 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-stack-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,894 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-dangle-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,897 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-triloop-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,900 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint2-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,904 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-dangle-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,908 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tloop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,911 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-stack-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,915 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-loop-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,918 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-sint4-rna.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,926 copying build/lib.linux-armv7l-cpython-39/hotknots/tstackcoax.dat -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,930 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-tstackh-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,934 copying build/lib.linux-armv7l-cpython-39/hotknots/turner-loop-rna.dg -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,937 copying build/lib.linux-armv7l-cpython-39/hotknots/mathews-sint4-dna.dh -> build/bdist.linux-armv7l/wheel/hotknots 2022-05-20T18:11:50,944 running install_egg_info 2022-05-20T18:11:52,211 running egg_info 2022-05-20T18:11:52,820 writing hotknots.egg-info/PKG-INFO 2022-05-20T18:11:53,392 writing dependency_links to hotknots.egg-info/dependency_links.txt 2022-05-20T18:11:56,855 writing top-level names to hotknots.egg-info/top_level.txt 2022-05-20T18:11:56,961 reading manifest file 'hotknots.egg-info/SOURCES.txt' 2022-05-20T18:11:57,001 reading manifest template 'MANIFEST.in' 2022-05-20T18:11:57,064 warning: no files found matching '*.c' under directory 'src' 2022-05-20T18:11:57,064 adding license file 'LICENSE' 2022-05-20T18:11:57,093 writing manifest file 'hotknots.egg-info/SOURCES.txt' 2022-05-20T18:11:57,097 Copying hotknots.egg-info to build/bdist.linux-armv7l/wheel/hotknots-2.4-py3.9.egg-info 2022-05-20T18:11:57,114 running install_scripts 2022-05-20T18:11:57,235 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.data 2022-05-20T18:11:57,236 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2022-05-20T18:11:57,239 copying build/scripts-3.9/hotknots.py -> build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts 2022-05-20T18:11:57,243 changing mode of build/bdist.linux-armv7l/wheel/hotknots-2.4.data/scripts/hotknots.py to 755 2022-05-20T18:11:57,270 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-05-20T18:11:57,281 creating build/bdist.linux-armv7l/wheel/hotknots-2.4.dist-info/WHEEL 2022-05-20T18:11:57,285 creating '/tmp/pip-wheel-yvvz1o90/hotknots-2.4-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-05-20T18:11:57,293 adding 'hotknots/CG_best_parameters_ISMB2007.txt' 2022-05-20T18:11:57,295 adding 'hotknots/__init__.py' 2022-05-20T18:11:57,298 adding 'hotknots/coaxial.dat' 2022-05-20T18:11:57,300 adding 'hotknots/coaxstack.dat' 2022-05-20T18:11:58,195 adding 'hotknots/hotknots.cpython-39-arm-linux-gnueabihf.so' 2022-05-20T18:11:58,234 adding 'hotknots/mathews-asint1x2-dna.dat' 2022-05-20T18:11:58,241 adding 'hotknots/mathews-asint1x2-dna.dh' 2022-05-20T18:11:58,244 adding 'hotknots/mathews-dangle-dna.dat' 2022-05-20T18:11:58,247 adding 'hotknots/mathews-dangle-dna.dh' 2022-05-20T18:11:58,249 adding 'hotknots/mathews-loop-dna.dat' 2022-05-20T18:11:58,251 adding 'hotknots/mathews-loop-dna.dh' 2022-05-20T18:11:58,254 adding 'hotknots/mathews-miscloop-dna.dat' 2022-05-20T18:11:58,256 adding 'hotknots/mathews-miscloop-dna.dh' 2022-05-20T18:11:58,259 adding 'hotknots/mathews-sint2-dna.dat' 2022-05-20T18:11:58,263 adding 'hotknots/mathews-sint2-dna.dh' 2022-05-20T18:11:58,269 adding 'hotknots/mathews-sint4-dna.dat' 2022-05-20T18:11:58,278 adding 'hotknots/mathews-sint4-dna.dh' 2022-05-20T18:11:58,282 adding 'hotknots/mathews-stack-dna.dat' 2022-05-20T18:11:58,284 adding 'hotknots/mathews-stack-dna.dh' 2022-05-20T18:11:58,286 adding 'hotknots/mathews-tloop-dna.dat' 2022-05-20T18:11:58,288 adding 'hotknots/mathews-tloop-dna.dh' 2022-05-20T18:11:58,291 adding 'hotknots/mathews-triloop-dna.dat' 2022-05-20T18:11:58,293 adding 'hotknots/mathews-triloop-dna.dh' 2022-05-20T18:11:58,295 adding 'hotknots/mathews-tstackh-dna.dat' 2022-05-20T18:11:58,298 adding 'hotknots/mathews-tstackh-dna.dh' 2022-05-20T18:11:58,300 adding 'hotknots/mathews-tstacki-dna.dat' 2022-05-20T18:11:58,303 adding 'hotknots/mathews-tstacki-dna.dh' 2022-05-20T18:11:58,305 adding 'hotknots/multirnafold.conf' 2022-05-20T18:11:58,309 adding 'hotknots/parameters_CC06.txt' 2022-05-20T18:11:58,313 adding 'hotknots/parameters_CC09.txt' 2022-05-20T18:11:58,316 adding 'hotknots/parameters_DP03.txt' 2022-05-20T18:11:58,318 adding 'hotknots/parameters_DP09.txt' 2022-05-20T18:11:58,321 adding 'hotknots/pkenergy.conf' 2022-05-20T18:11:58,323 adding 'hotknots/pkmodelCC2006.dat' 2022-05-20T18:11:58,326 adding 'hotknots/pkmodelDP.dat' 2022-05-20T18:11:58,328 adding 'hotknots/pkmodelRE.dat' 2022-05-20T18:11:58,331 adding 'hotknots/tstackcoax.dat' 2022-05-20T18:11:58,336 adding 'hotknots/turner-asint1x2-rna.dat' 2022-05-20T18:11:58,343 adding 'hotknots/turner-asint1x2-rna.dg' 2022-05-20T18:11:58,353 adding 'hotknots/turner-asint1x2-rna.dh' 2022-05-20T18:11:58,356 adding 'hotknots/turner-dangle-rna.dat' 2022-05-20T18:11:58,359 adding 'hotknots/turner-dangle-rna.dg' 2022-05-20T18:11:58,362 adding 'hotknots/turner-dangle-rna.dh' 2022-05-20T18:11:58,364 adding 'hotknots/turner-loop-rna.dat' 2022-05-20T18:11:58,366 adding 'hotknots/turner-loop-rna.dg' 2022-05-20T18:11:58,369 adding 'hotknots/turner-loop-rna.dh' 2022-05-20T18:11:58,371 adding 'hotknots/turner-miscloop-rna.dat' 2022-05-20T18:11:58,373 adding 'hotknots/turner-miscloop-rna.dg' 2022-05-20T18:11:58,376 adding 'hotknots/turner-miscloop-rna.dh' 2022-05-20T18:11:58,379 adding 'hotknots/turner-sint2-rna.dat' 2022-05-20T18:11:58,382 adding 'hotknots/turner-sint2-rna.dg' 2022-05-20T18:11:58,385 adding 'hotknots/turner-sint2-rna.dh' 2022-05-20T18:11:58,399 adding 'hotknots/turner-sint4-rna.dat' 2022-05-20T18:11:58,411 adding 'hotknots/turner-sint4-rna.dg' 2022-05-20T18:11:58,436 adding 'hotknots/turner-sint4-rna.dh' 2022-05-20T18:11:58,440 adding 'hotknots/turner-stack-rna.dat' 2022-05-20T18:11:58,443 adding 'hotknots/turner-stack-rna.dg' 2022-05-20T18:11:58,446 adding 'hotknots/turner-stack-rna.dh' 2022-05-20T18:11:58,448 adding 'hotknots/turner-tloop-rna.dat' 2022-05-20T18:11:58,450 adding 'hotknots/turner-tloop-rna.dg' 2022-05-20T18:11:58,452 adding 'hotknots/turner-tloop-rna.dh' 2022-05-20T18:11:58,454 adding 'hotknots/turner-triloop-rna.dat' 2022-05-20T18:11:58,456 adding 'hotknots/turner-triloop-rna.dg' 2022-05-20T18:11:58,458 adding 'hotknots/turner-triloop-rna.dh' 2022-05-20T18:11:58,461 adding 'hotknots/turner-tstackh-rna.dat' 2022-05-20T18:11:58,464 adding 'hotknots/turner-tstackh-rna.dg' 2022-05-20T18:11:58,466 adding 'hotknots/turner-tstackh-rna.dh' 2022-05-20T18:11:58,469 adding 'hotknots/turner-tstacki-rna.dat' 2022-05-20T18:11:58,472 adding 'hotknots/turner-tstacki-rna.dg' 2022-05-20T18:11:58,474 adding 'hotknots/turner-tstacki-rna.dh' 2022-05-20T18:11:58,477 adding 'hotknots/turner_parameters_fm363_constrdangles.txt' 2022-05-20T18:11:58,481 adding 'hotknots/turner_partypes_fm363.txt' 2022-05-20T18:11:58,483 adding 'hotknots/walter-coaxstack-rna.dat' 2022-05-20T18:11:58,488 adding 'hotknots-2.4.data/scripts/hotknots.py' 2022-05-20T18:11:58,506 adding 'hotknots-2.4.dist-info/LICENSE' 2022-05-20T18:11:58,509 adding 'hotknots-2.4.dist-info/METADATA' 2022-05-20T18:11:58,510 adding 'hotknots-2.4.dist-info/WHEEL' 2022-05-20T18:11:58,512 adding 'hotknots-2.4.dist-info/top_level.txt' 2022-05-20T18:11:58,515 adding 'hotknots-2.4.dist-info/RECORD' 2022-05-20T18:11:58,548 removing build/bdist.linux-armv7l/wheel 2022-05-20T18:11:58,843 Building wheel for hotknots (setup.py): finished with status 'done' 2022-05-20T18:11:58,874 Created wheel for hotknots: filename=hotknots-2.4-cp39-cp39-linux_armv7l.whl size=776853 sha256=c1e9c91c02634a50036bdada1cefe6c3fa08e3917ca4617f81b58564137af013 2022-05-20T18:11:58,876 Stored in directory: /tmp/pip-ephem-wheel-cache-d0ae0dbp/wheels/66/07/18/d19066fa6a2c469262783f2bc4d30c70c6ef0877fd53749131 2022-05-20T18:11:58,906 Successfully built hotknots 2022-05-20T18:11:58,972 Removed build tracker: '/tmp/pip-build-tracker-x0gs6kbx'