2023-09-17T12:06:12,658 Created temporary directory: /tmp/pip-build-tracker-e2i9gg7_ 2023-09-17T12:06:12,659 Initialized build tracking at /tmp/pip-build-tracker-e2i9gg7_ 2023-09-17T12:06:12,659 Created build tracker: /tmp/pip-build-tracker-e2i9gg7_ 2023-09-17T12:06:12,660 Entered build tracker: /tmp/pip-build-tracker-e2i9gg7_ 2023-09-17T12:06:12,661 Created temporary directory: /tmp/pip-wheel-gu6f61lz 2023-09-17T12:06:12,664 Created temporary directory: /tmp/pip-ephem-wheel-cache-y528gw_i 2023-09-17T12:06:12,687 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-17T12:06:12,691 2 location(s) to search for versions of pypulchra: 2023-09-17T12:06:12,691 * https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,691 * https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,691 Fetching project page and analyzing links: https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,692 Getting page https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,694 Found index url https://pypi.org/simple/ 2023-09-17T12:06:12,833 Fetched page https://pypi.org/simple/pypulchra/ as application/vnd.pypi.simple.v1+json 2023-09-17T12:06:12,835 Found link https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz (from https://pypi.org/simple/pypulchra/) (requires-python:>=3.7), version: 1.0.0 2023-09-17T12:06:12,836 Found link https://files.pythonhosted.org/packages/c7/60/4c39e247bd18cb845ffc8f55f3021a55db0b0ba8e3e481b4a4d641868fb4/pypulchra-1.0.1.tar.gz (from https://pypi.org/simple/pypulchra/) (requires-python:>=3.7), version: 1.0.1 2023-09-17T12:06:12,837 Fetching project page and analyzing links: https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,838 Getting page https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,839 Found index url https://www.piwheels.org/simple/ 2023-09-17T12:06:13,150 Fetched page https://www.piwheels.org/simple/pypulchra/ as text/html 2023-09-17T12:06:13,153 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp39-cp39-linux_armv7l.whl#sha256=e924917a730e5895e85d8e5768e339b83845808e32b55fbb3fe065485fed3bd7 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,154 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp39-cp39-linux_armv6l.whl#sha256=e924917a730e5895e85d8e5768e339b83845808e32b55fbb3fe065485fed3bd7 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,155 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=dd6c53f28a2abfdf39df68c00333a7e734f66ef9d486ac1f6f2a1737c476afb8 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,155 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=dd6c53f28a2abfdf39df68c00333a7e734f66ef9d486ac1f6f2a1737c476afb8 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,156 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=0470a8e044d39160d887c99766465e6c35ade8688d0c457e37ae37ce03b85472 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,157 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=0470a8e044d39160d887c99766465e6c35ade8688d0c457e37ae37ce03b85472 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,157 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=021994ea82be3c4909986db98b8c49e8149b7b4c033c1963bfd0232adf248683 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,158 Skipping link: No binaries permitted for pypulchra: https://www.piwheels.org/simple/pypulchra/pypulchra-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=021994ea82be3c4909986db98b8c49e8149b7b4c033c1963bfd0232adf248683 (from https://www.piwheels.org/simple/pypulchra/) (requires-python:>=3.7) 2023-09-17T12:06:13,159 Skipping link: not a file: https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:13,159 Skipping link: not a file: https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:13,177 Given no hashes to check 1 links for project 'pypulchra': discarding no candidates 2023-09-17T12:06:13,195 Collecting pypulchra==1.0.1 2023-09-17T12:06:13,198 Created temporary directory: /tmp/pip-unpack-fdrultc7 2023-09-17T12:06:13,673 Downloading pypulchra-1.0.1.tar.gz (1.9 MB) 2023-09-17T12:06:14,511 Added pypulchra==1.0.1 from https://files.pythonhosted.org/packages/c7/60/4c39e247bd18cb845ffc8f55f3021a55db0b0ba8e3e481b4a4d641868fb4/pypulchra-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-e2i9gg7_' 2023-09-17T12:06:14,516 Created temporary directory: /tmp/pip-build-env-gxbbu8or 2023-09-17T12:06:14,520 Installing build dependencies: started 2023-09-17T12:06:14,521 Running command pip subprocess to install build dependencies 2023-09-17T12:06:15,664 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-17T12:06:16,150 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-17T12:06:17,859 Collecting setuptools>=42 2023-09-17T12:06:17,861 Obtaining dependency information for setuptools>=42 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-17T12:06:17,867 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-17T12:06:18,080 Collecting wheel 2023-09-17T12:06:18,098 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-17T12:06:18,266 Collecting pybind11>=2.8.0 2023-09-17T12:06:18,294 Using cached https://www.piwheels.org/simple/pybind11/pybind11-2.11.1-py3-none-any.whl (227 kB) 2023-09-17T12:06:18,486 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-17T12:06:20,983 Installing collected packages: wheel, setuptools, pybind11 2023-09-17T12:06:21,208 Creating /tmp/pip-build-env-gxbbu8or/overlay/local/bin 2023-09-17T12:06:21,210 changing mode of /tmp/pip-build-env-gxbbu8or/overlay/local/bin/wheel to 755 2023-09-17T12:06:23,823 changing mode of /tmp/pip-build-env-gxbbu8or/overlay/local/bin/pybind11-config to 755 2023-09-17T12:06:23,849 Successfully installed pybind11-2.11.1 setuptools-68.2.2 wheel-0.41.2 2023-09-17T12:06:24,362 Installing build dependencies: finished with status 'done' 2023-09-17T12:06:24,365 Getting requirements to build wheel: started 2023-09-17T12:06:24,367 Running command Getting requirements to build wheel 2023-09-17T12:06:24,892 running egg_info 2023-09-17T12:06:24,899 writing pypulchra.egg-info/PKG-INFO 2023-09-17T12:06:24,902 writing dependency_links to pypulchra.egg-info/dependency_links.txt 2023-09-17T12:06:24,904 writing entry points to pypulchra.egg-info/entry_points.txt 2023-09-17T12:06:24,906 writing top-level names to pypulchra.egg-info/top_level.txt 2023-09-17T12:06:24,931 reading manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:24,933 reading manifest template 'MANIFEST.in' 2023-09-17T12:06:24,939 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,017 Getting requirements to build wheel: finished with status 'done' 2023-09-17T12:06:25,029 Created temporary directory: /tmp/pip-modern-metadata-g0c47p66 2023-09-17T12:06:25,032 Preparing metadata (pyproject.toml): started 2023-09-17T12:06:25,033 Running command Preparing metadata (pyproject.toml) 2023-09-17T12:06:25,514 running dist_info 2023-09-17T12:06:25,534 creating /tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info 2023-09-17T12:06:25,539 writing /tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/PKG-INFO 2023-09-17T12:06:25,543 writing dependency_links to /tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/dependency_links.txt 2023-09-17T12:06:25,544 writing entry points to /tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/entry_points.txt 2023-09-17T12:06:25,545 writing top-level names to /tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/top_level.txt 2023-09-17T12:06:25,547 writing manifest file '/tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,566 reading manifest file '/tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,568 reading manifest template 'MANIFEST.in' 2023-09-17T12:06:25,573 writing manifest file '/tmp/pip-modern-metadata-g0c47p66/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,574 creating '/tmp/pip-modern-metadata-g0c47p66/pypulchra-1.0.1.dist-info' 2023-09-17T12:06:25,752 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-17T12:06:25,757 Source in /tmp/pip-wheel-gu6f61lz/pypulchra_41c39ebd1c6d4e0783c730f8f57c9e16 has version 1.0.1, which satisfies requirement pypulchra==1.0.1 from https://files.pythonhosted.org/packages/c7/60/4c39e247bd18cb845ffc8f55f3021a55db0b0ba8e3e481b4a4d641868fb4/pypulchra-1.0.1.tar.gz 2023-09-17T12:06:25,757 Removed pypulchra==1.0.1 from https://files.pythonhosted.org/packages/c7/60/4c39e247bd18cb845ffc8f55f3021a55db0b0ba8e3e481b4a4d641868fb4/pypulchra-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-e2i9gg7_' 2023-09-17T12:06:25,763 Created temporary directory: /tmp/pip-unpack-4g87e3mf 2023-09-17T12:06:25,764 Created temporary directory: /tmp/pip-unpack-t_o2coce 2023-09-17T12:06:25,766 Building wheels for collected packages: pypulchra 2023-09-17T12:06:25,770 Created temporary directory: /tmp/pip-wheel-ol5s45fg 2023-09-17T12:06:25,771 Destination directory: /tmp/pip-wheel-ol5s45fg 2023-09-17T12:06:25,773 Building wheel for pypulchra (pyproject.toml): started 2023-09-17T12:06:25,774 Running command Building wheel for pypulchra (pyproject.toml) 2023-09-17T12:06:26,312 running bdist_wheel 2023-09-17T12:06:26,349 running build 2023-09-17T12:06:26,350 running build_py 2023-09-17T12:06:26,357 creating build 2023-09-17T12:06:26,358 creating build/lib.linux-armv7l-cpython-311 2023-09-17T12:06:26,358 creating build/lib.linux-armv7l-cpython-311/pypulchra 2023-09-17T12:06:26,360 copying pypulchra/__init__.py -> build/lib.linux-armv7l-cpython-311/pypulchra 2023-09-17T12:06:26,362 running build_ext 2023-09-17T12:06:26,367 building 'pypulchra._pypulchra' extension 2023-09-17T12:06:26,368 creating build/temp.linux-armv7l-cpython-311 2023-09-17T12:06:26,368 creating build/temp.linux-armv7l-cpython-311/bindings 2023-09-17T12:06:26,369 creating build/temp.linux-armv7l-cpython-311/bindings/python 2023-09-17T12:06:26,370 creating build/temp.linux-armv7l-cpython-311/src 2023-09-17T12:06:26,371 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.1 -Isrc -I/tmp/pip-build-env-gxbbu8or/overlay/local/lib/python3.11/dist-packages/pybind11/include -I/usr/include/python3.11 -c bindings/python/pulchra_bindings.cpp -o build/temp.linux-armv7l-cpython-311/bindings/python/pulchra_bindings.o -fvisibility=hidden -g0 -std=c++14 -static 2023-09-17T12:06:28,513 In file included from bindings/python/pulchra_bindings.cpp:5: 2023-09-17T12:06:28,514 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2023-09-17T12:06:28,515 src/pulchra.hpp:653:69: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-17T12:06:28,515 653 | res->type = AA_NUMS[pusetseq(resname)]; 2023-09-17T12:06:28,516 | ~~~~~~~~^~~~~~~~~ 2023-09-17T12:06:28,529 src/pulchra.hpp:594:22: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,530 594 | char version; 2023-09-17T12:06:28,531 | ^~~~~~~ 2023-09-17T12:06:28,531 src/pulchra.hpp:595:60: warning: unused variable ‘num’ [-Wunused-variable] 2023-09-17T12:06:28,532 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,532 | ^~~ 2023-09-17T12:06:28,533 src/pulchra.hpp:595:77: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,534 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,535 | ^ 2023-09-17T12:06:28,536 src/pulchra.hpp:595:80: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:28,536 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,537 | ^ 2023-09-17T12:06:28,538 src/pulchra.hpp:597:28: warning: unused variable ‘cc’ [-Wunused-variable] 2023-09-17T12:06:28,539 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,539 | ^~ 2023-09-17T12:06:28,540 src/pulchra.hpp:597:32: warning: unused variable ‘nres’ [-Wunused-variable] 2023-09-17T12:06:28,540 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,541 | ^~~~ 2023-09-17T12:06:28,542 src/pulchra.hpp:597:38: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:28,543 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,543 | ^~ 2023-09-17T12:06:28,544 src/pulchra.hpp:597:42: warning: unused variable ‘natom’ [-Wunused-variable] 2023-09-17T12:06:28,545 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,546 | ^~~~~ 2023-09-17T12:06:28,546 src/pulchra.hpp:602:24: warning: unused variable ‘dist’ [-Wunused-variable] 2023-09-17T12:06:28,547 602 | double dist; 2023-09-17T12:06:28,548 | ^~~~ 2023-09-17T12:06:28,548 src/pulchra.hpp:603:31: warning: unused variable ‘bin’ [-Wunused-variable] 2023-09-17T12:06:28,549 603 | unsigned char bin; 2023-09-17T12:06:28,550 | ^~~ 2023-09-17T12:06:28,550 src/pulchra.hpp:604:21: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,551 604 | int warn = 0; 2023-09-17T12:06:28,551 | ^~~~ 2023-09-17T12:06:28,552 src/pulchra.hpp:605:24: warning: unused variable ‘cutoff’ [-Wunused-variable] 2023-09-17T12:06:28,553 605 | double cutoff; 2023-09-17T12:06:28,553 | ^~~~~~ 2023-09-17T12:06:28,560 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2023-09-17T12:06:28,561 src/pulchra.hpp:775:24: warning: unused variable ‘theta0’ [-Wunused-variable] 2023-09-17T12:06:28,561 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,562 | ^~~~~~ 2023-09-17T12:06:28,563 src/pulchra.hpp:775:32: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:06:28,563 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,564 | ^~~~ 2023-09-17T12:06:28,565 src/pulchra.hpp:775:38: warning: unused variable ‘th’ [-Wunused-variable] 2023-09-17T12:06:28,565 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,566 | ^~ 2023-09-17T12:06:28,567 src/pulchra.hpp:775:42: warning: unused variable ‘aa’ [-Wunused-variable] 2023-09-17T12:06:28,567 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,568 | ^~ 2023-09-17T12:06:28,568 src/pulchra.hpp:775:46: warning: unused variable ‘bb’ [-Wunused-variable] 2023-09-17T12:06:28,569 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,569 | ^~ 2023-09-17T12:06:28,570 src/pulchra.hpp:775:50: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-17T12:06:28,570 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,571 | ^~ 2023-09-17T12:06:28,571 src/pulchra.hpp:776:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:06:28,572 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,572 | ^~~ 2023-09-17T12:06:28,573 src/pulchra.hpp:776:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:06:28,574 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,574 | ^~~ 2023-09-17T12:06:28,575 src/pulchra.hpp:776:34: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:06:28,575 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,576 | ^~~ 2023-09-17T12:06:28,576 src/pulchra.hpp:776:39: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:06:28,577 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,578 | ^~ 2023-09-17T12:06:28,578 src/pulchra.hpp:776:43: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:06:28,579 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,580 | ^~ 2023-09-17T12:06:28,581 src/pulchra.hpp:776:53: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:06:28,581 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,582 | ^~ 2023-09-17T12:06:28,583 src/pulchra.hpp:776:60: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:06:28,584 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,584 | ^~ 2023-09-17T12:06:28,585 src/pulchra.hpp:777:24: warning: unused variable ‘adiff’ [-Wunused-variable] 2023-09-17T12:06:28,586 777 | double adiff[3], bdiff[3]; 2023-09-17T12:06:28,586 | ^~~~~ 2023-09-17T12:06:28,587 src/pulchra.hpp:777:34: warning: unused variable ‘bdiff’ [-Wunused-variable] 2023-09-17T12:06:28,588 777 | double adiff[3], bdiff[3]; 2023-09-17T12:06:28,588 | ^~~~~ 2023-09-17T12:06:28,589 src/pulchra.hpp:778:24: warning: unused variable ‘deriv’ [-Wunused-variable] 2023-09-17T12:06:28,590 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,590 | ^~~~~ 2023-09-17T12:06:28,591 src/pulchra.hpp:778:38: warning: unused variable ‘dtheta’ [-Wunused-variable] 2023-09-17T12:06:28,592 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,592 | ^~~~~~ 2023-09-17T12:06:28,593 src/pulchra.hpp:778:46: warning: unused variable ‘len1’ [-Wunused-variable] 2023-09-17T12:06:28,594 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,595 | ^~~~ 2023-09-17T12:06:28,595 src/pulchra.hpp:778:52: warning: unused variable ‘len2’ [-Wunused-variable] 2023-09-17T12:06:28,596 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,596 | ^~~~ 2023-09-17T12:06:28,597 src/pulchra.hpp:779:24: warning: unused variable ‘dx1’ [-Wunused-variable] 2023-09-17T12:06:28,597 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,598 | ^~~ 2023-09-17T12:06:28,598 src/pulchra.hpp:779:29: warning: unused variable ‘dy1’ [-Wunused-variable] 2023-09-17T12:06:28,599 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,599 | ^~~ 2023-09-17T12:06:28,600 src/pulchra.hpp:779:34: warning: unused variable ‘dz1’ [-Wunused-variable] 2023-09-17T12:06:28,600 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,601 | ^~~ 2023-09-17T12:06:28,601 src/pulchra.hpp:780:24: warning: unused variable ‘dx2’ [-Wunused-variable] 2023-09-17T12:06:28,601 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,602 | ^~~ 2023-09-17T12:06:28,602 src/pulchra.hpp:780:29: warning: unused variable ‘dy2’ [-Wunused-variable] 2023-09-17T12:06:28,603 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,604 | ^~~ 2023-09-17T12:06:28,604 src/pulchra.hpp:780:34: warning: unused variable ‘dz2’ [-Wunused-variable] 2023-09-17T12:06:28,605 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,606 | ^~~ 2023-09-17T12:06:28,607 src/pulchra.hpp:781:24: warning: unused variable ‘dx3’ [-Wunused-variable] 2023-09-17T12:06:28,607 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,608 | ^~~ 2023-09-17T12:06:28,609 src/pulchra.hpp:781:29: warning: unused variable ‘dy3’ [-Wunused-variable] 2023-09-17T12:06:28,609 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,610 | ^~~ 2023-09-17T12:06:28,610 src/pulchra.hpp:781:34: warning: unused variable ‘dz3’ [-Wunused-variable] 2023-09-17T12:06:28,611 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,612 | ^~~ 2023-09-17T12:06:28,612 src/pulchra.hpp:782:24: warning: unused variable ‘vx1’ [-Wunused-variable] 2023-09-17T12:06:28,613 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,614 | ^~~ 2023-09-17T12:06:28,614 src/pulchra.hpp:782:29: warning: unused variable ‘vy1’ [-Wunused-variable] 2023-09-17T12:06:28,615 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,616 | ^~~ 2023-09-17T12:06:28,616 src/pulchra.hpp:782:34: warning: unused variable ‘vz1’ [-Wunused-variable] 2023-09-17T12:06:28,617 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,618 | ^~~ 2023-09-17T12:06:28,618 src/pulchra.hpp:783:24: warning: unused variable ‘vx2’ [-Wunused-variable] 2023-09-17T12:06:28,619 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,619 | ^~~ 2023-09-17T12:06:28,620 src/pulchra.hpp:783:29: warning: unused variable ‘vy2’ [-Wunused-variable] 2023-09-17T12:06:28,621 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,621 | ^~~ 2023-09-17T12:06:28,622 src/pulchra.hpp:783:34: warning: unused variable ‘vz2’ [-Wunused-variable] 2023-09-17T12:06:28,622 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,623 | ^~~ 2023-09-17T12:06:28,624 src/pulchra.hpp:784:24: warning: unused variable ‘vx3’ [-Wunused-variable] 2023-09-17T12:06:28,625 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,625 | ^~~ 2023-09-17T12:06:28,625 src/pulchra.hpp:784:29: warning: unused variable ‘vy3’ [-Wunused-variable] 2023-09-17T12:06:28,626 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,627 | ^~~ 2023-09-17T12:06:28,627 src/pulchra.hpp:784:34: warning: unused variable ‘vz3’ [-Wunused-variable] 2023-09-17T12:06:28,628 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,628 | ^~~ 2023-09-17T12:06:28,629 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2023-09-17T12:06:28,630 src/pulchra.hpp:937:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:06:28,630 937 | char buf[1000]; 2023-09-17T12:06:28,631 | ^~~ 2023-09-17T12:06:28,631 src/pulchra.hpp:938:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:28,632 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,632 | ^ 2023-09-17T12:06:28,633 src/pulchra.hpp:938:27: warning: unused variable ‘hx’ [-Wunused-variable] 2023-09-17T12:06:28,634 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,634 | ^~ 2023-09-17T12:06:28,635 src/pulchra.hpp:938:31: warning: unused variable ‘my_iter’ [-Wunused-variable] 2023-09-17T12:06:28,636 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,636 | ^~~~~~~ 2023-09-17T12:06:28,637 src/pulchra.hpp:939:46: warning: unused variable ‘dist2’ [-Wunused-variable] 2023-09-17T12:06:28,637 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,638 | ^~~~~ 2023-09-17T12:06:28,639 src/pulchra.hpp:939:53: warning: unused variable ‘dist3’ [-Wunused-variable] 2023-09-17T12:06:28,639 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,640 | ^~~~~ 2023-09-17T12:06:28,640 src/pulchra.hpp:939:67: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,641 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,641 | ^~~~~~ 2023-09-17T12:06:28,642 src/pulchra.hpp:940:31: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2023-09-17T12:06:28,643 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,643 | ^~~~~~~~~ 2023-09-17T12:06:28,644 src/pulchra.hpp:940:42: warning: unused variable ‘grad’ [-Wunused-variable] 2023-09-17T12:06:28,644 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,645 | ^~~~ 2023-09-17T12:06:28,646 src/pulchra.hpp:940:48: warning: unused variable ‘alpha’ [-Wunused-variable] 2023-09-17T12:06:28,646 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,647 | ^~~~~ 2023-09-17T12:06:28,647 src/pulchra.hpp:942:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:06:28,648 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,649 | ^~~ 2023-09-17T12:06:28,649 src/pulchra.hpp:942:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:06:28,650 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,650 | ^~~ 2023-09-17T12:06:28,651 src/pulchra.hpp:942:50: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:06:28,652 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,652 | ^~~~ 2023-09-17T12:06:28,653 src/pulchra.hpp:942:56: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:06:28,653 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,654 | ^~~ 2023-09-17T12:06:28,654 src/pulchra.hpp:942:61: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:06:28,655 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,655 | ^~ 2023-09-17T12:06:28,656 src/pulchra.hpp:942:65: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:06:28,656 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,657 | ^~ 2023-09-17T12:06:28,657 src/pulchra.hpp:943:40: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2023-09-17T12:06:28,658 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:06:28,658 | ^~~~~~~ 2023-09-17T12:06:28,659 src/pulchra.hpp:943:49: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-17T12:06:28,659 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:06:28,660 | ^~~ 2023-09-17T12:06:28,661 src/pulchra.hpp:944:24: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:06:28,661 944 | double f0[3], f2[3]; 2023-09-17T12:06:28,662 | ^~ 2023-09-17T12:06:28,662 src/pulchra.hpp:944:31: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:06:28,663 944 | double f0[3], f2[3]; 2023-09-17T12:06:28,663 | ^~ 2023-09-17T12:06:28,664 src/pulchra.hpp:945:24: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:28,665 945 | double x, y, z; 2023-09-17T12:06:28,665 | ^ 2023-09-17T12:06:28,666 src/pulchra.hpp:945:27: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:28,667 945 | double x, y, z; 2023-09-17T12:06:28,667 | ^ 2023-09-17T12:06:28,668 src/pulchra.hpp:945:30: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:28,668 945 | double x, y, z; 2023-09-17T12:06:28,669 | ^ 2023-09-17T12:06:28,670 src/pulchra.hpp:947:22: warning: unused variable ‘sec’ [-Wunused-variable] 2023-09-17T12:06:28,670 947 | int *sec; 2023-09-17T12:06:28,671 | ^~~ 2023-09-17T12:06:28,672 src/pulchra.hpp:948:79: warning: unused variable ‘tmp’ [-Wunused-variable] 2023-09-17T12:06:28,672 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2023-09-17T12:06:28,673 | ^~~ 2023-09-17T12:06:28,674 src/pulchra.hpp:949:25: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2023-09-17T12:06:28,674 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,675 | ^~~~~~~~~~~~~~~ 2023-09-17T12:06:28,676 src/pulchra.hpp:949:42: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2023-09-17T12:06:28,676 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,677 | ^~~~~~~ 2023-09-17T12:06:28,677 src/pulchra.hpp:949:51: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,678 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,678 | ^~~~~~~~~~ 2023-09-17T12:06:28,679 src/pulchra.hpp:953:23: warning: unused variable ‘inp’ [-Wunused-variable] 2023-09-17T12:06:28,680 953 | FILE *inp; 2023-09-17T12:06:28,680 | ^~~ 2023-09-17T12:06:28,681 src/pulchra.hpp:954:33: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:28,681 954 | int mnum, init, ok; 2023-09-17T12:06:28,682 | ^~ 2023-09-17T12:06:28,682 src/pulchra.hpp:958:24: warning: unused variable ‘w1’ [-Wunused-variable] 2023-09-17T12:06:28,683 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,683 | ^~ 2023-09-17T12:06:28,684 src/pulchra.hpp:958:28: warning: unused variable ‘w2’ [-Wunused-variable] 2023-09-17T12:06:28,685 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,685 | ^~ 2023-09-17T12:06:28,686 src/pulchra.hpp:958:32: warning: unused variable ‘w3’ [-Wunused-variable] 2023-09-17T12:06:28,686 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,687 | ^~ 2023-09-17T12:06:28,687 src/pulchra.hpp:960:21: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,688 960 | int mode, fcnt; 2023-09-17T12:06:28,688 | ^~~~ 2023-09-17T12:06:28,689 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2023-09-17T12:06:28,690 src/pulchra.hpp:1724:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:06:28,690 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,691 | ^ 2023-09-17T12:06:28,691 src/pulchra.hpp:1724:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:06:28,692 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,692 | ^ 2023-09-17T12:06:28,693 src/pulchra.hpp:1724:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:06:28,694 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,694 | ^~~~~ 2023-09-17T12:06:28,695 src/pulchra.hpp:1724:68: warning: unused variable ‘pro’ [-Wunused-variable] 2023-09-17T12:06:28,696 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,696 | ^~~ 2023-09-17T12:06:28,697 src/pulchra.hpp:1725:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:28,697 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,698 | ^~~~~ 2023-09-17T12:06:28,699 src/pulchra.hpp:1725:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:28,699 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,700 | ^~~~~ 2023-09-17T12:06:28,700 src/pulchra.hpp:1725:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:28,701 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,702 | ^~~ 2023-09-17T12:06:28,703 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2023-09-17T12:06:28,703 src/pulchra.hpp:1852:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:06:28,704 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,705 | ^ 2023-09-17T12:06:28,705 src/pulchra.hpp:1852:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:06:28,706 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,706 | ^ 2023-09-17T12:06:28,707 src/pulchra.hpp:1852:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:06:28,707 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,708 | ^~~~~ 2023-09-17T12:06:28,708 src/pulchra.hpp:1852:68: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,709 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,709 | ^~~ 2023-09-17T12:06:28,710 src/pulchra.hpp:1853:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:28,710 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,711 | ^~~~~ 2023-09-17T12:06:28,711 src/pulchra.hpp:1853:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:28,712 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,713 | ^~~~~ 2023-09-17T12:06:28,714 src/pulchra.hpp:1853:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:28,754 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,754 | ^~~ 2023-09-17T12:06:28,755 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2023-09-17T12:06:28,756 src/pulchra.hpp:2023:26: warning: unused variable ‘cacoords’ [-Wunused-variable] 2023-09-17T12:06:28,756 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,757 | ^~~~~~~~ 2023-09-17T12:06:28,758 src/pulchra.hpp:2023:38: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2023-09-17T12:06:28,758 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,759 | ^~~~~~~~~ 2023-09-17T12:06:28,760 src/pulchra.hpp:2023:51: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2023-09-17T12:06:28,760 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,761 | ^~~~~~~ 2023-09-17T12:06:28,761 src/pulchra.hpp:2024:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,762 2024 | double x1, y1, z1; 2023-09-17T12:06:28,763 | ^~ 2023-09-17T12:06:28,763 src/pulchra.hpp:2024:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,764 2024 | double x1, y1, z1; 2023-09-17T12:06:28,764 | ^~ 2023-09-17T12:06:28,765 src/pulchra.hpp:2024:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,766 2024 | double x1, y1, z1; 2023-09-17T12:06:28,766 | ^~ 2023-09-17T12:06:28,767 src/pulchra.hpp:2028:24: warning: unused variable ‘x5’ [-Wunused-variable] 2023-09-17T12:06:28,767 2028 | double x5, y5, z5; 2023-09-17T12:06:28,768 | ^~ 2023-09-17T12:06:28,768 src/pulchra.hpp:2028:28: warning: unused variable ‘y5’ [-Wunused-variable] 2023-09-17T12:06:28,769 2028 | double x5, y5, z5; 2023-09-17T12:06:28,771 | ^~ 2023-09-17T12:06:28,984 src/pulchra.hpp:2028:32: warning: unused variable ‘z5’ [-Wunused-variable] 2023-09-17T12:06:28,984 2028 | double x5, y5, z5; 2023-09-17T12:06:28,985 | ^~ 2023-09-17T12:06:28,985 src/pulchra.hpp:2029:24: warning: unused variable ‘r14’ [-Wunused-variable] 2023-09-17T12:06:28,986 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,986 | ^~~ 2023-09-17T12:06:28,987 src/pulchra.hpp:2029:29: warning: unused variable ‘r13_1’ [-Wunused-variable] 2023-09-17T12:06:28,987 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,988 | ^~~~~ 2023-09-17T12:06:28,988 src/pulchra.hpp:2029:36: warning: unused variable ‘r13_2’ [-Wunused-variable] 2023-09-17T12:06:28,989 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,989 | ^~~~~ 2023-09-17T12:06:28,990 src/pulchra.hpp:2030:24: warning: unused variable ‘dx’ [-Wunused-variable] 2023-09-17T12:06:28,990 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,991 | ^~ 2023-09-17T12:06:28,991 src/pulchra.hpp:2030:28: warning: unused variable ‘dy’ [-Wunused-variable] 2023-09-17T12:06:28,992 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,992 | ^~ 2023-09-17T12:06:28,993 src/pulchra.hpp:2030:32: warning: unused variable ‘dz’ [-Wunused-variable] 2023-09-17T12:06:28,993 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,994 | ^~ 2023-09-17T12:06:28,994 src/pulchra.hpp:2030:36: warning: unused variable ‘dd’ [-Wunused-variable] 2023-09-17T12:06:28,995 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,996 | ^~ 2023-09-17T12:06:28,996 src/pulchra.hpp:2031:29: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,997 2031 | double hit, besthit; 2023-09-17T12:06:28,997 | ^~~~~~~ 2023-09-17T12:06:28,998 src/pulchra.hpp:2032:21: warning: unused variable ‘exvol’ [-Wunused-variable] 2023-09-17T12:06:28,999 2032 | int exvol, bestpos; 2023-09-17T12:06:29,000 | ^~~~~ 2023-09-17T12:06:29,000 src/pulchra.hpp:2034:24: warning: unused variable ‘rmsd’ [-Wunused-variable] 2023-09-17T12:06:29,001 2034 | double rmsd, total; 2023-09-17T12:06:29,002 | ^~~~ 2023-09-17T12:06:29,003 src/pulchra.hpp:2034:30: warning: unused variable ‘total’ [-Wunused-variable] 2023-09-17T12:06:29,003 2034 | double rmsd, total; 2023-09-17T12:06:29,004 | ^~~~~ 2023-09-17T12:06:29,005 src/pulchra.hpp:2036:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:06:29,005 2036 | int nsc, nca; 2023-09-17T12:06:29,006 | ^~~ 2023-09-17T12:06:29,007 src/pulchra.hpp:2037:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:06:29,007 2037 | double cax, cay, caz; 2023-09-17T12:06:29,008 | ^~~ 2023-09-17T12:06:29,008 src/pulchra.hpp:2037:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:06:29,009 2037 | double cax, cay, caz; 2023-09-17T12:06:29,010 | ^~~ 2023-09-17T12:06:29,010 src/pulchra.hpp:2037:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:06:29,011 2037 | double cax, cay, caz; 2023-09-17T12:06:29,012 | ^~~ 2023-09-17T12:06:29,012 src/pulchra.hpp:2039:22: warning: unused variable ‘scn’ [-Wunused-variable] 2023-09-17T12:06:29,013 2039 | char scn[12][4]; 2023-09-17T12:06:29,014 | ^~~ 2023-09-17T12:06:29,014 src/pulchra.hpp:2040:21: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:29,015 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,016 | ^~ 2023-09-17T12:06:29,016 src/pulchra.hpp:2040:25: warning: unused variable ‘last_a’ [-Wunused-variable] 2023-09-17T12:06:29,017 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,017 | ^~~~~~ 2023-09-17T12:06:29,018 src/pulchra.hpp:2040:33: warning: unused variable ‘last_b’ [-Wunused-variable] 2023-09-17T12:06:29,018 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,019 | ^~~~~~ 2023-09-17T12:06:29,019 src/pulchra.hpp:2040:41: warning: unused variable ‘last_c’ [-Wunused-variable] 2023-09-17T12:06:29,020 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,021 | ^~~~~~ 2023-09-17T12:06:29,021 src/pulchra.hpp:2040:49: warning: unused variable ‘last_d’ [-Wunused-variable] 2023-09-17T12:06:29,022 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,022 | ^~~~~~ 2023-09-17T12:06:29,023 src/pulchra.hpp:2040:57: warning: unused variable ‘jpos’ [-Wunused-variable] 2023-09-17T12:06:29,023 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:29,024 | ^~~~ 2023-09-17T12:06:29,025 src/pulchra.hpp:2041:21: warning: unused variable ‘jx’ [-Wunused-variable] 2023-09-17T12:06:29,025 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,026 | ^~ 2023-09-17T12:06:29,026 src/pulchra.hpp:2041:25: warning: unused variable ‘jy’ [-Wunused-variable] 2023-09-17T12:06:29,027 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,028 | ^~ 2023-09-17T12:06:29,028 src/pulchra.hpp:2041:29: warning: unused variable ‘jz’ [-Wunused-variable] 2023-09-17T12:06:29,029 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,029 | ^~ 2023-09-17T12:06:29,030 src/pulchra.hpp:2041:33: warning: unused variable ‘jxi’ [-Wunused-variable] 2023-09-17T12:06:29,031 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,032 | ^~~ 2023-09-17T12:06:29,032 src/pulchra.hpp:2041:38: warning: unused variable ‘jyi’ [-Wunused-variable] 2023-09-17T12:06:29,033 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,033 | ^~~ 2023-09-17T12:06:29,034 src/pulchra.hpp:2041:43: warning: unused variable ‘jzi’ [-Wunused-variable] 2023-09-17T12:06:29,035 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,035 | ^~~ 2023-09-17T12:06:29,036 src/pulchra.hpp:2041:48: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:29,036 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,037 | ^~~~~ 2023-09-17T12:06:29,038 src/pulchra.hpp:2041:55: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:29,038 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,039 | ^~~~~ 2023-09-17T12:06:29,040 src/pulchra.hpp:2041:62: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:29,041 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,041 | ^~~ 2023-09-17T12:06:29,042 src/pulchra.hpp:2041:67: warning: unused variable ‘jm’ [-Wunused-variable] 2023-09-17T12:06:29,042 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:29,043 | ^~ 2023-09-17T12:06:29,043 src/pulchra.hpp:2042:27: warning: unused variable ‘bestrot’ [-Wunused-variable] 2023-09-17T12:06:29,044 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:29,044 | ^~~~~~~ 2023-09-17T12:06:29,045 src/pulchra.hpp:2042:36: warning: unused variable ‘minexvol’ [-Wunused-variable] 2023-09-17T12:06:29,046 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:29,046 | ^~~~~~~~ 2023-09-17T12:06:29,047 src/pulchra.hpp:2042:46: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,047 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:29,048 | ^~~~~~~~ 2023-09-17T12:06:29,048 src/pulchra.hpp:2042:56: warning: unused variable ‘rtried’ [-Wunused-variable] 2023-09-17T12:06:29,049 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:29,050 | ^~~~~~ 2023-09-17T12:06:29,050 src/pulchra.hpp:2044:24: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2023-09-17T12:06:29,051 2044 | double sort_rot[100][2]; 2023-09-17T12:06:29,052 | ^~~~~~~~ 2023-09-17T12:06:29,052 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2023-09-17T12:06:29,053 src/pulchra.hpp:2264:30: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:29,053 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:29,054 | ^ 2023-09-17T12:06:29,056 src/pulchra.hpp:2264:33: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:29,057 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:29,057 | ^ 2023-09-17T12:06:29,058 src/pulchra.hpp:2264:36: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:29,059 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:29,060 | ^ 2023-09-17T12:06:29,060 src/pulchra.hpp:2265:38: warning: unused variable ‘iter’ [-Wunused-variable] 2023-09-17T12:06:29,061 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:06:29,062 | ^~~~ 2023-09-17T12:06:29,062 src/pulchra.hpp:2265:44: warning: unused variable ‘maxcon’ [-Wunused-variable] 2023-09-17T12:06:29,063 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:06:29,063 | ^~~~~~ 2023-09-17T12:06:29,064 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:06:29,065 src/pulchra.hpp:2374:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:06:29,065 2374 | int i, j, x, y, z; 2023-09-17T12:06:29,066 | ^ 2023-09-17T12:06:29,067 src/pulchra.hpp:2374:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:29,067 2374 | int i, j, x, y, z; 2023-09-17T12:06:29,068 | ^ 2023-09-17T12:06:29,069 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2023-09-17T12:06:29,069 src/pulchra.hpp:2440:24: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,070 2440 | double min[3], max[3]; 2023-09-17T12:06:29,070 | ^~~ 2023-09-17T12:06:29,071 src/pulchra.hpp:2440:32: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,072 2440 | double min[3], max[3]; 2023-09-17T12:06:29,072 | ^~~ 2023-09-17T12:06:29,073 src/pulchra.hpp:2446:36: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:29,073 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:29,074 | ^ 2023-09-17T12:06:29,074 src/pulchra.hpp:2446:39: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:29,075 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:29,076 | ^ 2023-09-17T12:06:29,077 src/pulchra.hpp:2446:42: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:29,077 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:29,078 | ^ 2023-09-17T12:06:29,078 src/pulchra.hpp:2447:21: warning: unused variable ‘ii’ [-Wunused-variable] 2023-09-17T12:06:29,079 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:29,080 | ^~ 2023-09-17T12:06:29,080 src/pulchra.hpp:2447:25: warning: unused variable ‘jj’ [-Wunused-variable] 2023-09-17T12:06:29,081 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:29,081 | ^~ 2023-09-17T12:06:29,082 src/pulchra.hpp:2447:29: warning: unused variable ‘kk’ [-Wunused-variable] 2023-09-17T12:06:29,082 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:29,083 | ^~ 2023-09-17T12:06:29,083 src/pulchra.hpp:2450:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:06:29,084 2450 | int nsc, nca; 2023-09-17T12:06:29,085 | ^~~ 2023-09-17T12:06:29,085 src/pulchra.hpp:2451:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:06:29,086 2451 | double cax, cay, caz; 2023-09-17T12:06:29,087 | ^~~ 2023-09-17T12:06:29,087 src/pulchra.hpp:2451:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:06:29,088 2451 | double cax, cay, caz; 2023-09-17T12:06:29,089 | ^~~ 2023-09-17T12:06:29,089 src/pulchra.hpp:2451:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:06:29,090 2451 | double cax, cay, caz; 2023-09-17T12:06:29,091 | ^~~ 2023-09-17T12:06:29,091 src/pulchra.hpp:2453:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,092 2453 | double x1, y1, z1; 2023-09-17T12:06:29,093 | ^~ 2023-09-17T12:06:29,093 src/pulchra.hpp:2453:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,094 2453 | double x1, y1, z1; 2023-09-17T12:06:29,094 | ^~ 2023-09-17T12:06:29,095 src/pulchra.hpp:2453:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,096 2453 | double x1, y1, z1; 2023-09-17T12:06:29,097 | ^~ 2023-09-17T12:06:29,098 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2023-09-17T12:06:29,098 src/pulchra.hpp:2732:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:06:29,099 2732 | int i; 2023-09-17T12:06:29,099 | ^ 2023-09-17T12:06:29,100 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2023-09-17T12:06:29,101 src/pulchra.hpp:2828:42: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2023-09-17T12:06:29,101 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2023-09-17T12:06:29,102 | ^~~~~~~~~ 2023-09-17T12:06:29,102 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2023-09-17T12:06:29,103 src/pulchra.hpp:3042:24: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-17T12:06:29,104 3042 | int i, k, best; 2023-09-17T12:06:29,104 | ^ 2023-09-17T12:06:29,105 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2023-09-17T12:06:29,105 src/pulchra.hpp:3116:27: warning: unused variable ‘chain_length’ [-Wunused-variable] 2023-09-17T12:06:29,106 3116 | int const chain_length = chain->nres; 2023-09-17T12:06:29,106 | ^~~~~~~~~~~~ 2023-09-17T12:06:29,107 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2023-09-17T12:06:29,108 src/pulchra.hpp:3315:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘std::chrono::duration::rep’ {aka ‘long long int’} [-Wformat=] 2023-09-17T12:06:29,108 3315 | "Done. Reconstruction finished in %ld s.\n", 2023-09-17T12:06:29,109 | ~~^ 2023-09-17T12:06:29,110 | | 2023-09-17T12:06:29,110 | long int 2023-09-17T12:06:29,111 | %lld 2023-09-17T12:06:29,112 3316 | std::chrono::duration_cast(time1 - time0) 2023-09-17T12:06:29,112 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:06:29,113 3317 | .count()); 2023-09-17T12:06:29,114 | ~~~~~~~~ 2023-09-17T12:06:29,114 | | 2023-09-17T12:06:29,115 | std::chrono::duration::rep {aka long long int} 2023-09-17T12:06:29,116 src/pulchra.hpp:3145:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:06:29,116 3145 | char buf[100]; 2023-09-17T12:06:29,117 | ^~~ 2023-09-17T12:06:29,117 src/pulchra.hpp:3146:37: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:29,118 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2023-09-17T12:06:29,119 | ^~~~~~~~ 2023-09-17T12:06:29,119 src/pulchra.hpp:3147:23: warning: unused variable ‘ptr’ [-Wunused-variable] 2023-09-17T12:06:29,120 3147 | char *ptr, out_name[1000]; 2023-09-17T12:06:29,121 | ^~~ 2023-09-17T12:06:29,121 src/pulchra.hpp:3147:28: warning: unused variable ‘out_name’ [-Wunused-variable] 2023-09-17T12:06:29,122 3147 | char *ptr, out_name[1000]; 2023-09-17T12:06:29,123 | ^~~~~~~~ 2023-09-17T12:06:48,730 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.1 -Isrc -I/tmp/pip-build-env-gxbbu8or/overlay/local/lib/python3.11/dist-packages/pybind11/include -I/usr/include/python3.11 -c bindings/python/pypulchra_bindings.cpp -o build/temp.linux-armv7l-cpython-311/bindings/python/pypulchra_bindings.o -fvisibility=hidden -g0 -std=c++14 -static 2023-09-17T12:07:05,951 arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DVERSION_INFO=1.0.1 -Isrc -I/tmp/pip-build-env-gxbbu8or/overlay/local/lib/python3.11/dist-packages/pybind11/include -I/usr/include/python3.11 -c src/pulchra.cpp -o build/temp.linux-armv7l-cpython-311/src/pulchra.o -fvisibility=hidden -g0 -std=c++14 -static 2023-09-17T12:07:14,456 In file included from src/pulchra.cpp:20: 2023-09-17T12:07:14,457 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2023-09-17T12:07:14,458 src/pulchra.hpp:653:69: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-17T12:07:14,458 653 | res->type = AA_NUMS[pusetseq(resname)]; 2023-09-17T12:07:14,459 | ~~~~~~~~^~~~~~~~~ 2023-09-17T12:07:14,472 src/pulchra.hpp:594:22: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,473 594 | char version; 2023-09-17T12:07:14,473 | ^~~~~~~ 2023-09-17T12:07:14,474 src/pulchra.hpp:595:60: warning: unused variable ‘num’ [-Wunused-variable] 2023-09-17T12:07:14,474 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:14,475 | ^~~ 2023-09-17T12:07:14,476 src/pulchra.hpp:595:77: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,476 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:14,477 | ^ 2023-09-17T12:07:14,478 src/pulchra.hpp:595:80: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:14,479 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:14,479 | ^ 2023-09-17T12:07:14,480 src/pulchra.hpp:597:28: warning: unused variable ‘cc’ [-Wunused-variable] 2023-09-17T12:07:14,481 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:14,481 | ^~ 2023-09-17T12:07:14,482 src/pulchra.hpp:597:32: warning: unused variable ‘nres’ [-Wunused-variable] 2023-09-17T12:07:14,482 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:14,483 | ^~~~ 2023-09-17T12:07:14,484 src/pulchra.hpp:597:38: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:14,484 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:14,485 | ^~ 2023-09-17T12:07:14,486 src/pulchra.hpp:597:42: warning: unused variable ‘natom’ [-Wunused-variable] 2023-09-17T12:07:14,486 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:14,487 | ^~~~~ 2023-09-17T12:07:14,488 src/pulchra.hpp:602:24: warning: unused variable ‘dist’ [-Wunused-variable] 2023-09-17T12:07:14,488 602 | double dist; 2023-09-17T12:07:14,489 | ^~~~ 2023-09-17T12:07:14,490 src/pulchra.hpp:603:31: warning: unused variable ‘bin’ [-Wunused-variable] 2023-09-17T12:07:14,490 603 | unsigned char bin; 2023-09-17T12:07:14,491 | ^~~ 2023-09-17T12:07:14,491 src/pulchra.hpp:604:21: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,492 604 | int warn = 0; 2023-09-17T12:07:14,492 | ^~~~ 2023-09-17T12:07:14,493 src/pulchra.hpp:605:24: warning: unused variable ‘cutoff’ [-Wunused-variable] 2023-09-17T12:07:14,493 605 | double cutoff; 2023-09-17T12:07:14,494 | ^~~~~~ 2023-09-17T12:07:14,501 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2023-09-17T12:07:14,501 src/pulchra.hpp:775:24: warning: unused variable ‘theta0’ [-Wunused-variable] 2023-09-17T12:07:14,502 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,502 | ^~~~~~ 2023-09-17T12:07:14,503 src/pulchra.hpp:775:32: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:07:14,503 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,504 | ^~~~ 2023-09-17T12:07:14,504 src/pulchra.hpp:775:38: warning: unused variable ‘th’ [-Wunused-variable] 2023-09-17T12:07:14,505 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,505 | ^~ 2023-09-17T12:07:14,506 src/pulchra.hpp:775:42: warning: unused variable ‘aa’ [-Wunused-variable] 2023-09-17T12:07:14,507 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,507 | ^~ 2023-09-17T12:07:14,508 src/pulchra.hpp:775:46: warning: unused variable ‘bb’ [-Wunused-variable] 2023-09-17T12:07:14,509 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,510 | ^~ 2023-09-17T12:07:14,510 src/pulchra.hpp:775:50: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-17T12:07:14,511 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,512 | ^~ 2023-09-17T12:07:14,512 src/pulchra.hpp:776:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:07:14,513 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,514 | ^~~ 2023-09-17T12:07:14,514 src/pulchra.hpp:776:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:07:14,515 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,516 | ^~~ 2023-09-17T12:07:14,516 src/pulchra.hpp:776:34: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:07:14,517 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,518 | ^~~ 2023-09-17T12:07:14,518 src/pulchra.hpp:776:39: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:07:14,519 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,520 | ^~ 2023-09-17T12:07:14,520 src/pulchra.hpp:776:43: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:07:14,521 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,522 | ^~ 2023-09-17T12:07:14,522 src/pulchra.hpp:776:53: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:07:14,523 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,524 | ^~ 2023-09-17T12:07:14,525 src/pulchra.hpp:776:60: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:07:14,525 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,526 | ^~ 2023-09-17T12:07:14,526 src/pulchra.hpp:777:24: warning: unused variable ‘adiff’ [-Wunused-variable] 2023-09-17T12:07:14,527 777 | double adiff[3], bdiff[3]; 2023-09-17T12:07:14,527 | ^~~~~ 2023-09-17T12:07:14,528 src/pulchra.hpp:777:34: warning: unused variable ‘bdiff’ [-Wunused-variable] 2023-09-17T12:07:14,528 777 | double adiff[3], bdiff[3]; 2023-09-17T12:07:14,529 | ^~~~~ 2023-09-17T12:07:14,529 src/pulchra.hpp:778:24: warning: unused variable ‘deriv’ [-Wunused-variable] 2023-09-17T12:07:14,530 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,530 | ^~~~~ 2023-09-17T12:07:14,531 src/pulchra.hpp:778:38: warning: unused variable ‘dtheta’ [-Wunused-variable] 2023-09-17T12:07:14,531 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,532 | ^~~~~~ 2023-09-17T12:07:14,532 src/pulchra.hpp:778:46: warning: unused variable ‘len1’ [-Wunused-variable] 2023-09-17T12:07:14,533 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,533 | ^~~~ 2023-09-17T12:07:14,534 src/pulchra.hpp:778:52: warning: unused variable ‘len2’ [-Wunused-variable] 2023-09-17T12:07:14,535 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,535 | ^~~~ 2023-09-17T12:07:14,536 src/pulchra.hpp:779:24: warning: unused variable ‘dx1’ [-Wunused-variable] 2023-09-17T12:07:14,536 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,537 | ^~~ 2023-09-17T12:07:14,538 src/pulchra.hpp:779:29: warning: unused variable ‘dy1’ [-Wunused-variable] 2023-09-17T12:07:14,538 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,539 | ^~~ 2023-09-17T12:07:14,539 src/pulchra.hpp:779:34: warning: unused variable ‘dz1’ [-Wunused-variable] 2023-09-17T12:07:14,540 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,541 | ^~~ 2023-09-17T12:07:14,541 src/pulchra.hpp:780:24: warning: unused variable ‘dx2’ [-Wunused-variable] 2023-09-17T12:07:14,542 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,542 | ^~~ 2023-09-17T12:07:14,543 src/pulchra.hpp:780:29: warning: unused variable ‘dy2’ [-Wunused-variable] 2023-09-17T12:07:14,544 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,544 | ^~~ 2023-09-17T12:07:14,545 src/pulchra.hpp:780:34: warning: unused variable ‘dz2’ [-Wunused-variable] 2023-09-17T12:07:14,546 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,546 | ^~~ 2023-09-17T12:07:14,547 src/pulchra.hpp:781:24: warning: unused variable ‘dx3’ [-Wunused-variable] 2023-09-17T12:07:14,548 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,548 | ^~~ 2023-09-17T12:07:14,549 src/pulchra.hpp:781:29: warning: unused variable ‘dy3’ [-Wunused-variable] 2023-09-17T12:07:14,550 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,550 | ^~~ 2023-09-17T12:07:14,551 src/pulchra.hpp:781:34: warning: unused variable ‘dz3’ [-Wunused-variable] 2023-09-17T12:07:14,551 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,552 | ^~~ 2023-09-17T12:07:14,553 src/pulchra.hpp:782:24: warning: unused variable ‘vx1’ [-Wunused-variable] 2023-09-17T12:07:14,553 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,554 | ^~~ 2023-09-17T12:07:14,554 src/pulchra.hpp:782:29: warning: unused variable ‘vy1’ [-Wunused-variable] 2023-09-17T12:07:14,555 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,555 | ^~~ 2023-09-17T12:07:14,556 src/pulchra.hpp:782:34: warning: unused variable ‘vz1’ [-Wunused-variable] 2023-09-17T12:07:14,556 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,557 | ^~~ 2023-09-17T12:07:14,557 src/pulchra.hpp:783:24: warning: unused variable ‘vx2’ [-Wunused-variable] 2023-09-17T12:07:14,558 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,558 | ^~~ 2023-09-17T12:07:14,559 src/pulchra.hpp:783:29: warning: unused variable ‘vy2’ [-Wunused-variable] 2023-09-17T12:07:14,560 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,560 | ^~~ 2023-09-17T12:07:14,561 src/pulchra.hpp:783:34: warning: unused variable ‘vz2’ [-Wunused-variable] 2023-09-17T12:07:14,561 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,562 | ^~~ 2023-09-17T12:07:14,562 src/pulchra.hpp:784:24: warning: unused variable ‘vx3’ [-Wunused-variable] 2023-09-17T12:07:14,563 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,564 | ^~~ 2023-09-17T12:07:14,565 src/pulchra.hpp:784:29: warning: unused variable ‘vy3’ [-Wunused-variable] 2023-09-17T12:07:14,565 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,566 | ^~~ 2023-09-17T12:07:14,566 src/pulchra.hpp:784:34: warning: unused variable ‘vz3’ [-Wunused-variable] 2023-09-17T12:07:14,567 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,568 | ^~~ 2023-09-17T12:07:14,568 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2023-09-17T12:07:14,569 src/pulchra.hpp:937:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:07:14,570 937 | char buf[1000]; 2023-09-17T12:07:14,571 | ^~~ 2023-09-17T12:07:14,571 src/pulchra.hpp:938:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:14,572 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,572 | ^ 2023-09-17T12:07:14,573 src/pulchra.hpp:938:27: warning: unused variable ‘hx’ [-Wunused-variable] 2023-09-17T12:07:14,574 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,574 | ^~ 2023-09-17T12:07:14,575 src/pulchra.hpp:938:31: warning: unused variable ‘my_iter’ [-Wunused-variable] 2023-09-17T12:07:14,576 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,576 | ^~~~~~~ 2023-09-17T12:07:14,577 src/pulchra.hpp:939:46: warning: unused variable ‘dist2’ [-Wunused-variable] 2023-09-17T12:07:14,578 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,578 | ^~~~~ 2023-09-17T12:07:14,579 src/pulchra.hpp:939:53: warning: unused variable ‘dist3’ [-Wunused-variable] 2023-09-17T12:07:14,580 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,580 | ^~~~~ 2023-09-17T12:07:14,581 src/pulchra.hpp:939:67: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,582 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,582 | ^~~~~~ 2023-09-17T12:07:14,583 src/pulchra.hpp:940:31: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2023-09-17T12:07:14,584 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,584 | ^~~~~~~~~ 2023-09-17T12:07:14,585 src/pulchra.hpp:940:42: warning: unused variable ‘grad’ [-Wunused-variable] 2023-09-17T12:07:14,585 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,586 | ^~~~ 2023-09-17T12:07:14,586 src/pulchra.hpp:940:48: warning: unused variable ‘alpha’ [-Wunused-variable] 2023-09-17T12:07:14,587 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,587 | ^~~~~ 2023-09-17T12:07:14,588 src/pulchra.hpp:942:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:07:14,588 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,589 | ^~~ 2023-09-17T12:07:14,589 src/pulchra.hpp:942:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:07:14,590 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,590 | ^~~ 2023-09-17T12:07:14,591 src/pulchra.hpp:942:50: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:07:14,591 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,592 | ^~~~ 2023-09-17T12:07:14,592 src/pulchra.hpp:942:56: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:07:14,593 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,594 | ^~~ 2023-09-17T12:07:14,594 src/pulchra.hpp:942:61: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:07:14,595 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,596 | ^~ 2023-09-17T12:07:14,597 src/pulchra.hpp:942:65: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:07:14,597 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,598 | ^~ 2023-09-17T12:07:14,598 src/pulchra.hpp:943:40: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2023-09-17T12:07:14,599 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:07:14,599 | ^~~~~~~ 2023-09-17T12:07:14,600 src/pulchra.hpp:943:49: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-17T12:07:14,601 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:07:14,601 | ^~~ 2023-09-17T12:07:14,602 src/pulchra.hpp:944:24: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:07:14,602 944 | double f0[3], f2[3]; 2023-09-17T12:07:14,603 | ^~ 2023-09-17T12:07:14,604 src/pulchra.hpp:944:31: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:07:14,605 944 | double f0[3], f2[3]; 2023-09-17T12:07:14,605 | ^~ 2023-09-17T12:07:14,606 src/pulchra.hpp:945:24: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,607 945 | double x, y, z; 2023-09-17T12:07:14,607 | ^ 2023-09-17T12:07:14,608 src/pulchra.hpp:945:27: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,608 945 | double x, y, z; 2023-09-17T12:07:14,609 | ^ 2023-09-17T12:07:14,609 src/pulchra.hpp:945:30: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,610 945 | double x, y, z; 2023-09-17T12:07:14,610 | ^ 2023-09-17T12:07:14,611 src/pulchra.hpp:947:22: warning: unused variable ‘sec’ [-Wunused-variable] 2023-09-17T12:07:14,611 947 | int *sec; 2023-09-17T12:07:14,612 | ^~~ 2023-09-17T12:07:14,612 src/pulchra.hpp:948:79: warning: unused variable ‘tmp’ [-Wunused-variable] 2023-09-17T12:07:14,613 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2023-09-17T12:07:14,613 | ^~~ 2023-09-17T12:07:14,614 src/pulchra.hpp:949:25: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2023-09-17T12:07:14,614 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,615 | ^~~~~~~~~~~~~~~ 2023-09-17T12:07:14,616 src/pulchra.hpp:949:42: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2023-09-17T12:07:14,616 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,617 | ^~~~~~~ 2023-09-17T12:07:14,617 src/pulchra.hpp:949:51: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,618 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,618 | ^~~~~~~~~~ 2023-09-17T12:07:14,619 src/pulchra.hpp:953:23: warning: unused variable ‘inp’ [-Wunused-variable] 2023-09-17T12:07:14,620 953 | FILE *inp; 2023-09-17T12:07:14,620 | ^~~ 2023-09-17T12:07:14,621 src/pulchra.hpp:954:33: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:14,622 954 | int mnum, init, ok; 2023-09-17T12:07:14,622 | ^~ 2023-09-17T12:07:14,623 src/pulchra.hpp:958:24: warning: unused variable ‘w1’ [-Wunused-variable] 2023-09-17T12:07:14,624 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,625 | ^~ 2023-09-17T12:07:14,625 src/pulchra.hpp:958:28: warning: unused variable ‘w2’ [-Wunused-variable] 2023-09-17T12:07:14,626 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,626 | ^~ 2023-09-17T12:07:14,627 src/pulchra.hpp:958:32: warning: unused variable ‘w3’ [-Wunused-variable] 2023-09-17T12:07:14,628 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,628 | ^~ 2023-09-17T12:07:14,629 src/pulchra.hpp:960:21: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,629 960 | int mode, fcnt; 2023-09-17T12:07:14,630 | ^~~~ 2023-09-17T12:07:14,631 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2023-09-17T12:07:14,631 src/pulchra.hpp:1724:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:07:14,632 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,633 | ^ 2023-09-17T12:07:14,633 src/pulchra.hpp:1724:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:07:14,634 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,635 | ^ 2023-09-17T12:07:14,635 src/pulchra.hpp:1724:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:07:14,636 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,636 | ^~~~~ 2023-09-17T12:07:14,637 src/pulchra.hpp:1724:68: warning: unused variable ‘pro’ [-Wunused-variable] 2023-09-17T12:07:14,637 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,638 | ^~~ 2023-09-17T12:07:14,638 src/pulchra.hpp:1725:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,639 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,639 | ^~~~~ 2023-09-17T12:07:14,640 src/pulchra.hpp:1725:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,640 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,641 | ^~~~~ 2023-09-17T12:07:14,641 src/pulchra.hpp:1725:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,642 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,642 | ^~~ 2023-09-17T12:07:14,643 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2023-09-17T12:07:14,644 src/pulchra.hpp:1852:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:07:14,644 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,645 | ^ 2023-09-17T12:07:14,645 src/pulchra.hpp:1852:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:07:14,646 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,647 | ^ 2023-09-17T12:07:14,647 src/pulchra.hpp:1852:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:07:14,648 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,648 | ^~~~~ 2023-09-17T12:07:14,649 src/pulchra.hpp:1852:68: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,650 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,650 | ^~~ 2023-09-17T12:07:14,651 src/pulchra.hpp:1853:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,651 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,652 | ^~~~~ 2023-09-17T12:07:14,653 src/pulchra.hpp:1853:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,653 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,654 | ^~~~~ 2023-09-17T12:07:14,655 src/pulchra.hpp:1853:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,655 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,656 | ^~~ 2023-09-17T12:07:14,666 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2023-09-17T12:07:14,667 src/pulchra.hpp:2023:26: warning: unused variable ‘cacoords’ [-Wunused-variable] 2023-09-17T12:07:14,668 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,668 | ^~~~~~~~ 2023-09-17T12:07:14,669 src/pulchra.hpp:2023:38: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2023-09-17T12:07:14,670 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,671 | ^~~~~~~~~ 2023-09-17T12:07:14,671 src/pulchra.hpp:2023:51: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2023-09-17T12:07:14,672 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,672 | ^~~~~~~ 2023-09-17T12:07:14,673 src/pulchra.hpp:2024:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,673 2024 | double x1, y1, z1; 2023-09-17T12:07:14,674 | ^~ 2023-09-17T12:07:14,674 src/pulchra.hpp:2024:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,675 2024 | double x1, y1, z1; 2023-09-17T12:07:14,675 | ^~ 2023-09-17T12:07:14,676 src/pulchra.hpp:2024:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,676 2024 | double x1, y1, z1; 2023-09-17T12:07:14,677 | ^~ 2023-09-17T12:07:14,677 src/pulchra.hpp:2028:24: warning: unused variable ‘x5’ [-Wunused-variable] 2023-09-17T12:07:14,678 2028 | double x5, y5, z5; 2023-09-17T12:07:14,678 | ^~ 2023-09-17T12:07:14,679 src/pulchra.hpp:2028:28: warning: unused variable ‘y5’ [-Wunused-variable] 2023-09-17T12:07:14,679 2028 | double x5, y5, z5; 2023-09-17T12:07:14,680 | ^~ 2023-09-17T12:07:14,681 src/pulchra.hpp:2028:32: warning: unused variable ‘z5’ [-Wunused-variable] 2023-09-17T12:07:14,682 2028 | double x5, y5, z5; 2023-09-17T12:07:14,682 | ^~ 2023-09-17T12:07:14,683 src/pulchra.hpp:2029:24: warning: unused variable ‘r14’ [-Wunused-variable] 2023-09-17T12:07:14,683 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,684 | ^~~ 2023-09-17T12:07:14,685 src/pulchra.hpp:2029:29: warning: unused variable ‘r13_1’ [-Wunused-variable] 2023-09-17T12:07:14,685 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,686 | ^~~~~ 2023-09-17T12:07:14,686 src/pulchra.hpp:2029:36: warning: unused variable ‘r13_2’ [-Wunused-variable] 2023-09-17T12:07:14,687 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,688 | ^~~~~ 2023-09-17T12:07:14,688 src/pulchra.hpp:2030:24: warning: unused variable ‘dx’ [-Wunused-variable] 2023-09-17T12:07:14,689 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,690 | ^~ 2023-09-17T12:07:14,690 src/pulchra.hpp:2030:28: warning: unused variable ‘dy’ [-Wunused-variable] 2023-09-17T12:07:14,691 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,691 | ^~ 2023-09-17T12:07:14,692 src/pulchra.hpp:2030:32: warning: unused variable ‘dz’ [-Wunused-variable] 2023-09-17T12:07:14,692 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,693 | ^~ 2023-09-17T12:07:14,694 src/pulchra.hpp:2030:36: warning: unused variable ‘dd’ [-Wunused-variable] 2023-09-17T12:07:14,694 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,695 | ^~ 2023-09-17T12:07:14,695 src/pulchra.hpp:2031:29: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,696 2031 | double hit, besthit; 2023-09-17T12:07:14,697 | ^~~~~~~ 2023-09-17T12:07:14,697 src/pulchra.hpp:2032:21: warning: unused variable ‘exvol’ [-Wunused-variable] 2023-09-17T12:07:14,698 2032 | int exvol, bestpos; 2023-09-17T12:07:14,698 | ^~~~~ 2023-09-17T12:07:14,699 src/pulchra.hpp:2034:24: warning: unused variable ‘rmsd’ [-Wunused-variable] 2023-09-17T12:07:14,699 2034 | double rmsd, total; 2023-09-17T12:07:14,700 | ^~~~ 2023-09-17T12:07:14,700 src/pulchra.hpp:2034:30: warning: unused variable ‘total’ [-Wunused-variable] 2023-09-17T12:07:14,701 2034 | double rmsd, total; 2023-09-17T12:07:14,701 | ^~~~~ 2023-09-17T12:07:14,702 src/pulchra.hpp:2036:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:07:14,702 2036 | int nsc, nca; 2023-09-17T12:07:14,703 | ^~~ 2023-09-17T12:07:14,703 src/pulchra.hpp:2037:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:07:14,704 2037 | double cax, cay, caz; 2023-09-17T12:07:14,704 | ^~~ 2023-09-17T12:07:14,705 src/pulchra.hpp:2037:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:07:14,705 2037 | double cax, cay, caz; 2023-09-17T12:07:14,706 | ^~~ 2023-09-17T12:07:14,707 src/pulchra.hpp:2037:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:07:14,707 2037 | double cax, cay, caz; 2023-09-17T12:07:14,708 | ^~~ 2023-09-17T12:07:14,709 src/pulchra.hpp:2039:22: warning: unused variable ‘scn’ [-Wunused-variable] 2023-09-17T12:07:14,709 2039 | char scn[12][4]; 2023-09-17T12:07:14,710 | ^~~ 2023-09-17T12:07:14,710 src/pulchra.hpp:2040:21: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:14,711 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,712 | ^~ 2023-09-17T12:07:14,712 src/pulchra.hpp:2040:25: warning: unused variable ‘last_a’ [-Wunused-variable] 2023-09-17T12:07:14,713 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,713 | ^~~~~~ 2023-09-17T12:07:14,714 src/pulchra.hpp:2040:33: warning: unused variable ‘last_b’ [-Wunused-variable] 2023-09-17T12:07:14,715 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,715 | ^~~~~~ 2023-09-17T12:07:14,716 src/pulchra.hpp:2040:41: warning: unused variable ‘last_c’ [-Wunused-variable] 2023-09-17T12:07:14,717 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,717 | ^~~~~~ 2023-09-17T12:07:14,718 src/pulchra.hpp:2040:49: warning: unused variable ‘last_d’ [-Wunused-variable] 2023-09-17T12:07:14,719 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,719 | ^~~~~~ 2023-09-17T12:07:14,720 src/pulchra.hpp:2040:57: warning: unused variable ‘jpos’ [-Wunused-variable] 2023-09-17T12:07:14,720 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,721 | ^~~~ 2023-09-17T12:07:14,722 src/pulchra.hpp:2041:21: warning: unused variable ‘jx’ [-Wunused-variable] 2023-09-17T12:07:14,722 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,723 | ^~ 2023-09-17T12:07:14,724 src/pulchra.hpp:2041:25: warning: unused variable ‘jy’ [-Wunused-variable] 2023-09-17T12:07:14,724 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,725 | ^~ 2023-09-17T12:07:14,726 src/pulchra.hpp:2041:29: warning: unused variable ‘jz’ [-Wunused-variable] 2023-09-17T12:07:14,727 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,727 | ^~ 2023-09-17T12:07:14,728 src/pulchra.hpp:2041:33: warning: unused variable ‘jxi’ [-Wunused-variable] 2023-09-17T12:07:14,728 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,729 | ^~~ 2023-09-17T12:07:14,729 src/pulchra.hpp:2041:38: warning: unused variable ‘jyi’ [-Wunused-variable] 2023-09-17T12:07:14,730 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,730 | ^~~ 2023-09-17T12:07:14,731 src/pulchra.hpp:2041:43: warning: unused variable ‘jzi’ [-Wunused-variable] 2023-09-17T12:07:14,731 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,732 | ^~~ 2023-09-17T12:07:14,732 src/pulchra.hpp:2041:48: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,733 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,734 | ^~~~~ 2023-09-17T12:07:14,734 src/pulchra.hpp:2041:55: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,735 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,735 | ^~~~~ 2023-09-17T12:07:14,736 src/pulchra.hpp:2041:62: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,737 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,738 | ^~~ 2023-09-17T12:07:14,738 src/pulchra.hpp:2041:67: warning: unused variable ‘jm’ [-Wunused-variable] 2023-09-17T12:07:14,739 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,743 | ^~ 2023-09-17T12:07:14,743 src/pulchra.hpp:2042:27: warning: unused variable ‘bestrot’ [-Wunused-variable] 2023-09-17T12:07:14,747 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,747 | ^~~~~~~ 2023-09-17T12:07:14,748 src/pulchra.hpp:2042:36: warning: unused variable ‘minexvol’ [-Wunused-variable] 2023-09-17T12:07:14,749 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,749 | ^~~~~~~~ 2023-09-17T12:07:14,750 src/pulchra.hpp:2042:46: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,751 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,751 | ^~~~~~~~ 2023-09-17T12:07:14,752 src/pulchra.hpp:2042:56: warning: unused variable ‘rtried’ [-Wunused-variable] 2023-09-17T12:07:14,752 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,753 | ^~~~~~ 2023-09-17T12:07:14,753 src/pulchra.hpp:2044:24: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2023-09-17T12:07:14,754 2044 | double sort_rot[100][2]; 2023-09-17T12:07:14,755 | ^~~~~~~~ 2023-09-17T12:07:14,755 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2023-09-17T12:07:14,756 src/pulchra.hpp:2264:30: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,757 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,758 | ^ 2023-09-17T12:07:14,758 src/pulchra.hpp:2264:33: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,759 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,759 | ^ 2023-09-17T12:07:14,760 src/pulchra.hpp:2264:36: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,760 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,761 | ^ 2023-09-17T12:07:14,761 src/pulchra.hpp:2265:38: warning: unused variable ‘iter’ [-Wunused-variable] 2023-09-17T12:07:14,762 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:07:14,762 | ^~~~ 2023-09-17T12:07:14,763 src/pulchra.hpp:2265:44: warning: unused variable ‘maxcon’ [-Wunused-variable] 2023-09-17T12:07:14,763 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:07:14,764 | ^~~~~~ 2023-09-17T12:07:14,764 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:07:14,765 src/pulchra.hpp:2374:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:07:14,766 2374 | int i, j, x, y, z; 2023-09-17T12:07:14,766 | ^ 2023-09-17T12:07:14,767 src/pulchra.hpp:2374:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:14,767 2374 | int i, j, x, y, z; 2023-09-17T12:07:14,768 | ^ 2023-09-17T12:07:14,768 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2023-09-17T12:07:14,769 src/pulchra.hpp:2440:24: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,770 2440 | double min[3], max[3]; 2023-09-17T12:07:14,771 | ^~~ 2023-09-17T12:07:14,771 src/pulchra.hpp:2440:32: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,772 2440 | double min[3], max[3]; 2023-09-17T12:07:14,773 | ^~~ 2023-09-17T12:07:14,773 src/pulchra.hpp:2446:36: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,774 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,775 | ^ 2023-09-17T12:07:14,775 src/pulchra.hpp:2446:39: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,776 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,777 | ^ 2023-09-17T12:07:14,777 src/pulchra.hpp:2446:42: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,778 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,779 | ^ 2023-09-17T12:07:14,779 src/pulchra.hpp:2447:21: warning: unused variable ‘ii’ [-Wunused-variable] 2023-09-17T12:07:14,780 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,780 | ^~ 2023-09-17T12:07:14,781 src/pulchra.hpp:2447:25: warning: unused variable ‘jj’ [-Wunused-variable] 2023-09-17T12:07:14,782 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,782 | ^~ 2023-09-17T12:07:14,783 src/pulchra.hpp:2447:29: warning: unused variable ‘kk’ [-Wunused-variable] 2023-09-17T12:07:14,784 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,785 | ^~ 2023-09-17T12:07:14,785 src/pulchra.hpp:2450:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:07:14,786 2450 | int nsc, nca; 2023-09-17T12:07:14,787 | ^~~ 2023-09-17T12:07:14,787 src/pulchra.hpp:2451:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:07:14,788 2451 | double cax, cay, caz; 2023-09-17T12:07:14,788 | ^~~ 2023-09-17T12:07:14,789 src/pulchra.hpp:2451:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:07:14,789 2451 | double cax, cay, caz; 2023-09-17T12:07:14,790 | ^~~ 2023-09-17T12:07:14,790 src/pulchra.hpp:2451:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:07:14,791 2451 | double cax, cay, caz; 2023-09-17T12:07:14,791 | ^~~ 2023-09-17T12:07:14,792 src/pulchra.hpp:2453:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,792 2453 | double x1, y1, z1; 2023-09-17T12:07:14,793 | ^~ 2023-09-17T12:07:14,793 src/pulchra.hpp:2453:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,794 2453 | double x1, y1, z1; 2023-09-17T12:07:14,794 | ^~ 2023-09-17T12:07:14,795 src/pulchra.hpp:2453:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,795 2453 | double x1, y1, z1; 2023-09-17T12:07:14,796 | ^~ 2023-09-17T12:07:14,796 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2023-09-17T12:07:14,797 src/pulchra.hpp:2732:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:07:14,798 2732 | int i; 2023-09-17T12:07:14,798 | ^ 2023-09-17T12:07:14,799 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2023-09-17T12:07:14,800 src/pulchra.hpp:2828:42: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2023-09-17T12:07:14,800 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2023-09-17T12:07:14,801 | ^~~~~~~~~ 2023-09-17T12:07:14,802 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2023-09-17T12:07:14,802 src/pulchra.hpp:3042:24: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-17T12:07:14,803 3042 | int i, k, best; 2023-09-17T12:07:14,804 | ^ 2023-09-17T12:07:14,807 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2023-09-17T12:07:14,807 src/pulchra.hpp:3116:27: warning: unused variable ‘chain_length’ [-Wunused-variable] 2023-09-17T12:07:14,808 3116 | int const chain_length = chain->nres; 2023-09-17T12:07:14,809 | ^~~~~~~~~~~~ 2023-09-17T12:07:14,821 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2023-09-17T12:07:14,821 src/pulchra.hpp:3315:69: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘std::chrono::duration::rep’ {aka ‘long long int’} [-Wformat=] 2023-09-17T12:07:14,822 3315 | "Done. Reconstruction finished in %ld s.\n", 2023-09-17T12:07:14,823 | ~~^ 2023-09-17T12:07:14,823 | | 2023-09-17T12:07:14,824 | long int 2023-09-17T12:07:14,825 | %lld 2023-09-17T12:07:14,826 3316 | std::chrono::duration_cast(time1 - time0) 2023-09-17T12:07:14,827 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:14,828 3317 | .count()); 2023-09-17T12:07:14,828 | ~~~~~~~~ 2023-09-17T12:07:14,829 | | 2023-09-17T12:07:14,830 | std::chrono::duration::rep {aka long long int} 2023-09-17T12:07:14,831 src/pulchra.hpp:3145:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:07:14,831 3145 | char buf[100]; 2023-09-17T12:07:14,832 | ^~~ 2023-09-17T12:07:14,833 src/pulchra.hpp:3146:37: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,834 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2023-09-17T12:07:14,834 | ^~~~~~~~ 2023-09-17T12:07:14,835 src/pulchra.hpp:3147:23: warning: unused variable ‘ptr’ [-Wunused-variable] 2023-09-17T12:07:14,836 3147 | char *ptr, out_name[1000]; 2023-09-17T12:07:14,837 | ^~~ 2023-09-17T12:07:14,838 src/pulchra.hpp:3147:28: warning: unused variable ‘out_name’ [-Wunused-variable] 2023-09-17T12:07:14,839 3147 | char *ptr, out_name[1000]; 2023-09-17T12:07:14,840 | ^~~~~~~~ 2023-09-17T12:07:38,475 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:07:38,475 src/pulchra.hpp:2429:39: warning: ‘xgrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:38,476 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:38,476 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:38,477 2430 | zgrid); 2023-09-17T12:07:38,478 | ~~~~~~ 2023-09-17T12:07:38,479 src/pulchra.hpp:2365:21: note: ‘xgrid’ was declared here 2023-09-17T12:07:38,479 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,480 | ^~~~~ 2023-09-17T12:07:38,481 src/pulchra.hpp:2429:39: warning: ‘ygrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:38,482 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:38,482 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:38,483 2430 | zgrid); 2023-09-17T12:07:38,484 | ~~~~~~ 2023-09-17T12:07:38,485 src/pulchra.hpp:2365:28: note: ‘ygrid’ was declared here 2023-09-17T12:07:38,485 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,486 | ^~~~~ 2023-09-17T12:07:38,487 src/pulchra.hpp:2429:39: warning: ‘zgrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:38,487 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:38,488 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:38,489 2430 | zgrid); 2023-09-17T12:07:38,490 | ~~~~~~ 2023-09-17T12:07:38,490 src/pulchra.hpp:2365:35: note: ‘zgrid’ was declared here 2023-09-17T12:07:38,491 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,492 | ^~~~~ 2023-09-17T12:07:43,453 arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 build/temp.linux-armv7l-cpython-311/bindings/python/pulchra_bindings.o build/temp.linux-armv7l-cpython-311/bindings/python/pypulchra_bindings.o build/temp.linux-armv7l-cpython-311/src/pulchra.o -L/usr/lib/arm-linux-gnueabihf -o build/lib.linux-armv7l-cpython-311/pypulchra/_pypulchra.cpython-311-arm-linux-gnueabihf.so 2023-09-17T12:07:43,873 installing to build/bdist.linux-armv7l/wheel 2023-09-17T12:07:43,874 running install 2023-09-17T12:07:43,904 running install_lib 2023-09-17T12:07:43,911 creating build/bdist.linux-armv7l 2023-09-17T12:07:43,912 creating build/bdist.linux-armv7l/wheel 2023-09-17T12:07:43,913 creating build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,915 copying build/lib.linux-armv7l-cpython-311/pypulchra/__init__.py -> build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,917 copying build/lib.linux-armv7l-cpython-311/pypulchra/_pypulchra.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,980 running install_egg_info 2023-09-17T12:07:43,992 running egg_info 2023-09-17T12:07:43,996 writing pypulchra.egg-info/PKG-INFO 2023-09-17T12:07:43,999 writing dependency_links to pypulchra.egg-info/dependency_links.txt 2023-09-17T12:07:44,001 writing entry points to pypulchra.egg-info/entry_points.txt 2023-09-17T12:07:44,003 writing top-level names to pypulchra.egg-info/top_level.txt 2023-09-17T12:07:44,010 reading manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:07:44,013 reading manifest template 'MANIFEST.in' 2023-09-17T12:07:44,018 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:07:44,020 Copying pypulchra.egg-info to build/bdist.linux-armv7l/wheel/pypulchra-1.0.1-py3.11.egg-info 2023-09-17T12:07:44,034 running install_scripts 2023-09-17T12:07:44,079 creating build/bdist.linux-armv7l/wheel/pypulchra-1.0.1.dist-info/WHEEL 2023-09-17T12:07:44,082 creating '/tmp/pip-wheel-ol5s45fg/.tmp-ujaa5f7b/pypulchra-1.0.1-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-17T12:07:44,084 adding 'pypulchra/__init__.py' 2023-09-17T12:07:44,717 adding 'pypulchra/_pypulchra.cpython-311-arm-linux-gnueabihf.so' 2023-09-17T12:07:44,750 adding 'pypulchra-1.0.1.dist-info/METADATA' 2023-09-17T12:07:44,751 adding 'pypulchra-1.0.1.dist-info/WHEEL' 2023-09-17T12:07:44,752 adding 'pypulchra-1.0.1.dist-info/entry_points.txt' 2023-09-17T12:07:44,753 adding 'pypulchra-1.0.1.dist-info/top_level.txt' 2023-09-17T12:07:44,754 adding 'pypulchra-1.0.1.dist-info/RECORD' 2023-09-17T12:07:44,779 removing build/bdist.linux-armv7l/wheel 2023-09-17T12:07:44,874 Building wheel for pypulchra (pyproject.toml): finished with status 'done' 2023-09-17T12:07:44,926 Created wheel for pypulchra: filename=pypulchra-1.0.1-cp311-cp311-linux_armv7l.whl size=1940818 sha256=662327cbc653f6b70f3e0b55df636ac715fffb38855b8c574b9bc04335d506ea 2023-09-17T12:07:44,927 Stored in directory: /tmp/pip-ephem-wheel-cache-y528gw_i/wheels/25/b3/24/63b530944d3f3689aa8b540b51c5de3379470c537217362351 2023-09-17T12:07:44,938 Successfully built pypulchra 2023-09-17T12:07:44,991 Removed build tracker: '/tmp/pip-build-tracker-e2i9gg7_'