2023-09-17T12:06:12,380 Created temporary directory: /tmp/pip-build-tracker-9uem0i8v 2023-09-17T12:06:12,381 Initialized build tracking at /tmp/pip-build-tracker-9uem0i8v 2023-09-17T12:06:12,382 Created build tracker: /tmp/pip-build-tracker-9uem0i8v 2023-09-17T12:06:12,382 Entered build tracker: /tmp/pip-build-tracker-9uem0i8v 2023-09-17T12:06:12,383 Created temporary directory: /tmp/pip-wheel-a0ak7qd_ 2023-09-17T12:06:12,386 Created temporary directory: /tmp/pip-ephem-wheel-cache-bbebpikm 2023-09-17T12:06:12,408 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-17T12:06:12,411 2 location(s) to search for versions of pypulchra: 2023-09-17T12:06:12,411 * https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,411 * https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,412 Fetching project page and analyzing links: https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,413 Getting page https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,414 Found index url https://pypi.org/simple/ 2023-09-17T12:06:12,632 Fetched page https://pypi.org/simple/pypulchra/ as application/vnd.pypi.simple.v1+json 2023-09-17T12:06:12,634 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 2023-09-17T12:06:12,635 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 2023-09-17T12:06:12,636 Fetching project page and analyzing links: https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,636 Getting page https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,637 Found index url https://www.piwheels.org/simple/ 2023-09-17T12:06:12,931 Fetched page https://www.piwheels.org/simple/pypulchra/ as text/html 2023-09-17T12:06:12,935 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) 2023-09-17T12:06:12,935 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) 2023-09-17T12:06:12,936 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) 2023-09-17T12:06:12,937 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) 2023-09-17T12:06:12,937 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) 2023-09-17T12:06:12,938 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) 2023-09-17T12:06:12,938 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) 2023-09-17T12:06:12,939 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) 2023-09-17T12:06:12,940 Skipping link: not a file: https://www.piwheels.org/simple/pypulchra/ 2023-09-17T12:06:12,941 Skipping link: not a file: https://pypi.org/simple/pypulchra/ 2023-09-17T12:06:12,959 Given no hashes to check 1 links for project 'pypulchra': discarding no candidates 2023-09-17T12:06:12,977 Collecting pypulchra==1.0.0 2023-09-17T12:06:12,979 Created temporary directory: /tmp/pip-unpack-mvyziujj 2023-09-17T12:06:13,207 Downloading pypulchra-1.0.0.tar.gz (1.9 MB) 2023-09-17T12:06:13,749 Added pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-9uem0i8v' 2023-09-17T12:06:13,754 Created temporary directory: /tmp/pip-build-env-tezqktcm 2023-09-17T12:06:13,759 Installing build dependencies: started 2023-09-17T12:06:13,760 Running command pip subprocess to install build dependencies 2023-09-17T12:06:14,973 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-17T12:06:15,814 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-17T12:06:17,564 Collecting setuptools>=42 2023-09-17T12:06:17,565 Obtaining dependency information for setuptools>=42 from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-17T12:06:17,570 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-17T12:06:17,778 Collecting wheel 2023-09-17T12:06:17,807 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-17T12:06:17,979 Collecting pybind11>=2.8.0 2023-09-17T12:06:18,005 Using cached https://www.piwheels.org/simple/pybind11/pybind11-2.11.1-py3-none-any.whl (227 kB) 2023-09-17T12:06:18,193 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-17T12:06:20,646 Installing collected packages: wheel, setuptools, pybind11 2023-09-17T12:06:20,869 Creating /tmp/pip-build-env-tezqktcm/overlay/local/bin 2023-09-17T12:06:20,871 changing mode of /tmp/pip-build-env-tezqktcm/overlay/local/bin/wheel to 755 2023-09-17T12:06:23,223 changing mode of /tmp/pip-build-env-tezqktcm/overlay/local/bin/pybind11-config to 755 2023-09-17T12:06:23,245 Successfully installed pybind11-2.11.1 setuptools-68.2.2 wheel-0.41.2 2023-09-17T12:06:23,835 Installing build dependencies: finished with status 'done' 2023-09-17T12:06:23,838 Getting requirements to build wheel: started 2023-09-17T12:06:23,839 Running command Getting requirements to build wheel 2023-09-17T12:06:24,400 running egg_info 2023-09-17T12:06:24,407 writing pypulchra.egg-info/PKG-INFO 2023-09-17T12:06:24,409 writing dependency_links to pypulchra.egg-info/dependency_links.txt 2023-09-17T12:06:24,411 writing entry points to pypulchra.egg-info/entry_points.txt 2023-09-17T12:06:24,413 writing top-level names to pypulchra.egg-info/top_level.txt 2023-09-17T12:06:24,436 reading manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:24,438 reading manifest template 'MANIFEST.in' 2023-09-17T12:06:24,446 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:24,524 Getting requirements to build wheel: finished with status 'done' 2023-09-17T12:06:24,535 Created temporary directory: /tmp/pip-modern-metadata-zsjuf759 2023-09-17T12:06:24,537 Preparing metadata (pyproject.toml): started 2023-09-17T12:06:24,538 Running command Preparing metadata (pyproject.toml) 2023-09-17T12:06:25,053 running dist_info 2023-09-17T12:06:25,073 creating /tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info 2023-09-17T12:06:25,078 writing /tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/PKG-INFO 2023-09-17T12:06:25,081 writing dependency_links to /tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/dependency_links.txt 2023-09-17T12:06:25,083 writing entry points to /tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/entry_points.txt 2023-09-17T12:06:25,084 writing top-level names to /tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/top_level.txt 2023-09-17T12:06:25,086 writing manifest file '/tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,105 reading manifest file '/tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,107 reading manifest template 'MANIFEST.in' 2023-09-17T12:06:25,112 writing manifest file '/tmp/pip-modern-metadata-zsjuf759/pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:06:25,113 creating '/tmp/pip-modern-metadata-zsjuf759/pypulchra-1.0.0.dist-info' 2023-09-17T12:06:25,291 Preparing metadata (pyproject.toml): finished with status 'done' 2023-09-17T12:06:25,295 Source in /tmp/pip-wheel-a0ak7qd_/pypulchra_baedb3b1065b4f11a31794f980284ec2 has version 1.0.0, which satisfies requirement pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz 2023-09-17T12:06:25,296 Removed pypulchra==1.0.0 from https://files.pythonhosted.org/packages/f1/f9/07629a442c8da5001399ee88eb46f4b233b0ce71cc6c2b1a085c88805179/pypulchra-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-9uem0i8v' 2023-09-17T12:06:25,302 Created temporary directory: /tmp/pip-unpack-b5xiachp 2023-09-17T12:06:25,302 Created temporary directory: /tmp/pip-unpack-350na9v8 2023-09-17T12:06:25,305 Building wheels for collected packages: pypulchra 2023-09-17T12:06:25,309 Created temporary directory: /tmp/pip-wheel-2kqanhja 2023-09-17T12:06:25,310 Destination directory: /tmp/pip-wheel-2kqanhja 2023-09-17T12:06:25,312 Building wheel for pypulchra (pyproject.toml): started 2023-09-17T12:06:25,313 Running command Building wheel for pypulchra (pyproject.toml) 2023-09-17T12:06:25,846 running bdist_wheel 2023-09-17T12:06:25,880 running build 2023-09-17T12:06:25,881 running build_py 2023-09-17T12:06:25,888 creating build 2023-09-17T12:06:25,888 creating build/lib.linux-armv7l-cpython-311 2023-09-17T12:06:25,889 creating build/lib.linux-armv7l-cpython-311/pypulchra 2023-09-17T12:06:25,890 copying pypulchra/__init__.py -> build/lib.linux-armv7l-cpython-311/pypulchra 2023-09-17T12:06:25,892 running build_ext 2023-09-17T12:06:25,897 building 'pypulchra._pypulchra' extension 2023-09-17T12:06:25,898 creating build/temp.linux-armv7l-cpython-311 2023-09-17T12:06:25,898 creating build/temp.linux-armv7l-cpython-311/bindings 2023-09-17T12:06:25,899 creating build/temp.linux-armv7l-cpython-311/bindings/python 2023-09-17T12:06:25,900 creating build/temp.linux-armv7l-cpython-311/src 2023-09-17T12:06:25,901 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=1.0.0 -Isrc -I/tmp/pip-build-env-tezqktcm/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 2023-09-17T12:06:28,092 In file included from bindings/python/pulchra_bindings.cpp:5: 2023-09-17T12:06:28,093 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2023-09-17T12:06:28,094 src/pulchra.hpp:653:69: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-17T12:06:28,095 653 | res->type = AA_NUMS[pusetseq(resname)]; 2023-09-17T12:06:28,095 | ~~~~~~~~^~~~~~~~~ 2023-09-17T12:06:28,110 src/pulchra.hpp:594:22: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,111 594 | char version; 2023-09-17T12:06:28,112 | ^~~~~~~ 2023-09-17T12:06:28,112 src/pulchra.hpp:595:60: warning: unused variable ‘num’ [-Wunused-variable] 2023-09-17T12:06:28,112 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,113 | ^~~ 2023-09-17T12:06:28,113 src/pulchra.hpp:595:77: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,114 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,114 | ^ 2023-09-17T12:06:28,115 src/pulchra.hpp:595:80: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:28,115 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:06:28,116 | ^ 2023-09-17T12:06:28,116 src/pulchra.hpp:597:28: warning: unused variable ‘cc’ [-Wunused-variable] 2023-09-17T12:06:28,117 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,117 | ^~ 2023-09-17T12:06:28,118 src/pulchra.hpp:597:32: warning: unused variable ‘nres’ [-Wunused-variable] 2023-09-17T12:06:28,119 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,119 | ^~~~ 2023-09-17T12:06:28,120 src/pulchra.hpp:597:38: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:28,120 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,121 | ^~ 2023-09-17T12:06:28,122 src/pulchra.hpp:597:42: warning: unused variable ‘natom’ [-Wunused-variable] 2023-09-17T12:06:28,122 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:06:28,123 | ^~~~~ 2023-09-17T12:06:28,124 src/pulchra.hpp:602:24: warning: unused variable ‘dist’ [-Wunused-variable] 2023-09-17T12:06:28,125 602 | double dist; 2023-09-17T12:06:28,125 | ^~~~ 2023-09-17T12:06:28,126 src/pulchra.hpp:603:31: warning: unused variable ‘bin’ [-Wunused-variable] 2023-09-17T12:06:28,127 603 | unsigned char bin; 2023-09-17T12:06:28,128 | ^~~ 2023-09-17T12:06:28,128 src/pulchra.hpp:604:21: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,129 604 | int warn = 0; 2023-09-17T12:06:28,130 | ^~~~ 2023-09-17T12:06:28,130 src/pulchra.hpp:605:24: warning: unused variable ‘cutoff’ [-Wunused-variable] 2023-09-17T12:06:28,131 605 | double cutoff; 2023-09-17T12:06:28,132 | ^~~~~~ 2023-09-17T12:06:28,138 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2023-09-17T12:06:28,139 src/pulchra.hpp:775:24: warning: unused variable ‘theta0’ [-Wunused-variable] 2023-09-17T12:06:28,139 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,140 | ^~~~~~ 2023-09-17T12:06:28,141 src/pulchra.hpp:775:32: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:06:28,141 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,142 | ^~~~ 2023-09-17T12:06:28,143 src/pulchra.hpp:775:38: warning: unused variable ‘th’ [-Wunused-variable] 2023-09-17T12:06:28,144 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,145 | ^~ 2023-09-17T12:06:28,145 src/pulchra.hpp:775:42: warning: unused variable ‘aa’ [-Wunused-variable] 2023-09-17T12:06:28,146 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,146 | ^~ 2023-09-17T12:06:28,147 src/pulchra.hpp:775:46: warning: unused variable ‘bb’ [-Wunused-variable] 2023-09-17T12:06:28,147 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,148 | ^~ 2023-09-17T12:06:28,148 src/pulchra.hpp:775:50: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-17T12:06:28,149 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:06:28,149 | ^~ 2023-09-17T12:06:28,150 src/pulchra.hpp:776:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:06:28,150 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,151 | ^~~ 2023-09-17T12:06:28,151 src/pulchra.hpp:776:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:06:28,152 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,152 | ^~~ 2023-09-17T12:06:28,153 src/pulchra.hpp:776:34: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:06:28,153 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,154 | ^~~ 2023-09-17T12:06:28,154 src/pulchra.hpp:776:39: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:06:28,155 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,156 | ^~ 2023-09-17T12:06:28,156 src/pulchra.hpp:776:43: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:06:28,157 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,158 | ^~ 2023-09-17T12:06:28,158 src/pulchra.hpp:776:53: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:06:28,159 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,160 | ^~ 2023-09-17T12:06:28,160 src/pulchra.hpp:776:60: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:06:28,161 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:06:28,162 | ^~ 2023-09-17T12:06:28,163 src/pulchra.hpp:777:24: warning: unused variable ‘adiff’ [-Wunused-variable] 2023-09-17T12:06:28,163 777 | double adiff[3], bdiff[3]; 2023-09-17T12:06:28,164 | ^~~~~ 2023-09-17T12:06:28,164 src/pulchra.hpp:777:34: warning: unused variable ‘bdiff’ [-Wunused-variable] 2023-09-17T12:06:28,165 777 | double adiff[3], bdiff[3]; 2023-09-17T12:06:28,166 | ^~~~~ 2023-09-17T12:06:28,166 src/pulchra.hpp:778:24: warning: unused variable ‘deriv’ [-Wunused-variable] 2023-09-17T12:06:28,167 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,167 | ^~~~~ 2023-09-17T12:06:28,168 src/pulchra.hpp:778:38: warning: unused variable ‘dtheta’ [-Wunused-variable] 2023-09-17T12:06:28,169 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,169 | ^~~~~~ 2023-09-17T12:06:28,170 src/pulchra.hpp:778:46: warning: unused variable ‘len1’ [-Wunused-variable] 2023-09-17T12:06:28,171 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,171 | ^~~~ 2023-09-17T12:06:28,172 src/pulchra.hpp:778:52: warning: unused variable ‘len2’ [-Wunused-variable] 2023-09-17T12:06:28,172 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:06:28,173 | ^~~~ 2023-09-17T12:06:28,173 src/pulchra.hpp:779:24: warning: unused variable ‘dx1’ [-Wunused-variable] 2023-09-17T12:06:28,174 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,174 | ^~~ 2023-09-17T12:06:28,175 src/pulchra.hpp:779:29: warning: unused variable ‘dy1’ [-Wunused-variable] 2023-09-17T12:06:28,175 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,176 | ^~~ 2023-09-17T12:06:28,176 src/pulchra.hpp:779:34: warning: unused variable ‘dz1’ [-Wunused-variable] 2023-09-17T12:06:28,177 779 | double dx1, dy1, dz1; 2023-09-17T12:06:28,178 | ^~~ 2023-09-17T12:06:28,178 src/pulchra.hpp:780:24: warning: unused variable ‘dx2’ [-Wunused-variable] 2023-09-17T12:06:28,179 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,179 | ^~~ 2023-09-17T12:06:28,180 src/pulchra.hpp:780:29: warning: unused variable ‘dy2’ [-Wunused-variable] 2023-09-17T12:06:28,180 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,181 | ^~~ 2023-09-17T12:06:28,181 src/pulchra.hpp:780:34: warning: unused variable ‘dz2’ [-Wunused-variable] 2023-09-17T12:06:28,182 780 | double dx2, dy2, dz2; 2023-09-17T12:06:28,183 | ^~~ 2023-09-17T12:06:28,183 src/pulchra.hpp:781:24: warning: unused variable ‘dx3’ [-Wunused-variable] 2023-09-17T12:06:28,184 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,185 | ^~~ 2023-09-17T12:06:28,185 src/pulchra.hpp:781:29: warning: unused variable ‘dy3’ [-Wunused-variable] 2023-09-17T12:06:28,186 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,187 | ^~~ 2023-09-17T12:06:28,187 src/pulchra.hpp:781:34: warning: unused variable ‘dz3’ [-Wunused-variable] 2023-09-17T12:06:28,188 781 | double dx3, dy3, dz3; 2023-09-17T12:06:28,189 | ^~~ 2023-09-17T12:06:28,189 src/pulchra.hpp:782:24: warning: unused variable ‘vx1’ [-Wunused-variable] 2023-09-17T12:06:28,190 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,191 | ^~~ 2023-09-17T12:06:28,191 src/pulchra.hpp:782:29: warning: unused variable ‘vy1’ [-Wunused-variable] 2023-09-17T12:06:28,192 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,193 | ^~~ 2023-09-17T12:06:28,193 src/pulchra.hpp:782:34: warning: unused variable ‘vz1’ [-Wunused-variable] 2023-09-17T12:06:28,194 782 | double vx1, vy1, vz1; 2023-09-17T12:06:28,195 | ^~~ 2023-09-17T12:06:28,195 src/pulchra.hpp:783:24: warning: unused variable ‘vx2’ [-Wunused-variable] 2023-09-17T12:06:28,196 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,196 | ^~~ 2023-09-17T12:06:28,197 src/pulchra.hpp:783:29: warning: unused variable ‘vy2’ [-Wunused-variable] 2023-09-17T12:06:28,198 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,198 | ^~~ 2023-09-17T12:06:28,199 src/pulchra.hpp:783:34: warning: unused variable ‘vz2’ [-Wunused-variable] 2023-09-17T12:06:28,200 783 | double vx2, vy2, vz2; 2023-09-17T12:06:28,201 | ^~~ 2023-09-17T12:06:28,202 src/pulchra.hpp:784:24: warning: unused variable ‘vx3’ [-Wunused-variable] 2023-09-17T12:06:28,202 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,203 | ^~~ 2023-09-17T12:06:28,203 src/pulchra.hpp:784:29: warning: unused variable ‘vy3’ [-Wunused-variable] 2023-09-17T12:06:28,204 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,204 | ^~~ 2023-09-17T12:06:28,205 src/pulchra.hpp:784:34: warning: unused variable ‘vz3’ [-Wunused-variable] 2023-09-17T12:06:28,205 784 | double vx3, vy3, vz3; 2023-09-17T12:06:28,206 | ^~~ 2023-09-17T12:06:28,206 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2023-09-17T12:06:28,207 src/pulchra.hpp:937:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:06:28,207 937 | char buf[1000]; 2023-09-17T12:06:28,208 | ^~~ 2023-09-17T12:06:28,208 src/pulchra.hpp:938:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:28,209 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,209 | ^ 2023-09-17T12:06:28,210 src/pulchra.hpp:938:27: warning: unused variable ‘hx’ [-Wunused-variable] 2023-09-17T12:06:28,210 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,211 | ^~ 2023-09-17T12:06:28,211 src/pulchra.hpp:938:31: warning: unused variable ‘my_iter’ [-Wunused-variable] 2023-09-17T12:06:28,212 938 | int i, j, hx, my_iter; 2023-09-17T12:06:28,212 | ^~~~~~~ 2023-09-17T12:06:28,213 src/pulchra.hpp:939:46: warning: unused variable ‘dist2’ [-Wunused-variable] 2023-09-17T12:06:28,214 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,214 | ^~~~~ 2023-09-17T12:06:28,215 src/pulchra.hpp:939:53: warning: unused variable ‘dist3’ [-Wunused-variable] 2023-09-17T12:06:28,216 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,216 | ^~~~~ 2023-09-17T12:06:28,217 src/pulchra.hpp:939:67: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,218 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:06:28,218 | ^~~~~~ 2023-09-17T12:06:28,219 src/pulchra.hpp:940:31: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2023-09-17T12:06:28,220 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,221 | ^~~~~~~~~ 2023-09-17T12:06:28,221 src/pulchra.hpp:940:42: warning: unused variable ‘grad’ [-Wunused-variable] 2023-09-17T12:06:28,222 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,223 | ^~~~ 2023-09-17T12:06:28,223 src/pulchra.hpp:940:48: warning: unused variable ‘alpha’ [-Wunused-variable] 2023-09-17T12:06:28,224 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:06:28,225 | ^~~~~ 2023-09-17T12:06:28,225 src/pulchra.hpp:942:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:06:28,226 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,227 | ^~~ 2023-09-17T12:06:28,227 src/pulchra.hpp:942:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:06:28,228 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,229 | ^~~ 2023-09-17T12:06:28,230 src/pulchra.hpp:942:50: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:06:28,230 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,231 | ^~~~ 2023-09-17T12:06:28,231 src/pulchra.hpp:942:56: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:06:28,232 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,232 | ^~~ 2023-09-17T12:06:28,232 src/pulchra.hpp:942:61: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:06:28,233 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,233 | ^~ 2023-09-17T12:06:28,234 src/pulchra.hpp:942:65: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:06:28,235 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:06:28,235 | ^~ 2023-09-17T12:06:28,236 src/pulchra.hpp:943:40: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2023-09-17T12:06:28,236 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:06:28,237 | ^~~~~~~ 2023-09-17T12:06:28,237 src/pulchra.hpp:943:49: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-17T12:06:28,238 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:06:28,238 | ^~~ 2023-09-17T12:06:28,239 src/pulchra.hpp:944:24: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:06:28,240 944 | double f0[3], f2[3]; 2023-09-17T12:06:28,240 | ^~ 2023-09-17T12:06:28,241 src/pulchra.hpp:944:31: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:06:28,242 944 | double f0[3], f2[3]; 2023-09-17T12:06:28,243 | ^~ 2023-09-17T12:06:28,243 src/pulchra.hpp:945:24: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:28,244 945 | double x, y, z; 2023-09-17T12:06:28,245 | ^ 2023-09-17T12:06:28,246 src/pulchra.hpp:945:27: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:28,246 945 | double x, y, z; 2023-09-17T12:06:28,247 | ^ 2023-09-17T12:06:28,248 src/pulchra.hpp:945:30: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:28,248 945 | double x, y, z; 2023-09-17T12:06:28,249 | ^ 2023-09-17T12:06:28,250 src/pulchra.hpp:947:22: warning: unused variable ‘sec’ [-Wunused-variable] 2023-09-17T12:06:28,250 947 | int *sec; 2023-09-17T12:06:28,251 | ^~~ 2023-09-17T12:06:28,252 src/pulchra.hpp:948:79: warning: unused variable ‘tmp’ [-Wunused-variable] 2023-09-17T12:06:28,252 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2023-09-17T12:06:28,253 | ^~~ 2023-09-17T12:06:28,254 src/pulchra.hpp:949:25: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2023-09-17T12:06:28,254 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,255 | ^~~~~~~~~~~~~~~ 2023-09-17T12:06:28,256 src/pulchra.hpp:949:42: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2023-09-17T12:06:28,257 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,258 | ^~~~~~~ 2023-09-17T12:06:28,258 src/pulchra.hpp:949:51: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,259 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:06:28,259 | ^~~~~~~~~~ 2023-09-17T12:06:28,260 src/pulchra.hpp:953:23: warning: unused variable ‘inp’ [-Wunused-variable] 2023-09-17T12:06:28,260 953 | FILE *inp; 2023-09-17T12:06:28,261 | ^~~ 2023-09-17T12:06:28,261 src/pulchra.hpp:954:33: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:28,262 954 | int mnum, init, ok; 2023-09-17T12:06:28,262 | ^~ 2023-09-17T12:06:28,263 src/pulchra.hpp:958:24: warning: unused variable ‘w1’ [-Wunused-variable] 2023-09-17T12:06:28,263 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,264 | ^~ 2023-09-17T12:06:28,265 src/pulchra.hpp:958:28: warning: unused variable ‘w2’ [-Wunused-variable] 2023-09-17T12:06:28,265 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,266 | ^~ 2023-09-17T12:06:28,266 src/pulchra.hpp:958:32: warning: unused variable ‘w3’ [-Wunused-variable] 2023-09-17T12:06:28,267 958 | double w1, w2, w3, eps; 2023-09-17T12:06:28,267 | ^~ 2023-09-17T12:06:28,268 src/pulchra.hpp:960:21: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,268 960 | int mode, fcnt; 2023-09-17T12:06:28,269 | ^~~~ 2023-09-17T12:06:28,270 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2023-09-17T12:06:28,270 src/pulchra.hpp:1724:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:06:28,271 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,272 | ^ 2023-09-17T12:06:28,273 src/pulchra.hpp:1724:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:06:28,273 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,274 | ^ 2023-09-17T12:06:28,275 src/pulchra.hpp:1724:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:06:28,275 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,276 | ^~~~~ 2023-09-17T12:06:28,277 src/pulchra.hpp:1724:68: warning: unused variable ‘pro’ [-Wunused-variable] 2023-09-17T12:06:28,278 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,278 | ^~~ 2023-09-17T12:06:28,279 src/pulchra.hpp:1725:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:28,279 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,280 | ^~~~~ 2023-09-17T12:06:28,281 src/pulchra.hpp:1725:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:28,281 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,282 | ^~~~~ 2023-09-17T12:06:28,283 src/pulchra.hpp:1725:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:28,284 1725 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,284 | ^~~ 2023-09-17T12:06:28,285 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2023-09-17T12:06:28,286 src/pulchra.hpp:1852:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:06:28,287 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,287 | ^ 2023-09-17T12:06:28,288 src/pulchra.hpp:1852:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:06:28,288 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,289 | ^ 2023-09-17T12:06:28,289 src/pulchra.hpp:1852:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:06:28,290 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,291 | ^~~~~ 2023-09-17T12:06:28,291 src/pulchra.hpp:1852:68: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,292 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:06:28,292 | ^~~ 2023-09-17T12:06:28,293 src/pulchra.hpp:1853:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:28,293 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,294 | ^~~~~ 2023-09-17T12:06:28,294 src/pulchra.hpp:1853:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:28,295 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,296 | ^~~~~ 2023-09-17T12:06:28,296 src/pulchra.hpp:1853:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:28,297 1853 | int b13_1, b13_2, b14; 2023-09-17T12:06:28,297 | ^~~ 2023-09-17T12:06:28,298 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2023-09-17T12:06:28,299 src/pulchra.hpp:2023:26: warning: unused variable ‘cacoords’ [-Wunused-variable] 2023-09-17T12:06:28,300 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,300 | ^~~~~~~~ 2023-09-17T12:06:28,301 src/pulchra.hpp:2023:38: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2023-09-17T12:06:28,302 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,303 | ^~~~~~~~~ 2023-09-17T12:06:28,303 src/pulchra.hpp:2023:51: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2023-09-17T12:06:28,304 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:06:28,305 | ^~~~~~~ 2023-09-17T12:06:28,306 src/pulchra.hpp:2024:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,306 2024 | double x1, y1, z1; 2023-09-17T12:06:28,307 | ^~ 2023-09-17T12:06:28,307 src/pulchra.hpp:2024:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,308 2024 | double x1, y1, z1; 2023-09-17T12:06:28,309 | ^~ 2023-09-17T12:06:28,309 src/pulchra.hpp:2024:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,310 2024 | double x1, y1, z1; 2023-09-17T12:06:28,311 | ^~ 2023-09-17T12:06:28,312 src/pulchra.hpp:2028:24: warning: unused variable ‘x5’ [-Wunused-variable] 2023-09-17T12:06:28,313 2028 | double x5, y5, z5; 2023-09-17T12:06:28,313 | ^~ 2023-09-17T12:06:28,314 src/pulchra.hpp:2028:28: warning: unused variable ‘y5’ [-Wunused-variable] 2023-09-17T12:06:28,315 2028 | double x5, y5, z5; 2023-09-17T12:06:28,316 | ^~ 2023-09-17T12:06:28,316 src/pulchra.hpp:2028:32: warning: unused variable ‘z5’ [-Wunused-variable] 2023-09-17T12:06:28,317 2028 | double x5, y5, z5; 2023-09-17T12:06:28,317 | ^~ 2023-09-17T12:06:28,318 src/pulchra.hpp:2029:24: warning: unused variable ‘r14’ [-Wunused-variable] 2023-09-17T12:06:28,318 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,319 | ^~~ 2023-09-17T12:06:28,319 src/pulchra.hpp:2029:29: warning: unused variable ‘r13_1’ [-Wunused-variable] 2023-09-17T12:06:28,320 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,320 | ^~~~~ 2023-09-17T12:06:28,321 src/pulchra.hpp:2029:36: warning: unused variable ‘r13_2’ [-Wunused-variable] 2023-09-17T12:06:28,321 2029 | double r14, r13_1, r13_2; 2023-09-17T12:06:28,322 | ^~~~~ 2023-09-17T12:06:28,322 src/pulchra.hpp:2030:24: warning: unused variable ‘dx’ [-Wunused-variable] 2023-09-17T12:06:28,323 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,324 | ^~ 2023-09-17T12:06:28,324 src/pulchra.hpp:2030:28: warning: unused variable ‘dy’ [-Wunused-variable] 2023-09-17T12:06:28,325 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,325 | ^~ 2023-09-17T12:06:28,326 src/pulchra.hpp:2030:32: warning: unused variable ‘dz’ [-Wunused-variable] 2023-09-17T12:06:28,327 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,327 | ^~ 2023-09-17T12:06:28,328 src/pulchra.hpp:2030:36: warning: unused variable ‘dd’ [-Wunused-variable] 2023-09-17T12:06:28,329 2030 | double dx, dy, dz, dd; 2023-09-17T12:06:28,330 | ^~ 2023-09-17T12:06:28,330 src/pulchra.hpp:2031:29: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,331 2031 | double hit, besthit; 2023-09-17T12:06:28,331 | ^~~~~~~ 2023-09-17T12:06:28,332 src/pulchra.hpp:2032:21: warning: unused variable ‘exvol’ [-Wunused-variable] 2023-09-17T12:06:28,333 2032 | int exvol, bestpos; 2023-09-17T12:06:28,334 | ^~~~~ 2023-09-17T12:06:28,334 src/pulchra.hpp:2034:24: warning: unused variable ‘rmsd’ [-Wunused-variable] 2023-09-17T12:06:28,335 2034 | double rmsd, total; 2023-09-17T12:06:28,336 | ^~~~ 2023-09-17T12:06:28,337 src/pulchra.hpp:2034:30: warning: unused variable ‘total’ [-Wunused-variable] 2023-09-17T12:06:28,337 2034 | double rmsd, total; 2023-09-17T12:06:28,338 | ^~~~~ 2023-09-17T12:06:28,339 src/pulchra.hpp:2036:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:06:28,339 2036 | int nsc, nca; 2023-09-17T12:06:28,340 | ^~~ 2023-09-17T12:06:28,341 src/pulchra.hpp:2037:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:06:28,341 2037 | double cax, cay, caz; 2023-09-17T12:06:28,342 | ^~~ 2023-09-17T12:06:28,343 src/pulchra.hpp:2037:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:06:28,343 2037 | double cax, cay, caz; 2023-09-17T12:06:28,344 | ^~~ 2023-09-17T12:06:28,345 src/pulchra.hpp:2037:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:06:28,345 2037 | double cax, cay, caz; 2023-09-17T12:06:28,346 | ^~~ 2023-09-17T12:06:28,347 src/pulchra.hpp:2039:22: warning: unused variable ‘scn’ [-Wunused-variable] 2023-09-17T12:06:28,348 2039 | char scn[12][4]; 2023-09-17T12:06:28,348 | ^~~ 2023-09-17T12:06:28,349 src/pulchra.hpp:2040:21: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:06:28,349 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,350 | ^~ 2023-09-17T12:06:28,350 src/pulchra.hpp:2040:25: warning: unused variable ‘last_a’ [-Wunused-variable] 2023-09-17T12:06:28,351 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,351 | ^~~~~~ 2023-09-17T12:06:28,352 src/pulchra.hpp:2040:33: warning: unused variable ‘last_b’ [-Wunused-variable] 2023-09-17T12:06:28,352 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,353 | ^~~~~~ 2023-09-17T12:06:28,353 src/pulchra.hpp:2040:41: warning: unused variable ‘last_c’ [-Wunused-variable] 2023-09-17T12:06:28,354 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,354 | ^~~~~~ 2023-09-17T12:06:28,355 src/pulchra.hpp:2040:49: warning: unused variable ‘last_d’ [-Wunused-variable] 2023-09-17T12:06:28,355 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,356 | ^~~~~~ 2023-09-17T12:06:28,356 src/pulchra.hpp:2040:57: warning: unused variable ‘jpos’ [-Wunused-variable] 2023-09-17T12:06:28,357 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:06:28,358 | ^~~~ 2023-09-17T12:06:28,358 src/pulchra.hpp:2041:21: warning: unused variable ‘jx’ [-Wunused-variable] 2023-09-17T12:06:28,359 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,360 | ^~ 2023-09-17T12:06:28,360 src/pulchra.hpp:2041:25: warning: unused variable ‘jy’ [-Wunused-variable] 2023-09-17T12:06:28,361 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,362 | ^~ 2023-09-17T12:06:28,362 src/pulchra.hpp:2041:29: warning: unused variable ‘jz’ [-Wunused-variable] 2023-09-17T12:06:28,363 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,364 | ^~ 2023-09-17T12:06:28,364 src/pulchra.hpp:2041:33: warning: unused variable ‘jxi’ [-Wunused-variable] 2023-09-17T12:06:28,365 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,366 | ^~~ 2023-09-17T12:06:28,367 src/pulchra.hpp:2041:38: warning: unused variable ‘jyi’ [-Wunused-variable] 2023-09-17T12:06:28,367 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,368 | ^~~ 2023-09-17T12:06:28,368 src/pulchra.hpp:2041:43: warning: unused variable ‘jzi’ [-Wunused-variable] 2023-09-17T12:06:28,369 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,370 | ^~~ 2023-09-17T12:06:28,370 src/pulchra.hpp:2041:48: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:06:28,371 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,372 | ^~~~~ 2023-09-17T12:06:28,372 src/pulchra.hpp:2041:55: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:06:28,373 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,374 | ^~~~~ 2023-09-17T12:06:28,375 src/pulchra.hpp:2041:62: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:06:28,375 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,376 | ^~~ 2023-09-17T12:06:28,376 src/pulchra.hpp:2041:67: warning: unused variable ‘jm’ [-Wunused-variable] 2023-09-17T12:06:28,377 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:06:28,377 | ^~ 2023-09-17T12:06:28,378 src/pulchra.hpp:2042:27: warning: unused variable ‘bestrot’ [-Wunused-variable] 2023-09-17T12:06:28,378 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:28,379 | ^~~~~~~ 2023-09-17T12:06:28,379 src/pulchra.hpp:2042:36: warning: unused variable ‘minexvol’ [-Wunused-variable] 2023-09-17T12:06:28,380 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:28,380 | ^~~~~~~~ 2023-09-17T12:06:28,381 src/pulchra.hpp:2042:46: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,381 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:28,382 | ^~~~~~~~ 2023-09-17T12:06:28,382 src/pulchra.hpp:2042:56: warning: unused variable ‘rtried’ [-Wunused-variable] 2023-09-17T12:06:28,383 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:06:28,384 | ^~~~~~ 2023-09-17T12:06:28,384 src/pulchra.hpp:2044:24: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2023-09-17T12:06:28,385 2044 | double sort_rot[100][2]; 2023-09-17T12:06:28,386 | ^~~~~~~~ 2023-09-17T12:06:28,386 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2023-09-17T12:06:28,387 src/pulchra.hpp:2264:30: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:28,388 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:28,388 | ^ 2023-09-17T12:06:28,389 src/pulchra.hpp:2264:33: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:28,390 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:28,390 | ^ 2023-09-17T12:06:28,391 src/pulchra.hpp:2264:36: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:28,392 2264 | int i, j, k, x, y, z; 2023-09-17T12:06:28,392 | ^ 2023-09-17T12:06:28,393 src/pulchra.hpp:2265:38: warning: unused variable ‘iter’ [-Wunused-variable] 2023-09-17T12:06:28,394 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:06:28,394 | ^~~~ 2023-09-17T12:06:28,395 src/pulchra.hpp:2265:44: warning: unused variable ‘maxcon’ [-Wunused-variable] 2023-09-17T12:06:28,395 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:06:28,396 | ^~~~~~ 2023-09-17T12:06:28,397 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:06:28,398 src/pulchra.hpp:2374:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:06:28,398 2374 | int i, j, x, y, z; 2023-09-17T12:06:28,399 | ^ 2023-09-17T12:06:28,400 src/pulchra.hpp:2374:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:06:28,400 2374 | int i, j, x, y, z; 2023-09-17T12:06:28,401 | ^ 2023-09-17T12:06:28,402 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2023-09-17T12:06:28,403 src/pulchra.hpp:2440:24: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,403 2440 | double min[3], max[3]; 2023-09-17T12:06:28,404 | ^~~ 2023-09-17T12:06:28,404 src/pulchra.hpp:2440:32: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,405 2440 | double min[3], max[3]; 2023-09-17T12:06:28,405 | ^~~ 2023-09-17T12:06:28,406 src/pulchra.hpp:2446:36: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:06:28,406 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:28,407 | ^ 2023-09-17T12:06:28,407 src/pulchra.hpp:2446:39: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:06:28,408 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:28,408 | ^ 2023-09-17T12:06:28,409 src/pulchra.hpp:2446:42: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:06:28,409 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:06:28,410 | ^ 2023-09-17T12:06:28,410 src/pulchra.hpp:2447:21: warning: unused variable ‘ii’ [-Wunused-variable] 2023-09-17T12:06:28,411 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:28,412 | ^~ 2023-09-17T12:06:28,412 src/pulchra.hpp:2447:25: warning: unused variable ‘jj’ [-Wunused-variable] 2023-09-17T12:06:28,413 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:28,414 | ^~ 2023-09-17T12:06:28,414 src/pulchra.hpp:2447:29: warning: unused variable ‘kk’ [-Wunused-variable] 2023-09-17T12:06:28,415 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:06:28,416 | ^~ 2023-09-17T12:06:28,417 src/pulchra.hpp:2450:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:06:28,417 2450 | int nsc, nca; 2023-09-17T12:06:28,418 | ^~~ 2023-09-17T12:06:28,419 src/pulchra.hpp:2451:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:06:28,419 2451 | double cax, cay, caz; 2023-09-17T12:06:28,420 | ^~~ 2023-09-17T12:06:28,421 src/pulchra.hpp:2451:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:06:28,421 2451 | double cax, cay, caz; 2023-09-17T12:06:28,422 | ^~~ 2023-09-17T12:06:28,423 src/pulchra.hpp:2451:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:06:28,423 2451 | double cax, cay, caz; 2023-09-17T12:06:28,424 | ^~~ 2023-09-17T12:06:28,425 src/pulchra.hpp:2453:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,425 2453 | double x1, y1, z1; 2023-09-17T12:06:28,426 | ^~ 2023-09-17T12:06:28,427 src/pulchra.hpp:2453:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,427 2453 | double x1, y1, z1; 2023-09-17T12:06:28,428 | ^~ 2023-09-17T12:06:28,429 src/pulchra.hpp:2453:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,429 2453 | double x1, y1, z1; 2023-09-17T12:06:28,430 | ^~ 2023-09-17T12:06:28,431 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2023-09-17T12:06:28,432 src/pulchra.hpp:2732:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:06:28,432 2732 | int i; 2023-09-17T12:06:28,433 | ^ 2023-09-17T12:06:28,433 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2023-09-17T12:06:28,434 src/pulchra.hpp:2828:42: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2023-09-17T12:06:28,435 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2023-09-17T12:06:28,435 | ^~~~~~~~~ 2023-09-17T12:06:28,436 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2023-09-17T12:06:28,436 src/pulchra.hpp:3042:24: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-17T12:06:28,437 3042 | int i, k, best; 2023-09-17T12:06:28,437 | ^ 2023-09-17T12:06:28,438 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2023-09-17T12:06:28,438 src/pulchra.hpp:3116:27: warning: unused variable ‘chain_length’ [-Wunused-variable] 2023-09-17T12:06:28,439 3116 | int const chain_length = chain->nres; 2023-09-17T12:06:28,439 | ^~~~~~~~~~~~ 2023-09-17T12:06:28,440 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2023-09-17T12:06:28,440 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=] 2023-09-17T12:06:28,441 3315 | "Done. Reconstruction finished in %ld s.\n", 2023-09-17T12:06:28,442 | ~~^ 2023-09-17T12:06:28,442 | | 2023-09-17T12:06:28,443 | long int 2023-09-17T12:06:28,444 | %lld 2023-09-17T12:06:28,444 3316 | std::chrono::duration_cast(time1 - time0) 2023-09-17T12:06:28,445 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:06:28,446 3317 | .count()); 2023-09-17T12:06:28,447 | ~~~~~~~~ 2023-09-17T12:06:28,447 | | 2023-09-17T12:06:28,448 | std::chrono::duration::rep {aka long long int} 2023-09-17T12:06:28,448 src/pulchra.hpp:3145:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:06:28,449 3145 | char buf[100]; 2023-09-17T12:06:28,450 | ^~~ 2023-09-17T12:06:28,450 src/pulchra.hpp:3146:37: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:06:28,451 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2023-09-17T12:06:28,451 | ^~~~~~~~ 2023-09-17T12:06:28,452 src/pulchra.hpp:3147:23: warning: unused variable ‘ptr’ [-Wunused-variable] 2023-09-17T12:06:28,453 3147 | char *ptr, out_name[1000]; 2023-09-17T12:06:28,454 | ^~~ 2023-09-17T12:06:28,454 src/pulchra.hpp:3147:28: warning: unused variable ‘out_name’ [-Wunused-variable] 2023-09-17T12:06:28,455 3147 | char *ptr, out_name[1000]; 2023-09-17T12:06:28,456 | ^~~~~~~~ 2023-09-17T12:06:48,221 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=1.0.0 -Isrc -I/tmp/pip-build-env-tezqktcm/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 2023-09-17T12:07:05,442 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=1.0.0 -Isrc -I/tmp/pip-build-env-tezqktcm/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 2023-09-17T12:07:13,957 In file included from src/pulchra.cpp:20: 2023-09-17T12:07:13,958 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::read_pdb_buffer(std::stringstream&, std::shared_ptr)’: 2023-09-17T12:07:13,959 src/pulchra.hpp:653:69: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2023-09-17T12:07:13,959 653 | res->type = AA_NUMS[pusetseq(resname)]; 2023-09-17T12:07:13,960 | ~~~~~~~~^~~~~~~~~ 2023-09-17T12:07:13,974 src/pulchra.hpp:594:22: warning: variable ‘version’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:13,975 594 | char version; 2023-09-17T12:07:13,975 | ^~~~~~~ 2023-09-17T12:07:13,976 src/pulchra.hpp:595:60: warning: unused variable ‘num’ [-Wunused-variable] 2023-09-17T12:07:13,977 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:13,977 | ^~~ 2023-09-17T12:07:13,978 src/pulchra.hpp:595:77: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:13,979 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:13,980 | ^ 2023-09-17T12:07:13,980 src/pulchra.hpp:595:80: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:13,981 595 | int prevresnum, resnum, atmnum, locatmnum, num, locnum = 0, i, j; 2023-09-17T12:07:13,982 | ^ 2023-09-17T12:07:13,983 src/pulchra.hpp:597:28: warning: unused variable ‘cc’ [-Wunused-variable] 2023-09-17T12:07:13,983 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:13,984 | ^~ 2023-09-17T12:07:13,985 src/pulchra.hpp:597:32: warning: unused variable ‘nres’ [-Wunused-variable] 2023-09-17T12:07:13,985 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:13,986 | ^~~~ 2023-09-17T12:07:13,987 src/pulchra.hpp:597:38: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:13,987 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:13,988 | ^~ 2023-09-17T12:07:13,988 src/pulchra.hpp:597:42: warning: unused variable ‘natom’ [-Wunused-variable] 2023-09-17T12:07:13,989 597 | int sgnum, cc, nres, ok, natom; 2023-09-17T12:07:13,990 | ^~~~~ 2023-09-17T12:07:13,991 src/pulchra.hpp:602:24: warning: unused variable ‘dist’ [-Wunused-variable] 2023-09-17T12:07:13,992 602 | double dist; 2023-09-17T12:07:13,993 | ^~~~ 2023-09-17T12:07:13,993 src/pulchra.hpp:603:31: warning: unused variable ‘bin’ [-Wunused-variable] 2023-09-17T12:07:13,993 603 | unsigned char bin; 2023-09-17T12:07:13,994 | ^~~ 2023-09-17T12:07:13,994 src/pulchra.hpp:604:21: warning: variable ‘warn’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:13,995 604 | int warn = 0; 2023-09-17T12:07:13,995 | ^~~~ 2023-09-17T12:07:13,996 src/pulchra.hpp:605:24: warning: unused variable ‘cutoff’ [-Wunused-variable] 2023-09-17T12:07:13,996 605 | double cutoff; 2023-09-17T12:07:13,997 | ^~~~~~ 2023-09-17T12:07:14,005 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::calc_ca_energy(const std::vector >&, double**, double**, double**, double, double*, bool, int)’: 2023-09-17T12:07:14,006 src/pulchra.hpp:775:24: warning: unused variable ‘theta0’ [-Wunused-variable] 2023-09-17T12:07:14,006 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,006 | ^~~~~~ 2023-09-17T12:07:14,007 src/pulchra.hpp:775:32: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:07:14,007 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,008 | ^~~~ 2023-09-17T12:07:14,008 src/pulchra.hpp:775:38: warning: unused variable ‘th’ [-Wunused-variable] 2023-09-17T12:07:14,009 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,009 | ^~ 2023-09-17T12:07:14,010 src/pulchra.hpp:775:42: warning: unused variable ‘aa’ [-Wunused-variable] 2023-09-17T12:07:14,011 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,011 | ^~ 2023-09-17T12:07:14,012 src/pulchra.hpp:775:46: warning: unused variable ‘bb’ [-Wunused-variable] 2023-09-17T12:07:14,013 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,014 | ^~ 2023-09-17T12:07:14,015 src/pulchra.hpp:775:50: warning: unused variable ‘ab’ [-Wunused-variable] 2023-09-17T12:07:14,015 775 | double theta0, tdif, th, aa, bb, ab; 2023-09-17T12:07:14,016 | ^~ 2023-09-17T12:07:14,017 src/pulchra.hpp:776:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:07:14,018 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,019 | ^~~ 2023-09-17T12:07:14,019 src/pulchra.hpp:776:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:07:14,020 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,020 | ^~~ 2023-09-17T12:07:14,021 src/pulchra.hpp:776:34: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:07:14,022 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,022 | ^~~ 2023-09-17T12:07:14,023 src/pulchra.hpp:776:39: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:07:14,024 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,024 | ^~ 2023-09-17T12:07:14,025 src/pulchra.hpp:776:43: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:07:14,026 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,026 | ^~ 2023-09-17T12:07:14,027 src/pulchra.hpp:776:53: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:07:14,028 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,029 | ^~ 2023-09-17T12:07:14,029 src/pulchra.hpp:776:60: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:07:14,030 776 | double ff0, ff2, dth, m0, m2, grad, f0[3], f2[3]; 2023-09-17T12:07:14,030 | ^~ 2023-09-17T12:07:14,031 src/pulchra.hpp:777:24: warning: unused variable ‘adiff’ [-Wunused-variable] 2023-09-17T12:07:14,031 777 | double adiff[3], bdiff[3]; 2023-09-17T12:07:14,032 | ^~~~~ 2023-09-17T12:07:14,032 src/pulchra.hpp:777:34: warning: unused variable ‘bdiff’ [-Wunused-variable] 2023-09-17T12:07:14,033 777 | double adiff[3], bdiff[3]; 2023-09-17T12:07:14,034 | ^~~~~ 2023-09-17T12:07:14,034 src/pulchra.hpp:778:24: warning: unused variable ‘deriv’ [-Wunused-variable] 2023-09-17T12:07:14,034 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,035 | ^~~~~ 2023-09-17T12:07:14,036 src/pulchra.hpp:778:38: warning: unused variable ‘dtheta’ [-Wunused-variable] 2023-09-17T12:07:14,036 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,037 | ^~~~~~ 2023-09-17T12:07:14,037 src/pulchra.hpp:778:46: warning: unused variable ‘len1’ [-Wunused-variable] 2023-09-17T12:07:14,038 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,038 | ^~~~ 2023-09-17T12:07:14,039 src/pulchra.hpp:778:52: warning: unused variable ‘len2’ [-Wunused-variable] 2023-09-17T12:07:14,039 778 | double deriv, theta, dtheta, len1, len2, cos_theta, sin_theta; 2023-09-17T12:07:14,040 | ^~~~ 2023-09-17T12:07:14,040 src/pulchra.hpp:779:24: warning: unused variable ‘dx1’ [-Wunused-variable] 2023-09-17T12:07:14,041 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,042 | ^~~ 2023-09-17T12:07:14,042 src/pulchra.hpp:779:29: warning: unused variable ‘dy1’ [-Wunused-variable] 2023-09-17T12:07:14,043 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,044 | ^~~ 2023-09-17T12:07:14,044 src/pulchra.hpp:779:34: warning: unused variable ‘dz1’ [-Wunused-variable] 2023-09-17T12:07:14,045 779 | double dx1, dy1, dz1; 2023-09-17T12:07:14,046 | ^~~ 2023-09-17T12:07:14,046 src/pulchra.hpp:780:24: warning: unused variable ‘dx2’ [-Wunused-variable] 2023-09-17T12:07:14,047 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,048 | ^~~ 2023-09-17T12:07:14,048 src/pulchra.hpp:780:29: warning: unused variable ‘dy2’ [-Wunused-variable] 2023-09-17T12:07:14,049 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,050 | ^~~ 2023-09-17T12:07:14,050 src/pulchra.hpp:780:34: warning: unused variable ‘dz2’ [-Wunused-variable] 2023-09-17T12:07:14,051 780 | double dx2, dy2, dz2; 2023-09-17T12:07:14,052 | ^~~ 2023-09-17T12:07:14,052 src/pulchra.hpp:781:24: warning: unused variable ‘dx3’ [-Wunused-variable] 2023-09-17T12:07:14,053 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,054 | ^~~ 2023-09-17T12:07:14,055 src/pulchra.hpp:781:29: warning: unused variable ‘dy3’ [-Wunused-variable] 2023-09-17T12:07:14,056 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,056 | ^~~ 2023-09-17T12:07:14,057 src/pulchra.hpp:781:34: warning: unused variable ‘dz3’ [-Wunused-variable] 2023-09-17T12:07:14,058 781 | double dx3, dy3, dz3; 2023-09-17T12:07:14,058 | ^~~ 2023-09-17T12:07:14,059 src/pulchra.hpp:782:24: warning: unused variable ‘vx1’ [-Wunused-variable] 2023-09-17T12:07:14,060 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,060 | ^~~ 2023-09-17T12:07:14,061 src/pulchra.hpp:782:29: warning: unused variable ‘vy1’ [-Wunused-variable] 2023-09-17T12:07:14,061 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,062 | ^~~ 2023-09-17T12:07:14,062 src/pulchra.hpp:782:34: warning: unused variable ‘vz1’ [-Wunused-variable] 2023-09-17T12:07:14,063 782 | double vx1, vy1, vz1; 2023-09-17T12:07:14,063 | ^~~ 2023-09-17T12:07:14,064 src/pulchra.hpp:783:24: warning: unused variable ‘vx2’ [-Wunused-variable] 2023-09-17T12:07:14,064 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,065 | ^~~ 2023-09-17T12:07:14,065 src/pulchra.hpp:783:29: warning: unused variable ‘vy2’ [-Wunused-variable] 2023-09-17T12:07:14,066 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,067 | ^~~ 2023-09-17T12:07:14,067 src/pulchra.hpp:783:34: warning: unused variable ‘vz2’ [-Wunused-variable] 2023-09-17T12:07:14,068 783 | double vx2, vy2, vz2; 2023-09-17T12:07:14,068 | ^~~ 2023-09-17T12:07:14,069 src/pulchra.hpp:784:24: warning: unused variable ‘vx3’ [-Wunused-variable] 2023-09-17T12:07:14,070 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,070 | ^~~ 2023-09-17T12:07:14,071 src/pulchra.hpp:784:29: warning: unused variable ‘vy3’ [-Wunused-variable] 2023-09-17T12:07:14,072 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,073 | ^~~ 2023-09-17T12:07:14,073 src/pulchra.hpp:784:34: warning: unused variable ‘vz3’ [-Wunused-variable] 2023-09-17T12:07:14,074 784 | double vx3, vy3, vz3; 2023-09-17T12:07:14,075 | ^~~ 2023-09-17T12:07:14,076 src/pulchra.hpp: In member function ‘std::string pulchra::Pulchra::ca_optimize_from_mol(std::shared_ptr)’: 2023-09-17T12:07:14,076 src/pulchra.hpp:937:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:07:14,077 937 | char buf[1000]; 2023-09-17T12:07:14,078 | ^~~ 2023-09-17T12:07:14,078 src/pulchra.hpp:938:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:14,079 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,080 | ^ 2023-09-17T12:07:14,080 src/pulchra.hpp:938:27: warning: unused variable ‘hx’ [-Wunused-variable] 2023-09-17T12:07:14,081 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,082 | ^~ 2023-09-17T12:07:14,082 src/pulchra.hpp:938:31: warning: unused variable ‘my_iter’ [-Wunused-variable] 2023-09-17T12:07:14,083 938 | int i, j, hx, my_iter; 2023-09-17T12:07:14,083 | ^~~~~~~ 2023-09-17T12:07:14,084 src/pulchra.hpp:939:46: warning: unused variable ‘dist2’ [-Wunused-variable] 2023-09-17T12:07:14,085 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,085 | ^~~~~ 2023-09-17T12:07:14,086 src/pulchra.hpp:939:53: warning: unused variable ‘dist3’ [-Wunused-variable] 2023-09-17T12:07:14,087 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,088 | ^~~~~ 2023-09-17T12:07:14,089 src/pulchra.hpp:939:67: warning: variable ‘ddist2’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,089 939 | double dx, dy, dz, dd, dist, dist2, dist3, ddist, ddist2; 2023-09-17T12:07:14,090 | ^~~~~~ 2023-09-17T12:07:14,090 src/pulchra.hpp:940:31: warning: unused variable ‘new_e_pot’ [-Wunused-variable] 2023-09-17T12:07:14,091 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,091 | ^~~~~~~~~ 2023-09-17T12:07:14,092 src/pulchra.hpp:940:42: warning: unused variable ‘grad’ [-Wunused-variable] 2023-09-17T12:07:14,092 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,093 | ^~~~ 2023-09-17T12:07:14,093 src/pulchra.hpp:940:48: warning: unused variable ‘alpha’ [-Wunused-variable] 2023-09-17T12:07:14,093 940 | double e_pot, new_e_pot, grad, alpha, e_pot1, e_pot2, e_pot3; 2023-09-17T12:07:14,094 | ^~~~~ 2023-09-17T12:07:14,095 src/pulchra.hpp:942:24: warning: unused variable ‘ff0’ [-Wunused-variable] 2023-09-17T12:07:14,095 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,096 | ^~~ 2023-09-17T12:07:14,096 src/pulchra.hpp:942:29: warning: unused variable ‘ff2’ [-Wunused-variable] 2023-09-17T12:07:14,097 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,097 | ^~~ 2023-09-17T12:07:14,098 src/pulchra.hpp:942:50: warning: unused variable ‘tdif’ [-Wunused-variable] 2023-09-17T12:07:14,099 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,100 | ^~~~ 2023-09-17T12:07:14,100 src/pulchra.hpp:942:56: warning: unused variable ‘dth’ [-Wunused-variable] 2023-09-17T12:07:14,101 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,102 | ^~~ 2023-09-17T12:07:14,103 src/pulchra.hpp:942:61: warning: unused variable ‘m0’ [-Wunused-variable] 2023-09-17T12:07:14,103 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,104 | ^~ 2023-09-17T12:07:14,105 src/pulchra.hpp:942:65: warning: unused variable ‘m2’ [-Wunused-variable] 2023-09-17T12:07:14,106 942 | double ff0, ff2, aa, ab, bb, th, tdif, dth, m0, m2; 2023-09-17T12:07:14,106 | ^~ 2023-09-17T12:07:14,107 src/pulchra.hpp:943:40: warning: unused variable ‘maxgrad’ [-Wunused-variable] 2023-09-17T12:07:14,107 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:07:14,108 | ^~~~~~~ 2023-09-17T12:07:14,109 src/pulchra.hpp:943:49: warning: unused variable ‘sum’ [-Wunused-variable] 2023-09-17T12:07:14,109 943 | double theta0, deg_th, maxgrad, sum; 2023-09-17T12:07:14,110 | ^~~ 2023-09-17T12:07:14,110 src/pulchra.hpp:944:24: warning: unused variable ‘f0’ [-Wunused-variable] 2023-09-17T12:07:14,111 944 | double f0[3], f2[3]; 2023-09-17T12:07:14,112 | ^~ 2023-09-17T12:07:14,112 src/pulchra.hpp:944:31: warning: unused variable ‘f2’ [-Wunused-variable] 2023-09-17T12:07:14,113 944 | double f0[3], f2[3]; 2023-09-17T12:07:14,114 | ^~ 2023-09-17T12:07:14,115 src/pulchra.hpp:945:24: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,115 945 | double x, y, z; 2023-09-17T12:07:14,116 | ^ 2023-09-17T12:07:14,116 src/pulchra.hpp:945:27: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,117 945 | double x, y, z; 2023-09-17T12:07:14,117 | ^ 2023-09-17T12:07:14,118 src/pulchra.hpp:945:30: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,118 945 | double x, y, z; 2023-09-17T12:07:14,119 | ^ 2023-09-17T12:07:14,119 src/pulchra.hpp:947:22: warning: unused variable ‘sec’ [-Wunused-variable] 2023-09-17T12:07:14,120 947 | int *sec; 2023-09-17T12:07:14,120 | ^~~ 2023-09-17T12:07:14,121 src/pulchra.hpp:948:79: warning: unused variable ‘tmp’ [-Wunused-variable] 2023-09-17T12:07:14,121 948 | double **new_c_alpha, **gradient, **init_c_alpha, last_alpha, tmp, 2023-09-17T12:07:14,122 | ^~~ 2023-09-17T12:07:14,122 src/pulchra.hpp:949:25: warning: unused variable ‘last_good_alpha’ [-Wunused-variable] 2023-09-17T12:07:14,123 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,123 | ^~~~~~~~~~~~~~~ 2023-09-17T12:07:14,124 src/pulchra.hpp:949:42: warning: unused variable ‘d_alpha’ [-Wunused-variable] 2023-09-17T12:07:14,124 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,125 | ^~~~~~~ 2023-09-17T12:07:14,125 src/pulchra.hpp:949:51: warning: variable ‘last_e_pot’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,126 949 | last_good_alpha, d_alpha, last_e_pot; 2023-09-17T12:07:14,127 | ^~~~~~~~~~ 2023-09-17T12:07:14,127 src/pulchra.hpp:953:23: warning: unused variable ‘inp’ [-Wunused-variable] 2023-09-17T12:07:14,128 953 | FILE *inp; 2023-09-17T12:07:14,129 | ^~~ 2023-09-17T12:07:14,130 src/pulchra.hpp:954:33: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:14,130 954 | int mnum, init, ok; 2023-09-17T12:07:14,131 | ^~ 2023-09-17T12:07:14,132 src/pulchra.hpp:958:24: warning: unused variable ‘w1’ [-Wunused-variable] 2023-09-17T12:07:14,133 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,133 | ^~ 2023-09-17T12:07:14,134 src/pulchra.hpp:958:28: warning: unused variable ‘w2’ [-Wunused-variable] 2023-09-17T12:07:14,135 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,135 | ^~ 2023-09-17T12:07:14,136 src/pulchra.hpp:958:32: warning: unused variable ‘w3’ [-Wunused-variable] 2023-09-17T12:07:14,136 958 | double w1, w2, w3, eps; 2023-09-17T12:07:14,137 | ^~ 2023-09-17T12:07:14,138 src/pulchra.hpp:960:21: warning: variable ‘mode’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,138 960 | int mode, fcnt; 2023-09-17T12:07:14,139 | ^~~~ 2023-09-17T12:07:14,140 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::prepare_rbins(std::shared_ptr)’: 2023-09-17T12:07:14,140 src/pulchra.hpp:1724:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:07:14,141 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,142 | ^ 2023-09-17T12:07:14,142 src/pulchra.hpp:1724:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:07:14,143 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,144 | ^ 2023-09-17T12:07:14,144 src/pulchra.hpp:1724:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:07:14,145 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,145 | ^~~~~ 2023-09-17T12:07:14,145 src/pulchra.hpp:1724:68: warning: unused variable ‘pro’ [-Wunused-variable] 2023-09-17T12:07:14,146 1724 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,146 | ^~~ 2023-09-17T12:07:14,147 src/pulchra.hpp:1725:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,148 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,148 | ^~~~~ 2023-09-17T12:07:14,148 src/pulchra.hpp:1725:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,149 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,149 | ^~~~~ 2023-09-17T12:07:14,150 src/pulchra.hpp:1725:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,150 1725 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,151 | ^~~ 2023-09-17T12:07:14,151 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_backbone(std::shared_ptr)’: 2023-09-17T12:07:14,151 src/pulchra.hpp:1852:30: warning: unused variable ‘l’ [-Wunused-variable] 2023-09-17T12:07:14,152 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,153 | ^ 2023-09-17T12:07:14,153 src/pulchra.hpp:1852:33: warning: unused variable ‘m’ [-Wunused-variable] 2023-09-17T12:07:14,154 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,155 | ^ 2023-09-17T12:07:14,155 src/pulchra.hpp:1852:61: warning: unused variable ‘found’ [-Wunused-variable] 2023-09-17T12:07:14,156 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,157 | ^~~~~ 2023-09-17T12:07:14,157 src/pulchra.hpp:1852:68: warning: variable ‘pro’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,158 1852 | int i, j, k, l, m, bin13_1, bin13_2, bin14, found, pro; 2023-09-17T12:07:14,159 | ^~~ 2023-09-17T12:07:14,159 src/pulchra.hpp:1853:21: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,160 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,160 | ^~~~~ 2023-09-17T12:07:14,161 src/pulchra.hpp:1853:28: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,161 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,162 | ^~~~~ 2023-09-17T12:07:14,163 src/pulchra.hpp:1853:35: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,163 1853 | int b13_1, b13_2, b14; 2023-09-17T12:07:14,164 | ^~~ 2023-09-17T12:07:14,165 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::rebuild_sidechains(std::shared_ptr)’: 2023-09-17T12:07:14,166 src/pulchra.hpp:2023:26: warning: unused variable ‘cacoords’ [-Wunused-variable] 2023-09-17T12:07:14,166 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,167 | ^~~~~~~~ 2023-09-17T12:07:14,168 src/pulchra.hpp:2023:38: warning: unused variable ‘tmpcoords’ [-Wunused-variable] 2023-09-17T12:07:14,168 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,169 | ^~~~~~~~~ 2023-09-17T12:07:14,169 src/pulchra.hpp:2023:51: warning: unused variable ‘tmpstat’ [-Wunused-variable] 2023-09-17T12:07:14,170 2023 | double **cacoords, **tmpcoords, **tmpstat; 2023-09-17T12:07:14,170 | ^~~~~~~ 2023-09-17T12:07:14,171 src/pulchra.hpp:2024:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,171 2024 | double x1, y1, z1; 2023-09-17T12:07:14,172 | ^~ 2023-09-17T12:07:14,172 src/pulchra.hpp:2024:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,173 2024 | double x1, y1, z1; 2023-09-17T12:07:14,173 | ^~ 2023-09-17T12:07:14,174 src/pulchra.hpp:2024:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,174 2024 | double x1, y1, z1; 2023-09-17T12:07:14,175 | ^~ 2023-09-17T12:07:14,175 src/pulchra.hpp:2028:24: warning: unused variable ‘x5’ [-Wunused-variable] 2023-09-17T12:07:14,176 2028 | double x5, y5, z5; 2023-09-17T12:07:14,176 | ^~ 2023-09-17T12:07:14,177 src/pulchra.hpp:2028:28: warning: unused variable ‘y5’ [-Wunused-variable] 2023-09-17T12:07:14,177 2028 | double x5, y5, z5; 2023-09-17T12:07:14,178 | ^~ 2023-09-17T12:07:14,178 src/pulchra.hpp:2028:32: warning: unused variable ‘z5’ [-Wunused-variable] 2023-09-17T12:07:14,179 2028 | double x5, y5, z5; 2023-09-17T12:07:14,180 | ^~ 2023-09-17T12:07:14,180 src/pulchra.hpp:2029:24: warning: unused variable ‘r14’ [-Wunused-variable] 2023-09-17T12:07:14,181 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,181 | ^~~ 2023-09-17T12:07:14,182 src/pulchra.hpp:2029:29: warning: unused variable ‘r13_1’ [-Wunused-variable] 2023-09-17T12:07:14,183 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,183 | ^~~~~ 2023-09-17T12:07:14,184 src/pulchra.hpp:2029:36: warning: unused variable ‘r13_2’ [-Wunused-variable] 2023-09-17T12:07:14,185 2029 | double r14, r13_1, r13_2; 2023-09-17T12:07:14,185 | ^~~~~ 2023-09-17T12:07:14,186 src/pulchra.hpp:2030:24: warning: unused variable ‘dx’ [-Wunused-variable] 2023-09-17T12:07:14,187 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,187 | ^~ 2023-09-17T12:07:14,188 src/pulchra.hpp:2030:28: warning: unused variable ‘dy’ [-Wunused-variable] 2023-09-17T12:07:14,189 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,189 | ^~ 2023-09-17T12:07:14,190 src/pulchra.hpp:2030:32: warning: unused variable ‘dz’ [-Wunused-variable] 2023-09-17T12:07:14,191 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,191 | ^~ 2023-09-17T12:07:14,192 src/pulchra.hpp:2030:36: warning: unused variable ‘dd’ [-Wunused-variable] 2023-09-17T12:07:14,192 2030 | double dx, dy, dz, dd; 2023-09-17T12:07:14,193 | ^~ 2023-09-17T12:07:14,194 src/pulchra.hpp:2031:29: warning: variable ‘besthit’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,195 2031 | double hit, besthit; 2023-09-17T12:07:14,195 | ^~~~~~~ 2023-09-17T12:07:14,196 src/pulchra.hpp:2032:21: warning: unused variable ‘exvol’ [-Wunused-variable] 2023-09-17T12:07:14,197 2032 | int exvol, bestpos; 2023-09-17T12:07:14,198 | ^~~~~ 2023-09-17T12:07:14,198 src/pulchra.hpp:2034:24: warning: unused variable ‘rmsd’ [-Wunused-variable] 2023-09-17T12:07:14,199 2034 | double rmsd, total; 2023-09-17T12:07:14,199 | ^~~~ 2023-09-17T12:07:14,200 src/pulchra.hpp:2034:30: warning: unused variable ‘total’ [-Wunused-variable] 2023-09-17T12:07:14,200 2034 | double rmsd, total; 2023-09-17T12:07:14,201 | ^~~~~ 2023-09-17T12:07:14,201 src/pulchra.hpp:2036:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:07:14,202 2036 | int nsc, nca; 2023-09-17T12:07:14,202 | ^~~ 2023-09-17T12:07:14,203 src/pulchra.hpp:2037:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:07:14,203 2037 | double cax, cay, caz; 2023-09-17T12:07:14,204 | ^~~ 2023-09-17T12:07:14,204 src/pulchra.hpp:2037:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:07:14,205 2037 | double cax, cay, caz; 2023-09-17T12:07:14,206 | ^~~ 2023-09-17T12:07:14,206 src/pulchra.hpp:2037:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:07:14,207 2037 | double cax, cay, caz; 2023-09-17T12:07:14,207 | ^~~ 2023-09-17T12:07:14,208 src/pulchra.hpp:2039:22: warning: unused variable ‘scn’ [-Wunused-variable] 2023-09-17T12:07:14,209 2039 | char scn[12][4]; 2023-09-17T12:07:14,210 | ^~~ 2023-09-17T12:07:14,211 src/pulchra.hpp:2040:21: warning: unused variable ‘ok’ [-Wunused-variable] 2023-09-17T12:07:14,211 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,212 | ^~ 2023-09-17T12:07:14,213 src/pulchra.hpp:2040:25: warning: unused variable ‘last_a’ [-Wunused-variable] 2023-09-17T12:07:14,214 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,214 | ^~~~~~ 2023-09-17T12:07:14,215 src/pulchra.hpp:2040:33: warning: unused variable ‘last_b’ [-Wunused-variable] 2023-09-17T12:07:14,216 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,216 | ^~~~~~ 2023-09-17T12:07:14,217 src/pulchra.hpp:2040:41: warning: unused variable ‘last_c’ [-Wunused-variable] 2023-09-17T12:07:14,218 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,219 | ^~~~~~ 2023-09-17T12:07:14,219 src/pulchra.hpp:2040:49: warning: unused variable ‘last_d’ [-Wunused-variable] 2023-09-17T12:07:14,220 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,221 | ^~~~~~ 2023-09-17T12:07:14,221 src/pulchra.hpp:2040:57: warning: unused variable ‘jpos’ [-Wunused-variable] 2023-09-17T12:07:14,222 2040 | int ok, last_a, last_b, last_c, last_d, jpos; 2023-09-17T12:07:14,223 | ^~~~ 2023-09-17T12:07:14,223 src/pulchra.hpp:2041:21: warning: unused variable ‘jx’ [-Wunused-variable] 2023-09-17T12:07:14,224 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,224 | ^~ 2023-09-17T12:07:14,225 src/pulchra.hpp:2041:25: warning: unused variable ‘jy’ [-Wunused-variable] 2023-09-17T12:07:14,226 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,227 | ^~ 2023-09-17T12:07:14,228 src/pulchra.hpp:2041:29: warning: unused variable ‘jz’ [-Wunused-variable] 2023-09-17T12:07:14,228 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,229 | ^~ 2023-09-17T12:07:14,229 src/pulchra.hpp:2041:33: warning: unused variable ‘jxi’ [-Wunused-variable] 2023-09-17T12:07:14,230 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,230 | ^~~ 2023-09-17T12:07:14,231 src/pulchra.hpp:2041:38: warning: unused variable ‘jyi’ [-Wunused-variable] 2023-09-17T12:07:14,231 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,232 | ^~~ 2023-09-17T12:07:14,232 src/pulchra.hpp:2041:43: warning: unused variable ‘jzi’ [-Wunused-variable] 2023-09-17T12:07:14,233 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,234 | ^~~ 2023-09-17T12:07:14,234 src/pulchra.hpp:2041:48: warning: unused variable ‘b13_1’ [-Wunused-variable] 2023-09-17T12:07:14,235 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,235 | ^~~~~ 2023-09-17T12:07:14,235 src/pulchra.hpp:2041:55: warning: unused variable ‘b13_2’ [-Wunused-variable] 2023-09-17T12:07:14,236 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,236 | ^~~~~ 2023-09-17T12:07:14,237 src/pulchra.hpp:2041:62: warning: unused variable ‘b14’ [-Wunused-variable] 2023-09-17T12:07:14,237 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,238 | ^~~ 2023-09-17T12:07:14,239 src/pulchra.hpp:2041:67: warning: unused variable ‘jm’ [-Wunused-variable] 2023-09-17T12:07:14,240 2041 | int jx, jy, jz, jxi, jyi, jzi, b13_1, b13_2, b14, jm; 2023-09-17T12:07:14,240 | ^~ 2023-09-17T12:07:14,241 src/pulchra.hpp:2042:27: warning: unused variable ‘bestrot’ [-Wunused-variable] 2023-09-17T12:07:14,242 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,242 | ^~~~~~~ 2023-09-17T12:07:14,243 src/pulchra.hpp:2042:36: warning: unused variable ‘minexvol’ [-Wunused-variable] 2023-09-17T12:07:14,244 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,245 | ^~~~~~~~ 2023-09-17T12:07:14,245 src/pulchra.hpp:2042:46: warning: variable ‘totexvol’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,246 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,247 | ^~~~~~~~ 2023-09-17T12:07:14,247 src/pulchra.hpp:2042:56: warning: unused variable ‘rtried’ [-Wunused-variable] 2023-09-17T12:07:14,248 2042 | int crot, bestrot, minexvol, totexvol, rtried, pos, cpos; 2023-09-17T12:07:14,248 | ^~~~~~ 2023-09-17T12:07:14,249 src/pulchra.hpp:2044:24: warning: unused variable ‘sort_rot’ [-Wunused-variable] 2023-09-17T12:07:14,250 2044 | double sort_rot[100][2]; 2023-09-17T12:07:14,250 | ^~~~~~~~ 2023-09-17T12:07:14,251 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::get_conflicts(std::shared_ptr, pulchra::atom_list_3d, int, int, int)’: 2023-09-17T12:07:14,252 src/pulchra.hpp:2264:30: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,252 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,253 | ^ 2023-09-17T12:07:14,254 src/pulchra.hpp:2264:33: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,254 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,255 | ^ 2023-09-17T12:07:14,255 src/pulchra.hpp:2264:36: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,256 2264 | int i, j, k, x, y, z; 2023-09-17T12:07:14,256 | ^ 2023-09-17T12:07:14,257 src/pulchra.hpp:2265:38: warning: unused variable ‘iter’ [-Wunused-variable] 2023-09-17T12:07:14,257 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:07:14,258 | ^~~~ 2023-09-17T12:07:14,258 src/pulchra.hpp:2265:44: warning: unused variable ‘maxcon’ [-Wunused-variable] 2023-09-17T12:07:14,259 2265 | int ii, jj, kk, con, iter, maxcon, merged; 2023-09-17T12:07:14,259 | ^~~~~~ 2023-09-17T12:07:14,260 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:07:14,260 src/pulchra.hpp:2374:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:07:14,261 2374 | int i, j, x, y, z; 2023-09-17T12:07:14,261 | ^ 2023-09-17T12:07:14,262 src/pulchra.hpp:2374:24: warning: unused variable ‘j’ [-Wunused-variable] 2023-09-17T12:07:14,262 2374 | int i, j, x, y, z; 2023-09-17T12:07:14,263 | ^ 2023-09-17T12:07:14,264 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_exvol(std::shared_ptr)’: 2023-09-17T12:07:14,264 src/pulchra.hpp:2440:24: warning: variable ‘min’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,265 2440 | double min[3], max[3]; 2023-09-17T12:07:14,265 | ^~~ 2023-09-17T12:07:14,266 src/pulchra.hpp:2440:32: warning: variable ‘max’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,267 2440 | double min[3], max[3]; 2023-09-17T12:07:14,267 | ^~~ 2023-09-17T12:07:14,268 src/pulchra.hpp:2446:36: warning: unused variable ‘x’ [-Wunused-variable] 2023-09-17T12:07:14,269 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,269 | ^ 2023-09-17T12:07:14,270 src/pulchra.hpp:2446:39: warning: unused variable ‘y’ [-Wunused-variable] 2023-09-17T12:07:14,271 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,271 | ^ 2023-09-17T12:07:14,272 src/pulchra.hpp:2446:42: warning: unused variable ‘z’ [-Wunused-variable] 2023-09-17T12:07:14,272 2446 | int i, j, k, l, m, x, y, z; 2023-09-17T12:07:14,273 | ^ 2023-09-17T12:07:14,274 src/pulchra.hpp:2447:21: warning: unused variable ‘ii’ [-Wunused-variable] 2023-09-17T12:07:14,274 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,275 | ^~ 2023-09-17T12:07:14,275 src/pulchra.hpp:2447:25: warning: unused variable ‘jj’ [-Wunused-variable] 2023-09-17T12:07:14,276 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,277 | ^~ 2023-09-17T12:07:14,277 src/pulchra.hpp:2447:29: warning: unused variable ‘kk’ [-Wunused-variable] 2023-09-17T12:07:14,278 2447 | int ii, jj, kk, con, iter, maxcon, totcon; 2023-09-17T12:07:14,279 | ^~ 2023-09-17T12:07:14,280 src/pulchra.hpp:2450:26: warning: unused variable ‘nca’ [-Wunused-variable] 2023-09-17T12:07:14,281 2450 | int nsc, nca; 2023-09-17T12:07:14,281 | ^~~ 2023-09-17T12:07:14,282 src/pulchra.hpp:2451:24: warning: unused variable ‘cax’ [-Wunused-variable] 2023-09-17T12:07:14,282 2451 | double cax, cay, caz; 2023-09-17T12:07:14,283 | ^~~ 2023-09-17T12:07:14,283 src/pulchra.hpp:2451:29: warning: unused variable ‘cay’ [-Wunused-variable] 2023-09-17T12:07:14,284 2451 | double cax, cay, caz; 2023-09-17T12:07:14,284 | ^~~ 2023-09-17T12:07:14,285 src/pulchra.hpp:2451:34: warning: unused variable ‘caz’ [-Wunused-variable] 2023-09-17T12:07:14,285 2451 | double cax, cay, caz; 2023-09-17T12:07:14,286 | ^~~ 2023-09-17T12:07:14,287 src/pulchra.hpp:2453:24: warning: variable ‘x1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,287 2453 | double x1, y1, z1; 2023-09-17T12:07:14,288 | ^~ 2023-09-17T12:07:14,288 src/pulchra.hpp:2453:28: warning: variable ‘y1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,289 2453 | double x1, y1, z1; 2023-09-17T12:07:14,289 | ^~ 2023-09-17T12:07:14,290 src/pulchra.hpp:2453:32: warning: variable ‘z1’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,290 2453 | double x1, y1, z1; 2023-09-17T12:07:14,291 | ^~ 2023-09-17T12:07:14,291 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::chirality_check(std::shared_ptr)’: 2023-09-17T12:07:14,292 src/pulchra.hpp:2732:21: warning: unused variable ‘i’ [-Wunused-variable] 2023-09-17T12:07:14,293 2732 | int i; 2023-09-17T12:07:14,293 | ^ 2023-09-17T12:07:14,294 src/pulchra.hpp: In member function ‘double pulchra::Pulchra::hb_energy(std::shared_ptr, pulchra::atom_list_3d&, int, int, int)’: 2023-09-17T12:07:14,295 src/pulchra.hpp:2828:42: warning: unused variable ‘min_dist1’ [-Wunused-variable] 2023-09-17T12:07:14,295 2828 | double dx, dy, dz, dist, min_dist1, min_dist2; 2023-09-17T12:07:14,296 | ^~~~~~~~~ 2023-09-17T12:07:14,297 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::optimize_backbone(std::shared_ptr)’: 2023-09-17T12:07:14,297 src/pulchra.hpp:3042:24: warning: unused variable ‘k’ [-Wunused-variable] 2023-09-17T12:07:14,298 3042 | int i, k, best; 2023-09-17T12:07:14,299 | ^ 2023-09-17T12:07:14,299 src/pulchra.hpp: In member function ‘pulchra::PulchraResult pulchra::Pulchra::run_from_mol(std::shared_ptr)’: 2023-09-17T12:07:14,300 src/pulchra.hpp:3116:27: warning: unused variable ‘chain_length’ [-Wunused-variable] 2023-09-17T12:07:14,301 3116 | int const chain_length = chain->nres; 2023-09-17T12:07:14,301 | ^~~~~~~~~~~~ 2023-09-17T12:07:14,307 src/pulchra.hpp: In member function ‘int pulchra::Pulchra::main(int, char**)’: 2023-09-17T12:07:14,307 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=] 2023-09-17T12:07:14,308 3315 | "Done. Reconstruction finished in %ld s.\n", 2023-09-17T12:07:14,309 | ~~^ 2023-09-17T12:07:14,309 | | 2023-09-17T12:07:14,310 | long int 2023-09-17T12:07:14,311 | %lld 2023-09-17T12:07:14,312 3316 | std::chrono::duration_cast(time1 - time0) 2023-09-17T12:07:14,312 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:14,313 3317 | .count()); 2023-09-17T12:07:14,313 | ~~~~~~~~ 2023-09-17T12:07:14,313 | | 2023-09-17T12:07:14,314 | std::chrono::duration::rep {aka long long int} 2023-09-17T12:07:14,314 src/pulchra.hpp:3145:22: warning: unused variable ‘buf’ [-Wunused-variable] 2023-09-17T12:07:14,315 3145 | char buf[100]; 2023-09-17T12:07:14,315 | ^~~ 2023-09-17T12:07:14,315 src/pulchra.hpp:3146:37: warning: variable ‘ini_name’ set but not used [-Wunused-but-set-variable] 2023-09-17T12:07:14,316 3146 | char *name = NULL, *ini_name = NULL, *output_pdb_name=NULL, *output_traj_pdb_name=NULL; 2023-09-17T12:07:14,316 | ^~~~~~~~ 2023-09-17T12:07:14,317 src/pulchra.hpp:3147:23: warning: unused variable ‘ptr’ [-Wunused-variable] 2023-09-17T12:07:14,317 3147 | char *ptr, out_name[1000]; 2023-09-17T12:07:14,317 | ^~~ 2023-09-17T12:07:14,318 src/pulchra.hpp:3147:28: warning: unused variable ‘out_name’ [-Wunused-variable] 2023-09-17T12:07:14,318 3147 | char *ptr, out_name[1000]; 2023-09-17T12:07:14,319 | ^~~~~~~~ 2023-09-17T12:07:37,995 src/pulchra.hpp: In member function ‘void pulchra::Pulchra::allocate_grid(std::shared_ptr, pulchra::atom_list_3d&, int*, int*, int*)’: 2023-09-17T12:07:37,996 src/pulchra.hpp:2429:39: warning: ‘xgrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:37,996 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:37,997 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:37,998 2430 | zgrid); 2023-09-17T12:07:37,998 | ~~~~~~ 2023-09-17T12:07:37,999 src/pulchra.hpp:2365:21: note: ‘xgrid’ was declared here 2023-09-17T12:07:38,000 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,001 | ^~~~~ 2023-09-17T12:07:38,002 src/pulchra.hpp:2429:39: warning: ‘ygrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:38,002 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:38,003 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:38,004 2430 | zgrid); 2023-09-17T12:07:38,004 | ~~~~~~ 2023-09-17T12:07:38,005 src/pulchra.hpp:2365:28: note: ‘ygrid’ was declared here 2023-09-17T12:07:38,006 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,006 | ^~~~~ 2023-09-17T12:07:38,007 src/pulchra.hpp:2429:39: warning: ‘zgrid’ may be used uninitialized [-Wmaybe-uninitialized] 2023-09-17T12:07:38,008 2429 | printf("Grid already allocated (%d %d %d)\n", xgrid, ygrid, 2023-09-17T12:07:38,009 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-17T12:07:38,009 2430 | zgrid); 2023-09-17T12:07:38,010 | ~~~~~~ 2023-09-17T12:07:38,011 src/pulchra.hpp:2365:35: note: ‘zgrid’ was declared here 2023-09-17T12:07:38,012 2365 | int xgrid, ygrid, zgrid; 2023-09-17T12:07:38,012 | ^~~~~ 2023-09-17T12:07:42,973 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 2023-09-17T12:07:43,365 installing to build/bdist.linux-armv7l/wheel 2023-09-17T12:07:43,365 running install 2023-09-17T12:07:43,389 running install_lib 2023-09-17T12:07:43,396 creating build/bdist.linux-armv7l 2023-09-17T12:07:43,396 creating build/bdist.linux-armv7l/wheel 2023-09-17T12:07:43,397 creating build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,398 copying build/lib.linux-armv7l-cpython-311/pypulchra/_pypulchra.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,458 copying build/lib.linux-armv7l-cpython-311/pypulchra/__init__.py -> build/bdist.linux-armv7l/wheel/pypulchra 2023-09-17T12:07:43,460 running install_egg_info 2023-09-17T12:07:43,471 running egg_info 2023-09-17T12:07:43,476 writing pypulchra.egg-info/PKG-INFO 2023-09-17T12:07:43,479 writing dependency_links to pypulchra.egg-info/dependency_links.txt 2023-09-17T12:07:43,481 writing entry points to pypulchra.egg-info/entry_points.txt 2023-09-17T12:07:43,482 writing top-level names to pypulchra.egg-info/top_level.txt 2023-09-17T12:07:43,490 reading manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:07:43,492 reading manifest template 'MANIFEST.in' 2023-09-17T12:07:43,498 writing manifest file 'pypulchra.egg-info/SOURCES.txt' 2023-09-17T12:07:43,500 Copying pypulchra.egg-info to build/bdist.linux-armv7l/wheel/pypulchra-1.0.0-py3.11.egg-info 2023-09-17T12:07:43,511 running install_scripts 2023-09-17T12:07:43,556 creating build/bdist.linux-armv7l/wheel/pypulchra-1.0.0.dist-info/WHEEL 2023-09-17T12:07:43,558 creating '/tmp/pip-wheel-2kqanhja/.tmp-v6ckzgaf/pypulchra-1.0.0-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-09-17T12:07:43,561 adding 'pypulchra/__init__.py' 2023-09-17T12:07:44,193 adding 'pypulchra/_pypulchra.cpython-311-arm-linux-gnueabihf.so' 2023-09-17T12:07:44,226 adding 'pypulchra-1.0.0.dist-info/METADATA' 2023-09-17T12:07:44,228 adding 'pypulchra-1.0.0.dist-info/WHEEL' 2023-09-17T12:07:44,229 adding 'pypulchra-1.0.0.dist-info/entry_points.txt' 2023-09-17T12:07:44,230 adding 'pypulchra-1.0.0.dist-info/top_level.txt' 2023-09-17T12:07:44,231 adding 'pypulchra-1.0.0.dist-info/RECORD' 2023-09-17T12:07:44,263 removing build/bdist.linux-armv7l/wheel 2023-09-17T12:07:44,360 Building wheel for pypulchra (pyproject.toml): finished with status 'done' 2023-09-17T12:07:44,406 Created wheel for pypulchra: filename=pypulchra-1.0.0-cp311-cp311-linux_armv7l.whl size=1940793 sha256=b2e8b1821d02eab86c82ab2b3ce141e4593af0a46b6d77c5763d89b91159472f 2023-09-17T12:07:44,407 Stored in directory: /tmp/pip-ephem-wheel-cache-bbebpikm/wheels/7e/57/5e/4aba252d3bb4446f9d637c9ec5bb9c5d7e78d4f0ff44f2f31f 2023-09-17T12:07:44,418 Successfully built pypulchra 2023-09-17T12:07:44,468 Removed build tracker: '/tmp/pip-build-tracker-9uem0i8v'