Diff of the two buildlogs: -- --- b1/build.log 2025-11-27 06:33:20.007018904 +0000 +++ b2/build.log 2025-11-27 06:39:09.423417787 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 30 00:45:43 -12 2026 -I: pbuilder-time-stamp: 1798634743 +I: Current time: Thu Nov 27 20:33:40 +14 2025 +I: pbuilder-time-stamp: 1764225220 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying fix-gemmi-incompatibility.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1981773/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 27 06:33 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='144bb49615b6423984022921d77231c5' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1981773' - PS1='# ' - PS2='> ' + INVOCATION_ID=db5a392803cb459d856ec8580a2d3329 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=789579 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.f6qiBLMu/pbuilderrc_80XC --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.f6qiBLMu/b1 --logfile b1/build.log macromoleculebuilder_4.2+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.f6qiBLMu/pbuilderrc_6ZpF --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.f6qiBLMu/b2 --logfile b2/build.log macromoleculebuilder_4.2+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1981773/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -302,7 +334,7 @@ Get: 166 http://deb.debian.org/debian forky/main arm64 libstb0t64 arm64 0.0~git20250907.fede005+ds-1 [210 kB] Get: 167 http://deb.debian.org/debian forky/main arm64 libstb-dev arm64 0.0~git20250907.fede005+ds-1 [651 kB] Get: 168 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 107 MB in 1s (75.3 MB/s) +Fetched 107 MB in 1s (138 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19968 files and directories currently installed.) @@ -858,8 +890,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Dec 30 12:46:45 UTC 2026. -Universal Time is now: Wed Dec 30 12:46:45 UTC 2026. +Local time is now: Thu Nov 27 06:34:19 UTC 2025. +Universal Time is now: Thu Nov 27 06:34:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1010,7 +1042,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/macromoleculebuilder-4.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../macromoleculebuilder_4.2+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/macromoleculebuilder-4.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../macromoleculebuilder_4.2+dfsg-1_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1033,7 +1069,7 @@ -DOpenMM_INCLUDE_DIR=/usr/include \ -DSimTKmolmodel=/usr \ -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0" - cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0" .. + cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0" .. -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done @@ -1047,11 +1083,12 @@ -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found --- Configuring done (1.9s) +-- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: + BUILD_TESTING CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED @@ -1073,30 +1110,30 @@ make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu' -[ 3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Utils.cpp.o -MF CMakeFiles/MMB.dir/src/Utils.cpp.o.d -o CMakeFiles/MMB.dir/src/Utils.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Utils.cpp -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o +[ 3%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o +[ 6%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o +[ 12%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -MF CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp [ 9%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -MF CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o.d -o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/UnitCellParameters.cpp -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DisplacementContainer.cpp +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. 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-pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp -[ 15%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC 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-fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Repel.cpp.o -MF CMakeFiles/MMB.dir/src/Repel.cpp.o.d -o CMakeFiles/MMB.dir/src/Repel.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, @@ -1125,10 +1162,10 @@ | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/MoleculeContainer.h:6, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:3: + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1152,8 +1189,9 @@ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Utils.cpp:12: + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:14: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1177,22 +1215,9 @@ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, - from /usr/include/molmodel/molmodel/internal/Compound.h:36, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DisplacementContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DisplacementContainer.cpp:12: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /usr/include/molmodel/molmodel/internal/Compound.h:36, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:10: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1213,6 +1238,15 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:11: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) @@ -1233,8 +1267,8 @@ from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:12: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1259,7 +1293,7 @@ from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Utils.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1282,19 +1316,35 @@ | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:10: + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1303,22 +1353,10 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) @@ -1327,16 +1365,12 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:12: + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/MoleculeContainer.h:6, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:3: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1359,10 +1393,12 @@ | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp:11: + from /usr/include/simbody/SimTKsimbody.h:43, + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:4, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1388,7 +1424,8 @@ from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:14: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DisplacementContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DisplacementContainer.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -1409,42 +1446,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:17: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -1457,7 +1458,8 @@ 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -1469,16 +1471,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:12: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:11: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -1500,99 +1492,15 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] - 26 | bool myEndCapsOn; - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 70 | if(id < 0 || id >= contactWithinVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 77 | if(id < 0 || id >= contactWithinVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 275 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here - 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': -/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here - 1249 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here - 1258 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 129 | if(index < 0 || index >= constraintClassVector.size()) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | if(index < 0 || index >= constraintClassVector.size()) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here - 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': -/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here - 1249 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here - 1258 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp: In member function 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator; reference = BaseInteraction&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 44 | myBasePairVector.at(index); @@ -1604,8 +1512,6 @@ /usr/include/c++/15/bits/stl_vector.h:1313:7: note: declared here 1313 | at(size_type __n) | ^~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/MoleculeContainer.h:8: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -1613,15 +1519,47 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 284 | return 0; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 190 | if( (dist <= it->range) && + | ~~~~~~~~~~~~~~~~~~~~^~ + 191 | (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:12: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -1643,6 +1581,10 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -1664,14 +1606,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] - 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable 'biopolymerAtomTargetsIterator' set but not used [-Wunused-but-set-variable] - 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/PeriodicScrubber.h:16, @@ -1683,16 +1617,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 284 | return 0; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 190 | if( (dist <= it->range) && - | ~~~~~~~~~~~~~~~~~~~~^~ - 191 | (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': @@ -1702,27 +1626,32 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 284 | return 0; | ^~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/MoleculeContainer.h:8: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:324:15: warning: unused variable 'myAngle1' [-Wunused-variable] - 324 | Angle myAngle1 = 180*Deg2Rad; // this is a bond angle - | ^~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:11: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -1734,31 +1663,14 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here - 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': -/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here - 1249 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here - 1258 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 129 | if(index < 0 || index >= constraintClassVector.size()) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 146 | if(index < 0 || index >= constraintClassVector.size()) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': @@ -1798,20 +1710,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 18 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -1833,6 +1731,25 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:12: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -1862,10 +1779,35 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2172 | if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] + 26 | bool myEndCapsOn; + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 70 | if(id < 0 || id >= contactWithinVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 77 | if(id < 0 || id >= contactWithinVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:324:15: warning: unused variable 'myAngle1' [-Wunused-variable] + 324 | Angle myAngle1 = 180*Deg2Rad; // this is a bond angle + | ^~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} @@ -1874,14 +1816,30 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable 'myExtension' [-Wunused-variable] 65 | double myExtension = 0.0; | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:172:31: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] + 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); + | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteAtomSpring(int)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 194 | if(id < 0 || id >= atomSpringVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 275 | if(id < 0 || id >= residueStretchVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 201 | if(id < 0 || id >= atomSpringVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 283 | if(id < 0 || id >= residueStretchVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] + 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteThreading(int)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 260 | if(id < 0 || id >= threadingStructVector.size()){ @@ -1890,10 +1848,49 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 268 | if(id < 0 || id >= threadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] + 269 | ParameterReader * _parameterReader; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] + 259 | SimbodyMatterSubsystem _matter; + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] + 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), + | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:279:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 279 | if(id < 0 || id >= threadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:405:10: warning: variable 'readFromFile' set but not used [-Wunused-but-set-variable] + 405 | bool readFromFile = false; + | ^~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here + 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': +/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here + 1249 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here + 1258 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] + 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteGappedThreading(int)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:446:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 446 | if(id < 0 || id >= gappedThreadingStructVector.size()){ @@ -1934,38 +1931,39 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:172:31: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] - 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] - 269 | ParameterReader * _parameterReader; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] - 259 | SimbodyMatterSubsystem _matter; - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] - 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:405:10: warning: variable 'readFromFile' set but not used [-Wunused-but-set-variable] - 405 | bool readFromFile = false; - | ^~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here + 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': +/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here + 1249 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here + 1258 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable 'biopolymerAtomTargetsIterator' set but not used [-Wunused-but-set-variable] + 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 18 | if(id < 0 || id >= residueStretchVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2012,20 +2010,24 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 2172 | if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -2056,69 +2058,27 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:208:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 208 | for (int i = 0; i < interfaceContainer.numInterfaces(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:16: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here - 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 300 | for ( int j = 0 ; j < neighborList.size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]' - 2584 | residueStretchContainer.printResidueStretchVector(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2588:181: required from here - 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); - | ^ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' - 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here - 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 104 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4825:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' - 4825 | residueStretchContainer.printResidueStretchVector(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4828:213: required from here - 4828 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); - | ^ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here + 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': +/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here + 1249 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here + 1258 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; @@ -2185,6 +2145,32 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:16: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here + 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 300 | for ( int j = 0 ; j < neighborList.size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ [ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -MF CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o.d -o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MonoAtoms.cpp /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: @@ -2194,10 +2180,57 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ -[ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp -[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]' + 2584 | residueStretchContainer.printResidueStretchVector(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2588:181: required from here + 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); + | ^ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' + 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here + 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 104 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4825:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' + 4825 | residueStretchContainer.printResidueStretchVector(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4828:213: required from here + 4828 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); + | ^ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:17: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ +[ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:97:17: warning: 'bool compareUpper(const std::string&, const char*)' defined but not used [-Wunused-function] + 97 | static bool compareUpper( const string& param, const char* symbol ) { + | ^~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, @@ -2276,25 +2294,10 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ +[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp [ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BaseInteractionParameterReader.cpp -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:97:17: warning: 'bool compareUpper(const std::string&, const char*)' defined but not used [-Wunused-function] - 97 | static bool compareUpper( const string& param, const char* symbol ) { - | ^~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', @@ -2408,7 +2411,10 @@ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BaseInteractionParameterReader.cpp:17: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:17: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -2429,14 +2435,10 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/TetherForce.h:18, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp:11: + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BaseInteractionParameterReader.cpp:17: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -2457,19 +2459,13 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -[ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -2477,12 +2473,10 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 284 | return 0; | ^~~~~~ -[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/WaterDroplet.cpp /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2504,6 +2498,8 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Spiral.h:16: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] @@ -2516,14 +2512,10 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp +[ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp +[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/WaterDroplet.cpp /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function 'void Spiral::clear()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:92:12: warning: unused variable 'helixAdvancePerBasePair' [-Wunused-variable] 92 | double helixAdvancePerBasePair = -11111. ; // in nm // should be user specified. @@ -2532,48 +2524,10 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:124:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 124 | for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClassTwoTransformForces.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:140:10: warning: variable 'deltaZ' set but not used [-Wunused-but-set-variable] 140 | Vec3 deltaZ = Vec3(0,0,1) * sin(cylindricalSpiralSlopeAngle(pitch,radius))*helixAdvancePerBasePair ; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:238:16: warning: unused variable 'currentPhi' [-Wunused-variable] 238 | double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset); @@ -2581,6 +2535,8 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:221:12: warning: unused variable 'phiOffsetFromStartingTheta' [-Wunused-variable] 221 | double phiOffsetFromStartingTheta = phiFromTheta(startTheta, pitch, radius, 0.0, spiralIsRightHanded); // use offset = 0 to retreive the original, non-offset phi | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2606,9 +2562,8 @@ from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Water.h:1, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/WaterDroplet.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClassTwoTransformForces.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -2629,23 +2584,24 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::removeNonPriorityBasePairs(int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable 'oldDutyCyclePriority' [-Wunused-variable] - 727 | int oldDutyCyclePriority=0; - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 785 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:11: + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Water.h:1, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/WaterDroplet.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -2679,6 +2635,46 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/TetherForce.h:18, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp:11: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2700,10 +2696,58 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:11: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::removeNonPriorityBasePairs(int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable 'oldDutyCyclePriority' [-Wunused-variable] + 727 | int oldDutyCyclePriority=0; + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 785 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:1578:17: warning: unused variable 'myForceConstant' [-Wunused-variable] 1578 | double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later. | ^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2084:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 2084 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ @@ -2716,9 +2760,9 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2750:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 2750 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/TetherForce.h:19: +[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:16: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -2731,7 +2775,8 @@ 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; @@ -2748,13 +2793,32 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityForce.h:19, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp:11: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2776,6 +2840,16 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/TetherForce.h:19: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -2797,6 +2871,10 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClassTwoTransformForces.h:17: @@ -2811,53 +2889,33 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:814:42: required from here - 814 | physicsContainer.deleteResidueStretch(index); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ @@ -2870,18 +2928,10 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:16: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) @@ -2893,6 +2943,29 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:814:42: required from here + 814 | physicsContainer.deleteResidueStretch(index); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; @@ -2900,21 +2973,37 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:17: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: 'std::vector > >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 177 | if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here + 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': +/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here + 1249 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': +/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here + 1258 | { return completeEllipticIntegralsKE_T(m); } + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ +/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 181 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable 'dutyCycle' set but not used [-Wunused-but-set-variable] 279 | double dutyCycle; //must be between 0 and 1. at 1, force is applied all the time. at 0, basically never applied. @@ -2943,53 +3032,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: 'std::vector > >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 177 | if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 181 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityForce.h:19, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp:11: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::densityAutocorrelation(bool, bool) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:209:12: warning: unused variable 'ySquared' [-Wunused-variable] 209 | double ySquared = 0.; @@ -3022,6 +3064,12 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:319:12: warning: unused variable 'inverseNoiseTemperatureToPower4' [-Wunused-variable] 319 | double inverseNoiseTemperatureToPower4 = 1/pow(noiseTemperature,4); //Stefan–Boltzmann law says total radiance goes like T^4. So we normalize by this number to keep noise sort of constant with temperatuere. Of course our oven has a maximum wavenumber, so this won't be perfect. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ElectrostaticPotentialGridForce.cpp +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable] + 689 | int densitiesPerLine = 6; + | ^~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -3043,10 +3091,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable] - 689 | int densitiesPerLine = 6; - | ^~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -3063,31 +3107,22 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here - 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]': -/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here - 1249 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]': -/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here - 1258 | { return completeEllipticIntegralsKE_T(m); } - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ -/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ElectrostaticPotentialGridForce.cpp -[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MMBLogger.cpp +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, @@ -3114,13 +3149,8 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ +[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MMBLogger.cpp [ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: @@ -3150,16 +3180,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, @@ -3188,6 +3208,14 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} @@ -3199,6 +3227,20 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -3220,49 +3262,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ProgressWriter.cpp -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /usr/include/molmodel/molmodel/internal/Compound.h:36, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/CifOutput.h:5, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp:1: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -3279,8 +3278,15 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp +[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', @@ -3358,30 +3364,23 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 116 | Rotation rotation2; | ^~~~~~~~~ +[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ProgressWriter.cpp +[ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized] 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here 167 | double myFrcScalar; | ^~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ElectrostaticPotentialGridForce.h:19: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:15: + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/CifOutput.h:5, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp:1: /usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) @@ -3402,6 +3401,20 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ElectrostaticPotentialGridForce.h:19: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCClassContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, @@ -3418,6 +3431,30 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:15: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} @@ -3443,17 +3480,32 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/SimTKsimbody.h:43, + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCClassContainer.cpp:13: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, @@ -3529,6 +3581,33 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72 319 | Rotation rotation2; | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': @@ -3547,55 +3626,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /usr/include/molmodel/molmodel/internal/Compound.h:36, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCClassContainer.cpp:13: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp: In member function 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 201 | if(myEnergies.size() > myParameterReader.convergenceTimeout) { @@ -3630,19 +3660,13 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -3659,6 +3683,21 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; @@ -3679,6 +3718,32 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, + from /usr/include/simbody/SimTKcommon.h:35, + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtCForces.h:12, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp:11: +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': +/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1169 | approxCompleteEllipticIntegralsKE(double m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1177 | approxCompleteEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1186 | approxCompleteEllipticIntegralsKE(int m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': +/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1257 | inline std::pair completeEllipticIntegralsKE(float m) + | ^ +/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': +/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1265 | inline std::pair completeEllipticIntegralsKE(int m) + | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -3700,21 +3765,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtC_Class_Container.h:14, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:16: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -3731,12 +3781,49 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtC_Class_Container.h:14, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:16: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 282 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 284 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NTC_FORCE_CLASS.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -3758,56 +3845,6 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/Simbody.h:38, - from /usr/include/molmodel/SimTKmolmodel.h:47, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtCForces.h:12, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp:11: -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(double)': -/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1169 | approxCompleteEllipticIntegralsKE(double m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1177 | approxCompleteEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::approxCompleteEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1186 | approxCompleteEllipticIntegralsKE(int m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(float)': -/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1257 | inline std::pair completeEllipticIntegralsKE(float m) - | ^ -/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair SimTK::completeEllipticIntegralsKE(int)': -/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1265 | inline std::pair completeEllipticIntegralsKE(int m) - | ^ -In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 282 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 284 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]': /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here 1178 | { return approxCompleteEllipticIntegralsKE_T(m); } @@ -3843,13 +3880,6 @@ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 262 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 261 | const char* spaces = " \t"; - | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtCForces.h:13: @@ -3910,6 +3940,13 @@ /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 262 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 261 | const char* spaces = " \t"; + | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -4375,7 +4412,7 @@ make[2]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-aarch64-linux-gnu' - dh_auto_test +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -4493,25 +4530,25 @@ dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against libz.so.1 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzgets used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzgets used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.1/usr/lib/aarch64-linux-gnu/libMMB.so.4.1 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'libmmb4.1' in '../libmmb4.1_4.2+dfsg-1_arm64.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.2+dfsg-1_arm64.deb'. dpkg-deb: building package 'libmmb4.1-dbgsym' in '../libmmb4.1-dbgsym_4.2+dfsg-1_arm64.deb'. -dpkg-deb: building package 'mmb-common' in '../mmb-common_4.2+dfsg-1_all.deb'. -dpkg-deb: building package 'mmb' in '../mmb_4.2+dfsg-1_arm64.deb'. dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.2+dfsg-1_arm64.deb'. -dpkg-deb: building package 'libmmb4.1' in '../libmmb4.1_4.2+dfsg-1_arm64.deb'. +dpkg-deb: building package 'mmb' in '../mmb_4.2+dfsg-1_arm64.deb'. +dpkg-deb: building package 'mmb-common' in '../mmb-common_4.2+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../macromoleculebuilder_4.2+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../macromoleculebuilder_4.2+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4519,12 +4556,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/789579/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1981773 and its subdirectories -I: Current time: Wed Dec 30 00:56:18 -12 2026 -I: pbuilder-time-stamp: 1798635378 +I: removing directory /srv/workspace/pbuilder/789579 and its subdirectories +I: Current time: Thu Nov 27 20:39:08 +14 2025 +I: pbuilder-time-stamp: 1764225548