Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 01:38:19.701539221 +0000 +++ b2/build.log 2024-05-07 01:42:35.606653420 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 8 19:57:27 -12 2025 -I: pbuilder-time-stamp: 1749455847 +I: Current time: Mon Jun 9 22:01:23 +14 2025 +I: pbuilder-time-stamp: 1749456083 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying bf1ab1ebf49bb9e48f4f133e155f9315cc37079d.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/888303/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3524854/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Jun 9 08:01 /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/3524854/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3524854/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' + 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]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c2c8c830d8c04de9b458edf938a902ae' - 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='888303' - PS1='# ' - PS2='> ' + INVOCATION_ID=d193df0b30b34660a1cbfa087c142d64 + 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=3524854 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.mZyLLA7S/pbuilderrc_DNNC --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZyLLA7S/b1 --logfile b1/build.log macromoleculebuilder_4.0.0+dfsg-3.1~exp1.dsc' - SUDO_GID='109' - 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.mZyLLA7S/pbuilderrc_715i --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZyLLA7S/b2 --logfile b2/build.log macromoleculebuilder_4.0.0+dfsg-3.1~exp1.dsc' + SUDO_GID=109 + 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 codethink01-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 5 13:57 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/888303/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 13:58 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3524854/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -308,7 +340,7 @@ Get: 171 http://deb.debian.org/debian unstable/main arm64 libstb-dev arm64 0.0~git20230129.5736b15+ds-1.2 [579 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] -Fetched 103 MB in 2s (62.1 MB/s) +Fetched 103 MB in 0s (207 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19744 files and directories currently installed.) @@ -875,8 +907,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 9 07:57:59 UTC 2025. -Universal Time is now: Mon Jun 9 07:57:59 UTC 2025. +Local time is now: Mon Jun 9 08:01:54 UTC 2025. +Universal Time is now: Mon Jun 9 08:01:54 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -1036,7 +1068,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/macromoleculebuilder-4.0.0+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_4.0.0+dfsg-3.1~exp1_source.changes +I: user script /srv/workspace/pbuilder/3524854/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/3524854/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/macromoleculebuilder-4.0.0+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_4.0.0+dfsg-3.1~exp1_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-3.1~exp1 dpkg-buildpackage: info: source distribution experimental @@ -1073,7 +1109,7 @@ -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found --- Configuring done (1.2s) +-- Configuring done (1.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1099,29 +1135,29 @@ make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu' -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o +[ 3%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/MobilizerContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp +[ 6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o [ 12%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -[ 15%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -[ 18%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -[ 21%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o +[ 9%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o +[ 18%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o +[ 18%] 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/Utils.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/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-4.0.0+dfsg/src/BiopolymerClass.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. 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-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-4.0.0+dfsg/src/DisplacementContainer.cpp -[ 25%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -[ 28%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -[ 31%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/MobilizerContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o +[ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody 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/usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/DensityContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DensityContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp +[ 31%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o +[ 31%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o +[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/BasePairContainer.cpp.o -MF CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/ContactContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ContactContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ConstraintContainer.cpp [ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ConstraintContainer.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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/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-4.0.0+dfsg/src/Repel.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, @@ -1152,11 +1188,8 @@ 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-4.0.0+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1207,8 +1240,7 @@ from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10: + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1232,10 +1264,9 @@ 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-4.0.0+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DisplacementContainer.cpp:12: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1259,8 +1290,11 @@ 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-4.0.0+dfsg/include/Utils.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:11: + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:4, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1283,10 +1317,10 @@ | ^ 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-4.0.0+dfsg/include/MoleculeContainer.h:6, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3: + from /usr/include/simbody/SimTKsimbody.h:43, + from /usr/include/molmodel/molmodel/internal/Compound.h:36, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1311,7 +1345,7 @@ from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:12: + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1334,10 +1368,10 @@ | ^ 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 /usr/include/molmodel/molmodel/internal/Compound.h:36, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:14: + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:6, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1360,10 +1394,11 @@ | ^ 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-4.0.0+dfsg/include/BasePairContainer.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1412,9 +1447,10 @@ | ^ 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-4.0.0+dfsg/include/Utils.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:11: + from /usr/include/simbody/Simbody.h:38, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -1448,8 +1484,6 @@ /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 /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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -1496,12 +1530,11 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -1517,26 +1550,27 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | 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 -/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 -/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 -/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] + 26 | bool myEndCapsOn; + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -1583,10 +1617,35 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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). + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -1604,6 +1663,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -1614,14 +1677,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { @@ -1630,6 +1693,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | 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 /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 @@ -1647,73 +1718,20 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:11: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] - 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] - 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; - | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+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()) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | 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 -/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 -/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 -/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} @@ -1742,6 +1760,127 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] + 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] + 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] + 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] + 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsPurine(char)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 51 | return c == 'A' | c == 'G'; + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsRNA(char)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 57 | c == 'A' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 59 | c == 'G' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 60 | c == 'U' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsDNA(char)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 67 | c == 'A' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 69 | c == 'G' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 70 | c == 'T' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsProtein(char)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 77 | c == 'C' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 79 | c == 'H' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 80 | c == 'I' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 86 | c == 'M' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 88 | c == 'V' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 89 | c == 'A' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 95 | c == 'G' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 97 | c == 'P' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 98 | c == 'T' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 104 | c == 'R' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 106 | c == 'Y' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 107 | c == 'W' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 113 | c == 'D' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 115 | c == 'E' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 116 | c == 'Q' | + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] + 117 | c == 'K' + | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; + | ~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; + | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteGappedThreading(int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:441:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 441 | if(id < 0 || id >= gappedThreadingStructVector.size()){ @@ -1761,21 +1900,20 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:489:24: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] 489 | (bIndex < length(thread.updThreadingPartner(1).sequence))) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 -/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 -/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 -/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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:127:41: warning: variable 'myChargedAtomTypeIndex' set but not used [-Wunused-but-set-variable] + 127 | DuMM::ChargedAtomTypeIndex myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0))); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable] + 135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any); + | ^~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable] + 147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid"); + | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicScrubber.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:24: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -1783,6 +1921,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); @@ -1798,40 +1944,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicScrubber.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:24: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::checkResidueNumbersAndInsertionCodes()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:244:15: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] + 244 | ResidueID myResidueID = getFirstResidueID(); + | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:17: @@ -1842,6 +1958,23 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | 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 +/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 +/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 +/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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); @@ -1850,6 +1983,32 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | 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 +/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 +/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 +/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 +/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 +/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 +/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 +/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -1857,6 +2016,13 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -1877,54 +2043,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; - | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] - 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] - 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : - | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; @@ -1949,6 +2075,13 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; @@ -1977,16 +2110,27 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:518:15: warning: variable 'myFirstResidueID' set but not used [-Wunused-but-set-variable] + 518 | ResidueID myFirstResidueID = getFirstResidueID() ; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable] + 520 | int numResidues = -1; + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] + 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ @@ -1995,36 +2139,24 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable 'biopolymerAtomTargetsIterator' set but not used [-Wunused-but-set-variable] + 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 /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 @@ -2051,6 +2183,64 @@ /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 /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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1053:9: warning: unused variable 'myResidueIndex' [-Wunused-variable] + 1053 | int myResidueIndex = getResidueIndex(myResidueID); + | ^~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1316:25: warning: variable 'myAtomIndex' set but not used [-Wunused-but-set-variable] + 1316 | Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName); + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable] + 1437 | double huntCrossleyDissipation =.0; + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] + 269 | ParameterReader * _parameterReader; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] + 259 | SimbodyMatterSubsystem _matter; + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] + 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+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())) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -2075,30 +2265,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/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 -/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 -/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 -/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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:172:31: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] - 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); - | ^~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -2114,26 +2280,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] - 269 | ParameterReader * _parameterReader; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] - 259 | SimbodyMatterSubsystem _matter; - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] - 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -2141,6 +2291,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::runAllSteps()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:1027:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1027 | for(; _nextFrame <= _parameterReader->numReportingIntervals; _nextFrame++){ + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector, WaterDropletContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:3577:23: warning: variable 'myLocation' set but not used [-Wunused-but-set-variable] + 3577 | Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm + | ^~~~~~~~~~ /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 /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 @@ -2154,28 +2312,6 @@ /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 /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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -2200,6 +2336,46 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | 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 +/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 +/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 +/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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:11: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -2224,31 +2400,25 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp:12: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::runAllSteps()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:1027:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1027 | for(; _nextFrame <= _parameterReader->numReportingIntervals; _nextFrame++){ - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] - 26 | bool myEndCapsOn; - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+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()) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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)) || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 /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 @@ -2262,101 +2432,41 @@ /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 /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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsPurine(char)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 51 | return c == 'A' | c == 'G'; - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsRNA(char)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 57 | c == 'A' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 59 | c == 'G' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 60 | c == 'U' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsDNA(char)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 67 | c == 'A' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 69 | c == 'G' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 70 | c == 'T' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsProtein(char)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 77 | c == 'C' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 79 | c == 'H' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 80 | c == 'I' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 86 | c == 'M' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 88 | c == 'V' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 89 | c == 'A' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 95 | c == 'G' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 97 | c == 'P' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 98 | c == 'T' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 104 | c == 'R' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 106 | c == 'Y' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 107 | c == 'W' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 113 | c == 'D' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 115 | c == 'E' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 116 | c == 'Q' | - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] - 117 | c == 'K' - | ~~^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:127:41: warning: variable 'myChargedAtomTypeIndex' set but not used [-Wunused-but-set-variable] - 127 | DuMM::ChargedAtomTypeIndex myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0))); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable] - 135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any); - | ^~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable] - 147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid"); - | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 +/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 +/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 +/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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4130:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable] + 4130 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4519:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable] + 4519 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); + | ^~~~~~~~~~~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MonoAtoms.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 /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 @@ -2370,71 +2480,6 @@ /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 /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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::checkResidueNumbersAndInsertionCodes()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:244:15: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] - 244 | ResidueID myResidueID = getFirstResidueID(); - | ^~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:518:15: warning: variable 'myFirstResidueID' set but not used [-Wunused-but-set-variable] - 518 | ResidueID myFirstResidueID = getFirstResidueID() ; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable] - 520 | int numResidues = -1; - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] - 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1053:9: warning: unused variable 'myResidueIndex' [-Wunused-variable] - 1053 | int myResidueIndex = getResidueIndex(myResidueID); - | ^~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1316:25: warning: variable 'myAtomIndex' set but not used [-Wunused-but-set-variable] - 1316 | Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName); - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable] - 1437 | double huntCrossleyDissipation =.0; - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector, WaterDropletContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:3577:23: warning: variable 'myLocation' set but not used [-Wunused-but-set-variable] - 3577 | Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm - | ^~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -2460,15 +2505,13 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 244 | for ( int j = 0 ; j < neighborList.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MonoAtoms.cpp -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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 ::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -2476,19 +2519,9 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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] -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4130:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable] - 4130 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4519:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable] - 4519 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); - | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -2496,19 +2529,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | 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 -/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 -/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 -/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -2516,6 +2536,25 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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] +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | 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, @@ -2541,8 +2580,26 @@ /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-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 ::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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(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/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]', @@ -2713,35 +2719,12 @@ /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object '' of size 72 201 | rotation = Rotation(); | ^ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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(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) @@ -2762,14 +2745,35 @@ /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-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | 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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:17: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) | ^ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+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 ) { + | ^~~~~~~~~~~~ /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) @@ -2786,77 +2790,20 @@ /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) | ^ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp [ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/TetherForce.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] - 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] - 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; - | ~~^~~~~~~~~~~~~~~~~ -/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 -/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 -/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 -/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 -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/WaterDroplet.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-4.0.0+dfsg/include/TetherForce.h:18, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11: + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -2881,8 +2828,8 @@ 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-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:18, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -2903,8 +2850,8 @@ /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) | ^ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -2912,34 +2859,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | 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-4.0.0+dfsg/include/Water.h:1, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+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) - | ^ -/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-4.0.0+dfsg/include/Spiral.h:16: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -2959,34 +2878,11 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/WaterDroplet.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.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-4.0.0+dfsg/include/Utils.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3011,16 +2907,46 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::clear()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:92:12: warning: unused variable 'helixAdvancePerBasePair' [-Wunused-variable] - 92 | double helixAdvancePerBasePair = -11111. ; // in nm // should be user specified. - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'double Spiral::harmonicThetaAdjustment(double)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:22, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:18: +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-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) + | ^ +/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 +/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 +/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 +/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 +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:16: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -3036,12 +2962,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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 ; - | ^~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/DensityForce.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -3073,6 +2993,45 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::clear()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:92:12: warning: unused variable 'helixAdvancePerBasePair' [-Wunused-variable] + 92 | double helixAdvancePerBasePair = -11111. ; // in nm // should be user specified. + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'double Spiral::harmonicThetaAdjustment(double)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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 ; + | ^~~~~~ +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-4.0.0+dfsg/include/Water.h:1, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) + | ^ +/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-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:238:16: warning: unused variable 'currentPhi' [-Wunused-variable] 238 | double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset); @@ -3080,6 +3039,8 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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 /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 @@ -3115,19 +3076,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.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 -/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 -/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 -/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3152,8 +3100,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': @@ -3168,12 +3114,17 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/DensityForce.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-4.0.0+dfsg/include/DensityForce.h:19, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11: + from /usr/include/simbody/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -3194,17 +3145,6 @@ /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) | ^ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::removeNonPriorityBasePairs(int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable 'oldDutyCyclePriority' [-Wunused-variable] 727 | int oldDutyCyclePriority=0; @@ -3217,12 +3157,16 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:1582:17: warning: unused variable 'myForceConstant' [-Wunused-variable] + 1582 | double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later. + | ^~~~~~~~~~~~~~~ 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-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:18, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:19, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) @@ -3243,16 +3187,17 @@ /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-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:1582:17: warning: unused variable 'myForceConstant' [-Wunused-variable] - 1582 | double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later. - | ^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2069:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 2069 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:17: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] + 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); + | ^~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable] + 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); + | ^~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:22, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:18: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -3268,6 +3213,9 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 2735 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) + | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -3299,48 +3247,9 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] - 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); - | ^~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable] - 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); - | ^~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 2735 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) - | ^ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+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. - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable] - 280 | double scrubberPeriod; - | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:16: +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:19: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -3348,6 +3257,18 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.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 /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 @@ -3361,6 +3282,58 @@ /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 /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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] + 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] + 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; + | ~~^~~~~~~~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:17: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); @@ -3369,6 +3342,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -3376,6 +3357,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3401,8 +3386,7 @@ 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:17: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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(); }; @@ -3419,20 +3403,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MMBLogger.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 /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 @@ -3446,9 +3416,78 @@ /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 /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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:20: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+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. + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable] + 280 | double scrubberPeriod; + | ^~~~~~~~~~~~~~ +/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 +/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 +/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 +/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 +/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 +/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 +/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 +/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 +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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, + from /usr/include/molmodel/SimTKmolmodel.h:47, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:18, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.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-4.0.0+dfsg/include/WaterDroplet.h:16: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) @@ -3456,18 +3495,21 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ -[ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/CifOutput.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -3475,21 +3517,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3510,23 +3537,56 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:17: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 ::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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] /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 /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 @@ -3540,6 +3600,35 @@ /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 /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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3560,57 +3649,22 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:19: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()': /build/reproducible-path/macromoleculebuilder-4.0.0+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/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/MMBLogger.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::densityAutocorrelation(bool, bool) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:209:12: warning: unused variable 'ySquared' [-Wunused-variable] 209 | double ySquared = 0.; @@ -3618,10 +3672,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:210:12: warning: unused variable 'zSquared' [-Wunused-variable] 210 | double zSquared = 0.; | ^~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::populateNoiseMap()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:307:12: warning: unused variable 'groundFrequencyX' [-Wunused-variable] 307 | double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2; @@ -3647,9 +3697,24 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:20: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::loadParametersAndDensity_CCP4MAP()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:13: warning: unused variable 'newU' [-Wunused-variable] 543 | int newU, newV, newW; @@ -3669,6 +3734,17 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:509:9: warning: unused variable 'zGridInds' [-Wunused-variable] 509 | int zGridInds = zDimInds; | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable] + 689 | int densitiesPerLine = 6; + | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -3693,16 +3769,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable] - 689 | int densitiesPerLine = 6; - | ^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+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 /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 @@ -3716,18 +3782,12 @@ /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 /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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ @@ -3736,75 +3796,21 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | 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 -/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 -/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 -/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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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] /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:19: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] - 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] - 1294 | String chain; - | ^~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] - 1292 | ResidueID residueID; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] - 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; - | ~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/CifOutput.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 /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 @@ -3818,6 +3824,8 @@ /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 /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 +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ProgressWriter.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': @@ -3825,29 +3833,28 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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 ::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-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:19: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ 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, @@ -3876,6 +3883,18 @@ /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-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.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, @@ -3903,52 +3922,41 @@ /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-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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 -/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 -/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 -/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 -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/ProgressWriter.cpp -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] + 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] + 1294 | String chain; + | ^~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] + 1292 | ResidueID residueID; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] + 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; + | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -3956,8 +3964,18 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]', @@ -4035,6 +4053,19 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 116 | Rotation rotation2; | ^~~~~~~~~ +/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 +/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 +/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 +/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -4048,6 +4079,20 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here 167 | double myFrcScalar; | ^~~~~~~~~~~ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NtCClassContainer.cpp +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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, @@ -4079,28 +4124,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 290 | if (derivComponents.size() == 1) - | ^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 292 | return 0; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] - 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 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, @@ -4176,6 +4199,56 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72 319 | Rotation rotation2; | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | 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-4.0.0+dfsg/include/BiopolymerClass.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) + | ^ +[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NtCForces.cpp +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 290 | if (derivComponents.size() == 1) + | ^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 292 | return 0; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { @@ -4213,8 +4286,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NtCClassContainer.cpp /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ @@ -4227,13 +4298,32 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | 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-4.0.0+dfsg/include/NtCForces.h:12, + from /build/reproducible-path/macromoleculebuilder-4.0.0+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) + | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp: In member function 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+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) { @@ -4260,53 +4350,6 @@ /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 /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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ -[ 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-4.0.0+dfsg/obj-aarch64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/src/NtCForces.cpp -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/BiopolymerClass.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+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 file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': @@ -4331,32 +4374,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.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-4.0.0+dfsg/include/NtCForces.h:12, - from /build/reproducible-path/macromoleculebuilder-4.0.0+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) - | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -4401,6 +4418,25 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 /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 @@ -4414,18 +4450,6 @@ /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 /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 -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/NtC_Class_Container.h:14, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:16: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': @@ -4480,6 +4504,18 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+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 /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 @@ -4493,13 +4529,6 @@ /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 /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 -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': @@ -4565,6 +4594,13 @@ /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 /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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NtCForces.h:13: @@ -4620,6 +4656,13 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+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-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ @@ -4639,13 +4682,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | 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 /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 @@ -5258,11 +5294,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1~exp1_arm64.deb'. dpkg-deb: building package 'mmb-common' in '../mmb-common_4.0.0+dfsg-3.1~exp1_all.deb'. -dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-3.1~exp1_arm64.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-3.1~exp1_arm64.deb'. +dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1~exp1_arm64.deb'. dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-3.1~exp1_arm64.deb'. +dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-3.1~exp1_arm64.deb'. dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-3.1~exp1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../macromoleculebuilder_4.0.0+dfsg-3.1~exp1_arm64.buildinfo dpkg-genchanges --build=binary -O../macromoleculebuilder_4.0.0+dfsg-3.1~exp1_arm64.changes @@ -5271,12 +5307,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3524854/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3524854/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/888303 and its subdirectories -I: Current time: Sun Jun 8 20:01:18 -12 2025 -I: pbuilder-time-stamp: 1749456078 +I: removing directory /srv/workspace/pbuilder/3524854 and its subdirectories +I: Current time: Mon Jun 9 22:05:34 +14 2025 +I: pbuilder-time-stamp: 1749456334