Diff of the two buildlogs: -- --- b1/build.log 2024-11-27 12:17:13.315566483 +0000 +++ b2/build.log 2024-11-27 12:52:50.343350334 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Nov 27 00:07:00 -12 2024 -I: pbuilder-time-stamp: 1732709220 +I: Current time: Tue Feb 2 15:03:29 +14 2027 +I: pbuilder-time-stamp: 1801530209 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying 27.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/588540/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1456170/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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 Feb 2 01:06 /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/1456170/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1456170/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='cfd4a62ec18343f9aa76cd76cd501b2e' - 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='588540' - PS1='# ' - PS2='> ' + INVOCATION_ID=12c64bf071e741fd86affc47a23c02ed + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=1456170 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.5vI0UiWo/pbuilderrc_bI95 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5vI0UiWo/b1 --logfile b1/build.log macromoleculebuilder_4.0.0+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.5vI0UiWo/pbuilderrc_vPrZ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5vI0UiWo/b2 --logfile b2/build.log macromoleculebuilder_4.0.0+dfsg-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/588540/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1456170/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -315,7 +347,7 @@ Get: 175 http://deb.debian.org/debian unstable/main amd64 libstb0t64 amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [220 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libstb-dev amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [654 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] -Fetched 121 MB in 13s (9169 kB/s) +Fetched 121 MB in 11s (10.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (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 ... 19972 files and directories currently installed.) @@ -903,8 +935,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Nov 27 12:10:26 UTC 2024. -Universal Time is now: Wed Nov 27 12:10:26 UTC 2024. +Local time is now: Tue Feb 2 01:09:52 UTC 2027. +Universal Time is now: Tue Feb 2 01:09:52 UTC 2027. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -1061,7 +1093,11 @@ 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-5_source.changes +I: user script /srv/workspace/pbuilder/1456170/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1456170/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-5_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -1098,8 +1134,8 @@ -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found --- Configuring done (3.8s) --- Generating done (0.2s) +-- Configuring done (7.3s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1112,7 +1148,7 @@ -- Build files have been written to: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg' dh_auto_build - cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -B/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1124,50 +1160,111 @@ make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-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-x86_64-linux-gnu' -[ 3%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -[ 6%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o +[ 6%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o +[ 6%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o +[ 12%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o +[ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o +[ 18%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o +[ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o +[ 21%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o +[ 25%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o +[ 28%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 +[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.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-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -MF CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp -[ 9%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -[ 18%] 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-x86_64-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 -fcf-protection -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 -/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-x86_64-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 -fcf-protection -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 +[ 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-x86_64-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 -fcf-protection -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 -[ 21%] 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-x86_64-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 -fcf-protection -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 -[ 28%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -[ 40%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -[ 40%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o -[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -[ 46%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o 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-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 -fcf-protection -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 +[ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o +[ 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-x86_64-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 -fcf-protection -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 +[ 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-x86_64-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 -fcf-protection -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 +[ 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-x86_64-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 -fcf-protection -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 +/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-x86_64-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 -fcf-protection -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 +[ 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-x86_64-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 -fcf-protection -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 +[ 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-x86_64-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 -fcf-protection -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/src/ContactContainer.cpp:11: +/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 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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:19, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: +/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 '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: 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: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/PeriodicScrubber.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:24, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:12: /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) @@ -1183,10 +1280,27 @@ /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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +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) + | ^~ +/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 '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: 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: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 ++) { | ~~^~~~~~~~~~~~~~~ @@ -1210,32 +1324,54 @@ /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); }; | ~~^~~~~~~~~~~~~~~~~ -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/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/AtomSpringContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:12: +/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/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/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/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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/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/CifOutput.h:5, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp: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) @@ -1243,23 +1379,62 @@ /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; + | ^~~~~ +/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 '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; + | ^~~~~ +/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 '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: 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/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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:12: + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11: /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) @@ -1267,9 +1442,38 @@ /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: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 '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); }; + | ~~^~~~~~~~~~~~~~~~~ +/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(); @@ -1285,9 +1489,48 @@ /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/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3: +/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 ++) { + | ~~^~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:11: +/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: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 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/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/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: /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) @@ -1303,6 +1546,30 @@ /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 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: 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; + | ^~~~~ +/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 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 ++) { @@ -1310,6 +1577,29 @@ /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::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) : + | ^~~~~~~~~~~ +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': +/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 '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: 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; @@ -1330,6 +1620,31 @@ /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 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/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: 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); }; + | ~~^~~~~~~~~~~~~~~~~ +/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; @@ -1340,10 +1655,6 @@ /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 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 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; @@ -1354,10 +1665,6 @@ /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 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; @@ -1378,10 +1685,30 @@ /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/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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:11: +/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/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); }; + | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:12: /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) @@ -1389,10 +1716,10 @@ /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 '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/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(); @@ -1407,13 +1734,90 @@ /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/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/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/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 /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: 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) : + | ^~~~~~~~~~~ +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, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp:11: +/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 '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: 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); }; + | ~~^~~~~~~~~~~~~~~~~ +/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/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:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:12: /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++){ @@ -1422,10 +1826,6 @@ /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/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; @@ -1436,6 +1836,14 @@ /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/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 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; @@ -1446,6 +1854,10 @@ /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/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 ; + | ^~~~~~ /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); }; @@ -1454,16 +1866,25 @@ /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/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/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/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 - | ^~~~~~~~ -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/src/AtomSpringContainer.cpp:12: +/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/MobilizerContainer.cpp:11: /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) @@ -1471,7 +1892,19 @@ /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/src/ContactContainer.cpp:11: +/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/MonoAtoms.cpp:11: +/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/WaterDroplet.h:16, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:11: /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) @@ -1499,46 +1932,39 @@ /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/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, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11: +/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/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/NTC_FORCE_CLASS.h:4, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp: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/src/AtomSpringContainer.cpp: In member function 'double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable 'myExtension' [-Wunused-variable] + 65 | double myExtension = 0.0; + | ^~~~~~~~~~~ +/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 '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/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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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/BasePairContainer.cpp: In member function 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator; reference = BaseInteraction&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] - 44 | myBasePairVector.at(index); - | ~~~~~~~~~~~~~~~~~~~^~~~~~~ -In file included from /usr/include/c++/14/vector:66, - from /usr/include/simbody/SimTKcommon/internal/Array.h:39, - from /usr/include/simbody/SimTKcommon/basics.h:53, - from /usr/include/simbody/SimTKcommon.h:32, - 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: -/usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here - 1180 | at(size_type __n) - | ^~ /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; @@ -1559,10 +1985,13 @@ /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 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: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 '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; @@ -1583,20 +2012,6 @@ /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/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/src/BiopolymerClass.cpp:14: -/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 '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 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(); @@ -1605,7 +2020,48 @@ /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 file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:12: +/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();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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); + | ^~~~~~~~~~ +/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/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/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 + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +/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::deleteAtomSpring(int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 194 | if(id < 0 || id >= atomSpringVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 201 | if(id < 0 || id >= atomSpringVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +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/PeriodicPdbAndEnergyWriter.h:13, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.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) @@ -1613,37 +2069,22 @@ /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 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: 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/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/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 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/DensityMap.cpp:11: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteThreading(int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 260 | if(id < 0 || id >= threadingStructVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 268 | if(id < 0 || id >= threadingStructVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/DisplacementContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DisplacementContainer.cpp:12: /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) @@ -1651,10 +2092,31 @@ /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 '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/src/MobilizerContainer.cpp:11: +/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 '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 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/src/NtCClassContainer.cpp:13: /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) @@ -1666,40 +2128,28 @@ /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 '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 '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/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/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: -/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 '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/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: 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 ++) { @@ -1707,17 +2157,6 @@ /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: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 '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; @@ -1738,18 +2177,10 @@ /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/src/MonoAtoms.cpp:11: -/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 '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: 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 ++) { @@ -1758,9 +2189,6 @@ /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: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:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ @@ -1777,38 +2205,6 @@ /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/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()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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: -/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; @@ -1833,13 +2229,70 @@ /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/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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:449:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 449 | if(id < 0 || id >= gappedThreadingStructVector.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/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::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:458:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 458 | if(id < 0 || id >= gappedThreadingStructVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:11: +/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/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:488:24: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] + 488 | while ((aIndex < length(thread.updThreadingPartner(0).sequence)) && + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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))) + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 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 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: +/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; @@ -1860,30 +2313,6 @@ /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 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/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 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); }; - | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable 'myExtension' [-Wunused-variable] - 65 | double myExtension = 0.0; - | ^~~~~~~~~~~ /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 ++) { @@ -1908,9 +2337,32 @@ /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: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) : + | ^~~~~~~~~~~ +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: 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); }; @@ -1935,6 +2387,13 @@ /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: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); }; + | ~~^~~~~~~~~~~~~~~~~ /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); }; @@ -1944,59 +2403,52 @@ /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/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 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/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(); | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteAtomSpring(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 194 | if(id < 0 || id >= atomSpringVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+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)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/src/ConstraintContainer.cpp:10: -/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/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 201 | if(id < 0 || id >= atomSpringVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+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/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/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++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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: 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/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/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; @@ -2017,26 +2469,16 @@ /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/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/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteThreading(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 260 | if(id < 0 || id >= threadingStructVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 268 | if(id < 0 || id >= threadingStructVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+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/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3: +/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/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; @@ -2047,10 +2489,22 @@ /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/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+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/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/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 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 ++) { @@ -2058,10 +2512,49 @@ /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::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)) || + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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: +/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/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/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/src/BiopolymerClass.cpp:14: +/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, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:17, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:11: +/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/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++){ @@ -2070,6 +2563,62 @@ /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 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 '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 '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/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)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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 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 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 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::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.; @@ -2077,30 +2626,30 @@ /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/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()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:449:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 449 | if(id < 0 || id >= gappedThreadingStructVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:458:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 458 | if(id < 0 || id >= gappedThreadingStructVector.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/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; | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:488:24: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] - 488 | while ((aIndex < length(thread.updThreadingPartner(0).sequence)) && - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:308:12: warning: unused variable 'groundFrequencyY' [-Wunused-variable] 308 | double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2; | ^~~~~~~~~~~~~~~~ @@ -2122,9 +2671,13 @@ /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/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))) - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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: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; @@ -2145,16 +2698,95 @@ /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/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)) || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: +/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 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/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/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 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: 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/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; + | ^~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:19: warning: unused variable 'newV' [-Wunused-variable] + 543 | int newU, newV, newW; + | ^~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:25: warning: unused variable 'newW' [-Wunused-variable] + 543 | int newU, newV, newW; + | ^~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:507:9: warning: unused variable 'xGridInds' [-Wunused-variable] + 507 | int xGridInds = xDimInds; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:508:9: warning: unused variable 'yGridInds' [-Wunused-variable] + 508 | int yGridInds = yDimInds; + | ^~~~~~~~~ +/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/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/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/ConstraintContainer.h:14, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10: /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) @@ -2162,10 +2794,106 @@ /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/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/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; + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)': +/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/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/src/BasePairContainer.cpp: In member function 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator; reference = BaseInteraction&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] + 44 | myBasePairVector.at(index); + | ~~~~~~~~~~~~~~~~~~~^~~~~~~ +In file included from /usr/include/c++/14/vector:66, + from /usr/include/simbody/SimTKcommon/internal/Array.h:39, + from /usr/include/simbody/SimTKcommon/basics.h:53, + from /usr/include/simbody/SimTKcommon.h:32, + 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: +/usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here + 1180 | at(size_type __n) + | ^~ +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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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/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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: +/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(); @@ -2174,6 +2902,31 @@ /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 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/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) { + | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable 'lastEnergy' [-Wunused-variable] + 202 | double lastEnergy = myEnergies.back(); + | ^~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable 'compoundNumber' [-Wunused-variable] + 49 | int compoundNumber = 1; + | ^~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable 'requiredPrecision' [-Wunused-variable] + 50 | int requiredPrecision = 12; + | ^~~~~~~~~~~~~~~~~ +/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 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'; @@ -2247,14 +3000,10 @@ /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/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 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/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 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))); @@ -2265,45 +3014,26 @@ /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/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/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; - | ^~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:19: warning: unused variable 'newV' [-Wunused-variable] - 543 | int newU, newV, newW; - | ^~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:25: warning: unused variable 'newW' [-Wunused-variable] - 543 | int newU, newV, newW; - | ^~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:507:9: warning: unused variable 'xGridInds' [-Wunused-variable] - 507 | int xGridInds = xDimInds; - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:508:9: warning: unused variable 'yGridInds' [-Wunused-variable] - 508 | int yGridInds = yDimInds; - | ^~~~~~~~~ -/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/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()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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 '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(); | ^~~~~~~~~~~ -/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; @@ -2336,6 +3066,22 @@ /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()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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()': @@ -2361,110 +3107,42 @@ /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/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) - | ^~ -/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/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/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/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/WaterDroplet.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:11: -/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/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/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: 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) : - | ^~~~~~~~~~~ +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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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/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 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() @@ -2479,58 +3157,25 @@ /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/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/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/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)) + | ^ /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/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/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); | ^~~~~~~~~~~ -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: -/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::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/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:16, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:11: -/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/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; - | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+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. @@ -2538,52 +3183,9 @@ /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; | ^~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)': -/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/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/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/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; | ^~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -2601,25 +3203,6 @@ /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 '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/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 ; - | ^~~~~~ -/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); - | ^~~~~~~~~~ -/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 - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 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]': @@ -2636,21 +3219,10 @@ /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 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/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)) - | ^ -/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 '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/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); | ^~~~~~~~~~ @@ -2660,6 +3232,32 @@ /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/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/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/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/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/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/ResidueStretchContainer.h: In instantiation of '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]' 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); @@ -2686,10 +3284,29 @@ /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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ -/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(); - | ^~~~~~~~~~~~~~~~~~~~ +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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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"; + | ^~~~~~ 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/src/BiopolymerClass.cpp:16: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': @@ -2699,18 +3316,9 @@ /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"; - | ^~~~~~ -/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: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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ -[ 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-x86_64-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 -fcf-protection -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: 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"; @@ -2758,6 +3366,36 @@ /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 '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]' + 2584 | residueStretchContainer.printResidueStretchVector(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here + 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); + | ^ +/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]' + 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here + 4682 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/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]' + 4827 | residueStretchContainer.printResidueStretchVector(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here + 4830 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); + | ^ +/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 ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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 - 814 | physicsContainer.deleteResidueStretch(index); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ -/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"; @@ -2839,16 +3452,6 @@ /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/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]' - 2584 | residueStretchContainer.printResidueStretchVector(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here - 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); - | ^ -/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]' - 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here - 4682 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/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]' - 4827 | residueStretchContainer.printResidueStretchVector(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here - 4830 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); - | ^ -/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::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, - inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, - inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | Rotation rotation2; - | ^~~~~~~~~ -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, - inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, - inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | Rotation rotation2; - | ^~~~~~~~~ -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, - inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, - inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | Rotation rotation2; - | ^~~~~~~~~ -In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', - inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, - inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, - inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | Rotation rotation2; - | ^~~~~~~~~ -In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', - inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, - inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, - inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | Rotation rotation2; - | ^~~~~~~~~ -In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', - inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, - inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, - inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, - inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: -/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] - 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 - 116 | 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"; @@ -2985,14 +3480,44 @@ /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:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized] - 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here - 167 | double myFrcScalar; - | ^~~~~~~~~~~ -[ 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-x86_64-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 -fcf-protection -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: 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"; + | ^~~~~~ +/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/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/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/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, from /usr/include/simbody/SimTKcommon.h:35, @@ -3106,8 +3631,123 @@ /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object '' of size 72 201 | rotation = Rotation(); | ^ -[ 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-x86_64-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 -fcf-protection -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 +/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 + 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/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 + 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) + | ~~~~~~~~~~~~~~~~~~~~^~~~ +/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 + 814 | physicsContainer.deleteResidueStretch(index); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ +/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/SmallMatrix.h:93, + from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, + 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: +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, + inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, + inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +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, + inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, + inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +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, + inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, + inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', + inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, + inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, + inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', + inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, + inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, + inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', + inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, + inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, + inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, + inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: +/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] + 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 + 116 | Rotation rotation2; + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized] + 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; + | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here + 167 | double myFrcScalar; + | ^~~~~~~~~~~ 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, @@ -3183,610 +3823,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72 319 | Rotation rotation2; | ^~~~~~~~~ -[ 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-x86_64-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 -fcf-protection -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: 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"; - | ^~~~~~ -[ 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-x86_64-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 -fcf-protection -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 -[ 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-x86_64-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 -fcf-protection -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: 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/DensityForce.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11: -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -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++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 /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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -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++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 /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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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/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/PeriodicPdbAndEnergyWriter.h:13, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.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) - | ^~ -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -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++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/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) { - | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable 'lastEnergy' [-Wunused-variable] - 202 | double lastEnergy = myEnergies.back(); - | ^~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable 'compoundNumber' [-Wunused-variable] - 49 | int compoundNumber = 1; - | ^~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable 'requiredPrecision' [-Wunused-variable] - 50 | int requiredPrecision = 12; - | ^~~~~~~~~~~~~~~~~ -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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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/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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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/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/CifOutput.h:5, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp: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; - | ^~~~~ -/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/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:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:12: -/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 /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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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': -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NTC_FORCE_CLASS.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp: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/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 /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/src/NtCClassContainer.cpp:13: -/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/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"; - | ^~~~~~ -/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, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp:11: -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -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++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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 /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 - 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/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 - 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) - | ~~~~~~~~~~~~~~~~~~~~^~~~ -/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: 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"; @@ -4230,7 +4266,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -B/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -4337,24 +4373,24 @@ dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against libz.so.1 (it uses none of the library's symbols) -dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzgets used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'mmb-common' in '../mmb-common_4.0.0+dfsg-5_all.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-5_amd64.deb'. +dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-5_amd64.deb'. -dpkg-deb: building package 'mmb-common' in '../mmb-common_4.0.0+dfsg-5_all.deb'. dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-5_amd64.deb'. -dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../macromoleculebuilder_4.0.0+dfsg-5_amd64.changes @@ -4363,12 +4399,14 @@ 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/1456170/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1456170/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/588540 and its subdirectories -I: Current time: Wed Nov 27 00:17:12 -12 2024 -I: pbuilder-time-stamp: 1732709832 +I: removing directory /srv/workspace/pbuilder/1456170 and its subdirectories +I: Current time: Tue Feb 2 15:38:40 +14 2027 +I: pbuilder-time-stamp: 1801532320