Diff of the two buildlogs: -- --- b1/build.log 2024-06-11 22:45:39.619710710 +0000 +++ b2/build.log 2024-06-11 22:53:09.160573542 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jul 14 17:05:39 -12 2025 -I: pbuilder-time-stamp: 1752555939 +I: Current time: Wed Jun 12 12:45:42 +14 2024 +I: pbuilder-time-stamp: 1718145942 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying bf1ab1ebf49bb9e48f4f133e155f9315cc37079d.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/496374/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3925597/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Jun 11 22:46 /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/3925597/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3925597/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=42 ' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + 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='6d682410f5c94a0992f2d42c30da914f' - 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='496374' - PS1='# ' - PS2='> ' + INVOCATION_ID=0fc690c776304e2fb2f3ee3e52b5ec39 + 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=3925597 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.WyYHH41Q/pbuilderrc_KErQ --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.WyYHH41Q/b1 --logfile b1/build.log macromoleculebuilder_4.0.0+dfsg-4.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://213.165.73.152:3128' + 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.WyYHH41Q/pbuilderrc_dU28 --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.WyYHH41Q/b2 --logfile b2/build.log macromoleculebuilder_4.0.0+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 5 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/496374/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3925597/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -310,7 +342,7 @@ Get: 171 http://deb.debian.org/debian unstable/main amd64 libstb-dev amd64 0.0~git20230129.5736b15+ds-1.2 [595 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] -Fetched 114 MB in 2s (66.5 MB/s) +Fetched 114 MB in 6s (18.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-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 ... 19713 files and directories currently installed.) @@ -878,8 +910,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jul 15 05:06:36 UTC 2025. -Universal Time is now: Tue Jul 15 05:06:36 UTC 2025. +Local time is now: Tue Jun 11 22:48:22 UTC 2024. +Universal Time is now: Tue Jun 11 22:48:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -1038,7 +1070,11 @@ 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-4_source.changes +I: user script /srv/workspace/pbuilder/3925597/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/3925597/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-4_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -1075,7 +1111,7 @@ -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found --- Configuring done (0.5s) +-- Configuring done (3.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -1089,7 +1125,7 @@ -- 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 -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "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 @@ -1101,109 +1137,50 @@ 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/Utils.cpp.o -[ 6%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o +[ 3%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o [ 9%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -[ 12%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.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 +[ 9%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.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 /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/MoleculeContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.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 -/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 -[ 18%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -[ 40%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -[ 40%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -[ 43%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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 -[ 46%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o +[ 12%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+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 +[ 18%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o +[ 18%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o +[ 25%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o +[ 28%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o +[ 34%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o +[ 37%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o +[ 40%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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 -[ 50%] Building CXX object 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/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.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/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/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/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: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)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -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: +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) @@ -1226,56 +1203,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -In file included from /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 '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 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); }; - | ~~^~~~~~~~~~~~~~~~~ -/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; @@ -1300,40 +1227,7 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:12: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/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: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; - | ^~~~~~~~~ -/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/NtC_Class_Container.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:16: +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) @@ -1341,10 +1235,12 @@ /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); }; - | ~~^~~~~~~~~~~~~~~~~ +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(); @@ -1353,64 +1249,13 @@ /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/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/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: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/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] - 26 | bool myEndCapsOn; - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 70 | if(id < 0 || id >= contactWithinVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 77 | if(id < 0 || id >= contactWithinVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 18 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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++){ @@ -1419,6 +1264,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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; @@ -1443,72 +1292,7 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 275 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | if(id < 0 || id >= residueStretchVector.size()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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/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 ++) { - | ~~^~~~~~~~~~~~~~~ -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: +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) @@ -1526,8 +1310,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 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: + 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) @@ -1547,107 +1331,16 @@ /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: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/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: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/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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: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::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/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:181:78: warning: comparison of integer expressions of different signedness: 'std::vector >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 181 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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; @@ -1672,17 +1365,11 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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.; - | ^~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:210:12: warning: unused variable 'zSquared' [-Wunused-variable] - 210 | double zSquared = 0.; - | ^~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In 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; @@ -1703,76 +1390,22 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/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/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/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/DensityMap.cpp:308:12: warning: unused variable 'groundFrequencyY' [-Wunused-variable] - 308 | double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:309:12: warning: unused variable 'groundFrequencyZ' [-Wunused-variable] - 309 | double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:311:12: warning: unused variable 'maxFrequencyX' [-Wunused-variable] - 311 | double maxFrequencyX = 1/unitCellParameters.geta()/2; - | ^~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:312:12: warning: unused variable 'maxFrequencyY' [-Wunused-variable] - 312 | double maxFrequencyY = 1/unitCellParameters.getb()/2; - | ^~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:313:12: warning: unused variable 'maxFrequencyZ' [-Wunused-variable] - 313 | double maxFrequencyZ = 1/unitCellParameters.getc()/2; - | ^~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:318:12: warning: variable 'signalToNoiseRatio' set but not used [-Wunused-but-set-variable] - 318 | double signalToNoiseRatio = 0.; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:319:12: warning: unused variable 'inverseNoiseTemperatureToPower4' [-Wunused-variable] - 319 | double inverseNoiseTemperatureToPower4 = 1/pow(noiseTemperature,4); //Stefan–Boltzmann law says total radiance goes like T^4. So we normalize by this number to keep noise sort of constant with temperatuere. Of course our oven has a maximum wavenumber, so this won't be perfect. - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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/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/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable 'dutyCycle' set but not used [-Wunused-but-set-variable] - 279 | double dutyCycle; //must be between 0 and 1. at 1, force is applied all the time. at 0, basically never applied. - | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable] - 280 | double scrubberPeriod; - | ^~~~~~~~~~~~~~ -/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; - | ^~~~~~~~~ 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: @@ -1783,13 +1416,10 @@ /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/src/DensityMap.cpp:509:9: warning: unused variable 'zGridInds' [-Wunused-variable] - 509 | int zGridInds = zDimInds; - | ^~~~~~~~~ -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: +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) @@ -1820,10 +1450,6 @@ /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/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 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 ++) { @@ -1831,6 +1457,14 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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::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; @@ -1851,6 +1485,10 @@ /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); }; + | ~~^~~~~~~~~~~~~~~~~ /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; @@ -1875,32 +1513,114 @@ /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/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/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: +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/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/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/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; + | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In 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 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/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/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 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/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/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'; @@ -1909,6 +1629,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 57 | c == 'A' | | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 59 | c == 'G' | | ~~^~~~~~ @@ -1929,6 +1653,10 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 77 | c == 'C' | | ~~^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 79 | c == 'H' | | ~~^~~~~~ @@ -1974,47 +1702,6 @@ /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' | ~~^~~~~~ -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) - | ^~ -/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 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:127:41: warning: variable 'myChargedAtomTypeIndex' set but not used [-Wunused-but-set-variable] - 127 | DuMM::ChargedAtomTypeIndex myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0))); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable] - 135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any); - | ^~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable] - 147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid"); - | ^~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::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/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; @@ -2035,112 +1722,6 @@ /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/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; - | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/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/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/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:518:15: warning: variable 'myFirstResidueID' set but not used [-Wunused-but-set-variable] - 518 | ResidueID myFirstResidueID = getFirstResidueID() ; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable] - 520 | int numResidues = -1; - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] - 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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 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; @@ -2165,10 +1746,36 @@ /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 '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 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/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:127:41: warning: variable 'myChargedAtomTypeIndex' set but not used [-Wunused-but-set-variable] + 127 | DuMM::ChargedAtomTypeIndex myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0))); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable] + 135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any); + | ^~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable] + 147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid"); + | ^~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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: 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; @@ -2189,103 +1796,6 @@ /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); }; - | ~~^~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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); - | ^~~~~~~~~~~~~~ -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/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1316:25: warning: variable 'myAtomIndex' set but not used [-Wunused-but-set-variable] - 1316 | Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName); - | ^~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/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/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/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/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/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] - 269 | ParameterReader * _parameterReader; - | ^~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] - 259 | SimbodyMatterSubsystem _matter; - | ^~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] - 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), - | ^~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:405:10: warning: variable 'readFromFile' set but not used [-Wunused-but-set-variable] - 405 | bool readFromFile = false; - | ^~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/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/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/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/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(); @@ -2294,56 +1804,25 @@ /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/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/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/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 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::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()){ - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: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::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/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/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 2172 | if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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/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; @@ -2368,44 +1847,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; - | ~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20, - 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/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:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector, WaterDropletContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:3577:23: warning: variable 'myLocation' set but not used [-Wunused-but-set-variable] - 3577 | Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm - | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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; @@ -2426,38 +1867,19 @@ /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::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/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/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/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/DensityForce.h:20, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11: +/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) ) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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) @@ -2465,8 +1887,16 @@ /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/ConstraintContainer.h:14, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10: +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/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /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) @@ -2474,6 +1904,10 @@ /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/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 '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(); @@ -2490,41 +1924,69 @@ /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 '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/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) - | ^~ -/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 ++) { - | ~~^~~~~~~~~~~~~~~ /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/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/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.; + | ^~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:210:12: warning: unused variable 'zSquared' [-Wunused-variable] + 210 | double zSquared = 0.; + | ^~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: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/Utils.cpp:12: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:518:15: warning: variable 'myFirstResidueID' set but not used [-Wunused-but-set-variable] + 518 | ResidueID myFirstResidueID = getFirstResidueID() ; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable] + 520 | int numResidues = -1; + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/DensityMap.cpp:308:12: warning: unused variable 'groundFrequencyY' [-Wunused-variable] + 308 | double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:309:12: warning: unused variable 'groundFrequencyZ' [-Wunused-variable] + 309 | double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:311:12: warning: unused variable 'maxFrequencyX' [-Wunused-variable] + 311 | double maxFrequencyX = 1/unitCellParameters.geta()/2; + | ^~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:312:12: warning: unused variable 'maxFrequencyY' [-Wunused-variable] + 312 | double maxFrequencyY = 1/unitCellParameters.getb()/2; + | ^~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:313:12: warning: unused variable 'maxFrequencyZ' [-Wunused-variable] + 313 | double maxFrequencyZ = 1/unitCellParameters.getc()/2; + | ^~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:318:12: warning: variable 'signalToNoiseRatio' set but not used [-Wunused-but-set-variable] + 318 | double signalToNoiseRatio = 0.; + | ^~~~~~~~~~~~~~~~~~ +/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/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable] + 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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) @@ -2536,86 +1998,27 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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: 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/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; - | ^~~~~~ -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 ++) { | ~~^~~~~~~~~~~~~~~ -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/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: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/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 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)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -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: +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) @@ -2623,34 +2026,10 @@ /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 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/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -2675,25 +2054,30 @@ /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: 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 '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 ++) { - | ~~^~~~~~~~~~~~~~~ /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: +/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/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: 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 ++) { @@ -2702,53 +2086,56 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 666 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ +/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: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: 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: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/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: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::loadParametersAndDensity_CCP4MAP()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:13: warning: unused variable 'newU' [-Wunused-variable] + 543 | int newU, newV, newW; + | ^~~~ +/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; + | ^~~~~~~~~ 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:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 670 | for (int i = 0; i < Chains.size(); i ++) { - | ~~^~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:11: + 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/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable 'dutyCycle' set but not used [-Wunused-but-set-variable] + 279 | double dutyCycle; //must be between 0 and 1. at 1, force is applied all the time. at 0, basically never applied. + | ^~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable] + 280 | double scrubberPeriod; + | ^~~~~~~~~~~~~~ /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; @@ -2759,10 +2146,6 @@ /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/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/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; @@ -2773,38 +2156,33 @@ /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/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()){ - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 785 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable 'biopolymerAtomTargetsIterator' set but not used [-Wunused-but-set-variable] + 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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; @@ -2825,10 +2203,6 @@ /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 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 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); }; @@ -2853,17 +2227,19 @@ /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/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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/ConstraintContainer.cpp:11: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; @@ -2888,6 +2264,88 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:12: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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/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/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 129 | if(index < 0 || index >= constraintClassVector.size()) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 146 | if(index < 0 || index >= constraintClassVector.size()) + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/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/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1316:25: warning: variable 'myAtomIndex' set but not used [-Wunused-but-set-variable] + 1316 | Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName); + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] + 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 666 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 670 | for (int i = 0; i < Chains.size(); i ++) { + | ~~^~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable] + 1437 | double huntCrossleyDissipation =.0; + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable] + 26 | bool myEndCapsOn; + | ^~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 70 | if(id < 0 || id >= contactWithinVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 77 | if(id < 0 || id >= contactWithinVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; @@ -2908,11 +2366,54 @@ /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) : | ^~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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 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/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 ++) { + | ~~^~~~~~~~~~~~~~~ +/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/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 18 | if(id < 0 || id >= residueStretchVector.size()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor '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; @@ -2937,14 +2438,82 @@ /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/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/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). + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 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/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/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/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder] + 269 | ParameterReader * _parameterReader; + | ^~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder] + 259 | SimbodyMatterSubsystem _matter; + | ^~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] + 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), + | ^~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:405:10: warning: variable 'readFromFile' set but not used [-Wunused-but-set-variable] + 405 | bool readFromFile = false; + | ^~~~~~~~~~~~ +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; + | ^~~~~~ +/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/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector, WaterDropletContainer&)': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:3577:23: warning: variable 'myLocation' set but not used [-Wunused-but-set-variable] + 3577 | Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm + | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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; @@ -2965,76 +2534,34 @@ /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/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/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 129 | if(index < 0 || index >= constraintClassVector.size()) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 146 | if(index < 0 || index >= constraintClassVector.size()) - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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++){ + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) : - | ^~~~~~~~~~~ -/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); }; - | ~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses] - 190 | if( (dist <= it->range) && - | ~~~~~~~~~~~~~~~~~~~~^~ - 191 | (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) || - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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/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++){ @@ -3043,30 +2570,57 @@ /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: 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/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 '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/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/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/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/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/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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +/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()){ + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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/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/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/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))) + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]': @@ -3079,51 +2633,10 @@ /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/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 - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -/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/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/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/include/Utils.h: At global scope: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] - 257 | const char* digits = "0123456789"; - | ^~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] - 256 | const char* spaces = " \t"; - | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: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)) | ^ @@ -3134,6 +2647,15 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] + 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); + | ^~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable] + 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); + | ^~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] + 2735 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) + | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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"; @@ -3141,13 +2663,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -In file included from /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]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: 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]' /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here @@ -3157,9 +2672,6 @@ /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/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 300 | for ( int j = 0 ; j < neighborList.size(); j++) { - | ~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here @@ -3177,29 +2689,12 @@ 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; @@ -3207,27 +2702,18 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 144 | if(id >= 0 && id < residueStretchVector.size()) - | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] - 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); - | ^~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable] - 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); - | ^~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] - 2735 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) - | ^ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 300 | for ( int j = 0 ; j < neighborList.size(); j++) { + | ~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ +[ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o +/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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/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 /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"; @@ -3260,18 +2746,64 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized] 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3366,6 +2920,162 @@ /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"; | ^~~~~~ +[ 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/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"; + | ^~~~~~ +[ 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 +[ 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 +[ 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/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)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +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/SimTKsimbody.h:43, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22: +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i R(0.0); + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i R(0.0); + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i R(0.0); + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i U(0.0); // initialize 2-d array + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i U(0.0); // initialize 2-d array + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: +/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::Mat<3, 3> [1]' [-Warray-bounds=] + 784 | { for(int i=0;i U(0.0); // initialize 2-d array + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: +/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' of size 72 + 201 | rotation = Rotation(); + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: +/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' of size 72 + 201 | rotation = Rotation(); + | ^ +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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: +/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' of size 72 + 201 | rotation = Rotation(); + | ^ +/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 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, @@ -3441,58 +3151,51 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72 319 | Rotation rotation2; | ^~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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"; - | ^~~~~~ -/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"; - | ^~~~~~ -/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: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/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"; @@ -3500,6 +3203,112 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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: 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"; @@ -3507,6 +3316,73 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor '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 +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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: 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"; @@ -3526,9 +3402,282 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here -/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] +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/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(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +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/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)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void 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(); }; + | ~~^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, + from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 144 | if(id >= 0 && id < residueStretchVector.size()) + | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] + 257 | const char* digits = "0123456789"; + | ^~~~~~ +/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] + 256 | const char* spaces = " \t"; + | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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"; @@ -3557,119 +3706,6 @@ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ -In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, - from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, - from /usr/include/simbody/SimTKcommon.h:35, - from /usr/include/simbody/SimTKsimbody.h:43, - from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22: -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i R(0.0); - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i R(0.0); - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i R(0.0); - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i U(0.0); // initialize 2-d array - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i U(0.0); // initialize 2-d array - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: -/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::Mat<3, 3> [1]' [-Warray-bounds=] - 784 | { for(int i=0;i U(0.0); // initialize 2-d array - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: -/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' of size 72 - 201 | rotation = Rotation(); - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: -/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' of size 72 - 201 | rotation = Rotation(); - | ^ -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 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: -/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' of size 72 - 201 | rotation = Rotation(); - | ^ /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"; @@ -4109,7 +4145,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - 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" + 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" 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 @@ -4215,15 +4251,15 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -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 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 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 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 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 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 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 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 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 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 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 dh_installdeb dh_gencontrol dh_md5sums @@ -4231,9 +4267,9 @@ dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-4_amd64.deb'. -dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-4_amd64.deb'. -dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'mmb-common' in '../mmb-common_4.0.0+dfsg-4_all.deb'. +dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-4_amd64.deb'. +dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../macromoleculebuilder_4.0.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../macromoleculebuilder_4.0.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -4241,12 +4277,14 @@ 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/3925597/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3925597/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/496374 and its subdirectories -I: Current time: Mon Jul 14 17:08:38 -12 2025 -I: pbuilder-time-stamp: 1752556118 +I: removing directory /srv/workspace/pbuilder/3925597 and its subdirectories +I: Current time: Wed Jun 12 12:53:08 +14 2024 +I: pbuilder-time-stamp: 1718146388