I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 5 03:05:22 +14 2026 I: pbuilder-time-stamp: 1767531922 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [macromoleculebuilder_4.0.0+dfsg-5.dsc] I: copying [./macromoleculebuilder_4.0.0+dfsg.orig.tar.xz] I: copying [./macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Nov 27 07:10:58 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macromoleculebuilder_4.0.0+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting macromoleculebuilder in macromoleculebuilder-4.0.0+dfsg dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch dpkg-source: info: applying 96da444290ab1af4385013c566079d381d8051b4.patch dpkg-source: info: applying bf1ab1ebf49bb9e48f4f133e155f9315cc37079d.patch dpkg-source: info: applying 27.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/392996/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 4 13:05 /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/392996/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/392996/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=25d92cb03c7f4c1786f3699f82bb5e3c 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=392996 PS4='+ ' 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.6CmBvtqs/pbuilderrc_5WvJ --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/b2 --logfile b2/build.log macromoleculebuilder_4.0.0+dfsg-5.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/392996/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19962 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on asciidoc-base; however: Package asciidoc-base is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on docbook-xml; however: Package docbook-xml is not installed. pbuilder-satisfydepends-dummy depends on gemmi-dev (>= 0.6.2+ds-2); however: Package gemmi-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimbody-dev; however: Package libsimbody-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimtkmolmodel-dev (>= 3.1.0); however: Package libsimtkmolmodel-dev is not installed. pbuilder-satisfydepends-dummy depends on libsimtkmolmodel-plugins; however: Package libsimtkmolmodel-plugins is not installed. pbuilder-satisfydepends-dummy depends on libstb-dev; however: Package libstb-dev is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: architecture-properties{a} asciidoc-base{a} asciidoc-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook-xml{a} docbook-xsl{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dev{a} libgl1-mesa-dri{a} libglapi-mesa{a} libgles-dev{a} libgles1{a} libgles2{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd-core-dev{a} libglvnd-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsimbody-dev{a} libsimbody3.7{a} libsimtkmolmodel-dev{a} libsimtkmolmodel-plugins{a} libsimtkmolmodel3.1t64{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libstb-dev{a} libstb0t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwayland-client0{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxml2-utils{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxslt1.1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} tao-pegtl-dev{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-dev{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget xmlto 0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 121 MB of archives. After unpacking 511 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.2.3 [2184 B] Get: 37 http://deb.debian.org/debian trixie/main amd64 asciidoc-common all 10.2.1-1 [104 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [99.4 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 asciidoc-base all 10.2.1-1 [84.9 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.5-1 [2223 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 72 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 docbook-xml all 4.5-13 [77.4 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 87 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.7-1 [37.9 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get: 101 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.4-1 [26.0 MB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.7-1 [9186 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.7-1 [42.8 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.7-1 [43.9 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.7-1 [154 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-1+b2 [139 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libglvnd-core-dev amd64 1.7.0-1+b2 [13.4 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 24.2.7-1 [133 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libegl-dev amd64 1.7.0-1+b2 [19.5 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libgles1 amd64 1.7.0-1+b2 [12.1 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libgles2 amd64 1.7.0-1+b2 [17.3 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libgles-dev amd64 1.7.0-1+b2 [50.8 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B] Get: 140 http://deb.debian.org/debian trixie/main amd64 libglvnd-dev amd64 1.7.0-1+b2 [5148 B] Get: 141 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dev amd64 24.2.7-1 [18.5 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b2 [185 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b2 [223 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.40.2-11 [47.2 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2+b1 [407 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-1+b2 [163 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-1+b2 [53.4 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.5+ds-2 [1139 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-1+b1 [1058 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-1+b1 [346 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b2 [22.3 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.2-1 [241 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b3 [65.2 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-3+b1 [3363 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-3+b1 [2728 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel3.1t64 amd64 3.1.0-4.1+b3 [667 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel-dev amd64 3.1.0-4.1+b3 [1864 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel-plugins amd64 3.1.0-4.1+b3 [19.6 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 libstb0t64 amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [220 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libstb-dev amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [654 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 121 MB in 1s (90.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19962 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (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 ... 20282 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21344 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. 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Selecting previously unselected package libstb0t64:amd64. Preparing to unpack .../153-libstb0t64_0.0~git20240715.f7f20f39fe4f+ds-1_amd64.deb ... Unpacking libstb0t64:amd64 (0.0~git20240715.f7f20f39fe4f+ds-1) ... Selecting previously unselected package libstb-dev:amd64. Preparing to unpack .../154-libstb-dev_0.0~git20240715.f7f20f39fe4f+ds-1_amd64.deb ... Unpacking libstb-dev:amd64 (0.0~git20240715.f7f20f39fe4f+ds-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../155-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libwayland-server0:amd64 (1.23.0-1+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b2) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libglvnd-core-dev:amd64 (1.7.0-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.3) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libuv1t64:amd64 (1.48.0-7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libopengl0:amd64 (1.7.0-1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libseqan2-dev (2.4.0+dfsg-16) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jan 4 13:06:01 UTC 2026. Universal Time is now: Sun Jan 4 13:06:01 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libgles2:amd64 (1.7.0-1+b2) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up uuid-dev:amd64 (2.40.2-11) ... Setting up libgles1:amd64 (1.7.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up autopoint (0.22.5-2) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libglapi-mesa:amd64 (24.2.7-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libvulkan1:amd64 (1.3.296.0-1) ... Setting up autoconf (2.72-3) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libxshmfence1:amd64 (1.3-1+b2) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b2) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libopengl-dev:amd64 (1.7.0-1+b2) ... Setting up libstb0t64:amd64 (0.0~git20240715.f7f20f39fe4f+ds-1) ... Setting up libopenmm8.1 (8.1.2+dfsg-1+b1) ... Setting up libdrm-common (2.4.123-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.4-1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.4.7-8) ... Setting up gemmi-dev (0.6.5+ds-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libopenmm-dev (8.1.2+dfsg-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libstb-dev:amd64 (0.0~git20240715.f7f20f39fe4f+ds-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libsm-dev:amd64 (2:1.2.4-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up xsltproc (1.1.35-1.1+b1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxfixes-dev:amd64 (1:6.0.0-2+b2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b2) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.30.5-1) ... Setting up libxi-dev:amd64 (2:1.8.2-1) ... Setting up mesa-libgallium:amd64 (24.2.7-1) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:amd64 (2:1.1.3-3+b3) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libgbm1:amd64 (24.2.7-1) ... Setting up python3.12 (3.12.7-3) ... Setting up libgl1-mesa-dri:amd64 (24.2.7-1) ... Setting up debhelper (13.20) ... Setting up libegl-mesa0:amd64 (24.2.7-1) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2+b1) ... Setting up libegl1:amd64 (1.7.0-1+b2) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libglx-mesa0:amd64 (24.2.7-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up python3 (3.12.6-1) ... Setting up libxmu-dev:amd64 (2:1.1.3-3+b3) ... Setting up asciidoc-common (10.2.1-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up libglut3.12:amd64 (3.4.0-1+b2) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-3+b1) ... Setting up libglx-dev:amd64 (1.7.0-1+b2) ... Setting up libgl-dev:amd64 (1.7.0-1+b2) ... Setting up libegl-dev:amd64 (1.7.0-1+b2) ... Setting up libsimtkmolmodel3.1t64:amd64 (3.1.0-4.1+b3) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b2) ... Setting up libgles-dev:amd64 (1.7.0-1+b2) ... Setting up libsimtkmolmodel-plugins (3.1.0-4.1+b3) ... Setting up libsimtkmolmodel-dev:amd64 (3.1.0-4.1+b3) ... Setting up libglvnd-dev:amd64 (1.7.0-1+b2) ... Setting up libgl1-mesa-dev:amd64 (24.2.7-1) ... Setting up libglut-dev:amd64 (3.4.0-1+b2) ... Setting up freeglut3-dev:amd64 (3.4.0-1+b2) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-3+b1) ... Processing triggers for libc-bin (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-7) ... Setting up sgml-data (2.0.11+nmu1) ... Setting up asciidoc-base (10.2.1-1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-13) ... Processing triggers for sgml-base (1.31) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/392996/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/392996/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../macromoleculebuilder_4.0.0+dfsg-5_source.changes dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=Release \ -DENABLE_LEPTON=OFF \ -DGEMMI_DIR=/usr \ -DOpenMM_INCLUDE_DIR=/usr/include \ -DSimTKmolmodel=/usr \ -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" .. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found gemmi version 0.6.5 -- Looking for copy_file_range -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found -- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED SimTKmolmodel -- 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 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 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/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake "--color=" 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/DisplacementContainer.cpp.o [ 15%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o [ 15%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o [ 15%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o [ 18%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o [ 21%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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 [ 25%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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 [ 34%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+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 [ 28%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o [ 34%] 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/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 [ 37%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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 /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 [ 40%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-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/DensityContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DensityContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp [ 46%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o [ 46%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o [ 50%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS 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/usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ContactContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp /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 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-DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp /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 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-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/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp /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 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CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp [ 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/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ProgressWriter.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp /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/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:14: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In 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/include/BiopolymerClassTwoTransformForces.h:17, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /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/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/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void 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: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/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/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/ConstraintContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /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/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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))) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsPurine(char)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 51 | return c == 'A' | c == 'G'; | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsRNA(char)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 57 | c == 'A' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 59 | c == 'G' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 60 | c == 'U' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsDNA(char)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 67 | c == 'A' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 69 | c == 'G' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 70 | c == 'T' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsProtein(char)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 77 | c == 'C' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 79 | c == 'H' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 80 | c == 'I' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 86 | c == 'M' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 88 | c == 'V' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | c == 'A' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 95 | c == 'G' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 97 | c == 'P' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 98 | c == 'T' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 104 | c == 'R' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 106 | c == 'Y' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 107 | c == 'W' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 113 | c == 'D' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 115 | c == 'E' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 116 | c == 'Q' | | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 117 | c == 'K' | ~~^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:324:15: warning: unused variable 'myAngle1' [-Wunused-variable] 324 | Angle myAngle1 = 180*Deg2Rad; // this is a bond angle | ^~~~~~~~ /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/BiopolymerClass.cpp: In member function 'int BiopolymerClass::checkResidueNumbersAndInsertionCodes()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:244:15: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] 244 | ResidueID myResidueID = getFirstResidueID(); | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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; | ^~~~~~ 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/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /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/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: 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/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 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/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 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void 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 '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/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; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:16, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:11: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ 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 '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; | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NTC_FORCE_CLASS.h:4, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:17: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: 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/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; | ^~~~~~ 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/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 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: 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 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/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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/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: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/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(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~ 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 constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp: In member function 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator; reference = BaseInteraction&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 44 | myBasePairVector.at(index); | ~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /usr/include/c++/14/vector:66, from /usr/include/simbody/SimTKcommon/internal/Array.h:39, from /usr/include/simbody/SimTKcommon/basics.h:53, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:16: /usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here 1180 | at(size_type __n) | ^~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1053:9: warning: unused variable 'myResidueIndex' [-Wunused-variable] 1053 | int myResidueIndex = getResidueIndex(myResidueID); | ^~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: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()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~~~~ 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 ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: 'std::vector > >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 177 | if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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) : | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: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/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; | ^~~~~ /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/BiopolymerClass.cpp: In member function 'void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable] 1437 | double huntCrossleyDissipation =.0; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:19, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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; | ^~~~~ /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/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/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/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; | ^~~~~ /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/src/ContactContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/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/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 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::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 member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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) | ^~ /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/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/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:140:10: warning: variable 'deltaZ' set but not used [-Wunused-but-set-variable] 140 | Vec3 deltaZ = Vec3(0,0,1) * sin(cylindricalSpiralSlopeAngle(pitch,radius))*helixAdvancePerBasePair ; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: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/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 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/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/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/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 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:221:12: warning: unused variable 'phiOffsetFromStartingTheta' [-Wunused-variable] 221 | double phiOffsetFromStartingTheta = phiFromTheta(startTheta, pitch, radius, 0.0, spiralIsRightHanded); // use offset = 0 to retreive the original, non-offset phi | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:1582:17: warning: unused variable 'myForceConstant' [-Wunused-variable] 1582 | double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later. | ^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/DensityMap.cpp: In member function 'void DensityMap::loadParametersAndDensity_CCP4MAP()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:13: warning: unused variable 'newU' [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:19: warning: unused variable 'newV' [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:25: warning: unused variable 'newW' [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:507:9: warning: unused variable 'xGridInds' [-Wunused-variable] 507 | int xGridInds = xDimInds; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:508:9: warning: unused variable 'yGridInds' [-Wunused-variable] 508 | int yGridInds = yDimInds; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:509:9: warning: unused variable 'zGridInds' [-Wunused-variable] 509 | int zGridInds = zDimInds; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable 'lastEnergy' [-Wunused-variable] 202 | double lastEnergy = myEnergies.back(); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable 'compoundNumber' [-Wunused-variable] 49 | int compoundNumber = 1; | ^~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable 'requiredPrecision' [-Wunused-variable] 50 | int requiredPrecision = 12; | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 666 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 292 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 77 | if(id < 0 || id >= contactWithinVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/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 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 670 | for (int i = 0; i < Chains.size(); i ++) { | ~~^~~~~~~~~~~~~~~ /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/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 386 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 275 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 283 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses] 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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/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/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In 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/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:172:31: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable] 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); | ^~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/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/ParameterReader.cpp:2069:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 2069 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/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/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/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/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/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/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/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector, double, SimTK::String)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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(); | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function '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/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable] 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable] 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); | ^~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] 2735 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/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/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 4682 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 300 | for ( int j = 0 ; j < neighborList.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here 470 | _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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: 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]' 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here 573 | _parameterReader-> physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]' 2584 | residueStretchContainer.printResidueStretchVector(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here 4682 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]' 4827 | residueStretchContainer.printResidueStretchVector(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here 4830 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); | ^ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here 814 | physicsContainer.deleteResidueStretch(index); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /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: 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/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' 264 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]' 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here 470 | _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 104 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27: required from 'void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' 264 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]' 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here 573 | _parameterReader-> physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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 & SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

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

& SimTK::Rotation_

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

& SimTK::Rotation_

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

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72 116 | Rotation rotation2; | ^~~~~~~~~ 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:201:33: /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:201:33: /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:201:33: /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/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized] 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here 167 | double myFrcScalar; | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:97:17: warning: 'bool compareUpper(const std::string&, const char*)' defined but not used [-Wunused-function] 97 | static bool compareUpper( const string& param, const char* symbol ) { | ^~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ 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 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ 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 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function 'SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44: /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&, double, double, const std::vector&, PdbStructureMapType&)': /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ 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 '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 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from 'SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from 'SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from 'SimTK::Rotation_

::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::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 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_ [1]'} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]', inlined from 'SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from 'SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from 'SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2210:56: /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